title: Androgen receptor-mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells (scRNA-seq)

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

department: School of Medicine

country: Finland

institute: University of Eastern Finland

summary: Steroid receptors are involved in a wide array of crosstalk mechanisms that regulate diverse biological processes, with significant implications in diseases, particularly in cancers. In prostate cancer, indirect crosstalk between androgen receptor (AR) and glucocorticoid receptor (GR) is well-documented, where GR replaces antiandrogen inactivated AR becoming the disease driver. However, the existence and impact of direct chromatin crosstalk between AR and GR in prostate cancer have remained elusive. Our genome-wide investigations reveal that AR activation significantly expands GR chromatin binding. Mechanistically, AR induces remodeling of closed chromatin sites, facilitating GR binding to normally inaccessible sites. Importantly, coactivation of AR and GR results in distinct transcriptional responses at both the population and single-cell levels. Intriguingly, genes and pathways affected by these transcriptional changes are generally associated with improved patient survival. Thus, the direct crosstalk between AR and GR yields markedly different outcomes from the known role of GR in circumventing AR blockade by antiandrogens.

overall_design: Examination of single cell gene expression profile by scRNA-seq from VCaP prostate cancer cells treated with vehicle (EtOH), dexamethasone (Dex), dihydrotestesterone (DHT), or Dex and DHT. Sequencing was done with Illumina NextSeq 2000.

first: Johannes

last: Hiltunen

first: Niina

last: Aaltonen

first: Laura

last: Helminen


title: Patterns of intra- and inter-tumor phenotypic heterogeneity in men with lethal prostate cancer

status: Public on May 22 2025

city: Seattle

first: Brian

last: Hanratty

state: WA

address: 1100 Fairview Avenue

department: Division of Human Biology

country: USA

institute: Fred Hutchinson Cancer Cancer

type: Expression profiling by high throughput sequencing

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Androgen receptor-mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells (ChIP-seq)

status: Public on May 21 2025

overall_design: Examination of GR, AR, SMARCA4, FOXA1 and BRD4 chromatin binding by ChIP-seq from VCaP prostate cancer cells treated with vehicle (EtOH), dexamethasone (Dex), dihydrotestesterone (DHT), or Dex and DHT. Sequencing was done with Illumina NextSeq 500. AR and SMARCA4 ChIP-seq in EtOH and DHT treated VCaP cells were from GSE136016. FOXA1 ChIP-seq in EtOH (rep2), Dex (rep2) and DHT exposed VCaP cells were from GSE214757.


title: Androgen receptor-mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells


title: Androgen receptor-mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells (GRO-seq)

overall_design: Examination of gene and enhancer activity by GRO-seq from VCaP prostate cancer cells treated with vehicle (EtOH), dexamethasone (Dex), dihydrotestesterone (DHT), or Dex and DHT. Sequencing was done with Illumina HiSeq 2000.


title: Myeloid ATG7 Functions as a Sentinel for Pulmonary Defense Against Infection with Nontuberculous Mycobacteria

status: Public on May 20 2025

city: Daejeon

first: Taylor

last: Roh

address: 266, Munhwa-ro

department: Microbiology

country: South Korea

institute: Chungnam National University

summary: Nontuberculous mycobacterial pulmonary diseases (NTM-PD) are becoming increasingly prevalent and incident, and heightened antibiotic resistance presents a considerable challenge to clinicians. Despite this, our understanding of the factor(s) contributing to host defense against NTM-PD remains incomplete. Herein, we report that the myeloid autophagy-related gene (ATG) 7 promotes host protective responses against NTM-PD by mitigating excessive pathological inflammation, oxidative stress, and cell death associated with neutrophil infiltration. Patients with NTM-PD displayed a notable reduction in ATG7 expression in peripheral blood mononuclear cells and in necrotic lesions at disease sites. Mice with deletion of Atg7 specifically in myeloid cells (Atg7 cKO) exhibited a significant increase in lung bacterial load during infection. Spatial and bulk RNA-seq analyses, as well as biological experiments, revealed heightened myeloid cell infiltration, excessive inflammation, and mitochondrial damage in Atg7 cKO lung tissues. Furthermore, ｍyeloid Atg7-deficient mice showed upregulated apoptosis, necrosis, and GSDME-associated cell death, along with the formation of neutrophil extracellular traps, in the lung tissues during NTM-PD. However, Atg7-deficient macrophages showed only marginal differences in inflammation and cell death in vitro during NTM infection. Our findings demonstrate that myeloid ATG7 plays a major role in non-cell-autonomous protection against NTM-PD by alleviating neutrophil-associated pathological inflammation and cell death.

overall_design: To investigate the function ATG7 in the NTM-infected mice, we established C57/BL6 mouse in which each ATG7 gene has been conditional knocked out.


title: STING agonists drive recruitment and intrinsic type I interferon responses in monocytic lineage cells for optimal anti-tumor immunity

city: Toronto

first: Melanie

last: Girard

address: 1 King's College Circle

department: Immunology

country: Canada

institute: University of Toronto

summary: The cyclic GMP-AMP synthase-stimulator of interferon genes (cGAS-STING) pathway, a sensor of cytosolic DNA, orchestrates the production of proinflammatory cytokines, chemokines, and type I interferons (IFN-Is), thereby contributing to spontaneous tumor surveillance. Intratumoral delivery of synthetic STING agonists induces IFN-I-dependent tumor regression in preclinical cancer models and is being tested clinically. In this study, we investigate the role of monocytic lineage cells (MCs) in response to STING agonist induced IFN-I signaling. We show that CCR2-deficient mice, lacking inflammatory MCs in the periphery, or Lyz2-Cre-IFNAR1fl/fl mice in which IFN-I signaling in monocytes is reduced, exhibit impaired responses to STING agonist therapy of MC38 and/or B16F10 tumors. STING agonist treatment induced CCR5-dependent migration of MCs carrying tumor antigen from the tumor to the lymph nodes. Single-cell RNA sequencing of CD45+ cells from lymph nodes and tumors of mice in which half the hematopoietic cells lack the IFNAR1 (interferon alpha/beta receptor 1) revealed that STING agonist therapy induces intrinsic IFNAR1-dependent acquisition of an inflammatory monocytic cell phenotype distinct from inflammatory classical dendritic cells (cDC) and a reduction in macrophages with a protumor TGFβ/angiogenesis transcriptome. Interleukin (IL)-18-IL-18R1 interaction was the top predicted interaction between monocytic lineage cells and CD8+ T cells or natural killer cells. Blocking IL-18 reduced IFN-γ production by CD8 T cells in lymph nodes and decreased the therapeutic efficacy of STING agonist treatment in Ccr2+/+ but not in Ccr2-/- mice. These findings support a pivotal role for IL-18 producing inflammatory monocytic lineage cells in CD8+ T cell control of melanoma following STING agonist treatment.

overall_design: Mice were reconstituted with a 1:1 mix of Ifnar1+/+ CD45.1 and Ifnar1-/- CD45.2 bone marrow cells, and chimerism in the blood was confirmed after 90 days. Ifnar1 mixed bone marrow chimeras were inoculated with 10^6 B16.OVA cells intradermally and a single dose of ADU-S100 was administered intratumorally on day 12. LNs and tumors were harvested at day 1 and day 2 post-treatment, respectively. For both the tumor and LN, equal amounts of cell suspension from 3 vehicle or 3 ADU-S100-treated mice were pooled into one vehicle sample and one ADU-S100 sample. Cells were stained with fluor-conjugated antibodies (for FACS) and TotalSeq-A antibodies (Biolegend) in D-PBS 2% FBS for 25 min on ice. Vehicle and ADU-S100 treated samples were labeled with distinct hashtag antibodies, while anti-CD45.1 and anti-CD45 barcoded antibodies were used to label Ifnar1+/+ and Ifnar1-/- cells. Cells were sorted on a BD FACS Aria IIu (tumor: live CD45+ cells; LN: live CD3- CD19- CD11b+ and/or MHCII+ cells). Vehicle and ADU-S100-treated samples were pooled together at a 1:1 ratio immediately before partitioning on the 10X chromium controller. The Chromium Single Cell 3’ Reagent Kits v3.1 were used according to the manufacturer’s user guide in conjunction with CITE-seq & Cell Hashing Protocol from the New York Genome Center Technology Innovation Lab.

first: Tania

last: Watts


title: Multi-Region Brain Organoid - Fusion Organoid with cerebral, Endothelial and Mid-Hindbrain Components

city: Baltimore

first: Annie

last: Kathuria

state: Maryland

address: 400 N Broadway, Office 6029

department: Biomedical Engineering

institute: Johns Hopkins University

summary: Brain organoid technology has revolutionized our ability to model human neurodevelopment in vitro. However, current techniques remain limited by their reliance on simplified endothelial cell populations rather than a complete endothelial system. We engineered Multi-Region Brain Organoids (MRBOs) that integrate cerebral, mid/hindbrain, and complex endothelial organoids into one structure. Different from the earlier approaches based on isolated HUVECs, our endothelial organoids contain diverse vascular cell types, including vascular progenitors, mature endothelial cells, pericytes, proliferating angiogenic cells and stromal cells. Our strategy employs a sequential modulation of key developmental pathways to generate individual organoids, followed by optimized fusion conditions that maintain regional identities while supporting cellular integration. Single-nucleus RNA sequencing shows that MRBOs develop discrete neural populations specific to each brain region alongside specialized endothelial populations that establish paracrine signalling networks. Integration analysis with human fetal brain data shows that MRBOs contribute to 80% of cellular clusters found in human fetal brain tissue (Carnegie stages 12-16), whereas CellChat analysis identifies 13 previously uncharacterized endothelial-neural signalling interactions. Notably, we uncover endothelial-derived factors that support the persistence of intermediate progenitor populations during mid/hindbrain development, thereby revealing a new role for complex endothelial populations in regional brain patterning. This effect was not observed in cerebral development. This platform enables matching multiple developmental regions, fully incorporating the endothelial nature at the same time. There are opportunities for studying neurodevelopmental disorders in which neural-endothelial interactions are disrupted. Our engineered MRBO system establishes a foundation for investigating complex neurodevelopmental processes, providing an enabling context closer to physiological relevance.

overall_design: The single-nucleus RNA sequencing (scRNA-seq) data were analyzed using the Seurat package (version 5.0) in R. Quality control measures were applied to filter low-quality cells, and cells were clustered based on their gene expression profiles. Dimensionality reduction was performed using Uniform Manifold Approximation and Projection (UMAP) to visualize cellular heterogeneity. Cell type annotations were assigned by identifying cluster-specific marker genes and comparing them to established brain cell type signatures, facilitated by the sc-type package.


title: The MAIT cell response to controlled oral enterotoxigenic E. coli challenge

city: silver spring

first: Dohoon

last: Kim

address: 503 BLDG, Walter Reed Army institute of research

institute: Henry M Jackson Foundation

summary: Mucosa-associated invariant T (MAIT) cells recognize conserved microbial antigens presented by the non-polymorphic MR1 molecules and play important roles in barrier immunity. Enterotoxigenic E. coli (ETEC) is a major cause of diarrheal disease especially among children in lower-income countries. Here we investigate the potential role of MAIT cells in ETEC infection using samples from a human experimental ETEC challenge study. MAIT cells were activated with elevated function and proliferation in blood on day 7 after challenge, reflected both at protein and transcript levels, a pattern most evident among individuals who developed mild to severe diarrhea (MSD). The MSD-positive group had elevated expression of CCR9 and α4β7 on MAIT cells and experienced expansion of the peripheral MAIT cell pool at day 28 after challenge. Finally, the size of the MAIT cell pool correlated with MSD disease severity score. These findings indicate that MAIT cells respond to ETEC infection in a way associated with the development of symptomatic disease.

overall_design: Peripheral blood MAIT cells were purified by sorting (2,304 - 88,172 total cells) using a FACS Aria SORP (BD Biosciences), pelleted, and overlaid with 250 μl of RNAlater (ThermoFisher) and frozen at -20°C. RNA was extracted using the RNeasy Mini Kit (Qiagen), and RNA quality and concentration were assessed with the Agilent 2100 Bioanalyzer Pico Chip. RNA-seq libraries were prepared using the SMART-Seq v4 Ultra Low Input RNA Kit (Clontech) according to the manufacturer’s instructions. Amplified material was purified using Agencourt AMPure XP beads (Beckman). cDNA quantity was assessed on a Qubit 3.0 (ThermoFisher) and fragment size was evaluated on a 2100 BioAnalyzer (Agilent). The PCR products were next indexed using the Nextera XT DNA Library Prep Kit (Illumina) according to the manufacturer’s instructions. Briefly, products were tagmented using the Amplicon tagment mix containing Tn5 transposase, and indexed using Nextera index 1 (i7) and index 2 (i5) primers. The libraries were again cleaned-up with Agencourt AMPure XP beads, quantified, pooled, and sequenced across 75 base pairs (bp) using a single-end strategy with a 75-cycle high output flow cell on a NextSeq 500 (Illumina). Fourteen biological replicates were sequenced per experiment, with two donor-matched time points corresponding to pre and 7-days post ETEC challenge. Median reads per sample was 22.9 million reads. The Unix based program Spliced Transcripts Alignment to a Reference (STAR) v.2.6.1 with human genome hg38 was used for alignment (36), and transcription mapping was performed using RNA-seq by Expectation Maximization (RSEM) v.1.3.1(37). The FeatureCounts program was used for counting mapped reads (38), and RUVSeq v1.12 was utilized to remove unwanted variation (39). A differentially expressed gene list was subsequently generated by edgeR v3.20. R package (40), and the GSEA method (31) was employed to find statistically significant pathways with 5917 gene sets of GO(Gene Ontology) in Molecular Signatures Database (MSigDB) issued by the Broad Institute.

first: Kerri

middle: G

last: Lal

first: Matthew

last: Creegan

first: Adam

last: Waickman

first: Jeffrey

middle: R

last: Currier

first: Dominic

last: Paquin-Proulx

first: Milton

last: Maciel

first: Michael

middle: A

last: Eller

first: Johan

middle: K

last: Sandberg


title: The nucleolar granular component mediates genome-nucleolus interactions and establishes their repressive chromatin states

city: Zurich

first: Raffaella

last: Santoro

address: Winterthurerstrasse 190

department: Dep. of Molecular Mechanisms  of Disease

country: Switzerland

institute: University of Zurich

summary: Repressive chromatin domains often localize to the nuclear lamina or nucleolus. Although nucleolar-associated domains (NADs) have recently been mapped, their mechanisms of nucleolar association and functional significance remain unclear. Here, we show that nucleophosmin (NPM1), a factor located in the granular component of the nucleolus, mediates NAD association in mouse embryonic stem cells. NPM1 binds NADs, interacts with the histone methyltransferase G9a (EHMT2), and is required for establishing H3K9me2 at NADs. Loss of NPM1 or expression of a DNA-binding-deficient mutant disrupts NAD-nucleolus association and reduces H3K9me2 specifically at NADs. G9a is dispensable for NAD-nucleolus contacts, indicating that H3K9me2 is acquired after NADs associate with NPM1 at nucleoli. These findings reveal mechanistic insights into how genomic domains associate with nucleoli and form repressive chromatin and indicate that the nucleolus not only serves as a scaffold for positioning repressive domains but also plays a direct role in establishing their repressive chromatin states.

first: Shivani

last: Gupta

first: Cristiana

last: Bersaglieri

first: Dominik

last: Bär

first: Mathieu

last: Raingeval

first: Luana

last: Schaab


title: HBO1 is an epigenetic determinant of hepatocyte-to-ductal reprogramming

city: Boston

first: Wei-Chien

last: Yuan

state: MA

address: 1 Blackfan Circle

institute: Boston Children's Hospital

summary: Spontaneous cellular reprogramming is rare, but has been observed in adult cells. This is most evident in the mammalian liver, where hepatocytes undergo physiological reprogramming to generate functional biliary epithelial cells (BECs) in response to injury. The underlying mechanisms driving this cell fate switch remain unclear, however. Here, we characterize epigenetic changes occurring during this transition at the single cell level, and show that reprogramming occurs synchronously and deterministically, though reprogrammed cells retain epigenetic hepatocyte memory. An in vivo CRISPR screen reveals the histone acetyltransferase-HBO1 functions as a critical barrier to hepatocyte reprogramming via acetylation of H3K14. HBO1 depletion accelerates BEC-specific chromatin remodeling and allows for the full resolution of the hepatocyte chromatin landscape. Mechanistically, HBO1 is recruited by the YAP to TEAD target sites to negatively its modulate chromatin-accessibility, DNA-binding, and transcriptional-output, thus acting as an epigenetic brake for YAP/TEAD function. Our work here delineates epigenetic trajectories of a physiological reprogramming process and identifies HBO1 as potential target for hepatocyte trans-differentiation therapeutic strategies.

sample_organism:
Escherichia coli
Mus musculus

platform_organism:
Escherichia coli
Mus musculus

overall_design: Single-cell ATAC-seq profile of sorted BEC and hepatocytes isolated from TetO-YAP S127A mice at different time point post Dox administration.   ATAC-seq, RNA-seq, and ChIP-seq was done for primary hepatocytes of TetO-YAP S127A mice with or without HBO1 KO place on Dox for different time points.  For in vivo CRISPR screen, GFP+/EPCAM+ hepatocytes were isolated and sorted from TetO-YAP S127A mice carrying different sgRNA libraries 6 weeks post Dox administration.

first: Alejo

middle: E

last: Rodriguez-Fraticelli

first: Fernando

middle: D

last: Camargo

first: Andrew

last: Earl


title: CCR2+ monocytes promote white matter injury and cognitive dysfunction after myocardial infarction

city: Chicago

first: Edward

last: Thorp

state: IL

address: 303 E Chicago Ave

institute: Northwestern University

summary: Survivors of myocardial infarction are at increased risk for vascular dementia. Neuroinflammation has been implicated in the pathogenesis of vascular dementia, yet little is known about the cellular and molecular mediators of neuroinflammation after myocardial infarction. Using a mouse model of myocardial infarction coupled with flow cytometric analyses and immunohistochemistry, we discovered increased monocyte abundance in the brain after myocardial infarction, which was associated with increases in brain-resident perivascular macrophages and microglia. Myeloid cell recruitment and activation was also observed in post-mortem brains of humans that died after myocardial infarction. Spatial and single cell transcriptomic profiling of brain-resident myeloid cells after experimental myocardial infarction revealed increased expression of monocyte chemoattractant proteins. In parallel, myocardial infarction increased crosstalk between brain-resident myeloid cells and oligodendrocytes, leading to neuroinflammation, white matter injury, and cognitive dysfunction. Inhibition of monocyte recruitment preserved white matter integrity and cognitive function, linking monocytes to neurodegeneration after myocardial infarction. Together, these preclinical and clinical results demonstrate that monocyte infiltration into the brain after myocardial infarction initiate neuropathological events that lead to vascular dementia.

overall_design: Adult C57BL/6J females were subjected to Sham or MI surgery (n=5 per group). 7 days after surgery, brains were collected and processed into single cell solutions using a Neuronal Tissue Dissociation Kit (P) following manufacturer's instructions. Myelin debris was removed by density gradient centrifugation and biological replicates were pooled together by condition for processing in the 10X Genomics Chromium System. A targeted number of 10,000 cells were loaded for each experimental condition. Single cell mRNA sequencing libraries were prepared using the 10X Genomics Chromium Next GEM Single Cell 3′ Library and Gel Bead Kit (v3.1) pipeline following manufacturer protocols.

middle: B

first: Mallory

last: Filipp

first: Maria

last: Dima

first: Chunfeng

last: Tan

first: Matthew

last: Feinstein

first: Brian

last: Popko

last: DeBerge


title: LATS1/2–integrin axis confers tumor-generated forces that activate neighboring fibroblasts

city: Kumamoto

first: Toshiro

last: Moroishi

address: 1-1-1 Honjo, Chuo-ku

country: Japan

institute: Kumamoto University

summary: Tumors generate various forces during growth and progression, which, in turn, promote tumor development. Although fibroblasts are considered the primary force generators in the tumor microenvironment, recent studies have shown that cancer cells also generate considerable tensile force. However, the role of these forces in the tumor microenvironment and the pathways regulating this process remain largely unknown. Here, we demonstrate that the Hippo pathway kinases LATS1/2 in cancer cells are essential for collective force generation and fibroblast activation via extracellular matrix-mediated cell–cell interactions. In murine breast cancer 4T1 spheroids, deletion of LATS1/2 dampens force generation and disrupts the reorganization of surrounding collagen matrix. The LATS1/2-mediated mechanical forces of the tumor are required for fibroblast activation and differentiation into mechanoresponsive fibroblasts. Mechanistically, LATS1/2 regulate tumor force generation through the expression of the collagen receptor integrins. Our findings not only identify the Hippo pathway as a critical regulator of tumor force generation, but also suggest potential strategies for targeting the Hippo pathway in cancer therapy from the mechanobiological perspective, offering new avenues in the fight against cancer.

overall_design: Comparative gene expression profiling analysis between cancer spheroids generated from wild-type or LATS1/2 double knock-out 4T1 cell lines.

first: Yanliang

last: Liu

first: Saisai

first: Moroishi

last: Toshiro


title: Gene expression profile at single cell level of sorted CD45+ cells from the GL261 tumor bearing hemisphere, treated with PBS / CSI / CSI+aPD1

status: Public on May 19 2025

city: Warsaw

first: Karol

last: Jacek

address: Ludwika Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: We performed scRNA-seq to assess the effect of CpG-STAT3ASO+anti-PD1 therapy on immune cells from GL261 high grade glioma model.

overall_design: The mice were implanted with GL261 cells. Subsequently, the mice received four intracranial treatments with either PBS, CpG-STAT3ASO, or CpG-STAT3ASO combined with anti-PD1, and were sacrificed on day 21. Tumor-bearing hemispheres were then isolated and dissociated. CD45+ cells were sorted and subjected to single-cell RNA sequencing (10X Genomics 3').

first: Chia-Yang

last: Hung

first: Marcin

last: Kortylewski


title: Prognostic Models and Signatures in Retroperitoneal Sarcoma

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: CINSARC (the Complexity Index in SARComas) is a transcriptomic profile that independently forecasts the risk of metastasis in soft tissue sarcoma patients. This study aimed to (1) deliver the first standalone validation of CINSARC in a group of patients with retroperitoneal sarcoma (RPS) and (2) investigate if integrating CINSARC could improve the predictive accuracy of the Sarculator model.

overall_design: The Istituto Nazionale Tumori (INT) group comprised patients with primary localized retroperitoneal sarcoma (RPS) who underwent curative surgery between 2011 and 2015, as part of the SARCOMICS study. Patients were divided into two categories based on their CINSARC status: low-risk (C1) and high-risk (C2). The main outcomes measured were overall survival (OS) and disease-free survival (DFS), with multivariable Cox models used for analysis. The accuracy of the Sarculator was evaluated based on its discriminatory power (using Harrell’s C-index) and calibration (assessed via calibration plots and the Brier score), both before and after incorporating CINSARC data. The study confirmed that CINSARC serves as a prognostic marker for OS and DFS in patients with primary RPS who received surgical treatment. However, adding CINSARC to the Sarculator did not enhance its discrimination or calibration, indicating that its integration may not offer additional clinical advantages.

first: Stefano

last: Percio


title: Intracellular accumulation of amyloid-ß is a marker of selective neuronal vulnerability in Alzheimer’s disease

city: London

first: Paul

middle: M

last: Matthews

address: White City

country: United Kingdom

institute: Imperial College London

summary: Defining how amyloid-β and pTau together lead to neurodegeneration is fundamental to understanding Alzheimer’s disease (AD). We used imaging mass cytometry to identify neocortical neuronal subtypes lost with AD in post-mortem brain middle temporal gyri from non-diseased and AD donors. Here we showed that L5,6 RORB+FOXP2+ and L3,5,6 GAD1+FOXP2+ neurons, which accumulate amyloid-β intracellularly from early Braak stages, are selectively vulnerable to degeneration in AD, while L3 RORB+GPC5+ neurons, which accumulate pTau but not amyloid-β, are not lost even at late Braak stages. We discovered spatial associations between activated microglia and these vulnerable neurons and found that vulnerable RORB+FOXP2+ neuronal transcriptomes are enriched selectively for pathways involved in inflammation and glycosylation and, with progression to AD, also protein degradation. Our results suggest that the accumulation of intraneuronal amyloid-β, which is associated with glial inflammatory pathology, may contribute to the initiation of degeneration of these vulnerable neurons.

overall_design:
This study was carried out in accordance with the Regional Ethics Committee and Imperial College Use of Human Tissue guidelines. This study was carried out in accordance with the Regional Ethics Committee and Imperial College Use of Human Tissue guidelines. Cases were selected based first on neuropathological diagnosis (non-disease control [NDC] or AD) from UK brain banks (London Neurodegenerative Diseases Brain Bank [King’s College London], Newcastle Brain Tissue Resource, Queen’s Square Brain Bank [University College London], Manchester Brain Bank, Oxford Brain Bank and South West Dementia Brain Bank [University of Bristol]. We excluded cases with clinical or pathological evidence for small vessel disease, stroke, cerebral amyloid angiopathy, diabetes, Lewy body pathology (TDP-43), or other neurological diseases. Where the information was available, cases were selected with a post mortem delay of less than 49 hours. The final cohort  was formed of non-diseased controls (Braak 0-II; 16 samples) and early (Braak III-IV; 4 samples) and late (Braak V-VI; 33 samples) AD human post-mortem FFPE middle temporal gyrus (MTG) samples. Of these, 5 controls and 10 late AD donors carried the AD high-risk R62H TREM2 variant, while 2 controls and 8 late AD donors carried the R47H variant.

***************************************************************
All raw data are submitted on Synapse.org under the accession id syn54083444 and is available upon completing the Data User Agreement.
***************************************************************

first: Alessia

last: Caramello

first: Nurun

middle: N

last: Fancy

first: Clotilde

last: Tournerie

first: Maxine

last: Eklund

first: Vicky

last: Chau

first: Emily

last: Adair

first: Marianna

last: Papageorgopoulou

first: Nanet

last: Willumsen

first: Johanna

middle: S

last: Jackson

first: John

last: Hardy


title: Resolve smFISH spatial transcriptomics on the GL261 tumor bearing hemisphere, treated with PBS / aPD1 / CSI / CSI+aPD1

summary: We performed Resolve Molecular Cartography to assess the effect of CpG-STAT3ASO+anti-PD1 therapy on immune cells from GL261 high grade glioma model.

overall_design: The mice were implanted with GL261 cells. Subsequently, the mice received four intracranial treatments with either PBS, anti-PD1,  CpG-STAT3ASO, or CpG-STAT3ASO combined with anti-PD1, and were sacrificed on day 21. Brains were isolated.


title: E-cadherin mechanotransduction activates EGFR-ERK signaling in epithelial monolayers by inducing ADAM-mediated ligand shedding

city: Utrecht

first: Martijn

last: Gloerich

state: Utrecht

address: Universiteitsweg 100

department: Center for Molecular Medicine

country: Netherlands

institute: University Medical Center Utrecht

summary: The behavior of cells is governed by signals originating from their local environment, including mechanical forces that cells experience. Forces are transduced by mechanosensitive proteins, which can impinge on signaling cascades that are also activated by growth factor receptors upon ligand binding. However, the interplay between these mechanical and biochemical signals in the regulation of intracellular signaling networks remains incompletely understood. To elucidate this mechanochemical crosstalk, we conducted phosphoproteomic and transcriptomic analyses on epithelial monolayers subjected to mechanical strain. This approach revealed ERK signaling as a predominant strain-activated hub, initiated at the level of the upstream EGF receptor. Strain-induced EGFR/ERK signaling relies on mechanosensitive E-cadherin adhesions, as this signaling is disrupted upon genetic modulation of force transduction by the E-cadherin complex. Proximity labeling identified a connection between E-cadherin and ADAM17, an enzyme that mediates the shedding of soluble EGFR ligands. We developed a novel ADAM activity probe to demonstrate that mechanical strain induces ADAM activation, which relays mechanosensitive signaling from E-cadherin adhesions towards EGFR/ERK. Collectively, our data demonstrate how mechanical strain transduced by E-cadherin adhesion modulates the presence of EGFR ligands to regulate downstream ERK activity. Our findings illustrate how mechanical signals and biochemical ligands can operate within a single, linear signaling cascade.

overall_design: Transcriptomic profiling of MDCK GII cells after 18% static strain application for 2 hours.

first: RM

last: Houtekamer

first: MC

last: van der Net

first: MJ

last: Vliem

first: TEJC

last: Noordzij

first: L

last: van Uden

last: van Es

first: JY

last: Sim

first: E

last: Deguchi

first: K

last: Terai

first: MA

last: Hopcroft

first: HR

last: Vos

first: BP

last: Pruitt

first: M

last: Matsuda

first: WJ

last: Pannekoek


title: Loss of SPHK1 recruits pro-tumorigenic macrophagese to drive lung adenocarcinoma

city: Vienna

first: Herwig

middle: P

last: Moll

address: Waehringer Strasse 13a

country: Austria

institute: Medical University of Vienna

summary: Altered lipid metabolism contributes to lung inflammation and drives lung tumorigenesis. A key factor maintaining homeostasis is Sphingosine Kinase 1 (SPHK1), which phosphorylates sphingosine to the bioactive lipid sphingosine-1-phosphate. Interruption of this synthesis pathway in lung tumor cells promotes a pro-tumorigenic microenvironment and hence drives tumor progression. To better understand this process, we performed RNAseq analysis of SPHK1 proficient and deficient mouse lung tumor cells harboring KrasG12D mutations.

overall_design: We established KrasG12D driven, p53 deficient lung tumor cell lines. Subsequently, we knocked out SPHK! In these cells. For RNAseq analysis, we harvested RNA before and after treatment witth 10% fetal calf serum.

first: Daniel

last: John

first: Andreea

middle: C

last: Luca

first: Emilio

last: Casanova


title: Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC [snRNA-Seq]

city: shenzhen

first: Minmin

last: Chen

state: GuangDong

address: Gaoke Innovation Center, Guangqiao Road, Guangming District, Shenzhen

country: China

institute: Shenzhen bay lab

summary: This study aims to explore the role of nerves in tumor biology, particularly focusing on their function and the impact of the neural microenvironment in cancer invasion. Utilizing multi-omics technologies, we have mapped the spatial transcriptomic landscape of nerve-associated cells in pancreatic ductal adenocarcinoma (PDAC). By analyzing tissue samples with varying degrees of neural invasion, we have uncovered the complex interactions between tumor cells, immune cells, and neurons, providing new insights into the mechanisms underlying nerve-tumor interactions. This research lays the groundwork for future studies in cancer neuroscience and potentially advances the development of novel therapeutic strategies.

overall_design:
We generated scRNA-seq and snRNA-seq data from 25 patients to investigate Neural Invasion in PDAC, including tumor and normal tissue.

***************************************************************
Raw data were deposited in the Genome Sequence Archive (GSA) with the accession number HRA008568.
***************************************************************

first: Min-Min

first: Qinhang

last: Gao

first: Huiheng

last: Ning

first: Kang

first: Yang

first: Chaoqun

last: Liu

first: Linnan

last: Zhu

first: Wei

last: Zhou

first: Jieying

last: Pan

first: Lusheng

last: Wei

first: Dingwen

last: Zhang

first: Min

last: Yu

first: Qingling

first: Rufu

first: Zemin


title: Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC [scRNA-Seq]


title: Assessing the Effects of Silver Nanoparticles on ARPE-19 Cells via High-Throughput Phenotypic Profiling with the Cell Painting Assay.

city: Durham

first: Joshua

last: Harrill

address: 109 TW Alexander Dr

institute: US EPA

summary: Increasing commercialization of silver nanoparticles (AgNPs) has resulted in elevated opportunity for human exposure and outpaced traditional risk assessment approaches that rely on in vivo testing. Therefore, efficient methods are needed to evaluate potential hazards of AgNPs. Previous studies identified particle size and surface charge as determinants of AgNP toxicity, which has primarily been attributed to reactive oxygen species generation. Those studies have generally focused on cytotoxicity or targeted cellular effects, potentially missing critical sub-cytotoxic effects. Here, high throughput phenotypic profiling (HTPP) with the Cell Painting assay was used to characterize the effects of 12 distinct AgNPs (≤ 30 µg/mL) on organelle morphology in human retinal pigmented epithelial cells (ARPE-19). Three coatings (branched polyethyleneimine, polyvinylpyrrolidone, citrate) were selected for their distinct surface charges and tested at 4 different sizes (40, 60, 80, 100 nm) to determine the effects of these properties on toxicity. HTPP was conducted in conjunction with a transcriptomic profiling experiment involving 60 nm particles of all coating types. This facilitated evaluation of mechanisms of action underlying morphological effects observed using HTPP. A cell viability and apoptosis assay was also run in parallel and used to exclude cytotoxic treatments from phenotypic and transcriptomic analyses. HTPP revealed concentration-dependent emergence of sub-cytotoxic phenotypic profiles that clustered by coating type, suggesting surface charge to be more influential than particle size in the determination of AgNP toxicity. The transcriptomic data highlighted oxidative stress and cell cycle alterations as fundamental underlying toxicity mechanisms of AgNPs.

overall_design: For the RNA-Seq assay, dosing was performed manually by removing half of the cell culture media from each flask and replacing it with an equivalent volume of 2X concentrated test particle or fresh cell culture media as a negative control. Initial 1 mg/mL AgNP solutions (polyethyleneimine (Ag-BPEI), polyvinylpyrrolidone (Ag-PVP) and citrate (Ag-Citrate) were diluted in media such that the final concentrations applied to cells were 0.3, 1, 3, 10, and 30 μg/mL. There were six technical replicates of each nanoparticle treatment and eleven negative controls. For this assay, cells were exposed for 24 hours.

first: Gabrielle

last: Byrd

first: Alice

last: Goldstein-Plesser

first: Jo

last: Nyffeler

first: Clinton

last: Willis

first: Anna

last: Fisher

first: William

last: Boyes


title: Analysis of a BCOR internal tandem duplication in mouse embryonic stem cell to neuronal precursor differentiation

first: Mitzi

middle: I

last: Kuroda

address: 77 Ave Louis Pasteur

department: Genetics and Medicine

institute: MGB

summary: BCOR (BCL-6 corepressor) is a component of variant Polycomb Repressive Complex 1.1 (vPRC1.1), one of several vPRC1 complexes that catalyze histone H2A ubiquitination thought to play an important role in PRC2 binding and the deposition of H3K27me3 to silence genes. The PCGF Ub-like Fold Discriminator (PUFD) domain at the C-terminus of BCOR forms a heterodimer with PCGF1, serving as a critical interface for its polycomb-dependent functions. Internal tandem duplication (ITD) mutations in BCOR, causing in-frame duplications of 20 to 40 amino acids in the PUFD domain, are observed in heterogenous tumors including sarcomas (kidney, bone and endometrium) and neuroepithelial tumors in the brain. To dissect the molecular mechanisms underlying aberrant function of BCOR-ITD mutants, we employed mouse embryonic stem (mES) cells expressing either transgenic or endogenous BCOR-ITD. Our results indicate that the BCOR-ITD mutation does not disrupt the BCOR-PCGF1 interaction, instead maintaining the integrity of the vPRC1.1 complex. While displaying subtle changes in imprinted gene expression during differentiation toward a neural lineage, BCOR-ITD mutants also had no growth phenotype in culture. Furthermore, we found that CD24+ cells were enriched, as expected, during neural progenitor differentiation in both wildtype and mutant cells. However, sensitization of BCOR-ITD mES cells with EZH2 inhibitor during differentiation resulted in an unexpected enrichment of a CD24+CD26+ subpopulation, indicating aberrant cell fate that was also prevalent in a BCOR truncation mutant. Together, our results suggest that BCOR-ITD may largely retain wildtype function, but with increased susceptibility to synergistic stress on the Polycomb pathway.

overall_design: RNA-seq profiles in wild type mouse embryonic stem cells (mESC) and knock-in derivate of BCOR-ITD and BCOR-TR mutant  at day 0 at  ES cell state  and at day6 neuronal precursor cells (NPC) differentiation state

first: Zuzer

last: Dhoondia


title: Androgen receptor-mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells (ATAC-seq)

city: Kuopio

first: Ville

last: Paakinaho

address: Yliopistonranta 8

institute: University of Eastern Finland

summary: Steroid receptors are involved in a wide array of crosstalk mechanisms that regulate diverse biological processes, with significant implications in diseases, particularly in cancers. In prostate cancer, indirect crosstalk between androgen receptor (AR) and glucocorticoid receptor (GR) is well-documented, where GR replaces antiandrogen inactivated AR becoming the disease driver. However, the existence and impact of direct chromatin crosstalk between AR and GR in prostate cancer have remained elusive. Our genome-wide investigations reveal that AR activation significantly expands GR chromatin binding. Mechanistically, AR induces remodeling of closed chromatin sites, facilitating GR binding to normally inaccessible sites. Importantly, coactivation of AR and GR results in distinct transcriptional responses at both the population and single-cell levels. Intriguingly, genes and pathways affected by these transcriptional changes are generally associated with improved patient survival. Thus, the direct crosstalk between AR and GR yields markedly different outcomes from the known role of GR in circumventing AR blockade by antiandrogens.

overall_design: Examination of chromatin accessibility by ATAC-seq from VCaP prostate cancer cells treated with vehicle (EtOH), dexamethasone (Dex), dihydrotestesterone (DHT), or Dex and DHT. Sequencing was done with Illumina NextSeq 500.

first: Johannes

last: Hiltunen

first: Niina

last: Aaltonen

first: Laura

last: Helminen


title: Quorum sensing regulation by the nitrogen phosphotransferase system in Pseudomonas aeruginosa

city: Stillwater

first: Matthew

last: Cabeen

state: Oklahoma

address: 307 Life Science East

department: Microbiology and Molecular Genetics

institute: Oklahoma State University

summary: This study was conducted to learn the transcriptional effects of deleting different components of the nitrogen-related phosphotransfer system (Nitro-PTS or PTS-Ntr) in Pseudomonas aeruginosa under infection-similar culture conditions using synthetic cystic fibrosis sputum medium (SCFM2). This system regulates a number of different genes and processes in different bacterial species, but few of its targets have been identified in P. aeruginosa. Because PtsP is required for PtsN phosphorylation, the ptsP mutant provides an opportunity to assess the impact of unphosphorylated PtsN (versus the ptsP ptsN double deletion). We also tested the transcriptional impact of adding 7.5 mM supplementary citrate to this medium. The different deletions showed distinct sets of differentially regulated genes that help yield insight into how the different components of the Nitro-PTS differentially influence expression. The results also aided in identifying previously unrecognized citrate transport proteins.

overall_design: Total RNA was extracted using an NEB Monarch kit from bacterial samples grown in liquid synthetic cystic fibrosis sputum medium (SCFM2). Transcriptomes from wild-type P. aeruginosa PA14 were compared with isogenic in-frame deletions of ptsP, ptsP, ptsN, or ptsP + ptsN or with wild-type PA14 grown in SCFM2+7.5 mM citrate.

first: Simon

last: Underhill

first: Samalee

last: Banerjee

first: Josephine

last: Chandler


title: Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC [ST]

first: Minmin

last: Chen

overall_design:
We generated Spatial Transcriptomics data from 21 slices to investigate Neural Invasion in PDAC

***************************************************************
Raw data were deposited in the Genome Sequence Archive (GSA) with the accession number HRA008568.
***************************************************************

first: Min-Min

first: Qinhang

last: Gao

first: Huiheng

last: Ning

first: Kang

first: Yang

first: Chaoqun

last: Liu

first: Linnan

last: Zhu

first: Wei

last: Zhou

first: Jieying

last: Pan

first: Lusheng

last: Wei

first: Dingwen

last: Zhang

first: Min

last: Yu

first: Qingling

first: Rufu

first: Zemin


title: Merlin Controls Limb Development and Thumb Formation by Regulating Primary Cilia-Hedgehog Signaling

city: hangzhou

first: shali

last: wu

address: YUHANGTANG  road 866

institute: zhejiang university

summary: Hedgehog (HH) signaling, transduced at the primary cilium, plays a crucial role in limb longitudinal growth and digit formation, yet its involvement in thumb development has been underestimated. This study identifies Merlin (Nf2) as a novel regulator of limb development, modulating the ciliary trafficking of the HH receptor, Smoothened. Merlin is predominantly expressed in limb buds and growth plates. Conditional knockout of Merlin in limb mesenchyme in mice results in dwarfism, brachydactyly, and thumb hypoplasia, with transcriptomic profiling and molecular analyses revealing disrupted HH signaling. Mechanistically, Merlin interacts with ARF6 to regulate the ciliary transport of Smoothened via RAB11+ vesicles. Importantly, pharmacological enhancement of HH signaling significantly corrected the limb defects caused by Merlin deletion. These findings highlight the essential role of Merlin in regulating longitudinal limb growth and thumb morphogenesis via primary cilia-HH signaling, suggesting potential therapeutic strategies for related limb dysplasias.

overall_design: RNA-seq profiling of Nf2f/f and Nf2f/f;Prx1-Cre primary cultured chondrocytes without differentiation.

first: Shali

last: Wu

first: Yan

last: Bian

first: Mengrui


title: Genomic and transcriptomic determinants of clinical outcomes in patients with AML and DNMT3A mutations

city: Taipei

first: Sao-Chih

last: Ni

address: Heping E. Rd

country: Taiwan

institute: National Taiwan University Hospital

summary: Acute myeloid leukemia (AML) and DNMT3A mutations (DNMT3Amut) are considered to carry intermediate risk under the 2022 European LeukemiaNet (ELN-2022) classification in the absence of other co-mutations or cytogenetic abnormalities. However, this group is highly heterogeneous. In this study, the genomic and transcriptomic features influencing outcomes in DNMT3A-mutated AML were examined in a cohort of 884 patients with AML receiving standard chemotherapy. Stratification by NPM1 and FLT3-ITD status revealed worse survival among patients with NPM1 mutations and wild-type FLT3-ITD (NPM1mut/FLT3-ITDwt) than patients in the ELN-2022 favorable risk group. The other three subgroups (NPM1mut/FLT3-ITDmut, NPM1wt/FLT3-ITDmut, and NPM1wt/FLT3-ITDwt) exhibited worse prognoses than patients in the ELN-2022 intermediate risk group. Additionally, the presence of TET2mut in patients with AML and DNMT3Amut/NPM1mut/FLT3-ITDwt led to reclassification from favorable risk to intermediate risk in the ELN-2022. RNA-sequencing analysis revealed a distinct transcriptomic profile in patients with TET2mut, highlighting the enrichment of leukemic stem cell signatures and dendritic cell migration, with MMP14, CD200, and CT45A5 identified as key differentially expressed genes. In conclusion, co-mutation patterns strongly affected AML outcomes in patients with DNMT3Amut. Patients with TET2mut constituted a unique subgroup within the ELN-2022 favorable DNMT3Amut/NPM1mut/FLT3-ITDwt group, characterized by distinct transcriptomic features and an unfavorable prognosis.

overall_design: Comparitive gene expression profiling of RNA-seq data for AML patients with DNMT3A mutation and DNMT3A wild-type

first: Feng-Ming

last: Tien


title: Effect of L-2-hydroxyglutarate on gene expression in mice round spermatids

city: Jerusalem

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

country: Israel

institute: HUJI

summary: 2-hydroxyglutarate (2HG) is known to function as an epigenetic regulator in cancer and certain transient biological processes. Among all organs in mice, the testis contains the highest baseline physiological levels of 2HG. We found that L-2HG is generated in specific stages of spermatogenesis namely starting from  pachytene  up to round spermatids.

overall_design: To investigate the impact of 2HG, we conducted experiments where we manipulated its content in cells. This was achieved either by incubating cells with the LDH pan inhibitor oxamate or by supplementing oxamate-treated cells with cell-permeable L2HG. In a previous study (GSE169015), we examined the effect of L-2HG on gene expression in the pachytene/diplotene/diakinesis population. In the current study, we extended our investigation to explore the same effect in round spermatids.

first: Eli

last: Pikarsky

first: Nina

last: Mayorek

first: Miriam

last: Schlossberg


title: Nanopore sequencing unveils the complexity of the murine brown adipose tissue transcriptome

city: Odense

first: Jan-Wilhelm

last: Kornfeld

address: Campusvej 55

department: BMB

country: Denmark

institute: University of Southern Denmark

summary: Alternative splicing contributes to transcriptomic complexity and plays a role in the regulation of cellular identity and function, but the correct assembly of transcripts of complex loci as well as their quantification based on short-read sequencing is non-trivial. Recent long-read sequencing methods such as those from ONT and PacBio overcome these problems by potentially sequencing full transcripts. The activation of brown adipose tissue e.g., by reduced ambient temperature (cold) exposure, positively affects metabolism by increasing energy expenditure and releasing endocrine factors and has been shown to involve specific alternative splicing events. Here we assessed important features of ONT long read sequencing protocols in relation to Illumina short read sequencing: (i) Alignment characteristics to the reference genome and transcriptome, (ii) Gene and transcript detection and quantification, (iii) Detection of differential gene and transcript expression events, (iv) Transcriptome reannotation and (v) Detection of differential transcript usage events. We find that ONT long-read sequencing is advantageous in terms of transcriptome reassembly, especially when the reads are enriched for full length reads. Illumina sequencing, due to the higher number of counts available, has a higher statistical power for calling differentiall expressed/used features, whereas long-read sequencing has a lower risk of calling false positive events due to the better ability to unambiguously map reads to transcripts. Finally we describe novel transcript isoforms in cold-activated murine iBAT reassembled from ONT long reads.

overall_design: PolyA RNA from epididymal white adipose tissue of 20 weeks old male wild type C57BL/6N mice singly housed at 4°C (n = 3) for a period of 24 h sequenced by Oxford Nanopore Technologies direct cDNA sequencing.

first: Christoph

last: Engelhard

first: Sajjad

last: Khani

first: Sophia

last: Derdak

first: Martin

last: Bilban


title: PAF1C-dependent activation of CDK12 is required for RNA polymerase II phosphorylation and transcript elongation

city: Copenhagen N

first: Jesper

last: Svejstrup

state: Denmark

address: Blegdamsvej 3, 18.6

department: Department of Cellular and Molecular Medicine

institute: University of Copenhagen

summary: The RNA polymerase II (RNAPII) transcription cycle is regulated by dynamic changes in RNAPII C-terminal domain (CTD) phosphorylation, and such modification is crucial for gene expression. However, the mechanisms regulating the transcription-specific cyclin-dependent kinases (CDKs) during the transcription cycle remain poorly understood. Here, we show that human CDK12 co-phosphorylates CTD Serine2 and Serine5. This di-phosphorylated Serine2-Serine5 CTD mark can then act as a precursor for Serine2 mono-phosphorylated CTD through Serine5 de-phosphorylation. Notably, CDK12 is specifically regulated by association with the elongation-specific factor PAF1C, in which the CDC73 subunit contains a metazoan-specific peptide motif, capable of allosteric CDK12/Cyclin K activation. This motif is essential for cell proliferation and required for normal cellular levels of CTD phosphorylation. It is also crucial for transcript elongation, particularly across long human genes. Together, these findings provide new insight into the mechanisms governing RNAPII phospho-CTD dynamics that ensure progression through the human transcription cycle.

overall_design: To investigate the role of CDC73-KIM for global RNA production, we first established a “switchover” system where endogenous CDC73 was knocked down by siRNA in HEK293 cells, and different recombinant, siRNA resistant, and Flag-tagged versions of CDC73 were inducibly expressed by doxycycline (Dox) addition. This was followed by metabolic labelling of nascent RNA using a short pulse of the uridine analog 4-thiouridine (4sU).  Transient Transcriptome chem-sequencing (TTchem-seq) was then used to affinity purify, fragment and sequence 4sU-labelled RNA for high-resolution profiles of nascent transcription.

first: David

last: Lopez Martinez

first: Izabela

last: Todorovski

first: Jesper Q


title: Single-cell RNA transcriptome defines the signaling networks stimulated by alkali burn

first: Han

last: Peng

address: 303 E Chicago Ave, Ward 9-120

institute: Feinberg School of Medicine, Northwestern University

summary: To understand the pathological mechanisms of alkali burn, mouse corneal epithelium was exposed to 1M NaOH for 30s . Corneas were processed for scRNA-seq using 10X genomics and data was analyzed using R with a Seurat package.

overall_design: Methods:We conducted scRNA-seq on ocular anterior segmental tissue from 1 uninjured wild-type and 1 NaOH injured wild type mice, using a 10X Gemomics pipeline. Cell populations were distinguished byUMAP embedding. Seurat analysis was conducted to compare gene expression profiles between these two groups of mice.

first: Nihal

last: Kaplan

first: Robert

last: Lavker


title: Single cell RNA-sequencing of testes from control and Brca1 germ cell-specific knockout mice

city: Hangzhou

first: Lin-Yu

last: Lu

state: Zhejiang

address: 268 Kaixuan Road, North Central Building, Room 536

institute: Zhejiang University

summary: To examine the role of BRCA1 during the formation of undifferentiated spermatogonia, we generated Brca1 germ cell-specific knockout mice, in which BRCA1 was undetectable when undifferentiated spermatogonia started to form at PD1. To analyze the defects comprehensively, we isolated testes from one pair of control and Brca1 germ cell-specific knockout mice male mice at PD7 and performed single-cell RNA sequencing (scRNA-seq) analyses using the 10× Genomics platform. In the study, we found that BRCA1 loss indeed disrupts early postnatal germ cell development.

overall_design: A pair of PD7 testes from different mice were isolated and single cells were generated for the downstream RNA-sequencing

first: Peng

last: Li

first: Yidan

last: Liu


title: Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC

first: Minmin

last: Chen

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

overall_design: Refer to individual Series


title: An engineered viral protein activates STAT5 to prevent T cell suppression

city: ANN ARBOR

first: Adam

last: Courtney

state: MI

address: 1150 W. Medical Center Dr., 2240 MSRB III

department: Pharmacology

institute: University of Michigan

summary: T cell therapy efficacy can be compromised if cytokine-induced Janus kinase (JAK)-signal transducer and activator of transcription (STAT) signaling is dysregulated or insufficient to sustain functionality. Here, we demonstrate that LCK kinase activity can be recruited to non-canonical protein substrates to directly activate targeted STAT proteins in T cells. STAT activation was accomplished by engineering the Herpesvirus saimiri (HVS) tyrosine kinase interacting protein (TIP) to provide a platform for the enforced recruitment of LCK to STAT proteins. We determined that a minimal region of TIP that binds to LCK could be combined with STAT binding sites derived from endogenous cytokine receptors. These constructs activated targeted STAT proteins in a cytokine-independent manner. We identified a STAT5 activator that sustained CD8+ T cell survival and cytotoxic function ex vivo in the absence of IL-2. Tumor outgrowth was reduced in vivo due to enhanced T cell persistence and functionality. Single-cell transcriptomics revealed the STAT5 activator prevented the expression of genes associated with an exhausted T cell fate. Our findings demonstrate that signaling pathways can be rewired in T cells to sustain their function in solid tumors.

overall_design: B16-OVA tumors were established in BoyJ (CD45.1+) mice prior to adoptive transfer of CD8+ OT-I T cells (ACT) transduced with empty vector, a STAT5 activator (aSTAT5), a minimal construct (PepControl), and constitutively active STAT5 (STAT5CA). Tumors were collected form 3 mice per treatument group 5- or 12-days post-ACT and CD45+ tumor infiltrating leukoctyes isolated by positive selection. Isolated cells were then stained with DNA barcoded antibodies (CD45.1, CD45.2, CD90.1, CD8a  TotalSeq-C antibodies and TotalSeq-C HashTag antibodies) and fluorescent antibodies (CD45, CD8a, CD8b, TCRb) prior to isolation of CD45+CD8+ T cells by FACS. Joint HTO and ADT libraries were prepared using the 10x Genomics platform.

first: Yating

last: Zheng

first: Monica

last: Chanda

first: Dana

last: King

middle: H


title: Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition (EM-Seq)

city: Kyoto

first: Yukihiro

last: Yabuta

state: Kyoto

address: Yoshida-Konoe-cho, Sakyo-ku

department: Anatomy and Cell Biology

institute: Kyoto University, Graduate school of medicine

type: Methylation profiling by high throughput sequencing

summary: In vitro oogenesis provides a platform to elucidate the mechanism of oocyte development and advance reproductive medicine. The prevalent in vitro oogenesis model requires ovarian somatic cells (OSCs) to support oocyte development, yet complex three-dimensional oocyte–OSC interactions pose difficulties in systems regulation and mechanistic understanding. Here, we present an OSC-free system of in vitro oogenesis: upon optimized provision of retinoic acid and bone morphogenetic protein on feeders, mouse primordial germ cell-like cells induced from embryonic stem cells propagate robustly, and enter/progress through meiotic prophase I, generating abundant fetal oocyte-like cells at diplotene arrest. With key cytokines, signaling activators, and antioxidants, they show prominent growth and differentiate into cells comparable to germinal-vesicle oocytes in morphology, transcriptome, and histone-modification profiles, with competence to resume meiosis with germinal-vesicle breakdown. By reconstituting major phases of oogenesis with minimal components, our study creates a foundation for OSC-free in vitro oogenesis in mammals, including humans.

overall_design: Transcriptome analysis of pre-antral oocytes from mouse embryonic stem cells under an ovarian soma-free condition

first: Yoshiaki

last: Nosaka

first: Masahiro

last: Nagano

first: Baku

last: Nakakita

first: So

last: Nagaoka

first: Ikuhiro

last: Okamoto

first: Hiromichi

last: Sasada

first: Ken

last: Mizuta

first: Fumiya

last: Umemura

first: Hiroto

last: Kuma

first: Yasushi

last: Okochi

first: Yoshitaka

last: Katou

first: Bernard

last: de Massy

first: Azusa

last: Inoue

first: Akihito

last: Horie

first: Masaki

last: Mandai

first: Hiroshi

last: Ohta

first: Mitinori

last: Saitou


title: Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition (SC3-Seq)

first: Yukihiro

last: Yabuta

first: Yoshiaki

last: Nosaka


title: Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition


title: Transcriptional profiling of U87 and U373 after 72 hours treatment of 1U/ml pegylated arginase I BCT-100.

city: Hong Kong SAR

first: Kwong Lam

last: Fung

address: L7-55 Paediatrics, Lab Block, Faculty of Medicine, 21 Sassoon Road, Pokfulam, Hong Kong

department: Paediatrics & Adolescent Medicine

country: Hong Kong

institute: University of Hong Kong

summary: In this study  the effect of pegylated arginasse I on global gene expression in U87 and U373 were examined. Both cells were cultured in complete medium with PBS control or 1U/ml pegylated arginase I (BCT-100) for 72 hours. Comparative transcriptome analysis of both cell lines in PBS control versus BCT-100 treatment were performed.

overall_design: Examination of gene expression in U87 and U373 after 72 hour pegylated arginase I treatment.

first: M

first: S

last: Chan

last: Sun

first: PD

last: Zhang

first: G

last: Leung


title: Porphyran from discolored nori prevents metabolic syndrome through microbiota-bile acid-ceramide pathway

city: Fujisawa

first: Yoko

last: Yokoyama

address: 5322 Endo

institute: Keio University

summary: To investigate nori (seaweed) effects on metabolic syndrome, we conducted microarray analysis.

overall_design: Male C57BL/6J mice of 5 weeks of age were fed with a control diet (10% kcal fat; n = 7), a high fat diet (60% kcal fat; n = 7), or a high fat supplemented with 2% w/w porphyran (n = 7) or with 2% w/w nori extract (n = 7) for 13 weeks. Tissues from the 7 mice in a group were pooled.

first: Mitsuhiro

last: Watanabe


title: Global transcriptional profiles of primary and secondary cellular senescence in vivo  by oncogene-induced senescence (OIS) and stress-induced senescence (SIS)

first: Takuya

last: Yamamoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

department: CiRA

institute: Kyoto University


title: Global transcriptional profiles of primary and secondary cellular senescence in vivo  by oncogene-induced senescence (OIS) and stress-induced senescence (SIS) [Bulk RNA-seq]

summary: The physiological roles of cellular senescence in vivo are largely unknown. Here, we report primary and secondary senescence-induced transcriptional alterations by oncogene-induced senescence (OIS, ERK activation) and stress-induced senescence (SIS, p38 activation) of liver, intestine, and MEF.

overall_design: Hepatocytes and colonic epithelial cells were isolated from double-coloured chimeric caMEK1 (OIS, ERK activation) and caMKK6 (SIS, p38 activation) mice. The mCherry-positive primary senescent cells and GFP-positive surrounding cells were collected using FACS, and total RNAs were extracted to perform RNA-seq. MEFs were analyzed as in vitro control.

first: Yuko

last: Sogabe

first: Mio

last: Kabata

first: Yasuhiro

last: Yamada


title: m6A profile of soybean tissues

status: Public on May 18 2025

city: beijing

first: li

last: yaping

address: 中关村南大街12号

institute: 中国农业科学院生物所

summary: Soybean is a critical source of vegetable protein, yet its proteome remains under-characterized. Here, we quantify 12,855 proteins across 14 soybean organs using 4D-data-independent acquisition mass spectrometry (4D-DIA-MS), creating the most extensive soybean proteome dataset to date. Organ-specific protein expression and co-expression analyses highlight functional specificity, with significant differences in protein-transcript abundance across organs. We also map N6-methyladenosine (m6A) modifications, identifying their key role in post-transcriptional protein regulation. Integrative analysis of proteome and m6A methylome identifies novel regulator in m6A methylation. This comprehensive proteomic and m6A landscape advances our understanding of soybean biology and provides a valuable resource for crop improvement.

overall_design: Different tissues from wild-type SoyC11 soybeans (Glycine max) were used and collected for proteome, m6A methylome and transcriptome analysis. The seedlings were grown in the greenhouse at 25℃. Mature plants were grown in soybean field located in Shijiazhuang (37°6′25″N, 114°42′47″E), Hebei province, China. Seeds of the soybean germinated in sterilized water for 1 days, the imbibition seeds (ISD) were transferred to soil. At V1 stage, unifoliolate leaf (ULF), seedling stem (SM), root (RT_V1), seedling cotyledon (CT_V1) and trifoliolate leaf (TLF) were collected. The flowers (FL_R2) were collected at R2 stage in soybean field, the roots (RT_R5) and the root nodules (RTN) at R5 stage, the pod (Pod) at R6 stage, green seed (GSD) at R7, mature seed (MSD) at R8 stage.


title: Generation of germinal-vesicle oocytes from mouse embryonic stem cells under an ovarian soma-free condition (CATCH-Seq)

overall_design: CATCH-seq against H3K4me3, H3K27me3, H3K36me3 in d4c7oogonia-like cells, d4c13oocyte-like cells, d4c34 oocyte-like cell, Oocyte (E18.5), GV Oocyte

first: Masahiro

last: Nagano

first: Baku

last: Nakakita

first: So

last: Nagaoka

first: Ikuhiro

last: Okamoto

first: Hiromichi

last: Sasada

first: Ken

last: Mizuta

first: Fumiya

last: Umemura

first: Hiroto

last: Kuma

first: Yasushi

last: Okochi

first: Yoshitaka

last: Katou

first: Bernard

last: de Massy

first: Azusa

last: Inoue

first: Akihito

last: Horie

first: Masaki

last: Mandai


title: Global transcriptional profiles of primary and secondary cellular senescence in vivo  by oncogene-induced senescence (OIS) and stress-induced senescence (SIS) [scRNA-seq]

first: Takuya

last: Yamamoto

summary: The physiological roles of cellular senescence in vivo are largely unknown. We report primary and secondary senescence-induced transcriptional alteration by oncogene-induced senescence (OIS, ERK activation) and stress-induced senescence (SIS, p38 activation) of mouse hepatocytes. Our analyses revealed that each senescence-induced cell displays different transcriptional profiles explaining various known senescent properties.

overall_design: Hepatocytes were isolated from double-coloured chimeric control, caMEK1 (OIS), and caMKK6 (SIS) mice. After mCherry-positive primary senescent cells and GFP-positive surrounding cells were collected by using FACS, the sorted cells were subjected to scRNAseq analyses.

first: Yuko

last: Sogabe

first: Mio

last: Kabata


title: Separation-of-function mutants reveal the NF-κB-independent involvement of IκBα in the regulation of intestinal stemness [ChIP-seq]

city: Barcelona

first: Lluis

last: Espinosa

state: Barcelona

address: Dr. Aiguader 88

department: Institut Municipal d'Investigacions Mèdiques, (IMIM)

country: Spain

institute: Hospital del Mar

summary: We previously demonstrated that the NF-κB inhibitor IκBα binds the chromatin together with PRC2 to regulate a subset of developmental- and stem cell-related genes. This alternative function has been elusive in both physiological and disease conditions because of the predominant role of IκBα as a negative regulator of NF-κB. We here uniquely characterize specific residues of IκBα that allow the generation of separation-of-function (SOF) mutants that are defective for either NF-κBrelated (SOF DeltaNF-κB) or chromatin-related (SOF DeltaH2A,H4) activities. Expression of IκBα SOF DeltaNF-κB, but not SOF DeltaH2A/H4, is sufficient to negatively regulate a specific stemness program in intestinal cells, thus rescuing the differentiation blockage imposed by IκBα deficiency. . By ChIP assay we demonstrated IκBα binding to several stem cell genes that are transcriptionally repressed following IκBα SOF DeltaNF-κB induction. Our data indicate that SOF mutants represent an exclusive tool for studying IκBα functions in physiology and disease.

overall_design: We performed IκBα ChIP-seq on FLAG IκBα samples from two different cell lines: HT29 and HCT116 (3x from each cell line).

first: Daniel

last: Álvarez-Villanueva

first: Luis

last: Galán-Palma

first: Teresa

last: Lobo-Jarne

first: María

last: Maqueda

first: Anna

last: Bigas


title: Interaction between long-range chromatin regulators Nipbl & Isl1 synergistically drives heart defects in mice

city: Irvine

first: Anne

last: Calof

state: CA

address: Biological Sciences III, 519 Ring Rd

department: Developmental & Cell Biology

institute: University of California, Irvine

summary: Congenital heart defects (CHDs) are frequently observed in the most common form of Cornelia de Lange Syndrome (CdLS), which is caused by haploinsufficiency for NIPBL, a gene involved in chromatin looping and cis-regulatory control of gene expression. Here, we surveyed cardiac defects in mice made Nipbl-haploinsufficient in the second heart field using two Cre drivers: Mef2c-Cre and Isl1-Cre. Only Isl1-Cre-driven Nipbl-haploinsufficiency resulted in CHDs – a finding we traced to the additional contribution of Isl1-haploinsufficiency caused by the Isl1-Cre allele. To test whether combined reduction of Nipbl and Isl1 cause CHDs, we made mice globally haploinsufficient for both genes. Indeed, Nipbl+/-; Isl1+/- mice exhibited a substantially higher frequency and severity of CHDs than mice haploinsufficient for either gene alone. As a member of the LIM-homeodomain transcription factor family, Isl1 is involved in chromatin looping and enhancer-promoter communication via a mechanism distinct from that of Nipbl. Nevertheless, when we performed RNA sequencing on E10.5 hearts from wildtype, Nipbl+/-, Isl1+/-, and Nipbl+/-; Isl1+/- embryos, we observed that combined haploinsufficiency resulted in largely additive gene expression changes, including dysregulation of known cardiac regulators (Irx4, Tbx1, Foxo6, Heyl, Bnc1, Sox17) and novel candidates (Gbx1, Csdc2, Myrf, Pou6f1, Zfp579, ad Zfp763). A subset of additive changes arose from opposing regulatory influences in single mutants that restored gene expression to WT levels in Nipbl⁺/⁻; Isl1⁺/⁻ hearts. For example, Hoxc4, Pitx2, Isl1 itself, and Pax6 (a known target of Isl1), were upregulated in Nipbl+/- hearts, downregulated in Isl1+/- hearts, but expressed at WT levels in Nipbl⁺/⁻; Isl1⁺/⁻ hearts. Since loss of Isl1 upregulation from Nipbl+/- to Nipbl+/-; Isl1+/- hearts coincided with a marked increase in CHDs, we propose that Isl1 upregulation compensates for the loss of cis-regulatory interactions due to Nipbl-haploinsufficiency, and protects hearts from severe CHD risk. Supporting this model, other LIM-homeodomain transcription factors (Lhx2, Lhx3, Lhx9) were also upregulated in Nipbl+/- hearts, with Lhx3 and Lhx9 showing even greater upregulation in Nipbl+/-; Isl1+/- hearts. Despite this, CHDs resulting from the combined loss of Nipbl and Isl1 were particularly severe. These findings suggest that heart development is exquisitely sensitive to small change in gene expression, leading to synergistic phenotypic interactions when relatively modest gene expression changes are combined.

overall_design: Stra8-iCre; Nipbl Flox/+ male mice were mated with Isl1 Cre/+ female mice. Stra8-iCre; Nipbl Flox/+ male mice produce sperm that are either Nipbl Flox (which is a wildtype allele) or Nipbl FIN (which is a null allele). Isl1 Cre/+ female mice encode a Cre-recombinase in one allele of Isl1 and are haploinsufficient for Isl1. As such, mating Stra8-iCre; Nipbl Flox/+ male mice with Isl1 Cre/+ female mice generates progeny of four genotypes: 1) Nipbl +/+; Isl1 +/+, 2) Isl1 +/-, 3) Nipbl +/-, and 4) Nipbl +/-; Isl1 +/-. Bulk paired-end RNA sequencing was performed on hearts dissected from embryos of all four genotypes at embryonic day E10.5.

first: Stephenson

last: Chea

first: Rosaysela

last: Santos

first: Martha

last: Lopez-Burks

first: Arthur

last: Lander

middle: L


title: Viral-mediated knockdown of Atxn2 attenuates TDP-43 pathology and muscle dysfunction in the PFN1C71G ALS mouse model

status: Public on May 17 2025

city: Cambridge

first: Deborah

last: Kwon

address: 225 Binney Street

institute: Biogen

summary: Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disorder characterized by progressive motor neuron loss and muscle atrophy. Hyperphosphorylated aggregation of the RNA-binding protein, TDP-43, in the motor cortex and spinal cord are defining molecular features of ALS, suggesting TDP-43 dysfunction underlies disease pathogenesis. This phenomenon, however, has been difficult to recapitulate endogenously in animal models, impeding characterization of TDP-43 pathobiology in neurodegeneration. In this study, we report age-dependent accumulation of TDP-43 pathology in the spinal cord and progressive muscle-related deficits in transgenic mice expressing the ALS-associated PFN1C71G mutant protein. We show that transgenic neuronal expression of PFN1C71G induces early hyperphosphorylation of endogenous TDP-43 in the spinal cord that augments over time, preceding accumulation of insoluble non-phosphorylated TDP-43 and the manifestation of muscle denervation and motor dysfunction. Sustained knockdown of Atxn2 in the central nervous system (CNS) in pre-symptomatic PFN1C71G mice by AAV-driven expression of an artificial microRNA (AAV-amiR-Atxn2) reduces aberrant TDP-43 in the spinal cord, while delaying neurodegeneration and improving muscle and motor function. RNA-sequencing analysis of spinal cord samples from PFN1C71G mice and ALS donors show shared patterns of transcriptional perturbation, including a pro-inflammatory gene signature that is attenuated by AAV-amiR-Atxn2. Notably, impaired regulation of the PFN1C71G skeletal muscle transcriptome exceeds that of the spinal cord and also improved by Atxn2 reduction in the CNS. Lastly, we find significant gene co-expression network homology between PFN1C71G mice and human ALS, with shared dysregulation of modules related to neuroinflammation and neuronal function and uncover novel hub genes that provide biological insight into ALS and potential drug targets that can be further investigated in this mouse model.

overall_design: RNA-seq profiling of C71G mutant PFN1 transgenic mice and age-matched wildtype FVB/NJ controls. Treated with AAV-amiR-Atxn2.

first: Zachary

last: Hawley

middle: Y


title: Separation-of-function mutants reveal the NF-κB-independent involvement of IκBα in the regulation of intestinal stemness

last: Alvarez- Villanueva

first: Joan

last: Bertrán

first: Laura

last: Solé


title: Genome-wide analysis of DNA methylation in pseudomyxoma peritonei originated from appendiceal cancer

city: Chiba

first: Masaki

last: Fukuyo

address: 1-8-1 Inohana, Chuo-ku

department: Department of Molecular Oncology

institute: Chiba University

type: Methylation profiling by genome tiling array

summary: Comprehensive DNA methylation analysis in the 15 tumors and eight non-cancerous colonic epithelial cells using Methylation EPIC array BeadChip (Infinium 850k) containing a total of 865,918 probes. The 15 PMP tumors contained four high-grade and 11 low-grade samples.

overall_design: Bisulphite converted DNA from the 23 samples were hybridised to the Infinium HumanMethylation850 BeadChip.

first: Kiyoko

last: Takane

first: Tingwei

last: Cai

first: Rei

last: Noguchi

first: Yoshimasa

last: Gohda

first: Tsuneo

last: Ikenoue

first: Kiyoshi

last: Yamaguchi

first: Yasunori

last: Ohta

first: Tomomichi

last: Kiyomatsu

first: Hideaki

last: Yano

first: Motoaki

last: Seki

first: Rahmutulla

last: Bahityar

first: Atsushi

last: Kaneda

first: Yoichi

last: Furukawa


title: Neuromuscular junction transcriptome analysis of spinal and bulbar muscular atrophy mice implicates sarcomere gene expression and calcium flux dysregulation in disease pathogenesis

status: Public on May 16 2025

city: IRVINE

first: Anastasia

last: Gromova

email: agromova@uci.edu, agromova@gmail.com

address: 419 South Circle View Drive

department: Pathology

institute: UC Irvine

summary: X-linked Spinal and Bulbar Muscular Atrophy (SBMA) is a rare, late-onset neuromuscular disease caused by a CAG repeat expansion mutation in the androgen receptor (AR) gene.  SBMA is characterized by progressive muscle atrophy of both neurogenic and myopathic etiologies.  Previous work has established that mutant AR expression in skeletal muscle could be a significant contributor to neuromuscular decline, yet the mechanisms involved remain ill-defined.  As AR is a nuclear hormone receptor transcription factor, we sought to define early changes in gene expression in skeletal muscle of pre-symptomatic SBMA mice, with a focus on transcriptional changes at the neuromuscular junction (NMJ).  We describe loss of key NMJ-specific genes in synaptic muscle regions of pre-symptomatic SBMA mice, while extrasynaptic muscle features a coordinated loss of sarcomere genes that coincides with ectopic re-expression of certain NMJ genes.  Furthermore, SBMA muscle prominently features dysregulated calcium flux, likely stemming from a compensatory response to early atrophy that greatly exacerbates over time.  The SERCA activator CDN1163 conferred a mild rescue in function and muscle size in SBMA mice, while genetic deletion of the gene encoding Myf6/MRF4, a negative regulator of sarcomere gene expression and predicted AR interactor, did not ameliorate muscle atrophy.  These studies suggest that modulation of calcium flux could be a promising pharmacological target in SBMA.

overall_design: Bulk RNA-Seq profiling of perisynaptic (NMJ-containing) and extrasynaptic (no NMJs) regions of the diaphgram muscle of BACfxAR121 mice and HSA-Cre;BACfxAR121 muscle-rescued littermate controls at 15 and 26 weeks of age.

first: Albert

last: La Spada


title: A hexamer tandem repeat RNA embedded within an SVA retrotransposon drives R-loop formation and neurodegeneration

city: Baltimore

first: Jennifer

last: Erwin

state: MD

address: 855 N Wolf St.

institute: Lieber Institute for Brain Development

summary: Retroelement activation is emerging as a significant factor in the pathogenesis of neurodegenerative diseases. SINE-VNTR-Alu (SVAs) are hominid-specific retroelements that create genetic variation through insertion polymorphisms and variable short tandem repeat (STR) lengths. We investigate how the SVA (CCCTCT)n STR contributes to the striatal neurodegenerative disorder X-linked Dystonia Parkinsonism (XDP), where the repeat expansion length within the pathogenic SVA is inversely correlated with disease onset age. Phenotypic and transcriptomic analysis of XDP and isogenic SVA-deleted striatal organoids revealed that the SVA insertion drives hallmarks of neurodegeneration, including transcriptional dysregulation, decreased neuronal activity, and apoptosis, which are ameliorated by SVA deletion. We identify a (AGAGGG)n hexamer-containing RNA in the SVA that increases expression during organoid maturation and drives R-loop formation in organoids and XDP brain tissue. Knockdown of the (AGAGGG)n hexamer-containing RNA by antisense oligonucleotides rescues apoptosis in the XDP organoids. We demonstrate that a retrotransposon-derived tandem repeat RNA could cause neurodegeneration.

overall_design:
We profiled gene expression of iPSC-derived ventral forebrain organoids over development (30-, 60-, 90-, and 120-days-old) and compared the gene expression of cell lines including XDP, ΔSVA-XDP, controls, and female carriers.

***************************************************************
There are patient privacy concerns regarding public access to the raw data.
***************************************************************

first: D'Ignazio

last: Laura

first: Lorenzetti

last: Alan

first: Penney

last: Ellen

first: Evans

last: Taylor

first: Qamar

last: Bareera

first: McCord

last: Alejandra

first: Feltrin

last: Arthur

first: Barbosa

last: Andre

first: Sheehan

last: Bonna

first: Araujo

last: Bruno

first: Giles

last: Hunter

first: Wang

last: Yanhong

first: Sawada

last: Tomoyo

first: Zabolocki

last: Michael

first: Murcar

last: Micaela

first: Fernandez-Cerado

last: Cara

first: Legarda

last: G. Paul

first: Sy

last: Michelle

first: Velasco-Andrada

last: M. Salvie

first: Munoz

last: Edwin

first: Ang

last: Mark

first: Diesta

last: Cid Czarina

first: Bardy

last: Cedric

first: Bragg

last: D. Cristopher

first: Paquola

last: Apua

first: Erwin

last: Jennifer


title: Molecule template estimation using Validator Barcodes as an alternative to UMIs in multiplex PCR for adaptive immune repertoire profiling

city: Mountain View

first: Kitt

last: Paraiso

address: 320 Logue Ave.

department: Bioinformatics

institute: Cellecta, Inc.

summary: TCR- and BCR-sequencing (TCR/BCR-seq) are two important technologies in studying the immune repertoire of samples such as PBMCs or tumors. In their most common form, these assays combine multiplex PCR of the repertoire using primers targeting regions of the V(D)J and the constant region with next-generation sequencing (NGS). The data produced by this assay provide a slew of information regarding immune repertoire(s) including the presence critical clonotypes, repertoire diversity, variable (V) gene usage, analysis of public clonotypes, etc. One issue that can arise during generation of the TCR/BCR-seq data is sequence bias during the PCR or NGS steps. To combat this, unique molecular identifiers (UMIs) have been used to identify and eliminate sequence bias. However, UMI fragments can be long and very diverse, resulting in the UMI sequences interfering with any of the multitude of primers during multiplex PCR. Here, we introduce Validator Barcodes (VBCs), a set of eight short barcodes (6-9 nucleotides in length). This compact set of barcodes improves PCR efficiency and facilitates PCR primer designs. Also, like UMIs, the VBCs may be used to estimate the number of template molecules (RNA or DNA). Using VBC-labeled primers for TCR and BCR repertoire profiling from PBMCs produces highly comparable results and similarly template values to those obtained through UMI-based assay counts. Overall, VBCs are a useful and simpler alternative to UMIs in assaying TCR and BCR repertoires.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human or mouse PBMCs are analyzed by multiplex PCR using V-gene forward primer and J or C gene reverse primers. The libraries either contain VBC or UMI sequences.

first: Alex

last: Chenchik


title: Single-cell RNA transcriptome shows IFITM1 regulates stem cell activation in limbal epithelium in response to alkali burn.

city: Chicago

first: Han

last: Peng

summary: To examine whether the upregulation of Ifitm1 is essential for the expansion of stem/early TA cells in response to corneal injury, wild type mouse eyes were topically treated with AAV-shRNA-Ifitm1 or AAV-empty vector (control) and subsequently were subjected to corneal NaOH burn. AAV-shRNA-Ifitm1 treatment downregulated Ifitm1 expression in mouse limbal epithelium . A scRNA-seq assay was conducted using cells isolated from corneal/limbal tissues at three days after corneas were injured. scRNA-seq assay identified stem/early TA cell population using Gpha2, a limbal epithelial stem /eTA cell marker. In AAV-EV treated mouse eyes, NaOH injury increased the numbers of the stem/eTA cells compared to uninjured eyes. Such expansion of stem/eTA cell population following corneal injury was markedly reduced in AAV-shRNA-Ifitm1 treated eyes. This suggests a positive role of Ifitm1 in stem/early TA cell expansion after corneal injury.

overall_design: Methods: We conducted scRNA-seq on ocular anterior segmental tissue from 2 uninjured wild-type, 2 NaOH injured AAV-empty vector-transduced, and 2 NaOH injured AAV-shRNA-Ifitm1 transduced mice, using a 10X Gemomics pipeline. Cell populations were distinguished by UMAP embedding. Seurat analysis was conducted to compare gene expression profiles between these groups of mice.

first: Huimin

last: Jiang

first: Nihal

last: Kaplan

first: Parisa

last: Foroozandeh

first: Robert

last: Lavker


title: Macropinocytosis maintains CAF subtype identity under metabolic stress in pancreatic cancer [RNA-seq]

city: La Jolla

first: Cosimo

last: Commisso

address: 10901 N. Torrey Pines Road

department: Cancer Metabolism and Microenvironment Program

institute: Sanford Burnham Prebys Medical Discovery Institute

summary: Pancreatic ductal adenocarcinoma (PDAC) tumors are deficient in glutamine, an amino acid that tumor cells and cancer-associated fibroblasts (CAFs) use to sustain their fitness. In PDAC, both cell types stimulate macropinocytosis as an adaptive response to glutamine depletion. CAFs play a critical role in sculpting the tumor microenvironment, yet how adaptations to metabolic stress impact the stromal architecture remains elusive. In this study, we find that macropinocytosis functions to control CAF subtype identity when glutamine is limiting. Our data demonstrate that metabolic stress leads to an intrinsic inflammatory CAF (iCAF) program driven by MEK/ERK signaling. Utilizing in vivo models, we find that blocking macropinocytosis triggers CAF subtype transitions and reorganizes the tumor stroma. Importantly, these changes in stromal architecture can be exploited to sensitize PDAC to immunotherapy and chemotherapy. Our findings demonstrate that metabolic stress plays a role in shaping the tumor microenvironment, and that this attribute can be harnessed for therapeutic impact.

overall_design: Gene expression comparisons of murine cancer associated fibroblasts (CAFs) treated with 0.2 mM glutamine + DMSO, 0.2 mM glutamine + 25 uM EIPA, 4 mM glutamine + DMSO, or 4 mM glutamine + DMSO + 25 pg/mL IL1a using bulk RNA sequencing (RNA-seq)

first: Yijuan

last: Zhang


title: Macropinocytosis maintains CAF subtype identity under metabolic stress in pancreatic cancer

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

overall_design: Refer to individual Series


title: Macropinocytosis maintains CAF subtype identity under metabolic stress in pancreatic cancer [scRNA-seq]

overall_design: Single cell gene expression profiling of KPC orthotopic tumors treated with DMSO or 10 mg/Kg EIPA


title: Separation-of-function mutants reveal the NF-κB-independent involvement of IκBα in the regulation of intestinal stemness [RNA-Seq]

first: Lluis

last: Espinosa

overall_design: 12 samples analyzed

last: Espinosa-Blay

first: Daniel

last: Álvarez-Villanueva

first: Maria

last: Maqueda

first: Teresa

last: Lobo-Jarne


title: Separation-of-function mutants reveal the NF-κB-independent involvement of IκBα in the regulation of intestinal stemness [RNAseq Knock-ins IKBa]

overall_design: We performed RNA-seq on Knock-in IκBα-SOF samples, in untreated and TNF-treated conditions: (2x conditions) 3x (replicates) IκBα WT, (2x) 3x IκBα N108 mutant and (2x) 3x IκBα M3 mutant (triple H84, E85, E86 to A mutant). All samples are derived from HCT116 cell line.

first: Luis

last: Galán-Palma

first: María

first: Laura

last: Solé

first: Anna

last: Bigas


title: Gene expression analysis of human parotid salivary glands in cases of Mucoepidermoid Carcinoma via bulk RNA sequencing

city: Tampa

first: Antonio

last: Amelio

state: Fl

address: 12902 USF Magnolia Drive

department: Tumor Biology

institute: Moffitt Cancer Center

summary: Mucoepidermoid carcinoma (MEC) is the most frequently occurring salivary gland malignancy. Here, we investigated transcriptomic profiles of human adult salivary glands and MEC tumors to assess programs involved in MEC progression. MEC tumors were stratified by disease grade and CRTC1/MAML2 fusion status. The bioinformatics of our study will provide critical steps in elucidating salivary MEC progression and suggest a new candidates for targeted therapies in the treatment of high-grade MEC.

overall_design: Expression profiling by bulk RNAsequencing

first: Adele

last: Musicant

first: Julia

last: Billington

first: Jennifer

last: Modliszewski

first: Jay

last: Mehta


title: Recurrent FGFR-alterations are frequent oncogenic drivers and therapeutic targets in pediatric low-grade gliomas [RNA-Seq 2]

city: Boston

first: April

last: Apfelbaum

address: 450 Brookline Ave

department: Pediatric Oncology

institute: Dana-farber Cancer Institute

summary: Alterations in Fibroblast growth factor receptor proteins frequently occur as oncogenes in many cancers. FGFR alterations have been reported in a subset of pediatric gliomas, representing a therapeutic target for precision medicine approaches. We performed a genomic analysis of 13,659 gliomas and found that 4.5% harbor FGFR alterations including structural variants and single nucleotide variants. FGFR family members are differentially enriched by age, tumor grade, and histological subtype. FGFR1 alterations are most frequent in pediatric gliomas, particularly pediatric low-grade gliomas, while FGFR3 drivers were associated with adult gliomas. In vitro and in vivo functional studies confirm FGFR1 alterations to be sufficient to activate MAPK and mTOR signaling, drive gliomagenesis and activate neuronal transcriptional programs. FGFR1-driven models showed sensitivity to MAPK pathway inhibitors, including panFGFR inhibitors that are FDA approved for use in other cancers. While early FGFR inhibition was sufficient to prolong survival of mice bearing FGFR-driven xenografts, this was insufficient to induce cures. Similarly, review of patients treated with currently available MAPK pathway or FGFR inhibitors revealed modest responses. This study provides key insights into the biology of FGFR1-altered gliomas and potential strategies to therapeutically target them.

overall_design: To investigate the role of FGFR1 alterations in gliomagenesis in pLGGs, we engineered mouse neural stem cells (NSCs) to overexpress FGFR1 or BRAF alterations found in pLGGs. We then performed RNA-seq to look at their transcriptional programs on 8 different conditions (3 replicates).

first: Pratiti

last: Bandopadhayay


title: EHMT1 mediates cellular motility in embryonal rhabdomyosarcoma by activating SOX8 expression.

city: Singapore

first: Reshma

last: Taneja

address: National University of Singapore Dept of Physiology, Blk MD9 Level 2, 2 Medical Drive,

department: Physiology

country: Singapore

institute: National University of Singapore

summary: In this study, we examined the role of EHMT1 in embryonal rhabdomyosarcoma (ERMS), the most frequent subtype of RMS. We report that EHMT1 plays a key role in the migratory and invasive capacity of ERMS cells in vitro and in vivo. Transcriptomic analysis of EHMT1-depleted cells revealed significant alteration in cell migration and invasion pathways. SOX8, a transcription factor that has key roles in cellular motility was significantly decreased upon EHMT1 loss. Consistently, SOX8 depletion phenotypically mimicked EHMT1 loss. Moreover, RNA-Sequencing of SOX8 depleted cells showed down regulation of several integrin genes. Mechanistically, we show that EHMT1 upregulates SOX8 via regulation of BRD4 expression, and consequently its occupancy at the promoter. Our study reveals a novel EHMT1-SOX8 axis that mediates metastasis in ERMS.

overall_design:
RD cells were treated with [1] control siRNA (siscr) or EHMT1-specific siRNA (siEHMT1), [2] control siRNA (siscr) or SOX8-specific siRNA (siSOX8) for 48 hours, after which total RNA was collected with TRIzol reagent. RNA was purified and quality of purified RNA was checked using Nanodrop and gel electrophoresis.
3 samples of siscr and 3 samples of siEHMT1 were used for sequencing analysis, done by Novogene.
3 samples of siscr and 3 samples of siSOX8 were used for sequencing analysis, done by Novogene.

first: Bajaj

last: Upasana

first: Taneja

last: Reshma


title: Analysis of transcriptomic and epitranscriptomic effects of the acute megakaryoblastic leukemia fusion protein RBM15-MKL1

city: New Haven

first: Giulia

last: Biancon

state: Connecticut

address: 300 George Street

department: Internal Medicine - Yale Cancer Center

country: USA

institute: Yale University

summary: The RBM15-MKL1 (RM) fusion protein causes acute megakaryoblastic leukemia (AMKL) primarily in infants. RBM15 recruits the m6A writer complex and is essential for determining the m6A epitranscriptome. MKL1 is a transcriptional cofactor important to megakaryopoiesis. Although the functions of the component proteins are well described, the mechanism whereby the RM fusion protein induces AMKL is unknown. We performed a high-resolution multi-omics analysis to identify the direct transcriptional, RNA-binding, and epitranscriptional targets of RM compared to RBM15. While RM maintains the RNA-binding and m6A modification capabilities of wildtype RBM15, it also has distinct RNA targets, many of which are upregulated and stabilized in RM-expressing cells. Among the top targets that are differentially bound, m6A modified, and upregulated by RM are the Frizzled genes, which encode receptors for the Wnt signalling pathway. To assess the role of RM-mediated m6A modifications in a physiologically relevant model, we treated two murine AMKL cell lines with STM3675, a novel METTL3 inhibitor. In vitro, METTL3 inhibition causes murine AMKL cells to undergo differentiation and apoptosis. In vivo treatment with METTL3 inhibitor prolongs survival of mice transplanted with murine AMKL cells. We additionally show that treatment with STM3675 decreases expression of key RM target genes, including Frizzled genes. Knockdown of Frizzled genes in RM-driven murine AMKL cells decreases their growth and survival, suggesting that RM-specific binding, m6A modification, and aberrant upregulation of the Wnt signaling pathway contribute to leukemogenesis and may represent targetable therapeutic pathways for treatment of children with RM-AMKL.

overall_design: We performed a multi-omics analysis of RBM15-MKL1 (RM)-AMKL using two cell models. (1) Human erythroleukemia (HEL) cells were stably transfected with empty vector or dox-inducible FLAG-RBM15, FLAG-RM. RNA-seq was performed on dox-treated and untreated cells in duplicate.  eCLIP-seq was performed on dox-treated cells in 2-3 replicates; pre-IP input was sequence for 1 replicate.  m6A eCLIP-seq was performed on dox-treated cells in 2-3 replicates.  TimeLapse-seq was performed on dox-treated, s4U-treated cells in triplicate with non-s4U-treated controls.  FLAG-MKL1 was included in RNA-seq experiments as an additional control.  (2) Two murine AMKL cell lines, 6133 (Mercher et al, 2009) and CAOM (this paper) were used in triplicate for RNAseq after vehicle or METTL3 inhibitor treatment.  We additionally performed RNAseq on sorted ERP (Lin−cKit+Sca−CD150+FcgRI/II−CD105+) and MKP (Lin−cKit+Sca−CD150+CD41+) from wildtype mice.

first: Madeline

last: Mayday

first: Manyi

last: Wei

first: Christian

last: Ramirez

first: Toma

last: Tebaldi

first: Stephanie

last: Halene

first: Diane

last: Krause


title: Recurrent FGFR-alterations are frequent oncogenic drivers and therapeutic targets in pediatric low-grade gliomas [RNA-seq]


title: Osteoclast-independent osteocyte dendrite defects in mice bearing the Osteogenesis Imperfecta-causing Sp7 R342C mutation

city: Dallas

first: Jialiang

last: Wang

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

summary: Osteogenesis imperfecta (OI) is a group of diseases caused by defects in type I collagen processing which result in skeletal fragility. While these disorders have traditionally been regarded as defects in osteoblast function, the role of matrix-embedded osteocytes, descendants of osteoblasts, in OI pathogenesis remains unknown. The homozygous human SP7 (c.946C > T, R316C) mutation results in a recessive form of osteogenesis imperfecta characterized by short stature, fragility fractures, low bone mineral density, and osteocyte dendrite defects. To better understand how the osteogenesis imperfecta-causingSP7 R316Cmutation affects the function of this transcription factor in different osteoblast lineage cells in bone, we generatedSp7 R342Cknock-in mice. Homozygous mutantSp7 R342C/R342Cmice demonstrate increased cortical porosity and reduced cortical bone mineral density, findings consistent with phenotypes observed in patients with this mutation.  Sp7 R342Cmice show osteocyte dendrite defects, increased osteocyte apoptosis, and intracortical bone remodeling characterized by ectopic intracortical osteoclasts and elevated Tnfsf11 expression by osteocytes. Remarkably, these overt defects in osteocyte function contrast to preserved osteoblast function, suggesting that this Sp7 point mutation selectively interferes with the function of this transcription factor in osteocytes but not osteoblasts. Osteocyte morphology changes in Sp7 R342C/R342Cmice were not restored by inhibiting osteoclast formation, indicating that dendrite defects lie upstream of high intra-cortical osteoclast activity in this model. Moreover, transcriptomic profiling reveals that the expression of a core set osteocyte-enriched genes is highly dysregulated by the R342C mutation. Thus, this model supports a model in which osteocyte dysfunction can drive osteogenesis imperfecta pathogenesis, and provides a valuable resource to test novel therapeutic approaches and to understand the osteocyte-specific role of SP7 in bone homeostasis and remodeling.

overall_design: Adult female +/+ and R342C/R342C mice were euthanized at 10 weeks old. Enriched osteoblasts and osteocytes were extracted from right humeri for bulk RNA-seq.

first: Marc

last: Wein


title: Recurrent FGFR-alterations are frequent oncogenic drivers and therapeutic targets in pediatric low-grade gliomas [scRNA-seq]

overall_design: To investigate the role of FGFR1 alterations in gliomagenesis in pLGGs, we engineered mouse neural stem cells (NSCs) to overexpress FGFR1  alterations found in pLGGs. We then performed single-cell RNA-seq on the FGFR1-altered lines to  look at the heterogeneity in their  transcriptional programs


title: scCoBench: Benchmarking single cell RNA-seq co-expression using promoter-reporter lines

status: Public on May 15 2025

city: Blacksburg

first: Song

last: Li

state: Virginia

address: 1880 Pratt Drive Blacksburg

department: School of Plant and Environmental Sciences

institute: Virginia Tech

summary: We provide both raw and processed scRNA-seq data used to construct a transcriptomic atlas of the Arabidopsis root, incorporating various promoter-reporter GFP internal controls.

overall_design: Expression profiling by high throughput sequencing

first: Tran

last: Chau

first: Kook

last: Ryu

first: Razan

last: Alajoleen

first: Bastiaan

middle: O

last: Bargmann

first: John

last: Schiefelbein