title: PROTON GRADIENT REGULATION 5 enables efficient C4 photosynthesis under fluctuating light

city: Melbourne

first: Russell

last: Woodford

state: Victoria

address: 25 Rainforest Walk, Monash University, Clayton

department: School of Biological Sciences

institute: Monash University

summary: PROTON GRADIENT REGULATION 5 (PGR5) plays a critical role in generating proton motive force across thylakoid membranes and supporting photoprotection under fluctuating light in C3 plants. It is proposed that this function is achieved by regulating cyclic electron flow around Photosystem I. During the evolutionary transition from C3 to C4 photosynthesis, PGR5 abundance in leaves has increased, coinciding with an enhancement in cyclic electron flow rate. To investigate the role of PGR5 in C4 photosynthesis and photoprotection, we generated Setaria viridis (a model C4 monocot) lines with null PGR5 alleles. We demonstrate that loss of PGR5 severely impairs the establishment of proton motive force, photosynthetic control, and energy-dependent non-photochemical quenching at high irradiances, leading to a loss of Photosystem I activity under light stress. Furthermore, plants lacking PGR5 exhibit drastically reduced growth and photosynthesis when grown under fluctuating daylight; however, they are less severely affected than C3  pgr5 mutants. This relative tolerance arises from the ability of S. viridis lacking PGR5 to maintain significant levels of photosynthetic control, in contrast to C3 mutants. Additionally, in the absence of PGR5 and qE, a slower-relaxing, zeaxanthin-dependent form of non-photochemical quenching supports survival under fluctuating light, albeit at the cost of reduced photochemical efficiency and assimilation. Our findings highlight the essential role of PGR5 in enabling efficient C4 photosynthesis under fluctuating light by regulating photosynthetic control and energy-dependent non-photochemical quenching. This study also uncovers the interplay between multiple photoprotective mechanisms safeguarding C4 photosynthesis under light stress.

overall_design: PolyA-enriched RNA-seq was performed on S. viridis leaf discs harvested from WT, null NdhO and null PGR5 plants. Plants were germinated in 0.5 L pots with seed raising mix (Debco, Tyabb, Australia) containing 5 g L-1 of Osmocote fertiliser (Scotts, Bella Vista, Australia). Seeds were covered with inverted plastic cups to maintain humidity, with the cups removed one week after germination. Plants were grown in a controlled-environment chamber with a 16 h light/8 h dark photoperiod, an irradiance of 380 µmol m−2 s−1, ambient CO2, 28°C day, 22°C night and 60% humidity. The position of WT and edited plants within the chamber was blocked and randomised to minimise positional effects. Plants were analysed 3-4 weeks after sowing, with the youngest fully expanded leaves used for analysis. WT S. viridis plants were used as a control for all experiments.

first: Jacinta

last: Watkins

first: Marten

last: Moore

last: Nix

first: Suyan

last: Yee

first: Kai

middle: X

last: Chan

first: Barry

last: Pogson

first: Susanne

last: von Caemmerer

first: Robert

middle: T

last: Furbank

first: Maria

last: Ermakova


title: FIBo-seq in Tet1/2/3 CTRL and TKO mESC

status: Public on Oct 21 2025

city: Mainz

first: Alexandr

last: Gopanenko

address: Ackermannweg 4

country: Germany

institute: Institute of Molecular Biology gGmbH (IMB)

summary: The RNA modification 5-formylcytidine (f5C) is poorly explored in mammals. Low f5C levels reported in mRNA may reflect spurious 5-methylcytidine (m5C) oxidation or targeted demethylation by TET or ALKBH1 dioxygenases. Here we analyze f5C in RNA of mouse embryonic stem cells (mESCs) using LC-MS/MS and chemical-assisted sequencing. We reveal that the previously reported pyridine-borane-sequencing method misidentifies N4-acetylcytidine (ac4C) and unmodified, hyper-reactive cytidines in a CUMC context as f5C. To overcome these limitations, we developed FIBo-seq with enhanced specificity and sensitivity for f5C-sequencing. We find no evidence for a role of TET enzymes in generating f5C, unlike for ALKBH1. Moreover, no f5C sites are detectable in mRNA. Instead, the bulk of mammalian f5C resides in the well-established mitochondrial tRNA Methionine (mt-tRNAMet) and is mediated by ALKBH1. The results argue against an instructive function for f5C outside tRNA in mammals.

overall_design: FIBo-seq (f5C-immunoprecipitation-pyridine-borane sequencing) of RNA from Tet1/2/3 control (CTRL) mouse embryonic stem cells (mESCs) and their corresponding Tet1/2/3 triple knockout (TKO) mESCs.

first: Jasmin A.

last: Dehnen

first: Alexandr V.

first: Carola

last: Scholz

first: Michael U.

last: Musheev

first: Christof

last: Niehrs


title: Glucocorticoids unleash immune-dependent melanoma control through inhibition of the GARP/TGFβ axis [RNA-seq]

city: Manchester

first: Santiago

last: Zelenay

address: Wilmslow Rd, Manchester M20 4BX

country: United Kingdom

institute: Cancer Research UK Manchester Institute

type: Expression profiling by high throughput sequencing

summary: Glucocorticoids were found to trigger immune-dependent control of an orthotopic melanoma model. This was found to be dependent on glucocorticoid receptor expression in the tumor cells. We used whole exome RNAseq of parental and glucocorticoid receptor knockout tumor cells in vivo and in vitro to identify the transcriptional changes induced following glucocorticoid treatment.

overall_design: 10 mice were implanted with 20967 parental or 20967 GRKO melanoma tumours intradermally. 5 mice from each group were treated with control drug and 5 with glucocorticoid (clobetasol priopionate). These tumours were harvested, digested, RNA extracted, cDNA produced and sent for bulk sequencing. Additionally, 20967 parental and 20967 GRKO melanoma cells were cultured in vitro and treated with control (DMSO) or clobetasol propionate (1µM) prior to RNA collection and sequencing.

first: Charles

middle: H

last: Earnshaw

first: Agrin

last: Moeini

first: Richard

last: Reeves

last: Sellers

first: Sudhakar

last: Sahoo


title: Uli-Epic: A cutting-edge library construction strategy for profiling ultra-limited RNA modifications [Uli-Epic GLORI]

city: shanghai

first: Xu

last: Chu

address: Dong'an Road

country: China

institute: Fudan University Shanghai Cancer Center

summary: RNA modifications have important function in nearly every aspect of RNA biology. Epitranscriptome RNA modifications detected by high-throughput sequencing technologies is critical for understanding the distribution, regularity, stoichiometry, function of RNA modifications. One of disadvantages about these high-throughput sequencing technologies is needing high-input RNA. Here we use poly(A) tailing, template switching by reverse transcription during DNA synthesis and in vitro transcription (IVT) to develop a cutting-edge library construction strategy for profiling ultra-limited RNA modifications (Uli-Epic). We apply Uli-Epic for RNA-seq using 100 pg of poly A+ RNA. We also apply Uli-Epic to combine with BID-seq to characterize dynamics of pseudouridine in neural stem cells (NSC) and sperm under normal and fetal growth restriction (FGR) mice using as low as 100 pg of rRNA-depleted RNA. In addition, we combined Uli-Epic and GLORI to quantify the m6A methylomes of sperm and NSC under normal and FGR mice using 10ng of rRNA-depleted RNA. Summary, Uli-Epic is a strand-specific, high throughput and low input RNA library construction strategy which is compatible with many RNA modifications detected technologies.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: m6A detection by bulk GLORI and Uli-epic GLORI in HEK293T mRNA. m6A detection by Uli-epic GLORI in ribominus RNA of mouse sperm and NSC

first: He

last: Weizhi


title: Single-cell profiling of liver in offspring with intrauterine hyperglycemia reveals acute-phase response deficiency

city: Shanghai

first: Jiahang

last: Mo

address: No.131 Dong'an Road

department: Institute of Reproduction and Development

institute: Obstetrics and gynecology Hospital of Fudan University

summary: Gestational diabetes mellitus (GDM) has long-term effects on the offspring health. Among these chronic diseases, inflammatory profiles play important roles in their development. Assessment for inflammatory status of GDM offspring is limited. Thus, the single cell RNA sequencing (scRNA-seq) was conducted to delineate the inflammatory characteristics of offspring with intrauterine hyperglycemia (IHG). scRNA-seq analysis of mice liver revealed myeloid polarization and multiple lineages developmental retardationwas identified in IHG offspring. Proinflammatory potential of myeloid cells seemed to be deeply imprinted in the liver of adult offspring with IHG.

overall_design: To assess the hepatic inflammatory characteristics of offspring with IHG. Livers of fetal male offspring (E18.5) and adult male offspring (8 w) with Ctrl and IHG morther were enrolled for scRNA-seq analysis.


title: A unified workflow to define multipotent progenitor hierarchies (TEA-Seq)

city: Cincinnati

first: Nathan

last: Salomonis

state: OH

address: 3333 Burnet Avenue

department: Biomedical Informatics

country: USA

institute: Cincinnati Children's Hospital

summary: Multipotent hematopoietic progenitors with coherent developmental transcriptional programs are defined by their ability to give rise to distinct cell lineages. While the identification of multilineage progenitors is aided by single-cell technologies, new techniques are required for their rigorous delineation and isolation. We describe a new approach to dissect and contrast well-defined and newly proposed immunophenotypically defined hematopoietic progenitors using integrative multimodal single-cell genomics and linked high-dimensional flow cytometry. The lineage potential of implicated multi-lineage progenitors could be resolved through their sequential isolation, lineage tracing, genetic reporters, in vitro differentiation and gene-regulatory prediction analyses. These analyses implicate coordinated transcription factors operating on composite elements for distinct multilineage cell states. A newly identified precursor of the neutrophil-monocytic bipotential (MultiLin-1) was confirmed to be transcriptionally reprogrammed by Th2 cytokines following infection, to produce the successive waves of neutrophils, basophils and eosinophils. This work supports a stepwise model of hematopoiesis in which lineage transitions occur as discrete, isolatable cell states.

overall_design: A five-fold molecular titration of BioLegend antibodies was performed in murine bone marrow to develop an optimized CITE-Seq panel (10x Genomics) of 112 cell surface markers.

first: Kyle

last: Ferchen

first: Xuan

last: Zhang

first: H

middle: L

last: Grimes


title: Alveolar macrophages critically control infection by seasonal human coronavirus OC43 to avoid severe pneumonia [scRNA-seq]

city: Beijing

first: Chen

last: Dong

address: Haidian District

institute: Tsinghua University

summary: Seasonal coronaviruses, similar to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), only cause severe respiratory symptoms in a small fraction of infected individuals. However, the host factors that determine the variable responses to coronavirus infection remain unclear. Here, we use seasonal human coronavirus OC43 (HCoV-OC43) infection as an asymptomatic model that triggers both innate and adaptive immune responses in mice. Interestingly, innate sensing pathways as well as adaptive immune cells are not essential in protection against HCoV-OC43. Instead, alveolar macrophage (AMΦ) deficiency in mice results in COVID-19-like severe pneumonia post HCoV-OC43 infection, with abundant neutrophil infiltration, neutrophil extracellular trap (NET) release, and exaggerated pro-inflammatory cytokine production. Mechanistically, AMΦ efficiently phagocytose HCoV-OC43, effectively blocking virus spread, whereas, in their absence, HCoV-OC43 triggers Toll-like receptor (TLR)-dependent chemokine production to cause pneumonia. These findings reveal the central role of AMΦ in defending against seasonal HCoV-OC43 with clinical implications for human immunopathology associated with coronavirus infection.

overall_design: Lungs from uninfected or HCoV-OC43-infected WT or Csf2rb-/- mice were collected and digested into single-cell suspensions, and CD45+ cells were sorted for single-cell RNA sequencing.

last: Zhong

first: Tian

last: Xie


title: Pilot FIBo-seq in Tet1/2/3 CTRL and TKO mESC

first: Alexandr

last: Gopanenko

summary: The RNA modification 5-formylcytidine (f5C) is poorly explored in mammals. Low f5C levels reported in mRNA may reflect spurious 5-methylcytidine (m5C) oxidation or targeted demethylation by TET or ALKBH1 dioxygenases. Here we analyze f5C in RNA of mouse embryonic stem cells (mESCs) using LC-MS/MS and chemical-assisted sequencing. We reveal that the previously reported pyridine-borane-sequencing misidentifies N4-acetylcytidine (ac4C) and unmodified, hyper-reactive cytidines in a CUMC context as f5C. To overcome these limitations, we developed FIBo-seq with enhanced specificity and sensitivity for f5C-sequencing. We find no evidence for a role of TET enzymes in generating f5C, unlike for ALKBH1. Moreover, no f5C sites are detectable in mRNA. Instead, the bulk of mammalian f5C resides in the well-established mitochondrial tRNA Methionine (mt-tRNAMet) and is mediated by ALKBH1. The results argue against an instructive function for f5C outside tRNA in mammals.

overall_design: FIBo-seq (f5C-immunoprecipitation-pyridine-borane sequencing) of RNA from Tet1/2/3 control (CTRL) mouse embryonic stem cells (mESCs) and their corresponding Tet1/2/3 triple knockout (TKO) mESCs. Pilot experiment, no rRNA depletion.

first: Jasmin A.

last: Dehnen

first: Alexandr V.

first: Carola

last: Scholz

last: Musheev

last: Niehrs


title: A unified workflow to define multipotent progenitor hierarchies

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

overall_design: Refer to individual Series


title: A unified workflow to define multipotent progenitor hierarchies [Fluidigm]


title: A unified workflow to define multipotent progenitor hierarchies (CITE-Seq and CellTag)


title: Alveolar macrophages critically control infection by seasonal human coronavirus OC43 to avoid severe pneumonia [I]

overall_design: Alveolar macrophages were sorted from C57BL/6 mice infected with HCoV-OC43 at different time points (0, 3, and 5 days) and isolated total RNA for RNA-seq analysis.


title: CRISPR Screen Identifies HDAC3 as a Novel Radiosensitizing Target in Small Cell Lung Cancer

city: Toronto

first: Benjamin

last: Lok

state: ON

address: 101 College Street, PMCRT, 13-307

country: Canada

institute: Princess Margaret Cancer Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Small cell lung cancer (SCLC) is an aggressive malignancy, with most patients presenting with prognostically poor extensive-stage disease. Limited progress in standard care stresses the urgent need for novel therapies. Radiotherapy offers some survival benefit for select SCLC patients but could be enhanced with radiosensitizers. Here, we identify HDAC3 as a novel radiosensitizing target in SCLC using a CRISPR knockout screen and demonstrate its efficacy and mechanism. SBC5 cells were transduced with a custom EpiDrug sgRNA library and treated with ionizing radiation (IR). Cells were collected and sequenced at multiple timepoints to identify radiosensitizing genes. To validate this target, HDAC3 functional loss was generated by genetic knockdown (KD) and RGFP966 inhibition in several SCLC cell lines. HDAC3 KD and RGFP966 inhibition increased radiosensitivity, as shown by cell viability (dose[1]modification factor [DMF]10 = 1.14-1.69) and clonogenic assays (DMF10 = 1.16-1.41). We evaluated changes in chromatin accessibility by ATAC-seq, and IR-induced DNA damage and repair using γH2AX foci detection and double-strand break (DSB) repair assays. Cells with HDAC3 functional loss demonstrated increased chromatin accessibility which was associated with more IR-induced DNA DSBs, and impaired DSB repair function leading to persisting DNA damage. In SCLC xenograft models, HDAC3 KD or RGFP966, combined with IR, enhanced radiosensitivity and achieved significant tumor growth inhibition. Taken together, we identified HDAC3 as a novel radiosensitizing target in SCLC. Its functional loss increases the generation and persistence of IR-induced DNA DSBs, effectively sensitizing SCLC cell lines and xenografts to IR, providing a potential radiosensitization strategy to treat SCLC.

overall_design: ATAC-seq of SBC5 small cell lung cancer cells treated with shRNA to knockdown expression of HDAC3 or treated with 2µM or 5µM of the HDAC3 inhibitor RGFP966.

first: Ujas

last: Patel

first: Kevin

middle: C

last: Nixon

first: Troy

last: Ketela


title: Gene expression of TPO-stimulated HSC-derived murine Evi1+AML

city: Basel

first: Jonathan

last: Seguin

address: Spitalstrasse 33

country: Switzerland

institute: UKBB-DBM

summary: To characterize the cellular origin of ecotropic virus integration site 1 (EVI1)-expressing aggressive KMT2A-rearranged acute myeloid leukaemia (AML), we integrated an Evi1-GFP reporter allele in the inducible iKMT2A-MLLT3 mouse model. Single injection of thrombopoietin (TPO) was done to observe the effects on Evi1+ haematopoietic stem cells (HSC) and its consequences on AML. To better characterized the effects of Evi1 and TPO, gene expression was determined by RNA sequencing from HSC-derived iKMT2A-MLLT3-driven AML expressing different levels of Evi1 (GFP+ , GFP- and bulk fractions) treated or not with TPO.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HSC-derived murine AML with or without Evi1+ (GFP+) expression treated or not with TPO

first: Hugues-Etienne

last: Chatel-Soulet

first: Athimed

last: El Taher

first: Juerg

last: Schwaller


title: A unified workflow to define multipotent progenitor hierarchies (HIVE)

first: Nathan

last: Salomonis

first: Kyle

last: Ferchen

last: Zhang

last: Grimes


title: Alveolar macrophages critically control infection by seasonal human coronavirus OC43 to avoid severe pneumonia

last: Dong

overall_design: Lung-derived samples from WT-PBS, WT-OC43, Csf2rb KO-PBS and Csf2rb KO-OC43 groups.

first: Xuan

last: Zhong

last: Xie


title: RNA next-generation sequencing of cardiac fibroblasts isolated from young and old mice 7 days post-MI

city: Bucharest

first: Evelyn-Gabriela

last: Nastase-Rusu

state: Romania

address: B.P. Hasdeu St

country: Romania

institute: The Institute of Cellular Biology and Pathology "Nicolae Simionescu"

summary: Despite recent advances in pre-clinical research on cardiac remodeling following myocardial infarction (MI), the precise molecular pathways remain poorly understood, and effective therapies for heart failure are still delayed in development. The use of young animal models fails to mirror the clinical scenario of aged human patients, as aging is associated to less well-defined cellular identities that can alter the overall picture of cardiac repair. Here, we explore the active role of cardiac fibroblasts in post-MI ventricular remodeling, aiming to identify fibroblast-specific pathways through the lens of aging that enhance translational relevance. Cardiac fibroblasts were isolated from mice with MI through 5 day-culture of total interstitial population of cardiac cells under fibroblast-favoring conditions. The expression profiling of these cells was conducted as the initial approach to depict fibroblasts-specific changes that are common to young and old animals. For a translational perspective of the study, a group of young animals that endured MSC therapy after MI surgery was also included, to help identify the molecular changes that are amenable for therapeutic modulation. This analysis revealed GLIPR1 as being activated in cardiac fibroblasts within the infarct zone during the maturation phase post-MI, thus suggesting a role in the fibrotic process. Further investigations indicated that the inflammatory environment post-MI induced the upregulation of GLIPR1 in the myofibroblast subpopulation of infarcted cardiac fibroblasts, which promoted matrix reorganization by increase in TIMP3 expression. Our study shows a key role of GLIPR1 in modulating the matrix remodeling during cardiac repair post-MI. The data presented here provide a fundamental cellular and molecular knowledge that paves the way for further exploration of GLIPR1 as a potential therapeutic target to reduce cardiac fibrosis.

overall_design: mRNA profiles of cardiac fibroblasts isolated either from normal mice or after 7 days post-myocardial infraction (MI) and spited intro 6 experimental groups: Young-no-MI operated mice (5 biological replicates), Young-Sham-MI (5 biological replicates), Young-MI (5 biological replicates), Young-MI+MSC (5 biological replicates), Old-Sham (2 biological replicates) and Old-MI (3 biological replicates) C57Bl/6J mice were generated by next-generation sequencing.

first: Alexandrina

last: Burlacu

first: Catalina I.

last: Marinescu-Colan

first: Evelyn

last: G Nastase-Rusu

first: Bogdan

last: Preda

first: Laudy

last: Cherry


title: Uli-Epic: A cutting-edge library construction strategy for profiling ultra-limited RNA modifications [Uli-Epic BID-seq]

first: Xu

last: Chu

overall_design: Ψ detection by bulk BID-seq and Uli-epic BID-seq in HEK293T mRNA. Ψ detection by Uli-epic BID-seq in ribominus RNA of mouse sperm and NSC

first: He

last: Weizhi


title: Systemic proteomic and small RNA profile analysis of extracellular vesicles derived from Theileria annulata

city: Lanzhou

first: Yijun

last: Chai

state: Gansu

address: No.1 Xujiaping, Gansu Lanzhou

institute: Lanzhou Veterinary Research Institute, CAS

type: Non-coding RNA profiling by high throughput sequencing

summary: Extracellular vesicles (EVs) are key mediators of intercellular communication, and often play critical roles in host-parasite interactions by facilitating parasite’s physiology and pathogenesis. Theileria annulata, an apicomplexan parasite, induces profound changes in host cells, leading to uncontrolled proliferation, apoptosis resistance, and increased invasiveness. In this study, we performed the comprehensive proteomic and small RNA analysis of EVs isolated from a T. annulata Kashi isolate-infected bovine lymphocyte cell line (TaXJS), B cell line (TaBC), dendritic cell line (TaDC), and from the sera of cattle before and after infection. Our label-free LC-MS/MS proteomics identified 2580 proteins, while small RNA sequencing revealed 6635 miRNAs associated with parasite development, host invasion, and immune evasion. Functional enrichment analyses recognized vesicular components involved in key pathways of the parasite-host such as ECM-receptor interaction, oxidative phosphorylation, and proton transport. These findings highlight the potential of Theileria-derived EVs in modulating host responses and their potential as therapeutic and vaccine targets.

overall_design: In this study,we performed the comprehensive proteomic and small RNA analysis of EVs isolated from a T. annulata Kashi isolate-infected bovine lymphocyte cell line (TaXJS), B cell line (TaBC), dendritic cell line (TaDC), and from the sera of cattle before and after infection.


title: Expression profiles in Chd7 knockdown astrocytes

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: Tebiro 6-10-1

department: New Projects Development Division

country: Japan

institute: Toray Industries,Inc.

summary: Chd7 is an ATP-dependent chromatin-remodeling enzyme. We performed a microarray analysis to examine changes in gene expression between control and Chd7 knockdown astrocytes. The results provide insight into the function of Chd7 in astrocytes.

overall_design: Astrocytes derived from P0 Chd7flox/flox mouse cortex were infected with control or Cre lentiviruses and were cultured with 10% FBS, FGF2, EGF, and B-27 supplement. Three days after infection, the virus-infected astrocytes were harvested.

first: Motoshi

last: Nagao


title: Diverse transcriptional alterations in V2a propriospinal neurons following spinal cord injury

first: Steven

middle: Allen

last: Crone

address: 3333 Burnet Ave, MLC 7007

department: Pediatric Neurosurgery

institute: Cincinnati Children's Hospital Medical Center

summary: The V2a neurons contribute significantly to recovery of locomotor and respiratory function after injury in animal models. We used single nucleus RNA sequencing of enriched cervical V2a neurons to analyze the diversity of these neurons and their response to spinal cord injury.

overall_design: Nuclei from Chx10Cre/+; ROSA26CAG-LSL-Sun1-sfGFP-Myc/+ mouse cervical spinal cords were isolated from uninjured mice or 5 days post C2 hemisection spinal cord injury. Fluorescence-activated nuclei sorting (FANS) was used to isolate V2a (GFP+) nuclei. The sorted nuclei were then subjected to single nucleus RNA sequencing using 10X Chromium 3v3.

first: Christina

last: Thapa

middle: A


title: RNA-seq study of a helicon peptide targeting β-Catenin/TCF transcription factor [in vivo]

city: Cambridge

first: YaGuang

last: Si

state: MA

address: 30 Acorn Park Dr

institute: Fogpharma

summary: Genetic and epigenetic alterations in the Wnt signaling pathway leading to constitutive activation of the driver oncogene β-catenin occur in at least 20% of all human cancers. Pharmacologic suppression of aberrant β-catenin transcriptional activity through direct targeting of its downstream effectors has proven elusive despite decades of effort.  We developed conformationally hyperstabilized α-helical peptides – which we refer to as Helicons – that directly bind β-catenin with sub-nanomolar affinity and exhibit good cytosolic exposure.   COLO320DM is a human colorectal cancer line with an activated Wnt/ β-catenin pathway driven by an APC mutation. Here, we characterize the global effects of Helicon treatment on COLO320DM xenograft tumor by whole-transcriptome RNA sequencing. Forty-eight hours after a single dose of Helicon 4 at 30 mg/kg, treatment significantly down-regulates many Wnt/β-catenin and MYC-related gene sets in tumors, consistent with the mechanism of action of the Helicon as a β-catenin/TCF interaction inhibitor

overall_design: COLO320DM xenograft tumor model was prepared by Avastus Preclinical Services. Mice were randomized and adminstrated when the average tumor size is about 300mm3

first: Peicheng

last: Du

first: Minjung

last: Choi


title: RNA-seq study of a helicon peptide targeting β-Catenin/TCF transcription factor [shRNA]

summary: Constitutive activation of Wnt/β-catenin signaling drives tumor initiation, maintenance, and metastasis in numerous preclinical models. Within the nucleus, β-catenin interacts with transcription factors of the TCF/LEF (T cell factor/lymphoid enhancer factor, TCFs) family. The transcriptional program mediated by these β-catenin/TCF interactions promotes cell proliferation, epithelial-mesenchymal transition (EMT), and a cancer stem-cell phenotype.   COLO320DM is a human colorectal cancer line with an activated Wnt/ β-catenin pathway driven by an APC mutation. Here, we apply a doxycycline-inducible shRNA to knockdown (KD) CTNNB1 (encoding β-catenin) and study the impact on the global transcriptome of COLO320DM. We also design and express an shRNA-resistant rescue cDNA to rule out any potential off-target effect. The results reveal a global gene expression change upon CTNNB1-KD that is consistent with β-catenin’s role in serving as a signal hub downstream of the canonical Wnt pathway.

overall_design: COLO320DM xenograft tumor models were prepared by WuXi AppTec (HongKong). Mice were randomized and a doxycycline-containing diet was introduced when the average tumor size reaches 150mm3. Tumor samples were collected on day 3 post dox treatment and flash-frozen until RNA extraction


title: RNA Sequencing dataset of Claudin-low Breast Cancer Cell Lines with Neuropilin-1 Knockdown

city: Brisbane

first: Colleen

last: Nelson

state: Queensland

address: 199 Ipswich Road

department: Institute of Health and Biomedical Innovation; Vancouver Prostate Centre

country: Australia

institute: Queensland University of Technology; University of British Columbia

summary: Triple-negative breast cancers (TNBC) are a particularly aggressive breast cancer subtype with poor prognosis and high relapse rates. Due to a lack of identified targeted therapies, chemotherapy currently remains as the primary treatment for TNBC. Approximately 25-39% of TNBC are claudin-low breast cancers, which are mainly defined by low expression of cell-cell adhesion proteins and enrichment of mesenchymal signatures. Functional studies have demonstrated the potential role of the transmembrane-coreceptor, Neuropilin-1 (NRP1) in regulating the progression of these tumours. However, there have been no high-throughput studies to date that comprehensively investigate NRP1-modulated cell signalling across multiple claudin-low cell lines. Therefore, we knocked-down NRP1 by two small-interfering RNA (siRNA) or two short-hairpin RNA (shRNA) sequences in each of HS578T, MDA-MB-231 and SUM159PT claudin-low cell lines and followed this with Bulk-RNA sequencing. We present this comprehensive transcriptomic data set which provides a valuable resource for the analysis of NRP1-regulated signalling pathways in claudin-low breast cancer, paving the way for future studies of its potential as a targeted therapeutic.

overall_design: 52 samples. 2-3 biological replicates of each treatment group. Three claudin-low breast cancer cell lines (HS578T, MDA-MB-231, SUM159PT) were treated with two siRNA and two shRNA sequences (3 and 5) that target NRP1, as well as respective non-targeting (NT) controls.

first: Layla-Rose

last: Lynam

first: Anja

last: Rockstroh

first: Melanie

last: Lehman

first: Marianna

last: Volpert

first: Brett

last: Hollier


title: Expression data from different CLL incidences in Asian and Western populations.

city: Guangzhou

first: YAO

last: LUO

address: Dong Feng East Road

institute: SYSUCC

summary:
Certain non-coding microRNAs play a major role in CLL pathogenesis, we postulate that a differential expression of microRNAs in different ethnic groups could potentially account for the different CLL incidences.
Using GeneChip® miRNA Array to analyze the global miRNA expression profiles in B lymphocytes from Asian and Western CLL patients and healthy individuals.

overall_design: Six CLL blood samples were obtained from Asian patients (Sun Yat-sen University Cancer Center), nine CLL blood samples were obtained from Western patients (MD Anderson Cancer Center); nine normal blood samples were obtained from Asian healthy donors, six normal blood samples were obtained from Western healthy donors. We  analyzed the global miRNA expression profiles to reveal key microRNAs that contribute to different CLL incidences in Asian and Western populations using GeneChip® miRNA Array.

first: Peng

last: Huang

first: Panpan

last: Liu


title: RNA-seq study of a helicon peptide targeting β-Catenin/TCF transcription factor [in vitro]

summary: Genetic and epigenetic alterations in the Wnt signaling pathway leading to constitutive activation of the driver oncogene β-catenin occur in at least 20% of all human cancers. Pharmacologic suppression of aberrant β-catenin transcriptional activity through direct targeting of its downstream effectors has proven elusive despite decades of effort.  We developed conformationally hyperstabilized α-helical peptides – which we refer to as Helicons – that directly bind β-catenin with sub-nanomolar affinity and exhibit good cytosolic exposure.   COLO320DM is a human colorectal cancer line with an activated Wnt/ β-catenin pathway driven by an APC mutation. Here, we characterize the global effects of Helicon treatment on COLO320DM cells in vitro by whole-transcriptome RNA sequencing. As expected, Helicon 4 treatment had both time- and dose-dependent effects on the COLO320DM transcriptional profile. In particular, the Hallmark Wnt/β-catenin gene set was significantly down-regulated as early as six-hour at 10uM. The result validates the on-target inhibition of β-catenin signaling through disruption of its interaction with TCF/LEF transcription factors by active Helicons.  COLO320DM is a human colorectal cancer line with an activated Wnt/ β-catenin pathway driven by an APC mutation. Here, we characterized the global effects of Helicon treatment on COLO320DM cells in vitro by whole-transcriptome RNA sequencing. As expected, Helicon 4 treatment had both time- and dose-dependent effects on the COLO320DM transcriptional profile. In particular, the Hallmark Wnt/β-catenin gene set was significantly down-regulated in as early as six -hours at 10 μuM. The result validates the on-target inhibition of β-catenin signaling through disruption of its interaction with TCF/LEF transcription factors by active Helicons.

overall_design: COLO320DM cell line was maintained in RPMI with 4%FBS. Cells were treated by Helicon 4, Helicon 4-neg or DMSO at indicated dose and timepoint, followed by RNA extraction and Sequencing

first: Erica

last: Visness


title: Multiomic analyses on the contribution of transposable elements to the cis-regulatory landscape of different types of immune cells[ChIP-seq]

city: Yangzhou

first: Cui

state: Jiangsu

address: NO.88 University South Road

institute: Yangzhou University

summary: Transposable elements (TEs) are key contributors to genetic novelty. Despite increasing evidence of their importance, their roles in shaping the regulatory landscape of different immune cell populations remain largely unclear. Using single-cell multiome from human peripheral blood mononuclear cells, we annotated the cell-specific cis-regulatory elements for diverse immune cells and identified a highly cell-specific signature regarding overrepresented TE families. Focusing on monocytes that bear fast-evolving transcriptomes, we found that high proportions of their enhancers are TE-derived and bound by multiple pioneer transcription factors. Among them, we confirmed that the core myeloid regulator SPI1 can bind and regulate hundreds of TE-derived enhancers, which affect the expression of adjacent immune genes. Interspecies comparison reveals that non-conserved monocyte enhancers are frequently generated by lineage-specific TE insertions, and correlate with the evolved gene expression between human and mouse. Our study highlights the importance of TEs in shaping the regulatory landscape of diverse immune cells.

overall_design: Two biological replicates were used per sample of siSPI1(SPI1 knockdown) ChIP-seq for H3K27ac in THP-1 cells.

first: Hairui

last: Fan

first: Wenbin

last: Bao

first: Ming-an

last: Sun


title: Multiomic analyses on the contribution of transposable elements to the cis-regulatory landscape of different types of immune cells[RNA-seq]

overall_design: Three biological replicates were used per sample of siSPI1(SPI1 knockdown) RNA-seq in THP-1 cells.


title: Immunoresponsive gene 1 like/itaconate axis promotes neuromast size via metabolic reprogramming to induce Yap signaling

city: Nantong City

first: Xin

last: Wang

state: Jiangsu Province

address: No.9, Seyuan Road

institute: Nantong University

summary: The organ size control and tissue homeostasis maintenance are vital in the formation of vertebrate sensory organs, which are tightly regulated. Here, we identify a metabolic regulatory axis, Irg1l, a zebrafish homologue of the mammalian mitochondrial enzyme immunoresponsive gene 1, and its product itaconate in neuromast development. It was demonstrated that irg1l was found to be highly and specifically expressed in supporting cells of developing neuromast, and decreased along the hair cell trajectory. Loss-of-function of irg1l caused neuromast size reduction and auditory dysfunction. Conversely, gain-of-function of irg1l increased the neuromast size. We found that excessive proliferation of supporting cells results in the larger neuromast. Notably, 4-octyl itaconate (4-OI), an itaconate derivative, recapitulates the phenotype of irg1l overexpression and increases the neuromast size. Mechanistically, Irg1l and itaconate induce succinate accumulation, which could lead to disruptions of the TCA cycle. It was confirmed by transcriptome sequencing and metabolic pathway inhibitor treatment. Inhibiting and activating YAP, respectively, can rescue the up- or down-regulation of Irg1l/itaconate-induced phenotypes, suggesting that YAP signaling acts downstream of metabolic reprograming induced by irg1l/ITA axis. Collectively, these results provide a novel insight into the role of metabolic signaling and its transduction during sensory organ development. Targeting this metabolic regulatory pathway within supporting cells may prove useful in further regulating sensory hair cell development and regeneration.

overall_design: This experimental study aimed to investigate a role of Irg1l/itaconate axis in zebrafish neuromast development using RNA-seq analysis. At 5dpf, Larvae treated with 4-octyl itaconate was preformed to subsequent transcriptomic analysis.

first: Rui-jun

last: Shi

first: Yu-Qing

last: Xiang

first: Dong


title: Loss of FBXO11 establishes a stem cell program in acute myeloid leukemia by dysregulating LONP1 [array]

city: Vancouver

first: Aly

last: Karsan

address: 675 West 10th Avenue

institute: Canada's Michael Smith Genome Sciences Centre

summary:
Purpose: The goals of this study are to compare the transcriptome profile of human cord blood derived CD34+ cells expressing shRNA targeting FBXO11 or non-targeting shRNA by microarray.
Methods: mRNA profiles of CD34+ cord blood cells expressing non-targeting shRNA or shRNA targeting FBXO11 were generated by microarray sequencing.

overall_design: CD34+ cord blood expressing non-targeting shRNA or shRNA targeting human FBXO11.

first: Hayle

last: Kincross


title: Systematic Pan-cancer Functional Inference and Validation of Hyper, Hypo and Neomorphic Mutations

city: New York

first: Somnath

last: Tagore

state: NY

address: 650W, 168th Street

institute: Columbia University

summary: While the functional effects of many recurrent cancer mutations have been characterized, the TCGA repository comprises more than 10M non-recurrent events, whose function is unknown. We propose that the context specific activity of transcription factor (TF) proteins—as measured by expression of their transcriptional targets—provides a sensitive and accurate reporter assay to assess the functional role of oncoprotein mutations. Analysis of differentially active TFs in samples harboring mutations of unknown significance—compared to established gain (GOF/hypermorph) or loss (LOF/hypomorph) of function—helped functionally characterize 577,866 individual mutational events across TCGA cohorts, including identification of mutations that are either neomorphic (gain of novel function) or phenocopy other mutations (mutational mimicry). We performed RNA-seq profiles were generated by Pooled Library Amplification for Transcriptome Expression (PLATE-Seq), a highly controlled microfluidic assays for 37 breast cancer-specific PIK3CA mutations in MCF10A cell line. Validation using mutation knock-in assays confirmed 15 out of 15 predicted gain and loss of function mutations and 15 of 20 predicted neomorphic mutations.  This could help determine targeted therapy in patients with mutations of unknown significance in established oncoproteins.

overall_design:
To prospectively validate our functional inference for PIK3CA mutational status, we selected 37 breast cancer specificPIK3CAmutations, comprising 9 GOF, 5 LOF, and 20 NEO predicted events, whose functional relevance had not been previously assessed in the FASMIC repository. For this purpose, differential gene expression signatures were generated from MCF10 cell, following lentivirus-mediated knock-in of mutant PIK3CA cDNA vs. mock cDNA as negative control. RNA-seq profiles were generated by Pooled Library Amplification for Transcriptome Expression (PLATE-Seq), a highly controlled microfluidic assay described in Bush et al., 2017 (PMID: 28740083), for 37 breast cancer-specific PIK3CA mutations in MCF10A cell line.
*** Submitter declares that raw files will be deposited in dbGAP. ***

first: Samuel

last: Tsang

first: Gordon

last: B Mills

first: Andrea

last: Califano


title: 3D Bioprinted Endometrial Patch Enhances Regeneration and Fertility through Organotypic Endometrial Architecture

status: Public on Oct 20 2025

city: Sungnam

first: Danbi

last: Lee

address: sampyeongro 335, Seongnam-Si, Kyounggido, Republic of Korea

department: Department of biological sciences

country: South Korea

institute: CHA university

summary: Intrauterine adhesions (IUA), a severe condition of endometrial injury, remains a major cause of female infertility due to the lack of effective long-term regenerative therapies. To address this unmet clinical need, we develop an engineered endometrial patch (EEP) fabricated by three-dimensional bioprinting of a porcine endometrium-derived decellularized extracellular matrix bioink loaded with endometrial epithelial organoids, stromal-immune populations, and endothelial cells. The spatially organized, tri-layered construct recapitulates the native architecture of the endometrium and supports epithelial polarity, vascularization, immune modulation, and hormone responsiveness. In a rat model of IUA, EEP transplantation markedly reduced fibrosis and rescued fertility with healthy offspring across generation by restoring endometrial receptivity and tissue integrity. Transcriptomic analysis revealed activation of stem cell proliferation, epithelial development and angiogenesis pathways, highlighting a mechanistic alignment with native tissue repair. Scalable fabrication of human cell-based patches which was administered into the cavity of the endometrium of IUA rabbit model further demonstrated translational adaptability. Together, our findings establish the EEP as a clinically applicable and customizable therapeutic strategy for endometrial regeneration for patients with infertility.

overall_design: 8-week-old of female rats were anesthetized via intraperitoneal injection of 2,2,2-Tribromoethanol (250 mg/kg). A small incision was made along both sides of the lateral abdominal midline to expose the uterine horns. A 23G needle bent at a 45° angle was used to mechanically abrade the endometrial lining in all directions until the surface appeared bloody and pale. Two days after IUA induction, the EEP was carefully inserted into one uterine horn, while the contralateral horn served as an internal control or given transplantation control patch (CP; Endo-UdECM printed without cells). For RNA sequencing, uterine tissues from each experimental group were harvested and total RNA was extracted. Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit (Lexogen, Inc., Austria) according to the manufacturer’s instructions, and sequenced on a NextSeq500 (Illumina, Inc., USA) in single-end mode (75 bp). Sequencing reads were aligned to the reference genome or transcriptome using Bowtie2. Transcript assembly, quantification, and identification of DEGs were performed using Bedtools and EdgeR (Bioconductor).

first: Tugce

last: Sen

first: Yu-Gyeong

first: Sun-Young

last: Hwang

first: Jae Yun

last: Kim

first: Jongmin

first: Jinah

last: Jang

first: Youn-Jung

last: Kang

first: Dong-Woo

last: Cho


title: A platelet transcriptomic signature of thromboinflammation predicts cardiovascular risk

first: Jeffrey

last: Berger

address: 435 E. 30th Street  Science Building, 723L

department: Department of Cardiology

institute: NYU Langone Health

summary: The CHOlesterol Reduction and Residual Risk in type 2 Diabetes (CHORD) study was a prospective study that investigated the effect of lipid lowering therapieis in participants with LDL-C >100 mg/dL without cardiovascular disease, off all antiplatelet therapy. Individuals with MPA levels, defined as CD14+CD16+ cells, were measured before and after four weeks of lipid lowering therapy. Patients were categorized as MPAhigh or MPAlow based on consistently high or low MPA levels accross timepoints. MPAhigh individuals exhibited an enrichment of immune signaling pathway. We developed a 42/gene Thromboinflammation Platelet Signature (TIPS), which correlated with MPA levels in multiple cohorts. TIPS was significantly elevated in patients with COVID-19 and myocardial infarction and predicted future cardiovascular events in patients who underwent lower extremity revascularization after a median follow-up of 18 months. Notably, TIPS was modifiable by ticagrelor. These findings introduce TIPS as a novel platelet RNA signature that captures platelet-immune activity and offers a promising tool for cardiovascular risk stratification.

overall_design:
RNA-seq profiling of platelets in individuals with LDL >120mg/dl before and four weeks after lipid-lowering medication
The current dataset represents 'baseline visit' samples.

middle: S

first: Matthew

last: Muller

first: Antonia

last: Beitzen-Heineke


title: Persistent Activation of Chronic Inflammatory Pathways in Long Covid

city: Boston

first: Dan

last: Barouch

address: 3 Blackfan Cir

department: CVVR

institute: Beth Israel Deaconess Medical Center

summary: Long Covid, or Post-Acute Sequelae of COVID-19 (PASC), involves a spectrum of chronic symptoms following resolution of acute SARS-CoV-2 infection. Current hypotheses for the pathogenesis of Long Covid include persistent SARS-CoV-2, activation of other viruses, tissue damage, autoimmunity, endocrine insufficiency, immune dysfunction, and complement activation. We evaluated 142 participants, including uninfected controls (N=35), acutely infected patients (N=54), convalescent controls (N=25), and Long Covid patients (N=28), using comprehensive immunologic, virologic, transcriptomic, and proteomic analyses. Long Covid patients were characterized by persistent inflammatory pathways compared with convalescent controls and uninfected controls, including upregulation of IL-6 and JAK-STAT pathways as well as activation of coagulation, complement, metabolism, and T cell exhaustion pathways. Moreover, excessive activation of these pathways during acute COVID-19 infection correlated with subsequent development of Long Covid. In an independent validation cohort (N=47), Long Covid patients had higher levels of plasma IL-6R compared with convalescent controls and uninfected controls. These data show that Long Covid is characterized by persistent activation of chronic inflammatory pathways, suggesting novel therapeutic strategies and targets.

overall_design: Blood samples were collected from 178 patients --- 120 of whom were previously infected with SARS-CoV-2, and suffering from known long COVID symptoms. Severity of long COVID was determeined by self-reporting, and validated by a clinician's assessment. PBMCs were harvested and RNA was extracted, and used for total RNA-seq.

first: Malika

last: Aid


title: SOX2 confers tumour permissiveness in a specific skin progenitor population

city: Glasgow

first: Patricia

last: Centeno

state: Scotland

address: Switchback Rd, Bearsden, Glasgow

institute: Beatson Institute for Cancer Research

summary: The skin’s continuous renewal relies on stem and progenitor cells, yet their differential susceptibility to oncogenic mutations in cutaneous squamous cell carcinoma (cSCC) remains poorly understood. Rapid cSCC development occurs in melanoma patients treated with BRAF inhibitors, driven by paradoxical MAPK activation. To model this in mice, we use two complementary approaches: HRASG12V with BRAFi to mimic paradoxical MAPK activation, and BRAFV600E, which drives MAPK hyperactivation without further treatment. We target these mutations to the interfollicular stem and differentiation-committed progenitors of the basal epidermis. While stem cells rapidly form tumours, progenitors exhibit long-latency resistance despite retaining mutations and repopulating the basal layer. Ultimately, both populations produce similar tumours, revealing a shared transformation programme. However, SOX2 is uniquely upregulated in tumours from the progenitor population. SOX2 is expressed in 20% of human cSCC, suggesting that it could mark tumours originating from committed progenitors. Here, we show that SOX2 overexpression in progenitors induces a stem-like state and renders this otherwise resistant population permissive to transformation.

overall_design: We conducted RNAseq in tumours driven by BRAFV600E expressed in the  IVL population in the presence and absence of SOX2 overexpressor

first: Centeno

last: Patricia P


title: Effects of attenuating astrocytic Ca2+ activity in the medial prefrontal cortex with iβARK on transcriptional profiles in 5xFAD mice (snRNA-seq)

first: Yamei

last: Tang

state: Guangdong

address: 107 Yan Jiang West Road

department: Department of Neurology

institute: Sun Yat-Sen Memorial Hospital

summary: We injected adeno-associated viruses (AAV2/5) carrying an inhibitory peptide derived from β-adrenergic receptor kinase 1 (iβARK), tagged with mCherry for identification, into the medial prefrontal cortex (mPFC) of 5xFAD mice. This strategy aimed to attenuate Gq GPCR-induced Ca2+ activity in astrocytes. In the control group, mice were injected with AAV2/5 expressing only mCherry. Subsequently, snRNA sequencing analysis was conducted on the mPFC tissue samples from these mice, enabling a comparative assessment of transcriptomic alterations and an exploration of the potential implications resulting from the modulation of Gq-GPCR signaling.

overall_design: Comparative gene expression profiling analysis of snRNA-seq data for WT-mCherry, WT-iβARK, 5xFAD-mCherry, and 5xFAD-iβARK.

first: Zhan

last: Zhang

first: You

last: Zuo

first: Wei-Jye

last: Lin


title: RNA-seq study of a helicon peptide targeting β-Catenin/TCF transcription factor [PDX]

first: YaGuang

last: Si

overall_design:
A colorectal cancer patient-derived xenograft tumor model was prepared by WuXi AppTec. Mice were randomized and adminstrated when the average tumor size is about 500mm3
***Submitter declares that the raw data is not provided due to Chinese laws prohibiting sharing genetic information with third party****

first: Peicheng

last: Du

first: Minjung

last: Choi


title: Periostin promotes sarcoma growth by increasing tumor associated macrophages. [CITE-Seq]

city: Houston

first: Jlenia

last: Guarnerio

state: TX

address: 6767 Bertner Ave

department: Genetics

institute: MD Anderson Cancer Center

summary: Soft tissue sarcomas (STS) are characterized by abundant extracellular matrix (ECM) deposition, yet the functional contribution of specific ECM components remains poorly understood. Here, we identify Periostin (POSTN), a matricellular protein, as a regulator of sarcoma progression and the tumor immune microenvironment. Analysis of human sarcoma datasets revealed that high POSTN expression correlates with poor prognosis and elevated expression of ECM-related and myeloid cell-associated genes. In murine genetic models of sarcoma, tumors expressing high levels of Postn displayed enhanced expression of ECM genes and monocyte-recruiting cytokines. Functional silencing of Postn in vivo reduced tumor growth without altering tumor cell proliferation or intrinsic signaling pathways, suggesting a non-cell-autonomous mechanism. Instead, Postn-deficient tumors showed increased infiltration of CD4+ and CD8+ T cells and reduced proportions of immunosuppressive myeloid cells, including tumor-associated macrophages (TAMs). Single-cell RNA sequencing revealed that Postn silencing reprograms the myeloid compartment, increasing interferon-responsive and pro-inflammatory subsets. Mechanistically, recombinant POSTN promoted monocyte migration and maturation into macrophages in vitro, supporting its role as a chemoattractant and differentiation cue. Therapeutic neutralization of POSTN partially recapitulated the immunologic remodeling but was insufficient to reduce tumor burden as monotherapy.

overall_design: Single-cell RNA-seq of the myeloid cell compartment FACS-enriched from Postn-WT and Postn-silenced tumors, using the p53KO Ccne1OE mouse model of undifferentiated pleiomorphic sarcoma (UPS).

first: Emily

middle: Y

last: Ko

first: Jin-Fen

last: Xiao


title: RNA Sequencing of Liver and Skeletal Muscle from WT and Heterozygous IGF-1R Mutant Mice

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

summary: This dataset includes gene expression profiles from liver and skeletal muscle samples of young female and male C57BL/6J mice with heterozygous IGF-1R R1096C mutation, along with age-matched wild-type controls.

overall_design: Young (4-month-old) female and male wildtype (WT) and heterozygous IGF-1R R1096C (IGF-1R Het) C57BL/6J mice. 48 biological replicates: 5-6 liver and 5-7 skeletal (gastrocnemius) muscle samples per genotype and sex.

first: Ulalume

last: Hernández-Arciga

first: Alibek

last: Moldakozhayev

first: Vadim

middle: N

last: Gladyshev

first: Andrey

last: Parkhitko


title: C9orf72 hexanucleotide repeat expansions impair microglial response in models of ALS [RNA]

city: Antwrepen

first: Renzo

last: Mancuso

address: Universiteitsplein 1

country: Belgium

institute: Vlaams Instituut voor Biotechnologie

summary: The involvement of microglia and neuroinflammation in amyotrophic lateral sclerosis (ALS) is well recognized, but the precise underlying molecular mechanisms remain elusive. We generated single-nuclei transcriptomic profiles from the spinal cord and motor cortex of sporadic (sALS) and C9orf72 (C9-ALS) ALS patients. We confirmed that C9orf72 is highly expressed in microglia and observed that the hexanucleotide repeat expansion (HRE) results in haploinsufficiency specifically in these cells. Whereas sALS microglia transitioned towards classically defined disease-associated transcriptomic profiles, C9orf72 HRE microglia exhibited a diminished response, with alterations in phagocytic and lysosomal pathways. We confirmed these observations using a human microglia xenograft model, which showed that C9orf72 loss-of-function leads to a reduced baseline activation, with lower expression of antigen-presenting related genes. We also confirmed the alterations in the endolysosomal pathway in C9orf72-HRE and C9orf72-deficient induced pluripotent stem cell (iPSC)-derived microglia. In addition, we observed a diminished response of astrocytes in C9orf72-HRE carriers and provided an extensive map of dysregulated ligand-receptor pairs in microglia and astrocyte indicating an altered cell-cell communication in both C9orf72 and sALS. This complex cellular interplay highlights variations in the cellular substrate of sporadic and inherited forms of ALS, providing valuable insights for patient stratification and for selecting appropriate treatments.

overall_design: iPSC' derived microglia were either sequenced for bulk RNA sequencing, or xenotransplanted into the mouse brain of Rag2-/- hCSF1KI with either a C9of72 KO or C9orf72 hexanucleotide repeat expansion cell line and their controls. Mice were sacrificed at 3 and 6 months.

first: Pegah

last: Masrori

first: Baukje

last: Bijnens

first: Laura

last: Fumagalli

first: Kristofer

last: Davie

first: Suresh Kumar

last: Poovathingal

first: Tim

last: Meese

first: Annet

last: Storm

first: Nicole

last: Hersmus

first: Raheem

last: Fazal

first: Diede

last: van den Biggelaar

first: Bob

last: Asselbergh

first: Roxane

last: Gruel

first: Johanna

last: Van Den Daele

first: Heidi

last: Denton

first: Paula

last: Polanco Miquel

first: Simona

last: Manzella

first: Winnok H.

last: De Vos

first: Siddarthan

last: Chandran

first: Ludo

last: Van Den Bosch

first: Dietmar Rudolf

last: Thal

first: Philip

last: Van Damme


title: C9orf72 hexanucleotide repeat expansions impair microglial response in models of ALS [scRNA]

first: Renzo

last: Mancuso

first: Pegah

last: Masrori

first: Baukje

last: Bijnens

first: Laura

last: Fumagalli

first: Kristofer

last: Davie

first: Suresh Kumar

last: Poovathingal


title: RNA-seq study of a helicon peptide targeting β-Catenin/TCF transcription factor

first: YaGuang

last: Si

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

overall_design: Refer to individual Series


title: lncNEAT1 regulates the transcriptional level of MAN1A1 to affect endometrial decidualization

city: Dalian

first: aihui

last: Zhang

state: Liaoning province

address: Longtou Subdistrict

institute: Dalian Medical University

type:
Expression profiling by array
Non-coding RNA profiling by array

summary:
Long noncoding RNAs (lncRNAs) are a class of RNAs with a length of more than 200 nucleotides. LncRNAs regulate gene expression by chromatin remodeling, transcriptional activation/interference, and mRNA processing and translation by interaction with DNA, mRNA, microRNA, and protein.  Increasing evidence also proposes the crucial role of lncRNAs in reproductive processes. In addition, lncRNAs regulate multiple steps of the biosynthesis of N- and O-glycans. In the current study, we hypothesized that specific lncRNA was involved in decidualization by regulating the expression of MAN1A1. Serum samples were collected from healthy and infertile women for RNA sequencing, and the screening of lncRNAs showed that lncNEAT1 level was increased in the serum and decidua of miscarriage patients, and negatively correlated with MAN1A1 expression. Further studies revealed that specific binding of lncNEAT1 with nucleophosmin (NPM1)-SP1 transcription complex inhibited MAN1A1 expression and hampered endometrial decidualization and embryo implantation potential. The study suggests the new insights into the function of high-mannose glycans/MAN1A1 modification during endometrial decidualization.
Compare the serum samples of healthy women and women with infertility to identify differentially expressed lncRNAs, and explore their role in endometrial decidualization

overall_design: Serum samples were collected from healthy individuals and infertile patients respectively. The samples submitted for testing consist of 2 groups of mixed serum samples: Group 1 is the mixed serum sample from healthy individuals, and Group 2 is the mixed serum sample from infertile patients.

first: Shai

last: Liu

first: Siyi

last: Chen


title: Senotoxins target senescence via lipid binding specificity, ion imbalance and lipidome remodelling.

city: madrid

first: gonzalo

last: colmenarejo

address: carretera cantoblanco s/n

country: Spain

institute: imdea food

summary: A total of 16 samples were processed for RNA sequencing. Sequencing data passed quality control was referred to as clean data. In this project, a total of 386.81 M Reads (115.24 Gb) Clean Data were obtained with minimum yield of 6.02 Gb clean data per sample. Percentage of Q30 bases in each sample was above 93.64 %.

overall_design: Cellular senescence was induced by incubation with 5 microM palbociclib in 75 cm2 flask (DMEM 10% FBS, 1% penicillin-streptomycin and 1% non-essential aminoacids)  Senescent SKMel147 cells (570x10e3 cell/well) were treated with StnI 100nM following a time course at 0, 3, 6 and 12 h. We investigated mRNA changes over thr time course of the treatments with the senotoxin StnI  1.3.1 RNA Quality Assessment Purity, concentration and integrity of RNA sample were examined by NanoDrop, Qubit 2.0, Agilent 2100, etc. Only RNA with good quality could move on to following procedures.  1.3.2 RNA Library Construction Qualified RNA were processed for library construction. The procedures are described as follow:  (1) mRNA was isolated by Oligo(dT)-attached magnetic beads.  (2) mRNA was then randomly fragmented in fragmentation buffer.  (3) First-strand cDNA was synthesized with fragmented mRNA as template and random hexamers as primers, followed by second-strand synthesis with addition of PCR buffer, dNTPs, RNase H and DNA polymerase I. Purification of cDNA was processed with AMPure XP beads.  (4) Double-strand cDNA was subjected to end repair. Adenosine was added to the end and ligated to adapters. AMPure XP beads were applied here to select fragments within certain size range.  (5) cDNA library was obtained by certain rounds of PCR on cDNA fragments generated from step 4.  1.3.3 Library Quality Assessment In order to ensure the quality of library, Qubit 2.0 and Agilent 2100 were used to examine the concentration of cDNA and insert size. Q-PCR was processed to obtain a more accurate library concentration and assure adequate library concentration.  1.3.4 Sequencing Qualified libraries were uploaded on Illumina NovaSeq 6000 platform for sequencing with read length of PE150.  2 Data Quality Control 2.1 Sequencing Data In next generation sequencing, e.g. Illumina NovaSeq 6000, etc., bases are inferred from light intensity signals generated by Illumina sequencing platform, which is known as base calling. Data generated directly from base calling is referred to as Raw data or Raw reads. Raw data was normally provided in FASTQ(fq) format, containing sequences and corresponding quality information. A demo FASTQ file is shown as below.  2.1.1 Sequence Quality Phred quality score described above represents the probability of an error base calling. Correspondence table of Qphred was shown below.  TIn NovaSeq 6000 sequencing, one DNA library template is firstly captured on flowcell and generats a cluster. The first cour cycels are used for cluster calling and establishing more suitable parameter setting based on current flowcell. Therefore, Base-calls of first several bases, which are generated relying on a standard parameter setting, are usually of low quality. The Q-score will increased back to normal with calibrated setting. Besides, it is also common to see that error rate climbs in the last few bases due to comsumption of reagents. Despite this, Q-score of most bases are higher than Q30.

first: Javier

last: Moral-Sanz

first: Isabel

first: Maria

middle: P

last: Ikonomopoulou


title: γδ T Cells Target and Ablate Senescent Cells in Aging and Alleviate Pulmonary Fibrosis

city: Mountain View

first: Gabriel

last: Meca-Laguna

state: CA

address: 110 Pioneer Way, Suite J

institute: Lifespan Research Institute

summary: A variety of physiological and pathological stimuli elicit the cellular senescence response. Immune cells are known to execute surveillance of infected, cancerous, and senescent cells, and yet senescent cells accumulate with age and drive inflammation and age-related disease. Understanding the roles of different immune cells in senescent cell surveillance could enable the development of immunotherapies against biological aging and age-related disease. Here, we report the role of human gamma delta (γδ) T cells in eliminating senescent cells. Human donor Vγ9vδ2 T cells selectively remove senescent cells of different cell types and modes of induction while sparing healthy cells, with parallel findings in mouse cells. We find that senescent cells express high levels of multiple γδ T cell ligands, including cell-surface BTN3A1. Individually blocking NKG2D or γδ TCR of γδ T cells only partially reduces Vγ9vδ2 T cell cytotoxicity, evidencing their versatility in senescence removal. γδ T cells expand in response to the induction of a mouse model of idiopathic pulmonary fibrosis (IPF), accompanied by the emergence of senescent cells, and colocalize with senescent cells in lung tissue from patients with IPF. Finally, we show that adoptive cell transfer of γδ T cells into an IPF mouse model reduces the number of p21-expressing senescent cells in affected lung tissue and improves outcomes. γδ T cells or modalities that activate their surveillance activity present a potent approach for removing senescent cells and their attendant contribution to aging and disease.

overall_design: Non-senescent (NS) and senescent (SEN, 24 hours of doxorubicin 300 nM and cultured for 9 more days) IMR-90 fibroblasts were used for single-nucleus RNA-Sequencing. For nuclei isolation, fibroblasts were transferred into pre-chilled 1.5 mL Eppendorf tubes and dissociated using the 10x Genomics Nuclei Isolation Kit (10X Genomics; Cat# PN: 1000494). Single-cell libraries were prepared using the Chromium Next GEM Single Cell Fixed RNA Sample Preparation Kit (10X Genomics; Cat# PN: 1000323) on the Chromium X instrument, following the manufacturer’s protocol. Sequencing was performed by SeqMatic (Fremont, CA, USA) on one lane of a NovaSeq X 10B system using 2 × 150 bp paired-end reads. Barcodes, matrix, and feature files were generated using Cell Ranger. The snRNA-Seq. was processed, explored, and visualized using Trailmaker/Cellenics® community instance (https://scp.biomage.net/) hosted by Biomage (https://biomage.net/).

first: Meca-Laguna

last: Gabriel

first: Amit

last: Sharma


title: Evaluation of the pharmacological effects of oridonin on hepatic ischemia/reperfusion injury in vivo

city: fuzhou

first: qiyuan

last: Yang

state: Fujian Province

address: The First Affiliated Hospital of Fujian Medical University, Taijiang District, Fuzhou City, Fujian Province

summary: The study aims to explore the protective effects of oridonin against hepatic ischemia–reperfusion injury (IRI) and its underlying mechanisms. Hepatic IRI is a significant clinical issue that can lead to severe liver dysfunction. Oridonin (Ori), a natural diterpenoid compound, has shown promising therapeutic potential. In an in vivo model of hepatic IRI, oridonin (5 mg/kg) treatment significantly reduced serum levels of liver injury markers. In this study, we comprehensively investigated the pharmacological effects of oridonin in the treatment of liver IRI and clarified the potential molecular mechanisms.

overall_design: RNA sequencing was performed on liver tissue from wild-type C57BL/6 mice subjected to ischemia–reperfusion injury, with and without oridonin.

first: Qiyuan

first: Zhikun

last: Zhan

first: Hang

last: Wang

first: Siyu

first: Lingyan

first: Qiaoling

last: Wu


title: RNA-seq analysis of  BASP1B-KO and BASP1B-WT germinal center B cells

city: Pittsburgh

first: Mark

last: Shlomchik

state: PA

address: The Assembly, 5051 Centre Avenue

department: Department of Immunology

institute: University of Pittsburgh

summary: The goal of this study was to define differences in genes expression between BASP1-sufficient and BASP1-deficient germinal center B cells

overall_design: mRNA profiles of day 10 BASP1-sufficient and BASP1-deficient germinal center B cells from NP-KLH-immunized mice, were generated in three replicates, by sequencing on an Illumina NextSeq500 using PE 150 Cycles High Output flowcell.

first: Sean

last: Robert

first: Shuchi

last: Smita

middle: J


title: tert-Butylhydroquinone (TBHQ) suppresses LPS- and Poly (I: C)- induced RAW 264.7 macrophage activation through reduced NF-κB/type 1 interferon and enhanced antioxidant-related pathways

city: Clemson

first: Alyssa

middle: Marie

last: Whisel

state: SC

address: 132 Long Hall

department: Biological Sciences

institute: Clemson University

summary: The global demand for processed foods has increased reliance on synthetic phenolic antioxidants (SPAs), including tert-butylhydroquinone (TBHQ), a widely additive used to prevent lipid oxidation and extend shelf life. TBHQ is considered safe at present regulated levels; though studies suggest potential adverse effects, including oxidative stress, genotoxicity, and impacts on immune function, raising concerns about human health and ecological risks. Herein, we investigated the immunomodulatory effects of TBHQ on RAW 264.7 murine macrophages pre-exposed to TBHQ and then stimulated with lipopolysaccharide (LPS) or polyinosinic-polycytidylic acid (poly I:C, PIC) to model bacterial and viral immune challenges. We then used functional assays and transcriptomic profiling to assess inflammatory responses and oxidative stress signaling. TBHQ reduced nitric oxide production and IL-10 secretion at the highest non-cytotoxic dose, and enhanced phagocytosis and IL-6 secretion at the lowest concentrations. Overall, transcriptomics revealed significant downregulation of proinflammatory pathways and induction of glutathione and xenobiotic metabolism. Pre-treatment with TBHQ increased gene transcript counts of key metabolic genes/transporters such as Cbr3, Adh7, Gstp1/3, Gsta3, Hmox1, and Gclm prior to LPS or PIC treatments. Following treatment with LPS or PIC several genes for classical proinflammatory chemokines and cytokines such as Cxcl2, Ccl2, Ccl12, Acod1, Ptgs2, Nos2, and Il6 were downregulated.  Genes involved in N-κB signaling, such as Nfkbia, Nfkb1, and Ikbke were also downregulated.  Our study suggests that the induction of Nrf2-related antioxidant pathways by TBHQ is the main driver for reduced inflammatory signaling in macrophages.

overall_design: RNA-seq profiling of RAW 264.7 macrophages pre-treated with tert-butylhydroquinone (TBHQ) for 4 hours and/or stimulated with lipopolysaccharide (LPS) or polyinosinic:polycytidylic acid (poly I:C, PIC) for 12 hours.

middle: M

first: Charles

middle: D

last: Rice


title: Multi-modal Omics Analysis of a Paediatric Melanoma Highlights Mechanisms Underlying Treatment Resistance [methylation]

city: Augsburg

first: Pascal

middle: David

last: Johann

address: Stenglinstrasse 2

department: Paediatric Oncology

institute: University Hospital Augsburg

summary:
Background
Cutaneous malignant melanoma is a common cancer in adults but extremely rare in young children, affecting fewer than one child per million each year in Europe. Because of its rarity, most treatments for children are adapted from adult therapies, despite possible biological differences. This study aimed to explore the molecular features of a rare and aggressive melanoma in a 16-month-old patient to understand disease progression and treatment resistance.
Methods
We studied the tumour and metastases of a patient with a melanoma carrying an NRAS mutation, who received chemotherapy and immune checkpoint inhibitor treatment. The patient died 10 months after diagnosis. We used DNA methylation analysis, single nucleus RNA sequencing, and deep spatial transcriptomic profiling to examine genetic changes, gene activity, and their spatial distribution in both the primary tumour and lymph node metastases.
Results
Here we show that the tumour displayed high genetic and transcriptomic diversity. We identified increases in MITF and BRAF gene copies as likely key drivers of the aggressive disease, which were not detected at diagnosis. We also found activation of biological pathways, including VEGFA and WNT signalling, and abnormal activity of several genes linked to immune therapy response, with marked variation between tumour regions.
Conclusions
This case demonstrates that paediatric melanoma can harbour complex and spatially variable molecular changes that contribute to rapid disease progression and treatment failure. Our findings support incorporating detailed spatial transcriptional profiling into clinical assessment to better guide therapy in rare paediatric cancers.

overall_design: The submission includes DNA methylation profiling by Illumina EPIC v2 array of primary tumour, healthy lymph node and lymph node metastasis from the paediatric melanoma patient.

first: Marlena

last: Mucha

first: Sebastian

last: Buehner

first: Maurice

last: Lossner

first: Victoria

middle: E

last: Fincke

first: Nic

middle: G

last: Reitsam

first: Felix

last: Dorn

first: Dajana

last: Lobbes

first: Katharina

last: Gastberger

first: Tobias

last: Schuster

last: Dintner

first: Christopher

last: Schroeder

first: Ines

middle: B

last: Brecht

first: Bruno

last: Maerkl

first: Michael

last: Fruehwald


title: Periostin promotes sarcoma growth by increasing tumor associated macrophages. [RNA-Seq 2]

first: Jlenia

last: Guarnerio

overall_design: RNA-seq of mouse tumor cells sorted from whole tumors, comparing two genetic models of undifferentiated pleiomorphic sarcoma.

first: Emily

last: Ko


title: Effects of interference and overexpression of NUDT3 on fat deposition in porcine subcutaneous adipocytes of pigs

city: Yangling

first: ya

middle: long

last: an

address: Xinong No.22

institute: Northwest Agriculture & Forestry University

summary: The enforced expression of NUDT3 significantly suppressed adipogenesis and lipid accumulation in porcine subcutaneous adipocytes. In addition, exogenous expression of NUDT3 in adipose tissue significantly reduced fat expansion triggered by a high-fat diet in mice. Mechanistically, the DEGs affected by NUDT3 overexpression and interference were significantly enriched in the PI3K-Akt signaling pathway were revealed. Western blotting further confirmed that the phosphorylation of Akt was significantly increased by NUDT3 knockdown, and the levels of phosphorylated PI3K, Akt and mTOR were significantly decreased by the enforced expression of NUDT3 both ex vivo and in vivo.

overall_design: In this project, the mechanism of NUDT3 in porcine adipocytes was explored through interference and overexpression of NUDT3 in vitro.

first: Yalong

last: An

first: Xiao

last: Li

first: Haoran

first: Peiyuan

last: Han


title: In vivo model of progressive tumor development in the anorectal transition zone (TZ)

city: Bron

first: Hector

last: Hernandez-Vargas

state: Rhone

address: 36 bis Rue de la Batterie

country: France

institute: Genomics Consulting

summary: Epithelial junctions are areas of associated pathology in human and mouse. In the case of the anorectal junction there is an abrupt transition from a simple columnar to a stratified squamous epithelium. To identify new regulatory mechanisms during injury and tumorigenesis, we studied this so called anorectal transition zone (TZ) at the single cell level. To this end, we took advantage of a mouse injury model where TZ cells are traced with fluorescent kerating 17 (K17CreER T2 x LSL-EGFP) at different points during transformation.

overall_design: Anorectal TZ cells were isolated by Fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.

first: Geraldine

last: Guasch

first: Chloe

last: Petitpas


title: Long Hypocotyl 1 mediates light regulation of adventitious root development in Arabidopsis

city: Nanjing

first: xingliang

last: Duan

address: weigang 1

institute: Nanjing Agricultural University

summary: Adventitious root (AR) formation is controlled by both endogenous and environmental cues. Light is an important environmental factor that has been reported to promote plant root development. However, knowledge about the mechanisms controlling light-mediated AR formation in etiolated hypocotyl cuttings is not fully understood. In this study, we report that a light-induced photomorphogenic gene Long Hypocotyl 1 (HY1), regulates AR formation in Arabidopsis and rice. In Arabidopsis, plastid-localized AtHY1 in pericycle cells was capable of activating AR formation. Transcriptome profiling and genetic evidence revealed that Phytochrome B (AtPHYB) and Long Hypocotyl 5 (AtHY5) act downstream of HY1 to regulate AR formation, through the stimulation of auxin signaling and transport. However, in rice, AR emergence at stem node is inhibited by light upon submergence, opposite to its effects in Arabidopsis. We further showed that defective mutants of OsHY1, OsPHYB and OsHY5 showed enhanced AR emergence by upregulating the expression of OsGH3s and OsPIN1 genes. These findings uncover a opposite role of HY1 on AR development in responses to light between Arabidopsis and rice.

overall_design: Dark to light treatment for 0, 12, and 24h bwteen hy1 and WT

first: Xingliang


title: p300 catalytic inhibition selectively targets IRF4 oncogenic activity in multiple myeloma

city: Cambridge

first: Walter

last: Lenoir

address: 301 Binney St

institute: Kronos Bio


title: C9orf72 hexanucleotide repeat expansions impair microglial response in models of ALS

first: Renzo

last: Mancuso


title: Next Generation Sequencing Analysis of control and siHNRNPM treated RKO cells Transcriptomes

first: Weizhen

last: Liu

address: No.138,Xianlin Avenue,Qixia District

institute: Nanjing University Of Chinese Medicine

summary: We treated the RKO cells with siHNRNPM or control siRNA for 48 hours.Then, we extracted RNAs and performed next generation sequencing. By comparing sequencing data from control and siHNRNPM samples, we profiled the alternative splicing events and gene expression regulated by HNRNPM in CRC.

overall_design: RKO cells mRNA profiles of control and siHNRNPM were generated by deep sequencing, using HiSeq X(Illumina, San Diego, CA).

first: Linlin

last: Chen


title: Periostin promotes sarcoma growth by increasing tumor associated macrophages. [RNA-Seq 1]

overall_design: RNA-seq of Postn-WT and Postn-silenced mouse undifferentiated pleiomorphic sarcoma (UPS) cells, sorted from tumors ex vivo.

first: Jin-Fen

last: Xiao


title: Machine learning analysis of the orbitofrontal cortex transcriptome of human opioid users identifies Shisa7 as a translational target relevant for heroin-seeking leveraging a male rat model

city: New York

first: Yasmin

last: Hurd

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

summary: Background Identifying neurobiological targets predictive of the molecular neuropathophysiological signature of human opioid use disorder (OUD) could expedite new treatments. OUD is characterized by dysregulated cognition and goal-directed behavior mediated by the orbitofrontal cortex (OFC), and next-generation sequencing could provide insights regarding novel targets.  Methods Here, we used machine learning to evaluate human post-mortem OFC RNA-sequencing datasets from heroin-users and controls to identify transcripts predictive of heroin use. To determine a causal link to OUD-related behaviors, we examined the effects of overexpressing the top target gene in a translational rat model of heroin-seeking and behavioral updating. Additionally, we determined the effects of overexpression on the rat OFC transcriptome compared to that of human heroin users. Co-immunoprecipitation/mass-spectrometry from rat OFC elucidated the protein complex of the novel target.  Results Our machine learning approach identified SHISA7 as predictive of human heroin users. Shisa7 is understudied but appears to be an auxiliary protein of GABAA or AMPA receptors. In rats, Shisa7 expression positively-correlated with heroin-seeking behavior. Overexpressing Shisa7 in the OFC augmented heroin-seeking and impaired behavioral updating for sucrose-based operant contingency. RNA-sequencing of rat OFC revealed gene co-expression networks regulated by Shisa7-overexpression similar to human heroin-users. Finally, co-immunoprecipitation/mass-spectrometry showed that heroin influences Shisa7 binding to glutamatergic and GABAergic receptor subunits. Both gene expression signatures and Shisa7 protein complex emphasized perturbations of neurodegenerative and neuroimmune processes.  Conclusions Our findings suggest that OFC Shisa7 is a critical driver of neurobehavioral pathology related to drug-seeking behavior and behavioral updating, identifying a potential therapeutic target for OUD.

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design:
To investigate the effects of opioid use disorder and overdose on the human OFC transcriptome, we conducted RNA-seq on post-mortem OFC tissue from heroin users and controls. We then conducted machine learning experiments to identify genes predictive of experimental group.
To translate these findings, we used a rat heroin self-administration model to test the effects of Shisa7 (identified as predictive in the human data) overexpression in the OFC, and conducted RNA-seq on OFC tissue from these animals

first: Randall

last: Ellis

middle: L


title: Tackling the early lung graft immunity by preconditioning donors with corticosteroids

city: Jouy-en-Josas

first: Jouneau

last: Luc

address: Domaine de Vilvert

institute: INRA

summary: Though lung transplantation (LT) is increasingly used to treat end-stage lung diseases, the clinical outcomes are disappointing, underscoring the need for novel therapeutic strategies. Preclinical studies revealed the critical role of innate immunity in LT outcomes. While corticosteroid boluses are routinely given to recipients, we hypothesized that donor preconditioning with corticosteroid could improve early immune parameters, in the context of ongoing clinical trials exploring various preconditioning approaches. We used a cross-circulatory pig platform that consists in a donor lung placed extracorporeally and connected to the circulation of a recipient pig whose leukocytes are fluorescently labelled. Donor preconditioning reduced the presence of CD3pos T-cell in the graft from both the donor and recipient, and enhanced the anti-inflammatory profile of alveolar macrophages, at least during first 10 hours of donor-recipient interaction. The alveolar macrophages isolated from corticosteroid-preconditioned pig lungs exhibited decreased gene expression of T-cell attracting chemokines during the 10-hour reperfusion period, correlating with the reduced T-cell infiltration. Similarly, human lung macrophages showed lower expression of these T-cell-attracting chemokines and higher anti-inflammatory profiles upon corticosteroid treatment. Thus, the early immune status of lung grafts is improved by donor preconditioning with corticosteroids through macrophage-targeted mechanisms, holding promises for enhanced clinical outcomes.

overall_design: scRNA-seq of MHC class II-positive cells from one pig lung

first: Isabelle

last: Schwartz-Cornil

first: Claudia

last: Bevilacqua

first: Thien-Phong

last: Vu-Manh

first: Ludivine

last: Soubigou-Taconnat

first: Clément

last: Pichot

first: Yann

last: JASZCZYSZYN

first: Luc

last: Jouneau


title: Single-cell RNA sequencing of pulmonaly pleomorphic carcinoma

city: Okayama

first: Shuta

last: Tomida

state: Okayama

address: 2-5-1 Shikata-cho, Kita-ku

department: Center for Comprehensive Genomic Medicine

institute: Okayama University Hospital

summary: Single-cell RNA sequencing (scRNA-seq) of pulmonary pleomorphic carcinoma (PPC) patients was conducted using the 10x Genomics platform to reveal the clonal evolution of PPCs.

overall_design: Surgically resected fresh frozen primary PPC samples from four patients were used. After tissue fixation and dissociation, library preparation was processed according to the Chromium Fixed RNA Profiling Reagent Kits for Multiplexed Samples.

first: Atsushi

last: Matsuoka

first: Kazuhiko

last: Shien


title: Viral-directed augmentation of Kupffer cell cross-presentation provokes anti-tumor immunity against liver metastasis

city: Hefei

first: Chen

address: huang shan Road 443

institute: university of science and technology of china

summary: Liver metastasis is associated with poor prognosis and resistance to immune checkpoint inhibitors. Functional modulation of Kupffer cells (KCs) holds promise as an alternative immunotherapeutic approach. Leveraging their ability to capture circulating virions, we developed an oncolytic virus-based KC-targeting strategy that demonstrates efficacy and safety in treating multifocal liver metastasis. A single intravenous infusion of the M51R mutant vesicular stomatitis virus (VSV-M51R), but not wild-type (WT) VSV, induced significant tumor regression in mouse models of melanoma and colorectal cancer liver metastasis. The ineffectiveness of VSV-WT was ascribed to its rapid induction of KC apoptosis, whereas VSV-M51R transiently replicated within KCs without compromising their viability. Depleting KCs abolished the therapeutic effects of VSV-M51R. Mechanistically, VSV-M51R treatment promoted KCs proliferation in tumor-adjacent areas, enhancing their access to tumor foci, uptake of tumor-derived materials, and cross-presentation of tumor antigens, leading to a robust activation of hepatic anti-tumor CD8+T cell responses that required MAVS-dependent type I interferon triggering of KCs. Simultaneous blockade of PD-L1, which was upregulated on KCs during VSV-M51R treatment, achieved remarkable synergistic efficacy in late-stage liver metastasis. Our findings underscore the pivotal role of KCs in systemic oncolytic virotherapy and offers a potentially clinically applicable strategy for treating advanced liver metastasis.

overall_design: RNA-seq profiling of Kupffer cells isolated from metastatic B16F10 melanoma-bearing mice that were either untreated or treated with VSV-M51R for 3 days.

first: Qing

last: Zhang

first: Jiajia

last: Li

first: Xia

last: Zhou

first: Jizhou

last: Wang

first: Daxing

last: Gao

first: Lu


title: Spatial profiling of temporal artery biopsies from patients with giant cell arteritis using NanoString GeoMx Whole Transcriptome Atlas

city: GLASGOW

first: Cecilia

last: Ansalone

address: Sir Graeme Davies Building - 120 University Place Glasgow

department: School of Infection & Immunity

institute: University of Glasgow

summary: This study used the NanoString GeoMx Digital Spatial Profiler (DSP) platform to spatially profile gene expression in temporal artery biopsy tissue from patients with giant cell arteritis (GCA), taken at the time of diagnosis. Tissue sections were hybridised with the Human Whole Transcriptome Atlas panel and segmented to isolate immune-enriched (CD45⁺) and full-tissue regions across anatomical layers (adventitia, media, intima). Gene expression data were stratified according to clinical trajectory, comparing patients who later achieved sustained remission (SR) under glucocorticoid monotherapy with those who relapsed or failed to remit (non-remission, NR). Non-GCA controls (C) were also included for comparisons. Data from two sequencing batches were merged and normalised using DESeq2 for downstream analysis. This submission includes: (1) unnormalised digital counts and segment metadata; (2) normalised processed data and associated metadata; and (3) clinical information to aid re-analysis.

overall_design:
Formalin-fixed paraffin-embedded (FFPE) temporal artery biopsies were processed using the NanoString GeoMx DSP platform with the Human Whole Transcriptome Atlas. Regions of interest (ROIs) were selected based on CD45 immunofluorescence and annotated into anatomical compartments (adventitia, media, intima). Each ROI was segmented into immune-enriched (CD45⁺) and full-tissue areas.  A total of n = 18 donors had CD45⁺-enriched segments, and n = 23 donors had full tissue segments, including: n = 21 with adventitia (A), n = 22 with media (M), n = 20 with intima (I) Donors were stratified into: n = 9 GCA non-responders (NR), n = 12 GCA steroid responders (SR), n = 4  non-GCA controls (C). Samples were processed in two independent batches and sequenced externally using Illumina NovaSeq 6000. Raw FASTQ files were processed via the GeoMx NGS Pipeline (v2.3.4 and v2.3.3.10). Unnormalised count data were exported from GeoMx DSP Analysis Suite (v3.1.0.222), curated to include only samples relevant to this study [Raw_Batch1-2_ExpressionMatrix.csv, and associated Batch1_SegmentProperties.csv and Batch2_SegmentProperties.csv], and normalised using DESeq2 (v1.38.3) in R (v4.2.2) [processed_CD45_A_em.csv, processed_FULL_areas_em.csv, and associated metadata (ss)].

***************************************************************
Raw data (fastq files) not available to submitter
***************************************************************

first: Samuel

last: McAllister

first: John

last: Cole

first: Nigel

last: Jamieson

first: Carl

last: Goodyear

first: Neil

last: Basu


title: Spatial transcriptomics of pulmonary pleomorphic carcinoma

summary: Spatial transcriptomics of Pulmonary Pleomorphic Carcinoma (PPC) patients were conducted using the GeoMx Digital Spatial Profiler to reveal intratumoral heterogeneity of PPCs at molecular level. Hybridization was performed using the Human Whole Transcriptome Atlas, targeting human protein-coding transcripts.

overall_design: In this study, 125 Regions of Interest (ROIs) were selected from nine PPC patients based on pathologically defined tumor components (epithelial and sarcomatoid), adjacent normal lung tissue and mediastinal lymph node metastasis. As a sub-analysis, we performed region segmentation based on the presence or absence of the morphology marker CD45 and analyzed the tumor immune microenvironment.


title: Multi-modal Omics Analysis of a Paediatric Melanoma Highlights Mechanisms Underlying Treatment Resistance [Seq]

first: Pascal

last: Johann

overall_design: The submission includes multiple datasets generated from the same samples, from one patient. The datasets include: 1. Spatial transcriptomics (GeoMx DSP) of the primary tumour, lymph node metastasis, healthy lymph node and recurrence.   2. single nucleus RNA-Seq (10X Genomics) of the primary tumour (hg38, 2020-A).

first: Marlena

last: Mucha

first: Sebastian

last: Buehner

first: Maurice

last: Lossner

first: Victoria

last: Fincke

first: Nic

last: Reitsam

first: Felix

last: Dorn

first: Dajana

last: Lobbes

first: Katharina

last: Gastberger

first: Tobias

last: Schuster

last: Dintner

first: Christopher

last: Schroeder

first: Ines

last: Brecht

first: Bruno

last: Maerkl

first: Michael

middle: C

last: Fruehwald


title: The Proteostasis Network is a Therapeutic Target in Acute Myeloid Leukemia

city: La Jolla

first: Robert

last: Signer

address: 2880 Torrey Pines Scenic Drive

institute: University of California, San Diego

summary: Oncogenic growth typically places great strain and dependence on protein homeostasis (proteostasis) pathways. This has made proteostasis pathways attractive therapeutic targets in cancer, but efforts to drug components of these pathways have yielded largely disappointing clinical outcomes. One notable exception is proteasome inhibitors, which are approved for frontline treatment of multiple myeloma. Despite this success, proteasome inhibitors are largely ineffective in the treatment of other cancers, including acute myeloid leukemia (AML), although the reasons for these cancer-specific differences are unknown. Here, we determined that proteasome inhibitors are ineffective in AML due to their inability to disrupt proteostasis. In response to proteasome inhibition, human AML cells activated heat shock factor 1 (HSF1) and increased autophagic flux to preserve proteostasis. Genetic inactivation of HSF1 sensitized multiple human AML cell lines to proteasome inhibition, marked by accumulation of unfolded protein and activation of the PERK-mediated integrated stress response. This response was associated with severe reductions in protein synthesis, proliferation and cell survival in vitro and significant slowing of disease progression and extension of survival in AML xenografts in vivo. Similarly, pharmacological inhibition of autophagy sensitized human AML cells to proteasome inhibition by disrupting proteostasis. Combined autophagy and proteasome inhibition suppressed proliferation and synergistically killed human AML cells in vitro, and significantly reduced AML burden and extended survival in vivo. Furthermore, combined autophagy and proteasome inhibition preferentially suppressed protein synthesis and induced apoptosis in primary patient AML cells, including CD34+ AML stem and progenitor cells, without severely affecting normal hematopoietic stem and progenitor cells. Effects of combined autophagy and proteasome inhibition were associated with induction of a terminal integrated stress response, which, surprisingly, was not driven by a canonical unfolded protein response, but rather by Protein kinase R (PKR). Overall, these studies unravel how proteostasis pathways are co-opted to promote AML growth, progression and drug resistance, and reveal that disabling the proteostasis network is a promising strategy to therapeutically target AML.

overall_design:
To investigate the effects of proteostasis perturbation, we inhibited the proteasome, autophagy, and the heat shock respone in human AML cell lines. We treated human AML cell lines TF-1a and OCI-AML3 with proteasome inhibitor carfilzomib and/or autophagy inhibitor Lys05. To inhibit the heat shock response, we established TF-1a cell lines in which HSF1, the master transcription factor of the heat shock response, was knocked out by gRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of TF-1a and OCI-AML3 treated with carfilzomib and/or Lys05, and HSF1+/+ and HSF1-/- TF-1a treated with carfilzomib for 24 hours.
To investigate the effects of proteostasis perturbation, we inhibited the proteasome and autophagy in human AML cell lines. We treated human AML cell lines TF-1a with proteasome inhibitor carfilzomib and/or autophagy inhibitor Lys05. We then performed gene expression profiling analysis using data obtained from RNA-seq of TF-1a treated with carfilzomib and/or Lys05 for 24 hours.

first: Kentson

last: Lam

first: Yoon Joon

last: Kim


title: p300 catalytic inhibition selectively targets IRF4 oncogenic activity in multiple myeloma (PBMC_KB528_timeseries)

first: Walter

last: Lenoir

summary: The oncogenic transcription factor (TF) IRF4 is a universal multiple myeloma (MM) dependency that remains undrugged owing to its disordered structure. Using transcriptional regulatory network (TRN) mapping, an unbiased multi-omic approach to nominate druggable TF cofactors, we identified the chromatin coactivator lysine acetyltransferase (KAT) p300 as a key IRF4 partner. We developed KB528, a highly selective p300 KAT inhibitor to explore the regulatory relationship between IRF4 and p300. Instead of broadly inhibiting transcription, partial p300 KAT inhibition selectively downregulates IRF4 and its downstream gene expression program leading to apoptosis selectively in MM cells. IRF4 dependency is a hallmark of MM that exists downstream of existing MM therapies. Consequently, p300 KAT inhibition exhibits strong antiproliferative activity ex vivo and in vivo as a single agent as well as in combination regimens in treatment refractory models. p300 KAT inhibition is well-tolerated in vivo motivating further clinical development in MM.

overall_design: PBMC cells at 0 (DMSO), 1, 3, 6, and 24 hour treated with 100 nM KB528 (p300 KAT inhibitor).

first: Marek

last: Kobylarz

first: Michelle

last: Shum

first: W

middle: F

first: Pete

last: Rahl


title: p300 catalytic inhibition selectively targets IRF4 oncogenic activity in multiple myeloma (MM1S_KB528_timeseries)

overall_design: MM.1S cells at 0 (DMSO), 1, 3, 6, and 24 hour treated with 100 nM KB528 (p300 KAT inhibitor).


title: p300 catalytic inhibition selectively targets IRF4 oncogenic activity in multiple myeloma (RPMI8226_KB528_timeseries)

overall_design: RPMI-8226 cells at 0 (DMSO), 1, 3, 6, and 24 hour treated with 100 nM KB528 (p300 KAT inhibitor).


title: SOX2 confers tumour permissiveness in a specific skin progenitor population.

city: Glasgow

first: Patricia

last: Centeno

address: Switchback Rd, Bearsden, Glasgow

institute: Beatson Institute for Cancer Research

summary: The skin’s continuous renewal relies on stem and progenitor cells, yet their differential susceptibility to oncogenic mutations in cutaneous squamous cell carcinoma (cSCC) remains poorly understood. Rapid cSCC development occurs in melanoma patients treated with BRAF inhibitors, driven by paradoxical MAPK activation. To model this in mice, we use two complementary approaches: HRASG12V with BRAFi to mimic paradoxical MAPK activation, and BRAFV600E, which drives MAPK hyperactivation without further treatment. We target these mutations to the interfollicular stem and differentiation-committed progenitors of the basal epidermis. While stem cells rapidly form tumours, progenitors exhibit long-latency resistance despite retaining mutations and repopulating the basal layer. Ultimately, both populations produce similar tumours, revealing a shared transformation programme. However, SOX2 is uniquely upregulated in tumours from the progenitor population. SOX2 is expressed in 20% of human cSCC, suggesting that it could mark tumours originating from committed progenitors. Here, we show that SOX2 overexpression in progenitors induces a stem-like state and renders this otherwise resistant population permissive to transformation.

overall_design: We conducted RNAseq in tumours driven by BRAFV600E expressed in the K5, K14 and IVL population and in normal skin.

first: Patricia P