title: Trabectedin and olaparib combination primes cellular immunotherapy with HLA-independent killer lymphocytes against sarcoma preclinical models through the cGAS-STING pathway

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

institute: University of Turin

summary:
Background. Advanced sarcomas have a severe prognosis, limited therapeutic options, and are seldom sensitive to immunotherapy with checkpoint inhibitors. Novel strategies are urgently needed.
Methods. We set up a preclinical approach for testing the combination of chemotherapy (trabectedin) and PARP1 inhibitor (olaparib) to potentiate the HLA-independent cellular immunotherapy with natural killer (NK) or cytokine-induced killer (CIK) lymphocytes. The NK/CIK activators NKG2DLs were studied by qRT-PCR and flow cytometry. Drug-induced transcriptomic events were studied by RNA sequencing and the activation of the cytosolic DNA sensing pathway (cGAS-STING-IRF3-IFNβ) was explored. Focusing on the putative cancer stem cell (CSCs) subpopulation, OCT4 marker was evaluated. IRF3 silencing experiments were done to investigate the role of the cGAS-STING pathway in the control of NKG2DLs. NK/CIK killing activity on both bulk and OCT4-positive cells was tested by viability assay and flow cytometry, respectively.
Results. We obtained the enhancement of NK/CIK activity against sarcoma cell lines through an integrated approach based on the combination of trabectedin and olaparib. These drugs upregulated the NKG2DL expression at both mRNA and protein level by inducing the genotoxicity pathway (WP4286) and repressing the cellular response to DNA damage stimulus (GO:0006974). The drug treatment significantly increased the cytosolic DNA content and consequently activated the cGAS-STING-IRF3 pathway and IFNβ production. These molecular events significantly enhanced the antitumor activity of NK and CIK against drug-pretreated sarcoma cells. The OCT4-positive cell fraction was enriched after chemotherapy. Noteworthy, NK/CIK cells efficiently killed both the drug-surviving bulk and CSC subpopulation.
Conclusions. Trabectedin+olaparib treatment followed by NK/CIK-based immunotherapy is a promising therapeutic strategy against sarcomas, deserving further investigations.

overall_design: Duplicate total RNA-Seq of HT-1080, DMR, S018 cell lines treated with Trabectedin (PharmaMar, Madrid, Spain) and olaparib (Biosynth Carbosynth, Staad, Switzerland) alone, in combination, or untreated.

first: Giorgia

last: Giordano

first: Federica

last: Capozzi

first: Alessandra

last: Merlini

first: Cristina

last: Tucciarello

first: Shahab

last: Majidi

first: Giulia

last: Mesiano

first: Erika

last: Fiorino

first: Elisa

last: Prola

last: Galvagno

first: Annamaria

last: Massa

first: Maria

last: Centomo

first: Silvia

last: Brusco

first: Valeria

last: Leuci

first: Santina

last: Cutrupi

first: Michele

last: De Bortoli

first: Massimo

last: Aglietta

first: Lorenzo

last: D’Ambrosio

first: Dario

last: Sangiolo

first: Giovanni

last: Grignani

first: Ymera

last: Pignochino


title: The stringent response does not influence ribosome pausing in Bacillus subtilis [Ribo-Seq]

status: Public on May 01 2025

city: Amsterdam

first: Yaozu

last: Han

address: Science Park 904

country: Netherlands

institute: Unversity Of Amsterdam

summary: The stringent response represses translation and is activated when amino acid levels drop, for example during the stationary phase. Bacillus subtilis, a well-known industrial enzyme production organism, secretes most enzymes during the stationary phase. We were curious whether the stringent response affects ribosome pausing, and whether its absence improves protein production yields in the stationary phase. To investigate this, genome-wide ribosome profiling was used using a stringent response mutant that overexpressed the α-amylase AmyM. Although, blocking the stringent response did increases overall protein synthesis, the secretion of AmyM was actually reduced. The ribosome profiling data revealed that this was not caused by a reduction in translation. In fact, absence of the stringent response did not seem to markedly influence ribosome pausing. However, late in stationary phase an increased ribosome pausing at tryptophane codons emerges, suggesting a depletion of tryptophane. A strong suppression of tryptophane biosynthesis and acquisition genes, under control of the trp RNA-binding attenuation protein TRAP, likely accounts for this, although TRAP does not belong to the stringent response regulon of B. subtilis. Finally, the ribosome profiles revealed several genes with unusually low translation activities, illustrating the importance of translation initiation as a regulatory element of expression.

overall_design: A high-copy expression plasmid was used to overexpress the heterologous α-amylase AmyM from G. stearothermophilus. Throughout this study this strain is referred to as the wild type (WT) strain. To eliminate the stringent response, we took this strain and deleted rel, sasA and sasB. This mutant is referred to as the ppGpp0 strain. Both strains were grown in rich medium for 16 h at 30 °C with continuous shaking.

first: Alberto

last: Agnolin

first: Frans

last: van der Kloet

first: Christopher

last: Sauer

first: Paul

last: Igor Costea

first: Max

last: Fabian Felle

first: Mathis

last: Appelbaum

first: Leendert

middle: W

last: Hamoen


title: Site-specific phosphorylation of ERα determines sex-dependent metabolic, reproductive, and body compositional phenotypes in mice

city: New Orleans

first: Binghao

last: Zou

address: 1430 Tulane Ave

country: USA

institute: Tulane University

summary: Estrogen receptor alpha (ERα) phosphorylation modulates receptor activity and downstream signaling. Previous studies identified human phosphorylation sites, serine-167 (S167) and serine-212 (S212) as critical regulators of ERα-mediated gene expression. Serine(S) to alanine(A) phospho knock-in mouse models of the corresponding murine sites, S171 and S216, were generated to assess physiological impact. Compared to WT mice, ERα protein levels in tissues were altered in a sex- and phosphorylation site-dependent manner. S216A males exhibited reduced adipose and increased lean mass. S216A females exhibited decreased femur bone density whereas S171A females exhibited increased bone density. S216A females were subfertile with fewer pups/litter. Single-cell and spatial transcriptomics revealed markedly altered E2-regulated uterine gene expression in both models. S216A mice exhibited reduced plasma metabolites in several key metabolic pathways. This study identifies critical roles for site-specific ERα phosphorylation in modulating receptor level/activity and gene expression that has profound impact on murine body composition, fertility, and metabolism.

overall_design: This study employed NanoString CosMx spatial transcriptomics to analyze formalin-fixed, paraffin-embedded (FFPE) uterine sections from ovariectomized mice treated with either vehicle or estradiol (E2). A 1000-plex gene panel was used to capture spatial gene expression. Machine learning-based cell segmentation enabled the identification of individual cells. Data normalization, principal component analysis (PCA), and uniform manifold approximation and projection (UMAP) clustering delineated distinct cell populations. Differential gene expression analysis and module scoring revealed cell type-specific transcriptional changes between wild-type and ERα phosphorylation mutants (S171A and S216A).

first: Weiqiang

last: Lin

first: Muralidharan

last: Anbalagan

first: Brian

middle: G

last: Rowan


title: The stringent response does not influence ribosome pausing in Bacillus subtilis [RNA-Seq]

type: Expression profiling by high throughput sequencing


title: Microbiota-derived acetate protects against UPEC-epididymo-orchitis by improving the phagocytosis of testicular macrophages.

city: ZhengZhou

first: Ming

last: Wang

address: jianshe Road

country: China

institute: ZhengZhou university

summary: The gut microbiota is intimately associated with maintaining a stable intestinal immune balance. However, it remains unclear whether gut dysbiosis affects the homeostasis within the testes. In our DSS-induced colitis mouse model, we observed increased inflammatory cell infiltration within the mouse testes. Analysis of the gut microbiota in the feces of DSS colitis mice and mice treated with antibiotics revealed a significant decrease in the number of bacteria related to cellulose decomposition in the gut, as well as a decrease in the content of short-chain fatty acid salts in the peripheral blood of mice. In vitro experiments found that acetate can significantly improve the outcome of UPEC-induced bacterial epididymo-orchitis. Further in vitro experiments demonstrated that acetate can enhance the bacterial phagocytic ability of testicular macrophages (TM), accelerate the early clearance of bacteria within the testes, and thus reduce the degree of testicular inflammation. This study provides a link to explain the progression of bacterial epididymo-orchitis in relation to gut microbiota dysbiosis and offers new insights for the treatment of bacterial epididymo-orchitis.

overall_design: Transcriptome analysis of TM stimulated by UPEC and sodium acetate. Approximately 10^6 TM were isolated and inoculated into 6-well plates. Sodium acetate (10mM) was pre-treated for 30 minutes, followed by UPEC (MOI: 5) infection for 3 hours, after which the cells were collected for transcriptome sequencing; (C1-2: Control group. U1-2: UPEC infected. A1-2: UPEC infected + sodium acetate treatment).

first: Zhengguo

last: Zhang

first: Zhongyu

last: Fan


title: A humanized neuronal model system reveals key roles for the trace element manganese in neuronal endocytosis, calcium flux and mitochondrial bioenergetics

city: London

first: Dimitri

last: Budinger

address: 30 guilford street

country: United Kingdom

institute: university college london

summary: Manganese (Mn) is an essential trace metal that is necessary for life. Its duality as both a crucial micronutrient and potential neurotoxicant necessitates tight control of intracellular and extracellular Mn levels. Dysregulation of Mn is implicated in a broad range of human diseases, from neurodevelopmental sequelae related to Mn levels in drinking water, to acquired forms of manganism, rare inherited Mn transportopathies and more common disorders such as Parkinson’s and Alzheimer’s disease. Despite the clear association between Mn dysregulation and neurodevelopmental or neurodegenerative diseases, the underlying cellular mechanisms that govern neuropathology remain poorly understood. We established a humanised midbrain neuronal system to better understand the neuronal sequelae of Mn dysregulation. By integrating transcriptomic and functional approaches, we show that Mn dyshomeostasis leads to dysregulation of key cellular pathways that are crucial to normal neuronal function, including defects in mitochondrial bioenergetics, calcium signalling, endocytosis, and glycosylation, as well as cellular stress and early neurodegeneration. Our humanized model has enhanced understanding of the role of Mn in the human brain, and the consequences of both acquired and genetic disorders associated with Mn dysregulation. Better understanding of these underlying pathophysiological processes will identify potential targets for future therapeutic intervention.

overall_design: Aged-matched healthy Controls (2) and 6 patient lines with SLC39A14, SLC30A10 and SLC39A8 deficient patients iPSCs-derived midbrain dopaminergic neurons (3 biological replicates each). These lines were analysed in both basal condition and manganese toxic overexposure (100uM for 48h). Neurons were 65 days when collected.

first: Manju

last: Kurian


title: The nuclear cap-binding complex regulates subcellular RNA processing and surveillance of coding and noncoding RNAs

status: Public on May 09 2025

city: Canberra

first: Diep

middle: R

last: Ganguly

state: ACT

address: 46 Sullivans Creek Rd

department: Research School of Biology

country: Australia

institute: The Australian National University

summary: RNA cleavage is essential for processing and regulating all classes of RNA. Current methods profiling genome-wide RNA cleavage are biased towards cytoplasmic events and ignore compartmentalized differences. Here, we couple subcellular RNA fractionation with degradome profiling to detect genome-wide nucleoplasm- and cytoplasm-enriched RNA cleavage in Arabidopsis thaliana. While messenger RNA (mRNA) cleavage dominated cytoplasmic fractions, we captured a diverse array of nucleoplasm-enriched RNA cleavage events. These included pre-mRNA cleavage and noncoding RNA processing, including for microRNAs, ribosomal RNAs, small nucleolar RNAs, enhancer-associated RNAs, and retrotransposon-derived RNA. Furthermore, our findings suggest that CAP-BINDING PROTEIN80/ABA HYPERSENSITIVE1 regulates mRNA surveillance within the perinuclear cytoplasm during the pioneer round of translation. Our data also emphasized its role in stabilizing nucleoplasmic RNAs (e.g. mRNA-associated antisense RNAs) and affecting cytoplasmic mRNA cleavage. Overall, our results highlight the diversity of compartmentalized RNA cleavage and reveal that the nuclear cap-binding complex has numerous functions in subcellular RNA processing and surveillance.

overall_design: Subcellular RNA fractionation coupled with global mapping of uncapped and cleaved transcripts (subcellular GMUCT) to produce nucleoplasmic and cytoplasmic RNA-enriched degradomes was performed on early-stage flower buds of Arabidopsis WT and abh1 (abh1-8; Gregory et al 2008, Developmental Cell) plants in biological triplicate. In parallel, strand-specific mRNA sequencing was also performed on bulk RNA from WT and abh1 flower buds in biological triplicate.

middle: D

last: Gregory


title: RNA sequencing dataset of spontaneously immortalised pre-adipocyte line from pig

status: Public on Apr 30 2025

city: Roslin

first: F. Xavier

last: Donadeu

address: Easter Bush

institute: University of edinburgh

summary: We have derived a spontaneously immortalised pre-adipocyte line using sequential long-term passaging of porcine mesenchymal stromal cells. Uniquely, this cell line (named FaTTy) gained a high level of adipogenic capacity during immortalisation which was maintained over more than 200 population doublings. Here, we provide transcriptomic data (bulk RNA sequencing) from FaTTy and parental MSCs of origin.

overall_design: To identify transcriptional chages associated with immortalisation and enhanced adipogenesis in FaTTy, we performed comparative bulk RNA sequencing followed by differential gene expression analysis of 4 parental MSC samples and 4 FaTTy cell samples

first: Thomas

last: Thrower

first: Susanna

middle: E

last: Riley

first: Xavier


title: The stringent response does not influence ribosome pausing in Bacillus subtilis

first: Yaozu

last: Han

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

overall_design: Refer to individual Series


title: Computational design of potent and selective BAK and BAX binders

city: Seattle

first: David

last: Baker

state: WA

address: Molecular Engineering and Sciences, Box 351655

institute: University of Washington

summary: There are numerous binders of the pro-survival BCL2 family proteins such as BCL2, MCL1, and BCL-XL, but development of potent and selective binders of their pro-apoptotic counterparts BAK and BAX has remained a major unsolved challenge. We use computational protein design to generate 13 kDa binders of BAK and BAX with 400 pM and 3 nM affinity, orders of magnitude higher than any existing native or designed binder, and with greater than 100-fold specificity against pro-survival BCL2 family members. The crystal structure of the BAKᐧɑBAK2 complex is very close to the computational design model, with the binder making specific interactions extending out from the canonical BH3-binding groove. Liposome- and cell-based analyses reveal that ɑBAK2 inhibits membrane permeabilization when in excess of BAK, but activates BAK when BAK is in excess. Structural analyses indicate that binding of ɑBAK2 results in partial unfolding and exposure of BAK’s BH3 domain. Similar to ɑBAK2, ɑBAX2 activates BAX at low concentrations and does not activate BAX at high concentrations. This work provides valuable insight into design of small molecule or protein inhibitors of BAK and BAX; inhibition requires high affinity binding as well as a saturating concentration of binder at the site of action. Our designs are the first binders with the high specificity required for efficient modulation of apoptosis via direct interaction with BAK and BAX and they provide highly selective molecular probes for addressing outstanding cell biological questions about cell death.

overall_design: In the related work, proteins were computationally designed to bind BAK or BAX. Site-directed saturation mutagenesis libraries were generated based on the sequences of sub-optimal minibinders, transformed into yeast for surface display, and selected for high-affinity binding to each target, optionally in the presence of unlabeled competitors (other BCL2 homologs). Next generation sequencing analysis of the naive and selected pools was used to determine the fitness of each mutation for affinity and specificity.

first: Stephanie

last: Berger


title: Metabolic licensing of quiescent glioblastoma activation and immune evasion via astrocyte-mitochondria shuttle

city: Hefei

first: Li

address: No. 443, Mount Huangshan Road, Shushan District

institute: University of Science and Technology of China

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The reaction of quiescent tumor cell subpopulations at the invasive margin of glioblastoma (GBM) might be cleared by immune surveillance toward death or expand through immune escape, which can drive therapeutic resistance, tumor dissemination, and recurrence through phenotypic plasticity. However, the process and mechanisms underlying their activation remain largely unclear. This study revealed that astrocytes awaken quiescent GBM cells to cycling and immune-evasive phenotypes. Astrocytic mitochondria are indispensable in regulating the phenotypic changes. Specifically, the SHMT2 enzyme in astrocytic mitochondria catalyzes one-carbon metabolic products, which significantly promote synthetic metabolic activation and reactivation of quiescent GBM cells to immune evasion through intercellular mitochondrial transfer. Tumor cells that acquire astrocytic mitochondria enhanced one-carbon metabolism drives global hyperactive anabolic metabolism through YTHDC1-mediated transcriptional pause release of ribosomal and focal adhesion signaling genes, supporting rapid proliferation and conferring a potent immune-evasive phenotype. Therapeutically, pharmacologic or genetic inhibiting the astrocytic SHMT2 or blocking mitochondrial transfer markedly suppressed quiescent GBM cell activation and tumor progression. These findings elucidate a novel mechanism by which astrocytes in the tumor microenvironment drive GBM malignancy through metabolic symbiosis.

overall_design: Glioma was digested and dissociated single-cell suspensions were loaded to scRNA-seq. U87 cells from co-culture system of various groups were sorted using Fluorescence-activated cell sorting (FACS) and analyzed using CUT&Tag seq.

first: Hongrui

last: Zhu

first: Qingsong

last: Hu


title: Genome-scale knockout simulation and clustering analysis of drug-resistant breast cancer cells reveal drug sensitization targets

city: Daejeon

first: Hyun Uk

last: Kim

address: 291, Daehak-ro, Yuseong-gu

country: South Korea

institute: KAIST

summary: Anticancer chemotherapy is an essential part of cancer treatment, but the emergence of resistance remains a major hurdle. Metabolic reprogramming is a notable phenotype associated with the acquisition of drug resistance. Here, we develop a computational framework that predicts metabolic gene targets capable of reverting the metabolic state of drug-resistant cells to that of drug-sensitive parental cells, thereby sensitizing the resistant cells. The computational framework performs single-gene knockout simulation of genome-scale metabolic models that predicts genome-wide metabolic flux distribution in drug-resistant cells, and clusters the resulting knockout flux data using uniform manifold approximation and projection. From the clustering analysis, knockout genes that lead to the flux data near that of drug-sensitive cells are considered drug sensitization targets. This computational approach is demonstrated using doxorubicin- and paclitaxel-resistant MCF7 breast cancer cells. Drug sensitization targets are further refined based on proteome and metabolome data, which generate GOT1 for doxorubicin-resistant MCF7, GPI for paclitaxel-resistant MCF7, and SLC1A5 as a common target. These targets are experimentally validated where inhibiting their expression results in increased sensitivity of drug-resistant cells to doxorubicin or paclitaxel. Taken together, the computational framework predicts drug sensitization targets in an intuitive and cost-efficient manner and can be applied to overcome drug-resistant cells associated with various cancers and other metabolic diseases.

overall_design: RNA-seq profiling of parental (drug-sensitive), doxorubicin-resistant, and paclitaxel-resistant MCF7 cells.

first: JinA

last: Lim

first: Hae Deok

last: Jung

first: Soo Young

last: Park

first: Moonhyeon

last: Jeon

first: Da Sol

first: Ryeongeun

last: Cho

first: Dohyun

first: Han Suk

last: Ryu

first: Yoosik


title: Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program [RNA-Seq]

status: Public on Apr 29 2025

city: Los Angeles

first: Jonathan

last: DiRusso

state: California

address: 615 Charles E. Young Drive

department: Molecular, Cell and Developmental Biology

institute: University of California Los Angeles

summary: Transposable elements are increasingly appreciated as regulatory elements in early mammalian development, especially in cells which exhibit pluripotency. Mammalian primordial germ cells (PGCs) must exit latent pluripotency in a process termed determination before they are competent to differentiate and enter sex-specific developmental programs. Here, we find that determination is marked by large changes to the transposable element (TE) repertoire, a phenomenon driven by TRIM28, after which testicular and ovarian PGCs exhibit district transposable element repertoires. We find that loss of TRIM28 perturbs entry into determination as marked by expression of DAZL in a sex-specific manner, but does not result in a failure to downregulate markers of latent pluripotency, including SOX2 and NANOG in either sex. Despite downregulation of some early PGC markers, both ovarian and testicular PGCs fail to properly enter into their meiotic germ cell or prospermatogonial programs, respectively. Thus, we show that TRIM28-mediated reorganization of the TE repertoire is necessary to establish a PGC epigenome competent for proper germline commitment and gametogenesis.

overall_design: Prdm1-cre, Trim28 Δ/flox, males were paired with Trim28 flox/flox, oct4-eGFP females for time mated breeding. Day of plug was marked as E0.5. Resulting embryos were genotyped and control (prdm1-cre -, trim28 +/flox) and TIRM28 knockout (prdm1-cre +, Trim28 Δ/Δ) kept for library preparation. At the dissected end point, embryos were removed and the embryonic gonads dissected and dissociated before isolation of PGCs via FACS.

first: Lingyu

last: Zhan

first: Tao

last: Yu

first: Amander

last: Clark


title: Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program [ChIP-Seq]

overall_design: Embryonic gonads from 10 time-mated CD1 mice were collected according to visual sex of the embryonic gonad. Gonads were processed as below.


title: Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program


title: RBM47 Inhibits Hepatocellular Carcinoma Progression as a DNA/RNA Regulator

status: Public on Apr 28 2025

city: Weifang

first: Yingying

last: Jiang

state: Shandong

address: 7166 Baotong west Road

institute: Weifang Medical University


title: Using a modular massively parallel reporter assay to discover context-specific regulatory grammars in type 2 diabetes - Tovar library

status: Public on Apr 27 2025

city: Ann Arbor

first: Adelaide

middle: Erin

last: Tovar

state: Michigan

address: 100 Washtenaw Ave

department: Computational Medicine & Bioinformatics

institute: University of Michigan

summary: Recent genome-wide association studies have established that most complex disease-associated loci are found in noncoding regions where defining their function is nontrivial. In this study, we leverage a modular massively parallel reporter assay (MPRA) to uncover sequence features linked to context-specific regulatory activity. We screened enhancer activity across a panel of 198-bp fragments spanning over 10k type 2 diabetes- and metabolic trait-associated variants in the 832/13 rat insulinoma cell line, a relevant model of pancreatic beta cells. We explored these fragments’ context sensitivity by comparing their activities when placed up- or downstream of a reporter gene, and in combination with either a synthetic housekeeping promoter (SCP1) or a more biologically relevant promoter corresponding to the human insulin gene (INS). We identified clear effects of MPRA construct design on measured fragment enhancer activity. Specifically, a subset of fragments (n = 702/11,656) displayed positional bias, evenly distributed across up- and downstream preference. A separate set of fragments exhibited promoter bias (n = 698/11,656), mostly towards the cell-specific INS promoter (73.4%). To identify sequence features associated with promoter preference, we used Lasso regression with 562 genomic annotations and discovered that fragments with INS promoter-biased activity are enriched for HNF1 motifs. HNF1 family transcription factors are key regulators of glucose metabolism disrupted in maturity onset diabetes of the young (MODY), suggesting genetic convergence between rare coding variants that cause MODY and common T2D-associated regulatory variants. We designed a follow-up MPRA containing HNF1 motif-enriched fragments and observed several instances where deletion or mutation of HNF1 motifs disrupted the INS promoter-biased enhancer activity, specifically in the beta cell model but not in a skeletal muscle cell line, another diabetes-relevant cell type. Together, our study suggests that cell-specific regulatory activity is partially influenced by enhancer-promoter compatibility and indicates that careful attention should be paid when designing MPRA libraries to capture context-specific regulatory processes at disease-associated genetic signals.

sample_organism:
Rattus norvegicus
synthetic construct

platform_organism:
Rattus norvegicus
synthetic construct

overall_design:
We selected fragment sequences from the first library with strong INS promoter-biased activity that contained HNF1 motifs. We added barcodes to these fragments using PCR and cloned these fragments into an MPRA vector via Golden Gate cloning. We electroporated 30 ug of barcoded library into 30 million INS-1/832/13 rat insulinoma cells and harvested the cells 24 hours later. We isolated total RNA, generated sequencing libraries and performed paired-end sequencing on the Illumina NovaSeq instrument.

UPDATE: [Jan-28-2026] The GSE279071_tovar_library_barcode_pairing.txt.gz and GSE279071_tovar_library_counts.txt.gz files were updated to add additional barcodes and to correct mis-assigned barcodes.

first: Yasuhiro

last: Kyono

first: Kirsten

last: Nishino

first: Maya

last: Bose

first: Arushi

last: Varshney

first: Stephen

middle: C

last: Parker

first: Jacob

middle: O

last: Kitzman


title: Tranposable Element Control by TRIM28 Safeguards PGC Sex Determination Program [ATAC-Seq]


title: RBM47 Inhibits Hepatocellular Carcinoma Progression as a DNA/RNA Regulator [ChIP-seq]

summary: After ChIP assay, DNA sequencing was conducted to analyze the specific loci binding by RBM47 in HCCLM3 cells.

overall_design: ChIP-seq of human HCC cells

last: Guo

first: Ke

last: You

first: Xi

last: Chen


title: Nanog is repurposed after implantation to repress Sox2 and begin pluripotency extinction

status: Public on Apr 26 2025

city: Guangzhou

first: Man

last: Zhang

state: Guangdong

address: No.9, XingDaoHuanBei Road, Guangzhou International Bio-island, Haizhu District

department: Department of Basic Research

institute: Guangzhou Laboratory

summary: Loss of pluripotency is an essential step in postimplantation development that facilitates the emergence of somatic cell identities essential for gastrulation. Before implantation, pluripotent cell identity is governed by a gene regulatory network that includes the key transcription factors SOX2 and NANOG. However, it is unclear how the pluripotency gene regulatory network is dissolved to enable lineage restriction. Here we show that SOX2 is required for postimplantation pluripotent identity and cells that lose SOX2 expression in the posterior epiblast are no longer pluripotent. Using in vitro and in vivo analyses we demonstrate anticorrelated expression of Nanog and Sox2 preceding gastrulation, culminating in an early disappearance of pluripotent identity from posterior NANOGhigh/SOX2low epiblast. Surprisingly, Sox2 expression is repressed by NANOG and embryos with post-implantation deletion of Nanog maintain posterior SOX2 expression. Our results demonstrate that the distinctive features of post-implantation pluripotency are underpinned by altered functionality of pluripotency transcription factors, ensuring correct spatio-temporal loss of embryonic pluripotency.

overall_design: EpiLCs were differentiated by culturing naive ESCs for 48 hours in EpiLC conditions (N2B27+ 1%KSR + Activin and Fgf2) . Culturing EpiLCs for 24 hours in the presence of the Wnt/ß-catenin signalling agonist CHIR99021 and Activin, which mimics the signaling environment occurring in the Nanog-positive proximal posterior epiblast, efficiently upregulated Nanog as well as markers of mesoderm and endoderm. Notably, Sox2 mRNA was low and SOX2 was absent from most cells, appearing prominently in cells lacking NANOG and T . These features are reminiscent of posterior epiblast (posterior epiblast-like cells; pEpiLC). Conversely, 24-hour culture of EpiLCs in N2B27 basal media induced neural markers Sox1 and Pax6, mimicking anterior epiblast (anterior epiblast-like cells; aEpiLC). In these conditions, Sox2 was upregulated and Nanog was suppressed.

first: Frederick

last: C. K. Wong


title: The pioneer transcription factor PBX as a downstream target of MNX1 [ACT]

status: Public on Apr 24 2025

city: Gothenburg

first: Eric

last: Malmhäll-Bah

address: Bruna stråket 16

department: Laboratory Medicine

country: Sweden

institute: University of Gothenburg

summary: Recently we have identified the upregulation of the homebox domain protein MNX1 associated with the paediatric t(7;12) AML as the initiating event for Leukaemia in mice. We demonstrated that MNX1 triggers abnormal histone modifications, specifically H3K4me3 and H3K27me3, by interacting with SAM-dependent methyltransferases. In the current study our aim was investigate downstream targets of MNX1 and the relationship with histone modification. Employing TMT Mass spectrometry and RNA-Seq integrative analysis identified the pioneer transcription factor PBX1 as a downstream target of MNX1. We observe that MNX1 binds to the promoter region of PBX1, leading to increased expression of PBX1. This binding of MNX1 to the PBX1 promoter was associated with enhanced H3K4me3 and decreased H3K27me3 in the same promoter region. Interestingly, this binding of MNX1, but not the histone modification on the PBX1 promoter was transient and diminishes as MNX1-FL cells progress to leukaemia in mice. To gain further insight, we conducted a comparative analysis of H3K4me3 using ACT-Seq and RNA-Seq data between MNX preleukemia FL cells and leukaemia MNX1 BM blasts. Our results indicate that this phenomenon is not limited to PBX1 but is rather widespread throughout the genome, identifying several downstream targets for MNX1 mediated H3K4me3 modification. Investigating the PBX1 and 4 motifs identified from Chip-Seq, revealed a significant enrichment in MNX1 H3K4me3 and ATAC-seq peaks. This suggest that PBX family might play an important role in the function of MNX1, which was further confirmed by showing MNX1 induced PBX1 expression to be downregulated using the sinefungin inhibitor, which we have previously reported to inhibit leukemia induction by MNX1.

overall_design: Antibody-guided chromatin tagmentation sequencing (ACT-seq) fot histone variants H3K4me3, H3K4me1 and transcription factor MNX1 as well as IgG control, in bone marrow and non-transplanted fetal liver cells, transduced with MNX1 or empty vector control.

first: Lars

last: Palmqvist

first: Ahmed

last: Waraky

first: Dieter

last: Weichenhan

first: Christoph

last: Plass


title: The pioneer transcription factor PBX as a downstream target of MNX1 [ATAC]

overall_design: ATAC-seq of fetal liver cells, transduced with MNX1 or empty vector control.


title: WUSCHEL-dependent cis-regulation in maize inflorescence development at single-cell resolution

status: Public on Apr 25 2025

city: Athens

first: Robert

middle: J

last: Schmitz

state: GA

address: B416 Davison Life Sciences

department: Genetics

institute: University of Georgia

summary: WUSCHEL (WUS) is a key transcription factor essential for the homeostasis of stem cells in the inflorescence meristem. In maize, ZmWUS1 is expressed in the central zone harboring stem cells, and its overexpression induces significant phenotypic alterations during the early stages of ear development. Here, single-cell ATAC-seq analyses revealed that ZmWUS1 overexpression alters chromatin accessibility exclusively in the central zone. This alteration includes both open and closed chromatin regions, with a notable predominance of the CAATAATGC motif observed in the open chromatin regions. Conversely, the TGAATGAA motif, identified through ZmWUS1-DNA interactions genome-wide, is not prevalent in these open chromatin regions and exhibits lower activity in the central zone compared to other cells. Furthermore, we observed the closed chromatin regions in the central zone involved in regulating auxin response factors genes, illustrating its negative impact on auxin signaling. These findings suggest that ZmWUS1 employs central zone-specific motif utilization and cis-regulation.

overall_design: Comparing the chromatin accessibility between wild type and Bif3 of maize immature ear.


title: Olfactory Receptors as Tumor Suppressors in Cutaneous T-Cell Lymphoma via p38γ Pathway Modulation

status: Public on Apr 23 2025

city: Duarte

first: Hannah

state: CA

address: 1500 E Duarte Rd

department: Research-Rosen, Steven - MC

institute: City of Hope National Medical Center

summary:
We screened 270,000 compounds from an NCI library for the ability to dock with the non-ATP-binding site of p38γ using virtual screen.
The resulting candidate compounds were for cytotoxicity assays to the Hut78 CTCL cell line and identified CSH18 as one of the most promising agents.

overall_design: To show downstream pathway that CSH18-mediated targeting of p38γ, we first isolated RNA and subjected to microarray analysis of treated vs. control cells and observed upregulation of TNF alpha in several top hit  after assesments of its downstream pathways.

first: Xu Hannah

first: Xiwei

last: Wu

first: Steven

middle: T

last: Rosen


title: Bacillus subtilis root biofilm social interactions influence on potato transcriptome

city: Ljubljana

first: Marko

last: Petek

address: Večna pot 111

department: Department of Biotechnology and Systems Biology

country: Slovenia

institute: National Institute of Biology

summary: To investigate bacteria-plant social interactions and their influence on plant growth and immunity on transcriptional level, we performed RNA-seq analysis in plants inoculated with B. subtilis monocultures and their combinations. The results show differences in regulation in various social interactions both at the level of processes and at the level of individual genes.

overall_design: potato shoots and roots, non-inoculated control (incubated in MS30 medium without bacteria) and Bacillus subtilis inoculated samples. B. subtilis inoculations. Two experiments were performed: 'Monocultures', with individual strains (PS-216 YFP and PS-218 YFP), and control; and 'Interactions', with individual strains (PS-216 YFP, PS-218 YFP, PS-218 mKate2), an isogenic mixture of two strains (PS-218 mKate2 + PS-218 YFP), a non-kin mixture of strains (PS-218 mKate2 + PS-216 YFP), and control. Sampling was performed in 4 biological replicates per treatment group.

first: Tim

last: Godec

first: Katja

last: Stare

first: Tjaša

last: Lukan

first: Kristina

last: Gruden


title: Increased HSD11β1 Expression in Human Leiomyomatous Uteri: Implication for Enhanced Glucocorticoid Signaling

status: Public on Apr 21 2025

city: Tampa

first: Umit

middle: Ali

last: Kayisli

state: Florida

address: 560 Channelside Dr,

department: Ob/Gyn

institute: USF Morsani College of Medicine

summary: Abstract: FK506-binding-protein-51 (FKBP51) is a glucocorticoid-induced co-chaperone protein previously shown to bind glucocorticoid receptor (GR), inhibiting its transcriptional activity. We previously found increased FKBP51 levels in uterine leiomyoma versus paired myometrium. To test the hypothesis that elevated FKBP51 levels contribute to leiomyoma pathogenesis by altering GR signaling. Material Method: RNA-sequencing was performed in leiomyoma cell cultures transfected with scrambled or FKBP5-siRNA for 48-h, then treated with vehicle or dexamethasone (DEX) for 24-h. Differentially expressed genes, including HSD11B1, CNN1, and LAMA2 were analyzed by qPCR. Hydroxysteroid 11-beta dehydrogenase 1 (HSD11β1) expression was analyzed in leiomyoma, leiomyoma-adjacent paired myometrium, myometrium from patients without leiomyoma, and human endometrial stromal cells (HESC) by qPCR and immunohistochemistry in women with or without uterine leiomyoma. HSD11B1 mRNA and protein levels in leiomyoma, paired and normal myometrium, and HESC cells and tissue. Results: HSD11β1 expression was higher in paired myometrial and leiomyoma tissues versus normal myometrium (P<0.02). DEX treatment increased HSD11B1 transcription in normal myometrial and HESC cultures, but to a significantly greater extent in leiomyoma. However, FKBP5-silencing blunted DEX-induced HSD11B1 transcription. DEX-treatment reduced LAMA2 and increased CNN1 levels (coding for extracellular matrix and smooth muscle proteins, respectively) in FKBP5-silenced versus scrambled-siRNA leiomyoma cultures. Conclusions: FKBP51 not only inhibits but can augment GR-mediated transcription. Importantly, FKBP51-GR interactions increase HSD11B1 levels in leiomyoma cells, generating a pathological FKBP51-GR-HSD11β1 circle, altering transcription of downstream extracellular matrix and smooth muscle genes to induce a myofibroblast phenotype, thereby possibly contributing to leiomyoma pathogenesis.

overall_design: RNA-sequencing was performed in pooled samples from leiomyoma cell cultures transfected with scrambled or FKBP5-siRNA for 48-h, then treated with vehicle or dexamethasone (DEX) for 24-h (n=4/group).

first: Carrie

middle: A

last: Malcom

first: Ozlem

last: Guzeloglu‑Kayisli

first: Erika

middle: P

last: New

first: Xiaofang

last: Guo

first: Charles

last: J. Lockwood


title: The role of smooth muscle cell-derived IL-18 in uterine immune milieu and fetoplacental growth

status: Public on Apr 18 2025

city: Tokyo

first: Hajime

last: Ino

address: 1-1-5, Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

summary: There is a close relationship between pregnancy and immune responses. For example, an anti-inflammatory state is essential for maintaining pregnancy by promoting maternal tolerance toward the semi-allogeneic fetus, whereas pro-inflammatory conditions are crucial for processes such as maternal tissue remodeling during embryo implantation and the induction of labor. Increasing evidence suggests that various cell types within the uteroplacental immune environment contribute to these immune responses, and immunological approaches have been employed to investigate the pathophysiology and potential treatments of pregnancy-related complications. Interleukin-18 (IL-18) is a unique cytokine with both pro-inflammatory and anti-inflammatory properties; however, its roles during pregnancy remain largely unclear. We have found that smooth muscle cells (SMCs) in the uterine myometrium are an important source of IL-18, and that the homeostatic production of IL-18 promotes fetal development by supporting maternal uterine remodeling and placental growth. To further investigate the effects of IL-18 on the uterine immune milieu, we established SMC-specific Il18 conditional knockout (cKO) mice and performed RNA sequencing of uterine immune cells.

overall_design: RNA-sequencing profiles of uterine immune cells collected from Il18-floxed (control) mice and Il18-floxed;Sm22a-cre (SMC-specific Il18 cKO) mice.

first: Yasuyuki

last: Negishi

first: Yumi

last: Horii

first: Eri

last: Koike

first: Richard

last: Flavell

first: Shunji

last: Suzuki

first: Rimpei

last: Morita


title: TSG-6 activated MSC-derived Extracellular Vesicles present altered micro-RNA contents and ameliorate the inflammatory phenotype of macrophages in vitro

city: Rochester

first: Iker

last: Martinez-Zalbidea

state: New York

address: 1 Lomb Memorial Dr

department: Department of Biomedical Engineering

institute: Rochester Institute of Technology

type: Non-coding RNA profiling by high throughput sequencing

summary: Mesenchymal stem cell-derived extracellular vesicles (MSC-EVs) have shown promising immunomodulatory properties; however, strategies to enhance their therapeutic potential remain limited. Here, we employed CRISPR activation of the gene TSG-6 in MSCs to evaluate the impact of elevated TSG-6 on micro-RNA (miRNAs) EV cargo and immunomodulatory function in an in vitro macrophage model. CRISPR-mediated gene activation was confirmed by RT-qPCR, demonstrating more than an 1800-fold increase in TSG-6 mRNA compared to controls. EVs were isolated from TSG-6 overexpressing MSCs and thoroughly characterized by nanoparticle tracking analysis, transmission electron microscopy, and Western blot, confirming their typical size distribution, morphology, and surface markers. Small RNA sequencing of these EVs revealed 15 differentially expressed miRNAs relative to EVs from control MSCs. When THP-1–derived macrophages were stimulated with LPS and treated with TSG-6-overexpressing MSC-EVs, a marked reduction in pro-inflammatory cytokine gene expression (IL-1β, CCL2, CXCL10, and TNF-α) and secreted protein levels (CCL2, TNF-α, CXCL1, and MIP-3α) was observed. Taken together, these findings demonstrate that CRISPR-based TSG-6 activation reprograms MSC-EV miRNA cargo (as well as their protein cargo, as previously shown), which can boost their anti-inflammatory effects. These findings underscore the promise of CRISPR-activation as a novel platform for boosting the bioactive properties of MSC-EVs and enhancing immunotherapeutic efficacy.

overall_design: RNA-seq profiling of Extracellular Vesicles (EVs) obtained from 3 different populations of mesenchymal stem cells. These populations are: Wild-Type, Non-Target controls (a negative control), and TSG-6 activated (CRISPR activation of gene TNFAIP6/TSG-6). Samples are in triplicate, with miR samples labeled as follows: Non-Targets labeled: “NA1_NA2_NA3” “NB1_NB2_NB3” “NTA_EV_RNA_NTB_EV_RNA_NTC”; TSG-6 activated labeled: “TA1_TA2_TA3” “TB1_TB2_TB3” “TSGA_EV_RNA_TSGB_EV_RNA_TSGC_EV_RNA”; Wild type labeled:“WA1_WA2_WA3” “WB1_WB2_WB3” “WTA_EV_RNA_WTB_EV_RNA_WTC_EV_RNA”.

first: Alyssa

last: Rzasa

first: Varun

last: Puvanesarajah

first: Wolfgang

last: Hitzl

first: Karin

last: Wuertz‑Kozak


title: Effect of BAY2402234 treatment on gene expression in nasopharyngeal carcinoma C666-1 cells

status: Public on Apr 02 2025

city: Huai'an

first: Xingchen

last: Dong

state: Jiangsu Province

address: No.1 Huanghe West Road

department: Department of Otorhinolaryngology

institute: Huai'an No.1 People's Hospital

summary: The DHODH inhibitor BAY2402234 has shown promising anti-tumor effects in various cancer types, but its molecular mechanisms in nasopharyngeal carcinoma remain unclear. This study investigates the transcriptomic changes induced by BAY2402234 in C666-1 nasopharyngeal carcinoma cells. We performed RNA-seq analysis of C666-1 cells treated with 2nM BAY2402234 for 48 hours compared to untreated control cells. Differential gene expression analysis revealed significant alterations in multiple pathways, including p53 signaling, cell cycle regulation, apoptosis, and ribosome biogenesis. Our findings provide insights into the molecular mechanisms underlying BAY2402234's anti-tumor effects in nasopharyngeal carcinoma, highlighting its potential as a therapeutic agent through modulation of critical cellular pathways involved in cancer progression.

overall_design: RNA-seq profiling of C666-1 nasopharyngeal carcinoma cells treated with 2nM BAY2402234 for 48 hours compared to untreated control cells.


title: A Single-Cell Woodchuck Liver Atlas Identifies Healthy and Disease-related Cellular Programs Conserved in Human [scRNA-Seq]

status: Public on Apr 08 2025

city: Toronto

first: Zoe

middle: Alixandra

last: Clarke

state: Ontario

address: 27 King's College Cir

department: Molecular Genetics

country: Canada

institute: University of Toronto

summary: Background: The eastern woodchuck (Marmota monax), which can be naturally infected with woodchuck hepatitis virus (WHV), has served as a model for aspects of human hepatitis B virus (HBV) infection, including the establishment of chronic infection and progression from chronic hepatitis to liver cancer. However, the cellular landscape of the woodchuck liver and its parallels to HBV infection remain uncharacterized. Methods: We present a woodchuck single-cell and spatial transcriptomic atlas in health and chronic WHV infection, with a characterization of cell-type and infection-driven processes in hepatic (Healthy: 52,024 cells; Infected: 40,810 cells; n=8 each) and peripheral blood mononuclear cells (Healthy: 25,314 cells, n=7; Infected: 19,518 cells, n=8). We further examined shared WHV–HBV disease pathways transcriptionally and assessed woodchuck liver immune responses functionally using precision-cut woodchuck liver slice stimulation. Results:  We applied our generated atlas and found hepatic cellular and immune diversity in woodchuck liver was comparable to human livers. We found that immune cells in the PMA/IONO stimulated PCLS displayed a type I inflammatory response as expected, reinforcing our annotations. Our atlas further demonstrated transcriptional and cellular similarities between the HBV and WHV infected liver, including the activation of dendritic cells in the periportal region of the infected liver, and a restructuring of the T cell compartment in WHV infection from memory towards exhaustion, a hallmark of human HBV. Conclusions: We present a multi-omic atlas of healthy, diseased, and ex vivo–stimulated woodchuck liver. This work identified shared WHV–HBV pathological processes, reinforces the value of this preclinical model and provides a resource to advance HBV pathogenesis studies and therapeutic development.

overall_design: Cells from unsorted woodchuck PBMCs and liver tissue were dissociated and sequenced with 10X Genomics SingleCell 3' v2 chemistry.

first: Jawairia

last: Atif

first: Xinle

last: Wang

first: Lewis

middle: Y

last: Liu

first: Lawrence

last: Wood

first: Damra

last: Camat

first: Yijia

first: Ariya

last: Shiwram

first: Sharon

last: Hyduk

first: Sai

last: Chung

first: Xue-Zhong

last: Ma

first: Justin

last: Manuel

first: Si

last: Lok

first: Timothy

last: Lau

first: Cornelia

last: Thoeni

first: Tomasz

middle: I

last: Michalak

first: Ian

last: McGilvray

first: Gary

last: Bader

first: Sonya

last: MacParland


title: Ionizing radiation-Induced reprogramming of polarized Macrophages and their exosomes

status: Public on Apr 07 2025

city: Jeongeup-Si

first: Hyoung-woo

last: Bai

address: 29 Geumgu-gil

institute: Korea Atomic Energy Research Institute (KAERI)

summary: Macrophages play a central role in immune regulation by adopting distinct polarization states—pro-inflammatory M1 and anti-inflammatory M2 phenotypes. Ionizing radiation has emerged as a promising tool for modulating immune cell functions; however, its impact on macrophage polarization and associated molecular changes remains poorly understood. In this study, we investigated the transcriptional and functional alterations induced by gamma irradiation (10 Gy) in M1- and M2-polarized RAW 264.7 macrophages. Transcriptome analysis was performed to identify radiation-induced gene expression changes and to uncover key regulators driving these responses. Additionally, we explored the biological functions of exosomes derived from irradiated macrophages, given their potential as cell-free therapeutic agents that reflect parental cell status. Our findings provide new insights into how ionizing radiation reprograms polarized macrophages and modulates their cytokine signaling and exosomal profiles, highlighting novel targets and strategies for immune modulation and therapeutic development.

overall_design: Transcriptomic profiling of ionizing radiation-exposed M1/M2-polarized macrophages and their exosomes by RNA-seq

first: Hanui

last: Lee


title: A Single-Cell Woodchuck Liver Atlas Identifies Healthy and Disease-related Cellular Programs Conserved in Human [snRNA-Seq]

first: Zoe

last: Clarke

first: Jawairia

last: Atif

first: Xinle

last: Wang

first: Lewis

last: Liu

first: Lawrence


title: Autism spectrum disorder associated chromatin modifiers converge on transcription with sex-specific regulatory signatures

status: Public on Apr 16 2025

city: Philadelphia

first: Alekh

last: Paranjapye

state: Pennsylvania

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: We sought to understand the transcriptional disruptions and functional impacts of the loss of 9 autism spectrum disorder (ASD) risk genes that encode transcriptional regulators in neurons. In addition to understanding how these signature converge or diverge, we aimed to study how sex could modulate these consequences.

overall_design: Neurons were cultured from wildtype e16.5 mouse embryos seperated by males and females. Cultures were infected with lentivirus containing shRNA against a nontargetted control or each of 9 genes to deplete targets. Neurons were lysed at day in culture 10 to collect total RNA. RNA was reverse transcribed and RNA-seq libraries were prepared. (n  =  3 per condition, per sex)

first: Rili

last: Ahmad

first: Erica

last: Korb


title: DAXX governs the silencing of LINE1 during 1  spermatogenesis in mice

status: Public on Apr 01 2025

city: Wuhan

first: shen

last: jin

state: Hubei

address: No. 299, Bayi Road, Wuchang District, Wuhan City

institute: Wuhan university

type: Methylation profiling by high throughput sequencing

summary: The disinhibition of transposon elements (TEs) is a significant threat to male reproduction, particularly during the delicate process of spermatogenesis. Here we identify that Death associated protein 6 (Daxx), a potent transcription repressor and an H3.3 chaperone essential for the TEs silencing during spermatogenesis. DAXX-deficient mouse display delayed meiotic progression, reduced production of spermatids, deformed spermatozoa and age-dependent decline in male fertility. We demonstrate that young long-interspersed nuclear elements (LINE1) and endogenous retroviral elements (ERVs) subfamilies, were upregulated in meiotic spermatocytes of Daxx null testes. Further study found that the Daxx mutant meiotic cells exhibit DNA hypomethylation in TEs. In summary, we have identified DAXX as a previously unknown key regulator of spermatogenesis that may function as an epigenetic regulator to silence young LINE1 by DNA methylation.

overall_design: This submission includes RNA-Seq(3 replicates), smallRNA-Seq(2 replicates), ATAC-seq(3 replicates), and WGBS sequencing(2 replicates) data from testicular spermatogonia and round sperms derived from wild-type and DAXX gene knockout mice. The samples aim to investigate the effects of DAXX gene deletion on reproductive health. The dataset comprises biological replicates for each condition, including both control (wild-type) and experimental (knockout) groups, to ensure statistical robustness and reproducibility of results

first: Zejia

last: Li

first: Chaoyang

last: Xiong

first: Jin

last: Shen

first: Chen

last: Tan

first: Dupeng

last: Ma

first: Jun

last: Chen

first: Rong

first: Qi

last: Sun

first: Weihao

last: Gong

first: Wenming

last: Yuan

first: Mengya

last: Huang

first: Li

first: Yueqiu

first: Guohong

first: Mengcheng

last: Luo


title: Transcriptome profiles of mouse cortical cultures and the brain treated with fluoxetine, sertraline or citalopram

status: Public on Mar 30 2025

city: Sendai

first: Hajime

last: Yamamoto

address: 2-1-1 Katahira, Aoba-ku

institute: Tohoku university

summary: Selective serotonin reuptake inhibitors (SSRIs) are one of the most prescribed antidepressant classes in recent decades, with the development of numerous variants. While the primary action of these medications involves the inhibition of serotonin reuptake, the observed therapeutic efficacy exhibits interindividual variability. In order to elucidate the molecular mechanisms underlying their pharmacological actions, this study examined the alteration in the transcriptome following treatment of each SSRI—fluoxetine, sertraline, or citalopram— or vehicle in cultured cortical neurons and the medial prefrontal cortex (mPFC) of mice (Mus musculus, Slc:ICR).

overall_design: In vitro experiment: Cortical cultures were obtained from the mouse embryo on embryonic day 15. Fluoxetine, sertraline, or citalopram were administered for each culture for 24 hours from 16 days in vitro (div). In vivo experiment: Male mice at 8 weeks of age were isolated and treated with either fluoxetine, sertraline, or citalopram for 2 weeks via drinking water, and then their mPFC regions were dissected. Those samples were subjected to RNA extraction and library preparation.

first: Kentaro

last: Abe


title: A Single-Cell Woodchuck Liver Atlas Identifies Healthy and Disease-related Cellular Programs Conserved in Human [spatial transcriptomics]

first: Zoe

last: Clarke

overall_design: Unbiased spatial transcriptomics (Visium) was applied to ascribe a geographical pattern of the different cell types in the woodchuck liver.

first: Jawairia

last: Atif

first: Xinle

last: Wang

first: Lewis

last: Liu

first: Lawrence

last: Wood

first: Damra

last: Camat

first: Yijia

first: Ariya

last: Shiwram

first: Sharon

last: Hyduk

first: Sai

last: Chung

first: Xue-Zhong

first: Justin

last: Manuel

first: Si

last: Lok

first: Timothy

last: Lau

first: Cornelia

last: Thoeni

first: Tomasz

last: Michalak

first: Ian

last: McGilvray

first: Gary

last: Bader

first: Sonya

last: MacParland


title: De novo genome assembly of faba bean (Vicia faba L.) leaf transcriptome provide novel insights into the drought stress tolerance mechanisms

status: Public on Mar 31 2025

city: Gembloux

first: Yordan

last: Muhovski

address: Chaussee de Charleroi

department: Life Sciences

country: Belgium

institute: CRAW

summary: Drought is a major limiting constraint to faba bean production worldwide, including Tunisia. However, molecular mechanisms underlying faba bean responses to drought stress are not well understood. In this context, transcriptome analysis by RNA-seq was performed to investigate drought-related genes and construct a network of faba bean drought stress response and tolerance. De novo assembly of the transcriptome generated 26,728 differentially expressed genes (DEGs). Of these, 13,920 were up-regulated and 12,808 down-regulated in faba bean drought-stressed leaves. Moreover, a total of 10,800 simple sequence repeats (SSRs) and 2130 transcription factors involved in major metabolic pathways including abscisic acid (ABA)-dependent and -independent signaling pathway were identified. GO, KOG and KEGG enrichment analyses revealed that these DEGs were involved in several important processes including photosynthesis, flavonoid biosynthesis, response to stimulus and abiotic stress, reactive oxygen species (ROS) scavengers, signal transduction, biosynthesis of secondary metabolites and transporters, suggesting the involvement of these important pathways in faba bean response to water deficit. Various stress proteins such as late embryogenesis abundant proteins (LEA), dehydrins (DHNs) and heat shock proteins (HSPs) have been identified and their expression was robustly upregulated in drought-stressed leaves, indicating their key contribution to drought response and adaptation by conferring protection and providing stability to faba bean plant cellular processes under water deficit. The reliability of the RNA-seq results was confirmed by the analysis of 10 randomly selected genes using qRT-PCR. Taken together, these findings help advancing our knowledge and can guide breeding programs aimed at improving the tolerance of faba bean to drought stress.

overall_design: The goal of the study was to investigate the leaf transcriptomic changes of faba bean (Vicia faba) in response to drought stress and to perform de novo assembly. The collected leaf samples (stressed and control) were ground in liquid nitrogen and the resulting powder was then used for RNA extraction using NucleoSpin RNA Plant kit (Macherey-Nagel, Germany). Library construction and  RNA sequencing were carried out at Beijing Genomics Institute (BGI), China, at a sequencing depth of 40 million paired end reads.

first: Ghassen

last: Abid

first: Khaled

last: Sassi

first: Frédéric

last: Debode

first: Benjamin

last: Dubois

first: Rim

last: Nefiss-Ouertani

first: Emna

last: Ghouili

first: Souhir

last: Abdelkrim

first: Zhengguo

last: Li

first: Salwa

last: Harzalli-Jabara

first: Moez

last: Jabara


title: The syntenic long non-coding RNA DANCR is an essential regulator of zebrafish development and a human melanoma oncogene

status: Public on Mar 25 2025

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

institute: University of Bath

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

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

first: Stephanie

middle: M

last: Jones

first: Elizabeth

last: Coe

first: Michael

last: Shapiro

first: Igor

last: Ulitsky

first: Robert

middle: N

last: Kelsh


title: Transcriptomic profiling of baricitinib effects on host immune response to RVFV infection in A549 cells and organoids

status: Public on Mar 28 2025

city: Trondheim

first: Aleksandr

last: Ianevski

address: Høgskoleringen 1

country: Norway

institute: NTNU

summary: This study investigates the modulatory effects of baricitinib on the host immune response to Rift Valley Fever Virus (RVFV) infection. A549 cells and organoids were treated with 5 µM baricitinib or vehicle control prior to infection with recombinant RVFV (rRVFV) or mock treatment. Total RNA was isolated at 8 and 24 hours post-infection, and mRNA was enriched for transcriptome sequencing. We performed RNA-seq analysis to identify differentially expressed genes and pathways affected by baricitinib treatment during RVFV infection, providing insights into potential therapeutic mechanisms of JAK inhibition in viral infections.

overall_design: This study investigates the effects of baricitinib on the host immune response to Rift Valley Fever Virus (RVFV) infection. We employed a 2×2×2×2 factorial design examining the following variables: cell system (A549 cells vs. lung organoids), treatment (5 µM baricitinib vs. vehicle control), infection status (recombinant RVFV vs. mock infection), and time point (8h vs. 24h post-infection). Each condition was performed in biological triplicate.


title: The role of OASL in Helicobacter pylori infection and Gastric Cancer

status: Public on Mar 19 2025

city: Changsha

first: Fen

last: Wang

state: Hunan

address: 138 Tongzipo Road

institute: The Third Xiangya Hospital, Central South University

summary: Our previous studies have shown thatHelicobacter pylori can induce the expression of OASL, which plays a crucial role in gastritis-cancer progression. In order to further investigate the detailed mechanism of OASL, we constructed an OASL overexpression model in HGC27 cells.

overall_design: RNA-seq profiling of OASL-overexpressing HGC27 cells as well as corresponding controls.

first: Minglin

last: Zhang


title: Factors Driving Diversity in Gene Regulatory Networks at Genome Scale[ASE]

city: Cambridge

first: Jie

last: Yun

state: MA

address: 77 MASS

department: CEE

institute: MIT

summary: Gene expression is a quantitative trait under the control of genetic and environmental factors and their interaction, so-called GxE. Understanding the mechanisms driving GxE is fundamental for ensuring stable crop performance across environments, and for predicting the response of natural populations to climate change. Gene expression is regulated through complex molecular networks, however environmental and genotypic effects on genome-wide regulatory networks are rarely considered. In this study, we model genome-scale gene expression variation between two natural accessions of the model grass Brachypodium distachyon and their response to soil drying. We identified genotypic, environmental, and GxE responses in physiological, metabolic, and gene expression traits. We then identified gene regulation conservation and variation among conditions and genotypes, simplified as co-expression clusters found unique in or conserved across library types. Putative gene regulatory interactions are inferred as network edges with a graphical model approach, resulting in hypotheses about gene-gene interactions which are then found to be specific to or with higher affinity in one genotype (G regulation), one environmental treatment (E regulation), or in one genotype under treatment (GxE regulation). Some gene-gene interactions are conserved across conditions so the differential expression is accordingly transmitted to target genes. These variably detected edges cluster together in co-expression modules, suggestive of different constraints or selection strength acting on specific pathways. We further applied our graphical model approach to identify putative, E-dependent regulatory mechanisms of leaf glucose content as an exemplar metabolite. Our study highlights an approach to identify variable features of gene regulatory networks and thereby identify key components for later genomic intervention to elucidate function or modulate environmental response. Our results also suggest possible targets of evolutionary change in gene regulatory networks associated with environmental plasticity.

overall_design:
To study regulation mechanism of how different genotypes of Brachypodium (Bd21 and Bd3-1) response to soil water deficit differently, we generated hybrid of the two genotypes and applied same treatments and harvest samples for RNA sequencing. We started gradual dry-down on 33rd day with a soil water content ended up 55% for drought and 85% for control after 6 days. The youngest fully expanded leaves from 5 replicates of hybrids under drought and control treatment, and 2 control Bd3-1 samples were harvested at a single time point 1-2:30pm of the day for RNA sequencing. These along with 12 samples (each genotype and condition, replicated three times) from the main experiment with exact same treatments are sequenced.
We did gene expression profiling analysis and differential expression by fitting models using DESeq2 to infer gene regulation mechanism.

Grant: IOS 2239070
Grant title: NSF CAREER Award
Grantee: David Des Marais
Funding agency: National Science Foundation

first: Angela

last: Burnett

first: Alistair

last: Rogers

first: David

middle: L

last: Des Marais


title: UUO-rUUO single population RNA seq, Denby lab 2019

status: Public on Mar 27 2025

city: Edinburgh

first: Laura

last: Denby

state: Midlothian

address: Queen's Medical Research Institute, 47 Little France Cres

institute: University of Edinburgh

summary: RNA sequencing of sorted cell types, isolated from mice kidneys, after unilateral ureteral obstructive (UUO) surgery after 2 days, 7 days and a reversible (rUUO) 14 day model with corresponding sham operated mice. The goal of the study was to identify temporal gene expression changes in different cell types corresponding with kidney injury, in order to understand cell specific transcriptomic changes in the context of kidney injury and repair.

overall_design: Each group was sequenced from 4 mice, and 4 cell types. 2 day UUO kidneys were sorted into PDGFRβ+, F480+, LTL+ and CD31+ cell types before the RNA was extracted and small RNA sequenced for 4 mice. The same protocol was followed for 7 day UUO mice, rUUO mice, as well as sham operated mice for reference.

first: Oliver

last: Teenan

first: Katie

last: Connor

first: James

last: O'Sullivan


title: Anti-CD3 mAb treatment reshapes infiltrating T and beta cells in the islets in autoimmune diabetes

status: Public on Mar 24 2025

city: New Haven

first: Ying

last: Wu

state: CT

address: 300 George St

institute: Yale University

summary: Anti-CD3 mAb delays or prevents type 1 diabetes (T1D) by modulating the immune mediated destruction of beta cells. Our findings described the reshaping of islet-infiltrating T cells and beta cells that lead to operational, but tenuous tolerance to autoimmune diabetes following anti-CD3 mAb treatment.

overall_design: Islets and paired pancreatic draining lymph nodes were isolated from anti-CD3 treated NOD mice in remission and processed for single-cell 5' RNA sequencing. Each scRNAseq dataset is multiplexed and contains islet cells or pancreatic draining lymph nodes of 3 mice, each individually labeled by hashtag barcode.

first: Maxwell

last: Spurrell

first: Ana

last: Lledó-Delgado

first: Songyan

last: Deng

first: Dejiang

first: Yang

last: Liu

first: Mahsa

last: Nouri Barkestani

first: Ana Luisa

last: Perdigoto

first: Kevan

last: Herold


title: Single-cell RNA-Sequencing of Wild-type Perinatal Mice Thymi

city: Nashville

first: Bryan

middle: Robert

last: Helm

state: Tennessee

address: 2525 West End Avenue, Suite 1100

department: Center for Quantitative Science

institute: Vanderbilt University Medical Center

summary: We prepared enzymatically digested thymus single cell suspensions for scRNA-Seq. Cells were extracted from perinatal mice, and TEC cells were enriched via FACS using anti-EpCAM and Anti-CD45 to isolate EpCAM+ CD45- TECs.

overall_design: FACS purified TECs were obtained from P0, P3, P7, P10, P15 and P28 C57Bl6/J male and female thymuses. Supplicate experiments were performed for each time point except for P15.

first: Ellen

last: Richie

first: Anusha

last: Vasudev

first: Nandini

last: Singarapu

first: Qi

first: Ken

last: Lau


title: Factors Driving Diversity in Gene Regulatory Networks at Genome Scale[main]

first: Jie

last: Yun

overall_design:
To study how different genotypes of Brachypodium response to soil water deficit differently, we include two genotypes, i.e., Bd21 and Bd3-1, and two environment, i.e., drought and control samples. We started gradual dry-down on 33rd day after germination with a soil water content ended up 55% for drought and 85% for control after 6 days. The youngest fully expanded leaves from 48-59 replicated plants were harvested at a single time point 1-2:30pm of the day for RNA sequencing.
We did gene expression profiling analysis and differential expression among library types, especially interaction effect. The gene regulation network variation among library types are characterized based on gene expression clustering and its variation, infered gene regulations and its variation which is based on slope variation of multiple regression of target gene on its regulators.
Replicates are used for differential gene expression study, and variations among replicates are utilized for co-expression cluster, gene regulation inference, and multiple regression of gene expression.

Grant: IOS 2239070
Grant title: NSF CAREER Award
Grantee: David Des Marais
Funding agency: National Science Foundation

first: Angela

last: Burnett

first: Alistair

last: Rogers

first: David

last: Des Marais


title: Age-related reproductive performance and transcriptome profiling of testis in male blue catfish, Ictalurus furcatus

status: Public on Mar 17 2025

city: Auburn

first: Ian

last: Butts

state: Alabama

address: 203, Swingle Hall

department: School of Fisheries, Aquaculture & Aquatic Sciences

institute: Auburn University

summary: Catfish farming is the largest aquaculture industry in the U.S., where hybrid catfish produced by channel catfish, Ictalurus punctatus ♀ × blue catfish, I. furcatus ♂, represent >50% of the harvest. Typically, older blue catfish (≥5 years) are selected for artificial fertilization. However, observations at our facilities and reports from hatcheries indicate a high degree of variation in reproductive performance among individuals. Thus, it is essential to establish links between paternal age and reproductive success, as it is apparent that advanced paternal age leads to changes in reproductive performance. Since there are no prior studies regarding the changes in testis transcriptome in blue catfish males during aging, we evaluated global gene expression of testis at age 2,4,7 and 9. Significant differential expressed genes and gene ontology of pairwise comparisons between age 2 and each test age are presented and discussed.

overall_design: A total of 16 testis tissue samples from blue catfish males were used in this study, corresponding to ages 2, 4, 7 and 9. Age 2 was considered as the control group. Four testis tissue samples were collected per age group and extracted for RNA-seq.

first: Jason

last: Abernathy

first: Nithin

last: Sankappa

first: Samitha

last: Liyanage

first: Xu

last: Wang


title: RNA-Seq Reveals Enhanced Inflammation and Fibrosis in Alcohol-Induced Liver Injury of Apoe Knockout Mice

city: Rockville

first: Yukun

last: Guan

state: MD

address: 5625 Fishers Lane, Room 2S-30

institute: NIAAA

summary: Alcohol-related liver disease (ALD) involves inflammation, hepatocellular damage, and fibrosis. Apolipoprotein E (Apoe) plays a role in immune regulation and tissue repair, but its function in ALD remains unclear. To explore this, we performed RNA sequencing on liver tissues from wild-type (WT) and Apoe knockout (Apoe KO) mice subjected to a chronic-plus-binge ethanol model. Gene expression analysis revealed distinct clustering between groups and significant alterations in pathways related to neutrophil degranulation, extracellular matrix organization, and collagen formation, indicating heightened inflammation and fibrosis in Apoe KO mice. These findings offer insights into Apoe’s role in ALD and liver repair.

overall_design: Mice subjected to the chronic-plus-binge ethanol-feeding model were fed as described in our previous study. Briefly, 10–12-week-old female mice were acclimated by ad libitum feeding with the Lieber-DeCarli liquid diet (catalog #F1259SP, Bio-Serv) for five days. Following acclimatization, the ethanol-fed groups received a Lieber-DeCarli ethanol diet (catalog #F1258SP, Bio-Serv) containing 5% (v/v) ethanol for 10 days. On day 11, a single dose of ethanol (5 g/kg body weight) was administered via oral gavage in the early morning, and the mice were euthanized nine hours later. Pair-fed control mice were maintained on an isocaloric control diet for 10 days and, on the day of euthanasia, received an oral gavage of isocaloric dextrin-maltose (9 g/kg body weight).

last: GUAN

first: Yang

last: WANG

first: Bin

last: GAO


title: Harnessing Apple Cell Suspension Cultures in Bioreactors for Triterpene Production: Transcriptomic Insights into Biomass and Triterpene Biosynthesis

status: Public on Apr 17 2025

city: Belvaux

first: Sylvain

last: Legay

address: 41, rue du Brill

department: ERIN department

country: Luxembourg

institute: Luxembourg Institute of Science and Technology

summary: Plant cell suspension cultures offer a sustainable method for producing valuable secondary metabolites, such as bioactive pentacyclic triterpenes. This study established a high-triterpene-yielding cell suspension culture from the apple cultivar "Cox Orange Pippin." Through transcriptomic analysis and triterpene profiling across growth phases, we uncovered complex regulatory networks that govern biomass production and triterpene biosynthesis. Key biological processes, including cell cycle regulation, cell wall biosynthesis, lipid metabolism, and stress response mechanisms, play pivotal roles in culture dynamics. Differential gene expression linked to these processes revealed how the culture adapts to growth conditions and nutrient availability at each growth phase. Methyl jasmonate elicitation enhanced phenylpropanoid and flavonoid biosynthesis, along with specific triterpene production pathways, highlighting its potential for optimizing secondary metabolite production. Key enzymes, including oxidosqualene cyclase 4 and a putative C-2α hydroxylase, emerged as promising targets for future metabolic engineering of triterpene pathways. This study represents the first in-depth report on the molecular mechanisms underlying plant cell growth in bioreactors, specially focusing on a non-model plant species . These findings reveal key regulatory pathways in biomass accumulation and triterpene production, offering insights to optimize bioreactor cultures for industrial use. The research opens new avenues to enhance triterpene yields via targeted metabolic engineering and innovative bioprocessing strategies, paving the way for efficient large-scale production.

overall_design: A Malus x domestica cell line produced from the Cox orange Pippin variety was grown in bioreactors with three biological replicates. Cells were sampled during the course of the batch to investigate gene expression patterns being involved in the different growth stages (lag phase, exponential phase, stationnary phase, post elicitation)

first: Xuan

last: XU

first: Emmanuelle

last: COCCO

first: Gea

last: GUERRIERO

first: Kjell

last: SERGEANT

first: Samuel

last: JOURDAN

first: Jenny

last: RENAUT

first: Jean-Francois

last: HAUSMAN

last: LEGAY


title: The histone methyltransferases EHMT1 and EHMT2 repress the expression of genes related to excitability and cell death in oligodendrocyte progenitors [RNA-seq]

status: Public on Mar 14 2025

city: New York

first: Patrizia

last: Casaccia

state: NY

address: 85 St Nicholas Terrace

department: Neuroscience

institute: ASRC-CUNY

summary: Oligodendrocyte progenitor cells (OPCs) represent a population of electrically active and dividing cells, which are capable of responding to neuronal activity, by proliferating and differentiating. Here we report that the repressive euchromatic H3K9me2 histone mark, deposited by the histone mehyltransferases EHMT1 and EHMT2 enzymes, increases in proliferating OPCs in mice following optogenetic stimulation of neuronal activity. Using primary cultured OPCs with genetic deletion of Ehmt1 and Ehmt2, and pharmacological inhibition of EHMT enzymatic activity, we reveal the importance of these enzymes in repressing the expression of genes regulating cell death and electrical properties in proliferating OPCs. Consistent with these findings, we detect higher levels of cholinergic muscarinic receptors, fewer numbers of oligodendrocyte lineage cells and lower levels of the myelin basic protein (MBP) in mice with lineage specific ablation of Ehmt1 and Ehmt2. Together these data suggest that the repressive H3K9me2 histone mark, whose levels increase in proliferating OPCs after neuronal stimulation, is an important modulator of cell death and proteins regulating the electrical properties of OPCs.

overall_design: To investigate the role of EHMT1/EHMT2 in oligodendrocytes, we performed RNA-sequencing on mouse primary oligodendrocyte progenitors comparing Ehmt1/Ehmt2 knocked down samples to control. Knocked down of Ehmt1 and Ehmt2 was performed in vitro by infecting cells with an Adenovirus expressing Cre recombinase and a RFP protein (knockdown samples), or RFP only (control samples).

first: Mathilde

last: Pruvost

first: Hye-Jin

last: Park

first: Meng

last: Li

first: Jia

last: Liu


title: Beyond the plasma membrane disruption: Novel antifungal mechanism of Neosartorya (Aspergillus) fischeri antifungal protein 2 in Candida albicans

status: Public on Mar 03 2025

city: Szeged

first: Krisztián

last: Laczi

address: 52. Közép Fasor

department: Biotechnology and Microbiology

country: Hungary

institute: University of Szeged

summary: Candida albicans is the most prevalent human pathogenic fungus, responsible for drug-resistant and fatal invasive infections which show an increasing trend in the past two decades. A promising new therapeutic approach involves NFAP2, an antifungal protein secreted by Neosartorya (Aspergillus) fischeri. NFAP2 exhibits potent antifungal activity on both planktonic and biofilm-forming Candida cells in vitro and in vivo. Despite this promising feature,the exact antifungal mechanism of NFAP2 remains in the shadow which hampers its therapeutic application. Based on our recent observations, we suppose that NFAP2 is taken up by Candida cells, and has a long-term growth-slowing effect. Our objective was to understand the molecular mechanism of the long-term growth slowing effect of NFAP2 in C. albicans, therefore the transcriptome of the NFAP2-treated (below the minimum inhibitory concentration) C. albicans SC5314 cultures was compared to that of the untreated ones.The transcriptional responses to NFAP2 were further characterized using functional enrichment analyses of Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways.

overall_design: RNA-seq comparison of C. albicans SC5314 cells with NFAP2 treated C. albicans SC5314 cells

first: Kinga

last: Dán

first: Nóra

last: Zsindely

first: László

last: Bodai

last: Galgóczy


title: Urine Cell-Free RNA versus Plasma Cell-Free RNA for Monitoring of Immune and Urinary Tract Complications

status: Public on Mar 06 2025

city: Ithaca

first: Iwijn

last: De Vlaminck

address: 237 Tower Road, Weill Hall 301

department: Biomedical Engineering

institute: Cornell University

summary: While it is well known that cell-free RNA (cfRNA) can be isolated from urine, the diagnostic potential of this urine cfRNA, especially in comparison to plasma cfRNA, remains underexplored. Here, we directly compared the utility of urine cfRNA and plasma cfRNA for the monitoring of systemic and urinary tract related complications. We analyzed 297 matched plasma and urine cfRNA isolates obtained from three cohorts of patients: Hematopoietic Stem Cell Transplant (HSCT) recipients, patients with acute kidney injury (AKI), and healthy volunteers. The data highlight the unique cellular origins and properties of urinary and plasma RNA. Most importantly, we find that although plasma cfRNA is a superior analyte for monitoring immune and systemic complications, urinary cfRNA is more sensitive to complications of the urinary tract, including cell-type specific injury in the kidney. These findings highlight the potential of urine cfRNA as a novel analyte in diagnostic medicine.

overall_design:
We isolated and sequenced cell-free RNA from 297 matched plasma and urine samples from healthy volunteers (n=5), HSCT recipients (n=24), and patients who developed acute kidney injury (AKI) in the setting of receiving immune checkpoint inhibitor (ICI) therapy (n=46)

>>>Submitter states that raw data are not available due to patient privacy concerns<<<

first: Omary

last: Mzava

first: Conor

last: Loy

first: Isabel

middle: H

last: Gonzalez-Bocco

first: Liz-Audrey

last: Djomnang Kounatse

first: Andrew

last: Bliss

first: Sophia

last: Wells

first: Joan

last: Lenz

first: Emma

last: Belcher

first: Kaiwen

last: Chen

last: Koo

first: Lindsey

middle: R

last: Baden

first: Tinyi

last: Chu

first: Matthew

last: Cheng

first: Jerome

last: Ritz

first: Glory

middle: F

last: Agun


title: DNA methylation dynamics in the prenatal and postnatal human cortex

city: Exeter

first: Alice

last: Franklin

address: Stocker Road

institute: University of Exeter

summary: There is increasing recognition about the importance of epigenetic dysregulation in neurodevelopmental disorders including autism spectrum disorder and schizophrenia, yet little is known about patterns of gene regulation in the later stages of fetal development and the first decade of life. In this study we profiled changes in DNA methylation, an epigenetic modification to cytosine involved in mediating the developmental regulation of gene expression and function, across human brain development in cortex tissue from 107 human fetal and child donors spanning 6 post-conceptual weeks to 8 years old.

overall_design: DNA methylation of post-mortem bulk pre-frontal cortex tissue was profiled for 107 individuals: 95 fetal (6 - 33 post-conceptual weeks) and 12 child (0 - 8 years).

first: Jonathan

last: Mill

last: Dempster

last: Walker


title: Differential Cellular Mechanisms Underlie Language and Executive Decline in Amyotrophic Lateral Sclerosis [snRNAseq/snATACseq multiomics]

status: Public on Mar 01 2025

first: Christopher

last: Jackson

address: 101 Avenue of the Americas

department: Center for the Genomics of Neurodegenerative Disease

institute: New York Genome Center

summary: Half of all amyotrophic lateral sclerosis (ALS) patients demonstrate a spectrum of cognitive and behavioral changes over the course of the disease, but the mechanisms underlying this heterogeneity remain unclear. We assemble a high-resolution cellular map of prefrontal cortex regions of the ALS brain by integrating spatial and single-nucleus transcriptomic profiles of a cognitively stratified ALS patient cohort that includes non-neuropathological controls. We find cellular programs characteristic of ALS, including a frequent gliotic response. We also find that executive and language cognitive impairments differ from ALS without cognitive impairment, and from each other, in the extent and pattern of neuronal dysregulation and neuron-glial interactions across different brain regions. These findings reveal a relationship between cognitive phenotype and prefrontal cortex dysfunction in ALS.

overall_design: Single cell multiomic (transcriptomic and ATAC) libraries generated from 48 human donor prefrontal cortex samples (24 from BA44/45 and 24 from BA46), across a range of non-neuropathological sudden-death controls, ALS patients, and ALS patients who exhibit cognitive impairment on a standardized screening exam

first: Aidan

last: Daly

first: Cláudio

last: Roque

first: Joana

last: Petrescu

first: Hemali

last: Phatnani


title: Cell-type-specific DNA methylation dynamics in the prenatal and postnatal human cortex

summary: There is increasing recognition about the importance of epigenetic dysregulation in neurodevelopmental disorders including autism spectrum disorder and schizophrenia, although the cell-type specific changes in gene regulation across critical periods of brain development have not been fully elucidated. In this study we profiled DNA methylation of purified populations of neuronal (SATB2+) and non-neuronal (SATB2-) cell-types in 47 human fetal and child donors (8 post-conceptual weeks to 8 years old).

overall_design: Post-mortem pre-frontal cortex tissue was collected for 47 individuals: 38 fetal (8 - 28 post-conceptual weeks) and 9 child (0 - 8 years). Using a FANS protocol developed by our group (Davies et al. 2023), individual nuclei fractions (SATB2+, SATB2-) were isolated and DNA methylation profiled.


title: Effect of interleukin-1beta on confluent human lymphatic endothelial cells

status: Public on Feb 28 2025

city: Rouen

first: Ebba

last: Brakenhielm

address: Inserm U1096

country: France

institute: Inserm

summary: The goal of the study was to examine the transcriptional changes in human lymphatic endothelial cells (LEC) stimulated by interleukin-1beta

overall_design:
RNAseq profiling of human LECs (HMVEC-dLy) cultured until confluent and then serum-starved (1% FCS) overnight, followed by exposure  during 24h to 20 ng/mL human recombinant IL1beta. Controls were treated the same way without addition of IL1beta. N=3 samples per group.

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Submitter states that missing raw files are due to file loss.
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first: Coraline

last: Heron

first: Theo

last: Lemarcis

first: Oceane

last: Laguerre

first: Benjamin

last: Bourgeois

first: Corentin

last: Thuilliez

first: Chloe

last: Valentin

first: Anais

last: Dumesnil

first: Manon

last: Valet

first: David

last: Godefroy

first: Damien

last: Schapman

first: Gaetan

last: Riou

first: Sophie

last: Candon

first: Celine

last: Derambure

first: Caroline

last: Berard

first: Helene

last: Dauchel

first: Virginie

last: Tardif


title: Clonal cell states link gastroesophageal junction tissues, metaplasia, and cancer [scRNA-seq]

status: Public on Mar 05 2025

city: Philadelphia

first: Sydney

last: Shaffer

state: PA

address: 421 Curie Boulevard

department: Penn Medicine

institute: University of Pennsylvania

summary: Barrett's esophagus is a common type of metaplasia and a precursor of esophageal adenocarcinoma. However, the cell states and lineage connections underlying the origin, maintenance, and progression of Barrett’s esophagus have not been resolved in humans. Here, we performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue. Our analysis unexpectedly revealed that the squamous esophagus and gastric cardia contained cells belonging to common lineages that also included transitional basal progenitor cells; both esophageal and gastric tissues were also related to Barrett's esophagus. Barrett’s esophagus biopsies consisted of multiple clones, with lineages that contained all progenitor and differentiated cell types. In contrast, precancerous dysplastic lesions were initiated by the expansion of a single molecularly aberrant Barrett’s esophagus clone. Together, these findings provide a comprehensive view of the cell dynamics of Barrett's esophagus, linking cell states along the disease trajectory, from its origin to cancer.

overall_design: Performed single-cell lineage tracing and transcriptional profiling of patient cells isolated from metaplastic and healthy tissue.

first: Rodrigo

last: Gier

first: Raúl

last: Reyes Hueros

first: Jiazhen

last: Rong

first: Maureen

last: DeMarshall

last: Bracht

first: Tatiana

last: Karakasheva

first: Amanda

middle: B

last: Muir

first: Gary

middle: W

last: Falk

first: Nancy

last: Zhang


title: Lipid metabolism reprograming by SREBP1-PCSK9 targeting sensitizes pancreatic cancer to immunochemotherapy

city: Hangzhou

first: Mengyi

last: Lao

state: Zhejiang

address: Qingchun 79 road

institute: Zhejiang university

summary: Pancreatic ductal adenocarcinoma (PDAC) treatment is challenging. Determining the metabolic pathways that regulate lipids will provide new insights into PDAC therapeutic strategies. Sterol regulatory element binding transcription factor 1 (SREBP-1) regulates multiple cancer pathways; however, its role in the tumor immune microenvironment and cancer immunotherapy is unknown. Herein, we integrated our large PDAC cohort data and identified that SREBP-1, as a master transcriptional regulator of lipogenesis, aggravated lipid metabolism reprogramming in PDAC. Furthermore, interrupting lipid metabolism by targeting SREBP-1 suppressed PDAC cell growth and enhanced antitumor immunity in vitro and in vivo. We demonstrated that SREBP-1 binds to the PD-L1 (programmed cell death 1 ligand 1) promoter to suppress its transcription. Importantly, SREBP-1 binds to the PCSK9 (proprotein convertase subtilisin/kexin type 9) promoter, which regulated PD-L1 levels via lysosome-mediated degradation and aggravated tumor microenvironment immunosuppression. Targeting the SREBP-1- PCSK9 axis using available drugs sustained the remission of aggressive PDAC by synergizing with anti-PD-1 and gemcitabine. In summary, targeting lipid metabolism suppressed tumor growth and relieved tumor immunosuppression in PDAC.

overall_design: RNA-seq profiling of wildtype KPC and PANC02 cells and their knockdown derivatives (shSrebf1)


title: Sequential transcriptional programs underpin activation of quiescent hippocampal stem cells.

status: Public on Mar 16 2025

city: Brisbane

first: Lachlan

middle: Ian

last: Harris

state: QLD

address: 300 Herston Road

department: Cancer Research Program

institute: QIMR Berghofer MRI

summary: Postnatal neural stem cells are primarily quiescent, which is a cellular state that exists as a continuum from deep to shallow quiescence. The molecular changes that occur along this continuum are beginning to be understood but the transcription factor network governing these changes has not been defined. We show that these transitions are regulated by sequential transcription factor programs. Single-cell transcriptomic analyses of mice with loss- or gain-of-function of the essential activation factor Ascl1, reveal that Ascl1 promotes the activation of hippocampal neural stem cells by driving these cells out of deep quiescence, despite its low protein expression. Subsequently, during the transition from deep to shallow quiescence, Ascl1 induces the expression of Mycn, which drives progression through shallow states of quiescence towards an active state. Together, these results define the required sequence of transcription factors during hippocampal neural stem cell activation.

overall_design:
Each independent scRNA-seq experiment comprised a pooled group of 1-2 conditional knockout mice (of either Ascl1, Huwe1 or Mycn cKO genotype) with 1-2 controls that were prepared simultaneously to minimise processing artefacts. In total, 3 independent experiments were performed on Ascl1 cKO mice and controls, 2 independent experiments on Huwe1 cKO mice and controls and 2 independent experiments on Mycn cKO mice and controls. In the Ascl1 experiments, the cKO mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the the control mice were genetically identical but were wildtype for Ascl1 alleles. In the Huwe1 experiments, the male cKO mice were hemizygous for the floxed allele, heterozygous for Glast-creERT2 and homozygous for the cre-reporter YFP allele, while the male control mice were genetically identical but were wildtype for Huwe1. All mice received tamoxifen via oral gavage (100mg/kg) for 5 days starting from P30 (range from P27-P33) and were euthanised 12-days later. For the Mycn experiments, the cKO and control mice were homozygous for the floxed allele, heterozygous for Glast-creERT2 and heterozygous for Nestin-GFP. The Mycn cKO mice received tamoxifen and Mycn control mice received corn-oil via oral gavage for 5-days at P30 (range from P27-P30) before being euthanised 12-days later. Mice were euthanised by cervical dislocation, and the hippocampal dentate gyri were dissected. The dentate gyrus was disassociated using the Neural Tissue dissociation kit (P). The cells were then sorted on a MoFlo XDP (Bechman Coulter) using a 100um nozzle. Debris were removed, followed by two gates to remove aggregates and dead cells, based on DAPI fluorescence. Cells were then gated for YFP or GFP expression. The single-cell suspension (to a maximum of 10,000 cells) was then loaded into the 10x Chromium. On each experimental day, two libraries were prepared, one for each of the experimental groups to control for batch effects, which are strong in this type of data (i.e., cKO and control). All libraries were prepared with 10x Genomics Chemistry, Single Cell version 3.0.1. We also performed CUT&RUN on primary adult mouse hippocampal NSC cultures (AHNSCs), in two replicates. Cultured AHNSCs were collected and captured with ConA beads and incubated with anti-ASCL1 monoclonal antibody overnight at 4 °C in antibody buffer before completion of the protocol, preparation of the sequencing library and sequencing on the NovaSeq 6000 instrument, PE100.

**Please note that the processed data files for GSM8594263 sample have been replaced on April 29, 2025**

first: Piero

last: Rigo

first: Sara

last: Ahmed de Prado

first: Rebecca

last: Johnston

first: Chandra

last: Choudhury

first: François

last: Guillemot


title: Adverse outcome pathways of ionizing radiation investigated with multi-omics and benchmark dose modeling

city: Ottawa

first: Matthew

last: Meier

address: 251 Sir Frederick Banting Driveway

department: Health Canada

institute: Government of Canada

summary: Background/Issue and Objectives: Health risks from chronic low dose radiation exposures encountered in environmental and occupational settings are uncertain. A key aspect to understanding health risks is precise and accurate modelling of the dose-response relationship. Benchmark dose (BMD) modeling is an approach used in chemical hazard assessments to identify the dose at which a pre-defined (e.g., 10%) change relative to background occurs. Herein, this method is being explored for radiation hazard assessments along with Adverse Outcome Pathways (AOPs), a knowledge framework of causally linked chains of key events (KEs) from a molecular initiating event to an adverse outcome (AO). Design/Method/Description: Blood was drawn from human participants (6 females and 8 males), and lymphocytes were isolated, cultured and X-irradiated at a lower dose-rate (LDR: 0.05 Gy/minute) and higher dose-rate (HDR: 1 Gy/minute) across nine different doses (0, 0.05, 0.10 0.25, 0.5, 1, 2, 4 and 6 Gy).  Transcriptomic and proteomic changes were then assessed 24 hours post-exposure. Concurrently, cell membrane integrity and cellular ATP level were also measured, which are markers of radiation injuries. BMD values were then derived for each endpoint and pathways enriched in omics data were compared with Kes in an existing AOP to leukemia (www.aopwiki.org/aop/432). Conclusions/Impacts/Outcomes/Implications/Next Steps: By using AOPs as an organizational framework and BMD modeling for dose-response analysis, it provides a pragmatic platform to analyse complex data for radiation hazard assessment. Future work will entail in-depth analysis of the responses specific to LDR and HDR and effects of confounding factors on BMD values.

overall_design: Blood was drawn from human participants (6 females and 8 males), and lymphocytes were isolated, cultured and X-irradiated at 1 Gy/minute across nine different doses (0, 0.05, 0.10 0.25, 0.5, 1, 2, 4 and 6 Gy).  Transcriptomic and proteomic changes were then assessed 24 hours post-exposure. Concurrently, cell membrane integrity and cellular ATP level were also measured, as phenotypic indicators. BMD values were then derived for each endpoint and pathways enriched in omics data including the associated BMDs were aligned with KEs in an AOP to leukemia (www.aopwiki.org/aop/432)

first: Ngoc

middle: Q

last: Vuong

first: Saadia

last: Khilji

first: Andrew

last: Williams

first: Nadine

last: Adam

first: Danicia

last: Flores

first: Kelly

last: Fulton

first: Isabel

last: Baltat

first: Susan

last: Twine

first: Kathleen

last: Cook

first: Premkumari

last: Kumarathasan

first: Ruth

last: Wilkins

first: Carole

last: Yauk

first: Vinita

last: Chauhan