title: Modeling of lung-liver interaction during infection in a human fluidic organ-on-a-chip

status: Public on May 05 2025

city: Homburg

first: Christian

last: Herr

address: Kirrberger-Str. 100

department: Internal Medicine V

institute: Saarland University

summary: Respiratory infections, including pneumonia and COVID-19, are major causes of global mortality and morbidity. Recent advancements in organ-on-a-chip (OOC) technologies have paved the way for human-based disease models, offering new tools for studying disease mechanisms and accelerating drug development. The aim of this study was to establish a lung-liver fluidic system to study the interaction of both organ modules during infection. A two organ (lung / liver) fluidic system was established using primary human bronchial (HBECs) or alveolar type epithelial cells (AT) for the lung module and Huh-7 cells for the liver module. Inactivated non-typeable Haemophilus influenzae (NTHi) and Pseudomonas aeruginosa PAO1 (PAO1) were applied to the lung module. Secreted mediators were screened by dot-blot analysis and quantified. The impact of bacteria-exposed epithelial cells on the liver cell transcriptome was analyzed via mRNA sequencing. Lung and liver cells established stable cultures in a circulatory fluidic system. Activation of HBECs or ATCs with NTHi or PAO1 resulted in the secretion of multiple inflammatory mediators into the microfluidic medium including tumor necrosis factor-alpha (TNF-α), monocyte chemotactic protein-1 (MCP-1) and macrophage inflammatory protein-1-α (MIP-1α).  Addition of lung cells and application of bacterial onto the HBEC module led to significant transcriptomic alterations in the liver cell module. Gene ontology enrichment analysis showed the induction of various pathways involved in host defense, metabolism, repair, and acute phase response. In conclusion, a two-organ lung/liver fluidic system was established to study the interaction of the organ modules during infection. Mediators like cytokines are released from epithelial culture modules into the fluidic circulation after exposure to bacterial pathogens that significantly modify the gene expression patterns of liver cells.

first: Susanne

last: Reinhold

first: Yiwen

last: Yao

first: Mehdi

last: Pourrostami

first: Felix

last: Ritzmann

first: Thorsten

last: Lehr

first: Dominik

last: Selzer

first: Yvonne

last: Kohl

first: Daniela

last: Yildiz

first: Hortense

last: Slevogt

first: Christoph

last: Beisswenger

first: Robert

last: Bals


title: Characterization of leukocytes

status: Public on May 30 2025

city: Verona

first: Gabriela

last: Constantin

state: Verona

address: Strada le Grazie 8

department: Department of Medicine, Division of General Pathology

country: Italy

institute: University of Verona

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: GP130 Antagonism in Porcine RV Failure

status: Public on May 27 2025

city: Minneapolis

first: Kurt

last: Prins

state: MN

address: 2231 6th St Se

country: USA

institute: University of Minnesota

summary: We evaluated the effects of GP130 antagonism via the small molecule SC144 on the cellular landscape of the RV free wall using single nucleus RNAseq

overall_design: Control pigs, PAB pigs, and PAB-SC144 pigs had RV free wall nuclei isolated and were analyzed by single nucleus RNAseq


title: RNA-seq, miRNA-seq, and degradome-seq analysis of taproots and lateral roots of Quercus robur seedlings under well-watered and drought stress conditions [degradome]

status: Public on Apr 22 2025

city: Poznań

first: Paulina

last: Kościelniak-Wawro

address: Uniwersytetu Poznańskiego 6

department: Faculty of Biology, Institute of Human Biology and Evolution

country: Poland

institute: Adam Mickiewicz University

summary:
Identification of genes involved in the regulation of taproot and lateral root growth in Quercus robur seedlings under drought stress and well-watered conditions. Genes involved in the regulation of taproot and lateral root growth in Quercus robur seedlings were identified using RNA-seq, miRNA-seq, and degradome-seq. The analysis focused on the gene expression, miRNA regulation, and mRNA degradation profiles of taproots and lateral roots under both drought stress and well-watered conditions. Key genes and their regulatory miRNAs were identified, along with the role of mRNA degradation pathways in response to stress, providing insights into the molecular mechanisms controlling root growth and development in oak seedlings under varying water availability.

This research was funded by National Science Center, Poland [grant number 2021/41/N/NZ9/00433].

overall_design: The study employed a two-factor completely randomized design comparing container-grown versus rhizotron-sown Quercus robur seedlings under two watering regimes (optimal irrigation vs. 75% water reduction for 4 weeks), with sampling of both taproot and lateral root meristematic zones following an 8-week acclimatization period in standardized growth conditions (peat:perlite 5:1 substrate with controlled fertilization in a greenhouse environment). All plants were monitored for soil moisture (at 15 cm and 45 cm depths) and temperature throughout the experiment, with physiological (chlorophyll fluorescence measurements of PSII efficiency parameters) and molecular (transcriptome/miRNA) endpoints collected concurrently after drought treatment confirmation. The design incorporated triplicate biological replicates (10-15 root tips per replicate) and technical replication in sequencing (minimum 20 million 150bp paired-end reads od 50bp single-end reads per sample on Illumina NovaSeq), enabling statistically powered comparisons (α=0.05, 80% power to detect 1.5-fold expression changes) between cultivation methods, watering treatments, and root types while controlling for potential environmental variability through automated irrigation systems and continuous environmental monitoring. Key features included synchronization of molecular and physiological measurements, standardized transplantation protocols for container-grown seedlings, and integrated bioinformatics pipelines for multi-omics data analysis, providing a comprehensive framework to evaluate both nursery practice legacy effects and organ-specific drought responses.

first: Marcin

last: Zadworny


title: A targeted vector for brain endothelial cell gene delivery and cerebrovascular malformation modelling

status: Public on Apr 29 2025

city: Beijing

first: Xing-jun

last: Chen

address: Bldg.3, NO.9, YIKE Rd, Zhongguancun Life Science Park, Changping District

country: China

institute: Chinese Institute for Brain Research, Beijing(CIBR)

summary: In-depth analysis of the molecular mechanisms underlying the initiation and development of bAVM was conducted through single-nucleus RNA sequencing of cells from bAVM lesions in Braf-CAfl/fl mice locally injected with AAV-miniBEND.

overall_design: Differential expression analysis and Gene Set Enrichment Analysis of single-nucleus RNA sequencing data. We performed differential expression analysis of RNA seq data and Gene Set Enrichment Analysis obtained from bAVM lesions in Braf-CAfl/fl mice and normal brain region samples from the contralateral hemisphere of the same mice served as a control group.

first: Jun-Liszt

last: Li

first: Zhanying

last: Bi

first: Tianyue

last: Ming

first: Woo-ping

last: Ge


title: Visceral adipose tissue harbors pathogenic T cells in obesity that exacerbate inflammatory arthritis

status: Public on May 28 2025

city: Boston

first: Heather

last: Faust

state: MA

address: 60 Fenwood Road

institute: Brigham and Women's Hopsital

summary: Obesity worsens inflammatory arthritis severity, even in non-load bearing joints, but the mechanism is unknown. Here, we show that there is an immunological link mediated by T cells in adipose tissue and arthritis pathogenesis. Using an antigen-induced arthritis model with trackable, arthritis-inducing OT-I T cells, we found that OT-I T cells home to visceral adipose tissue (VAT) after arthritis induction and expand in the obese high-fat diet (HFD) context. Transplant of visceral adipose tissue from arthritic mice increased arthritis severity in naïve mice and was ameliorated by CD8 depletion. Bulk RNA-sequencing identified pro-inflammatory changes to OT-I T cells residing in peripheral lymph nodes and VAT characterized by increased interferon signaling after HFD. Intra-peritoneal injection of IFNα, but not IFNγ, expanded CD8 VAT T cell numbers. Using IFNAR1 blocking antibodies or IFNAR1-deficient mice confirmed that the increased number of CD8 T cells in VAT following HFD was IFNAR1 dependent. Our results show that VAT is a depot which can support a Type-1 interferon-driven expansion of a pool of CD8 T cells during obesity that are readily available to increase arthritic inflammation. These mechanisms may contribute to the increased frequency and severity of autoimmune diseases in obese patients.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data for  mouse lymph node or visceral adipose derived T cells from OT-I mice on lean or high fat diet for 8 weeks. Cells were cultured overnight before sorting a pure T cell population.

middle: J

first: Michael

middle: B

last: Brenner


title: RNA-seq, miRNA-seq, and degradome-seq analysis of taproots and lateral roots of Quercus robur seedlings under well-watered and drought stress conditions [RNA-seq]


title: Hypertension-Induced Neurovascular and Cognitive Dysfunction at Single-Cell Resolution

status: Public on Apr 17 2025

city: New York

first: Anthony

middle: G

last: Pacholko

state: NY

address: 465 Main Street

department: BMRI

institute: Weill Cornell Medicine

summary: Arterial hypertension is a leading cause of cognitive impairment, attributed to hemodynamic insufficiency, blood-brain barrier disruption, and white matter damage. However, the molecular mechanisms by which hypertension affects brain cells remain unclear. Using scRNA-seq in a mouse model of hypertension induced by angiotensin II, we mapped neocortical transcriptomic changes before (3 days) and after (42 days) onset of neurovascular and cognitive deficits. Surprisingly, evidence of endothelial transport disruption and senescence, stalled oligodendrocyte differentiation, interneuronal hypofunction and network imbalance emerged after just 3 days. By 42 days, when cognitive impairment becomes apparent, deficits in myelination and axonal conduction, as well as neuronal mitochondrial dysfunction, developed. These findings reveal a previously unrecognized early vulnerability of endothelial cells, interneurons, and oligodendrocytes, and provide the molecular bases for the subsequent neurovascular dysfunction and cognitive impairment in hypertension. In addition, the data constitute a valuable resource for future mechanistic studies and therapeutic target validation.

overall_design: After 3 or 42 days of treatment with angiotensin II (delivered via subcutaneously implanted osmotic minipump), mouse (6-8 weeks of age, male, C57Bl6) cortices were isolated and processed for single cell RNA sequencing.

first: Samantha

last: Schaeffer

first: Monica

last: Santisteban

first: Gang

last: Wang

first: Sung Ji

last: Ahn

first: Gianfranco

last: Racchumi

first: Giuseppe

last: Faraco

first: Laibaik

last: Park

first: Josef

last: Anrather

first: Costantino

last: Iadecola


title: Secreted chemokines and transcriptomic analyses reveal diverse inflammatory and degenerative processes in the intervertebral disc of the STZ-HFD mouse model of Type 2 diabetes

status: Public on Mar 25 2025

city: St Louis

first: Christian

middle: E

last: Gonzalez

state: MO

address: 450 S Euclid Ave

department: Orthopaedic Surgery

institute: Washington University in St Louis

summary: The chronic inflammation resultant from type 2 diabetes (T2D) is also associated with spinal pathologies, including intervertebral disc (IVD) degeneration and chronic neck and back pain.  Although confounding factors, such as increased weight gain in obesity, studies have shown that even after adjusting age, body mass index, and genetics (e.g. twins), patients with T2D suffer from disproportionately more IVD degeneration and back pain.  We hypothesize that chronic T2D fosters a proinflammatory microenvironment within the IVD that promotes degeneration and disrupts disc homeostasis. To test this hypothesis, we evaluated two commonly used mouse models of T2D – the leptin-receptor deficient mouse (db/db) and the chronic high-fat diet in mice with impaired beta-cell function (STZ-HFD).  STZ-HFD IVDs were more degenerated and showed differential expression of chemokines from the db/db models. Moreover, the RNAseq analysis revealed vast transcriptional dysregulation of many pathways in the STZ-HFD but not in the db/db tissues.  Taken together, the STZ-HFD may better recapitulates the complexities of the chronic inflammatory processes in the IVD during T2D

overall_design: Samples were derived from two cohorts. Cohort 1 is 3 db/db mice and 3 db/+ heterozygous mice as non-diabetic controls. Cohort 2 is 4 Streptozocin-High-Fat-Diet diabetic mice with 4 healthy wild-type C57BL/6J mice as control. Intervertebral discs were extracted, pulverized, and reconstiuted in TRIzol prior to RNA extraction via column extraction in accordance with manufacturer recommendation. RNA in H2O were submitted to the WashU in St Louis GTAC core for Illumina NovaSeq X Plus Analysis.

first: Rachana

last: Vaidya

first: Sade

last: Clayton

first: Simon

last: Tang


title: Parp7 generates an ADP-ribosyl degron that controls negative feedback of androgen signaling

status: Public on Jun 11 2025

city: Charlottesville

first: Krzysztof

last: Wierbiłowicz

state: VA

address: 1400 Jefferson Park Ave, PO Box 800577

department: Biochemistry and Molecular Genetics

institute: University of Virginia

summary: The androgen receptor (AR) transduces the effects of circulating and tumor-derived androgens to the nucleus through ligand-induced changes in protein conformation, localization, and chromatin engagement. Defining how these events are integrated with signal transduction is critical to understand how AR drives prostate cancer and unveil pathway features that are potentially amenable to therapeutic intervention. We describe a novel post-transcriptional mechanism that controls AR levels on chromatin and gene output based on highly selective, inducible degradation. We find that the mono-ADP-ribosyltransferase PARP7 generates an ADP-ribosyl degron in the DNA-binding domain of AR, which is recognized by the ADP-ribose reader domain in the ubiquitin E3 ligase DTX2 and degraded by the proteasome. Mathematical modeling of the pathway suggested that PARP7 ADP-ribosylates chromatin-bound AR, a prediction that was validated in cells using an AR DNA-binding mutant. Non-conventional ubiquitin conjugation to ADP-ribosyl-cysteine and degradation by the proteasome forms the basis of a negative feedback loop that regulates modules of AR target genes. Our data expand the repertoire of mono-ADP-ribosyltransferases to include gene regulation via highly selective protein degradation.

overall_design: To investigate the influence of PARP7 on AR-dependent transcription, we treated VCaP cells with vehicle control, R1881 (2 nM), RBN2397 (PARP7 inhibitor, 100 nM), and R1881+RBN2397 for 18h in biological triplicates.

last: Wierbilowicz

first: Chun-Song

last: Yang

first: Bryce

middle: M

last: Paschal

first: Aakrosh

last: Ratan


title: RNA-seq, miRNA-seq, and degradome-seq analysis of taproots and lateral roots of Quercus robur seedlings under well-watered and drought stress conditions [miRNA-seq]

first: Paulina

last: Kościelniak-Wawro

type: Non-coding RNA profiling by high throughput sequencing

first: Marcin

last: Zadworny


title: SCG2-LILRB4 interaction supports MDSCs suppressive function by upregulating IL-6-STAT3 signaling pathway

status: Public on Jan 07 2025

city: Dallas

first: Xing

state: TX

address: 5323 Harry Hines Blvd

department: Physiology

institute: University of Texas Southwestwen Mdeical Center

summary: SCG2 functionally interacts with leukocyte Ig-like receptor subfamily B4 (LILRB4) on monocytic cells. M-MDSCs were isolated from tumor bearing  WT, LILRB4+/+ or LILRB4+/+ SCG2-/- mice for RNA-seq. We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 replicates from each group.

overall_design: RNA-seq profiling of M-MDSCs isolated from tumor bearing WT, LILRB4+/+ or LILRB4+/+ SCG2-/- mice

first: Chengcheng

last: Zhang


title: Absent in melanoma 2: a potent suppressor of retinal pigment epithelial-mesenchymal transition and experimental proliferative vitreoretinopathy

status: Public on Dec 23 2024

city: wenzhou

first: yu

last: chen

address: 270 West Xueyuan Road

institute: Wenzhou Medical University

summary: Epithelial-to-mesenchymal transition (EMT) is a critical and complex process involved in normal embryonic development, tissue regeneration, and tumor progression. It also contributes to retinal diseases, such as age-related macular degeneration (AMD) and proliferative vitreoretinopathy (PVR). Although absent in melanoma 2 (AIM2) has been linked to inflammatory disorders, autoimmune diseases, and cancers, its role in the EMT of the retinal pigment epithelium (RPE-EMT) and retinal diseases remains unclear. The present study demonstrated that AIM2 functions as a potent suppressor of RPE cell proliferation and EMT to maintain retinal homeostasis. Transcriptome analysis using RNA-sequencing (RNA-Seq) revealed that AIM2 was significantly downregulated in primary human RPE (phRPE) cells undergoing EMT and proliferation. Consequently, Aim2-deficient mice showed morphological changes and increased FN expression in RPE cells under physiological conditions, whereas AIM2 overexpression in phRPE cells inhibited EMT. In a retinal detachment-induced PVR mouse model, AIM2 deficiency promotes RPE-EMT, resulting in severe experimental PVR. Clinical samples further confirmed the downregulation of AIM2 in the PVR membranes from patients. Kyoto Encyclopedia of Genes and Genome analysis revealed that the PI3K-AKT signaling pathway was significantly related to RPE-EMT and that AIM2 inhibited AKT activation in RPE cells by reducing its phosphorylation. Moreover, treatment with eye drops containing an AKT inhibitor alleviated RPE-EMT and the severity of experimental PVR. These findings provide new insights into the complex mechanisms underlying RPE-EMT and PVR pathogenesis, with implications for rational strategies for potential therapeutic applications in PVR by targeting RPE-EMT.

overall_design: To discover factors and gain a deeper understanding of the relevant genes and pathways involved in this RPE-EMT process, we used an approach in which RPE tissue was isolated from the donor’s eyes and subjected to enzymatic dissociation and passage to induce EMT and proliferation. Next, we used RNA sequencing (RNA-Seq) to analyze differential transcriptome profiles. This approach confirmed previously reported alterations in EMT genes and uncovered novel genes that have not been previously implicated.

first: Yu

last: Chen

first: Mingyuan

last: Jiang

first: Liping

last: Li

first: Ling

last: Hou


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

city: Bath

first: Keith

middle: William

last: Vance

state: Somerset

address: University of Bath

department: Department of Biology and Biochemistry

country: United Kingdom

institute: University of Bath

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

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

first: Stephanie

last: Jones

first: Elizabeth

middle: A

last: Coe

first: Michael

last: Shapiro

first: Igor

last: Ulitsky

first: Robert

middle: N

last: Kelsh

middle: W


title: RNA-seq of Tregs from injured mouse neonatal and adult tendon and spleen.

status: Public on Mar 01 2025

first: Varun

last: Arvind

address: 1 Gustave Levy Place

department: Orthopedics

institute: Icahn School of Medicine at Mount Sinai

summary: We report transcriptomic differences between neonatal and adult Treg responses to tendon jury using NGS sequencing. We performed tendon injuries to neonatal mice at P5 and 4-6 month old adult mice and isolated Tregs by FACS (CD4-PE+, Foxp3-GFP+) from injured tendons and autologus spleens 14 days after inury. We then performed RNA-sequencing with biological triplicates to distinguish unique transcriptomic signatures that can illuminate the role of Tregs in neonatal tendon regeneration. Tregs from neonatal tendon show a type 2 immune signatures with a unique gene signature that is distinc from canonical Treg activation, while adult Tregs demonstrate a type 1 signature.

overall_design: Examination of Tregs from neonatal and adult mice FACS sorted from injured tendon and spleen 14 days after injury.

first: Alice

middle: H

last: Huang


title: Dynamic control of transcriptional regulator BACH2 overcomes T cell dysfunction driven by tonic CAR signaling

status: Public on Jan 21 2025

city: St. Louis

first: Nathan

last: Singh

address: 660 S Euclid Ave

institute: Washington University School of Medicine in St Louis

summary: Chimeric antigen receptors (CARs) integrate multiple lymphocyte-derived functional domains to enable selective antigen binding and robust T cell activation in a single synthetic protein. Through various biochemical mechanisms, nearly all CARs activate intracellular signaling in the absence of antigen, referred to as “tonic signaling”. Previous work has shown that tonic signaling of CARs containing the CD28 costimulatory domain drives T cell exhaustion; in contrast, we have shown that tonic signaling of 41BB-containing CARs enhances T cell function. Using a model of tonically signaling CARs targeting the B cell antigen CD22, we undertook studies to determine the molecular determinants of the divergent impact of tonic CAR signaling on T cell fitness. We identified that tonic 41BB signaling induces activation of BACH2, a transcriptional regulator that directs stem and memory programs to maintain T cell homeostasis. Transgenic expression of BACH2 prevented the development of exhaustion and promoted memory-like programs in tonically signaling CD28-containing CAR T cells. This enhanced acute cytotoxic function but impaired durable anti-tumor function. We linked transgenic BACH2 to a degradation domain, enabling precise control of BACH2 expression and found that low-level expression of BACH2 enabled robust and persistent tumor control in multiple cancer models.

overall_design: At the conclusion of CAR T cell manufacturing, T cells were purified to enrich CAR+ cells using a truncated CD34 selection marker and BACH2+ cells using a truncated EGFR selection marker. From these purified populations, we isolated and sequenced RNA. Studies were performed in technical triplicate using cells manufactured from three independent donors.

first: Tien-ching

last: Chang

first: John

last: Warrington


title: Selective magnetic stimulation downregulates the GABAA receptor ε subunit in the left prelimbic cortex to alleviate schizophrenia-like behaviors in mice

status: Public on Jan 17 2025

city: Nanjing

first: Yunshan

middle: of

last: Hu

state: Jiangsu

address: No. 264 Guangzhou Road, Nanjing

institute: Nanjing Brain Hospital

summary: Schizophrenia (SCZ) is a prevalent and disabling mental disorder. Clinically, its complex symptoms, including negative symptoms and cognitive impairment, can be alleviated using electromagnetic techniques such as repetitive transcranial magnetic stimulation (rTMS). To investigate the neural mechanisms of magnetic stimulation and identify selective therapeutic targets, we employed combined magnetic stimulation system treatment (c-MSST). Targeting the left prelimbic cortex (PrL) of mice with c-MSST reversed the SCZ-like behaviors and synaptic abnormalities induced by MK-801 injection and normalized the regional increase in gamma-aminobutyric acid type A receptor subunit epsilon (GABRE) expression. Specific Gabre knockdown in the left PrL ameliorated MK-801-induced SCZ-like behaviors. Importantly, Gabre conditional knock-in mice exhibited SCZ-like behaviors and synaptic plasticity deficits, both of which were reversed by c-MSST. We further demonstrated that the ability of c-MSST to reduce GABRE protein expression may be related to p62/SQSTM1-mediated sequestration of GABARAP family. Our study improves the understanding of the therapeutic mechanisms of magnetic techniques and suggests that Gabre and related molecular circuits are promising targets for SCZ treatment.

overall_design: The mice were divided into four groups based on the model and intervention as follows: NS_S (Control, n=6), NS-M (Control+c-MSST, n=5), MK_S (SCZ, n=4), and MK_M (SCZ+c-MSST, n=4).On the 3rd day after surgery, PrL tissues were collected and RNA-seq was performed using Illumina HiSeq 2500.

first: Zixu

last: Wang

first: Zhijun

last: Zhang

first: Xiangrong


title: Phosphorylation of HP1/Swi6 relieves competition with Suv39/Clr4 on nucleosomes and enables H3K9 trimethyl spreading.

status: Public on Dec 02 2024

city: San Francisco

first: Bassem

last: Al-Sady

state: CA

address: 513 Parnassus Ave HSW 1501

institute: UCSF

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Heterochromatin formation in Schizosaccharomyces pombe requires the spreading of histone 3 (H3) Lysine 9 (K9) methylation (me) from nucleation centers by the H3K9 methylase, Suv39/Clr4, and the reader protein, HP1/Swi6. To accomplish this, Suv39/Clr4 and HP1/Swi6 have to associate with nucleosomes both nonspecifically, binding DNA and octamer surfaces and specifically, via recognition of methylated H3K9 by their respective chromodomains. However, how both proteins avoid competition for the same nucleosomes in this process is unclear. Here, we show that phosphorylation tunes the nucleosome affinity of HP1/Swi6 such that it preferentially partitions onto Suv39/Clr4’s trimethyl product rather than its unmethylated substrates. Preferential partitioning enables efficient conversion from di-to trimethylation on nucleosomes in vitro and H3K9me3 spreading in vivo. Together, our data suggests that phosphorylation of HP1/Swi6 creates a regime that relieves competition with the “read-write” mechanism of Suv39/Clr4 for productive heterochromatin spreading.

overall_design: Chromatin immunoprecipitation followed by sequencing (ChIP-seq) probing H3K9me2 and H3K9me3 levels in the context of delta swi6, wildtype swi6, or S18A/S24A swi6. Strain background contained our heterochromatin spreading sensor at the MAT locus.

first: Dana

last: Kennedy

first: Eric

last: Simental


title: Single-cell sequencing uncovers sensory neuron–mediated CGRP signaling as a driver of sarcoma progression

status: Public on Jan 04 2025

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

summary: Bone pain is a presenting feature of bone cancers such as osteosarcoma (OS), relayed by skeletal-innervating peripheral afferent neurons. Potential functions of tumor-associated sensory neurons in bone cancers beyond pain sensation are unknown. To uncover neural regulatory functions, a chemical-genetic approach in mice with a knock-in allele for TrkA was used to functionally perturb sensory nerve innervation during OS growth and disease progression. TrkA inhibition in transgenic mice led to significant reductions in sarcoma-associated sensory innervation and vascularization, skewed tumor associated macrophage polarization, reduced tumor growth and metastasis, and prolonged overall survival. Single-cell transcriptomics revealed that sarcoma denervation was associated with phenotypic alterations in both OS tumor cells and cells within the tumor microenvironment, and with reduced calcitonin gene-related peptide (CGRP) and vascular endothelial growth factor (VEGF) signaling. Multimodal and multiomics analyses of human OS bone samples further implicated peripheral innervation and neurotrophin signaling in OS tumor biology. Next and in two parallel approaches to inhibit nerve ingrowth, we repurposed FDA-approved bupivacaine liposomes and separately blocked CGRP signaling using FDA-approved Rimegepant. Both strategies led to significant reductions in sarcoma growth, vascularity, and sarcoma-induced hyperalgesia. In sum, TrkA-expressing peripheral neurons positively regulate key aspects of OS progression and sensory neural inhibition disrupts CGRP signaling within the sarcoma microenvironment leading to significantly reduced tumor growth and improved survival. These data suggest that interventions to prevent pathological innervation of OS represent an adjunctive therapy to improve clinical outcomes and survival.

overall_design: Tumor xenograft implants were dissected from TrkA^WT;NOD-Scid and TrkA^F592A; NOD-Scid animals at 12 d post-tumor cell innoculation for scRNA-Seq. The two sequenced samples were pooled triplicates of TrkA^WT and TrkA^F592A animals.

first: Sowmya

last: Ramesh

first: Zhao

last: Li

first: Qizhi

last: Qin


title: Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics (dscHi-C multiome)

status: Public on Jan 10 2025

first: Xiaoliang

middle: Sunney

last: Xie

state: Beijing

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

summary: Single-cell three-dimensional (3D) genome techniques have advanced our understanding of cell-type-specific chromatin structures in complex tissues, yet current methodologies are limited in cell throughput. Here we introduce a high-throughput single-cell Hi-C approach (dscHi-C) and its transcriptome co-assay (dscHi-C-multiome) using droplet microfluidics. Using dicHi-C, we investigated chromatin structural changes during mouse brain aging by profiling 32,777 single cells across three developmental stages (3 month, 12 month and 23 month), yielding a median of 78,220 unique contacts. Our results show that genes with significant structural changes are enriched in pathways related to metabolic process and morphology change in neurons, and innate immune response in glial cells, highlighting the role of 3D genome organization in physiological brain ageing. Furthermore, our multi-omics joint assay, dscHi-C-multiome, enables precise cell type identification in the adult mouse brain and uncovers the intricate relationship between genome architecture and gene expression. Collectively, we developed the sensitive, high-throughput dscHi-C and its multi-omics derivative, dscHi-C-multiome, demonstrating their potential for large-scale cell atlas studies in development and disease.

overall_design:
In this study, we performed droplet-based single-cell Hi-C (dscHi-C) and its transcriptome co-assay (dscHi-C-multiome) on human and mouse cell line, and mouse brain cortex tissues.

UPDATE: [Aug-27-2025] The GSM8698924_b3-month-BC-dscHiC-gDNA.metadata.txt file was corrected.

first: Honggui

last: Wu

first: Maoxu


title: Identification of conserved RNA regulatory switches in living cells using RNA secondary structure ensemble mapping and covariation analysis

status: Public on Sep 24 2024

city: Groningen

first: Danny

last: Incarnato

state: Netherlands

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: University of Groningen

summary: RNA molecules can populate ensembles of alternative structural conformations; however, comprehensively mapping RNA conformational landscapes within living cells presents notable challenges and has, as such, so far remained elusive. Here, we generate transcriptome-scale maps of RNA secondary structure ensembles in both Escherichia coli and human cells, uncovering features of structurally heterogeneous regions. By combining ensemble deconvolution and covariation analyses, we report the discovery of several bacterial RNA thermometers in the 5′ untranslated regions (UTRs) of the cspG, cspI, cpxP and lpxP mRNAs of Escherichia coli. We mechanistically characterize how these thermometers switch structure in response to cold shock and reveal the CspE chaperone-mediated regulation of lpxP. Furthermore, we introduce a method for the transcriptome-scale mapping of 5′ UTR structures in eukaryotes and leverage it to uncover RNA structural switches regulating the differential usage of open reading frames in the 5′ UTRs of the CKS2 and TXNL4A mRNAs in HEK293 cells. Collectively, this work reveals the complexity of RNA structural dynamics in living cells and provides a resource to accelerate the discovery of regulatory RNA switches.

sample_organism:
Escherichia coli
Homo sapiens

platform_organism:
Escherichia coli
Homo sapiens

overall_design:
RNA structure analysis of Escherichia coli  by DMS chemical probing and mutational profiling (DMS-MaPseq)

NOTE: The records have been updated with additional samples on June 17, 2025.

first: I.

last: Borovská

first: C.

last: Dülk

first: E.

last: Morandi

last: Cardoso

last: Bourkia

first: D.

last: van den Homberg

last: Wolfinger

last: Velema


title: Spermine Synthase Engages in Macrophages M2 polarization to Sabotage Antitumor Immunity in Hepatocellular Carcinoma

status: Public on Nov 11 2024

city: Guangzhou

first: Yining

last: Sun

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou

institute: Nanfang hospital, Southern medical university

summary: Disturbances in tumor cell metabolism reshape the tumor microenvironment (TME) and impair antitumor immunity, but the implicit mechanisms remain elusive. Here, we found that spermine synthase (SMS) was significantly upregulated in tumor cells, which correlated positively with immunosuppressive microenvironments and predicted poor survival in hepatocellular carcinoma (HCC) patients. Via “subcutaneous” and “orthotopic” HCC syngeneic mouse models and a series of in vitro coculture experiments, we identified elevated SMS level in HCC cells played a role in immune escape mainly through its metabolic product spermine, which induced tumor-associated macrophage (TAM) reprogramming and subsequently corresponded with a decreased antitumor functionality of CD8+ T cells. Mechanistically, we discovered that spermine reprogrammed TAM mainly by activating the PI3K-Akt-mTOR-S6K signaling pathway. Spermine inhibition in combination with immune checkpoint blockade effectively diminishes tumor burden in vivo. Our results expand the understanding of the critical role of metabolites in regulating cancer progression and anti-tumor immunity, and open new avenues for developing novel therapeutic strategies against HCC.

overall_design: To investigate how SMS regulated the tumor microenviroment, we estsblished overexpressed Sms (Sms-OE) cells by lentivirus, used them to construct orthotopic liver tumor model, and isolated macrophages (F4/80+ cells) in the tumor tissue.

first: Yuan

last: Fany

first: Peitao

last: Zhou

first: Dehua


title: Single-cell RNA Sequencing Reveals the Heterogeneity in Differentiation Trajectory and Tumor Microenvironment Leading to More Aggressive Phenotypes of Papillary Thyroid Cancer in Children and Young Adult Patients

status: Public on Jan 01 2025

city: Shanghai

first: KAI

last: GUO

state: Shanghai

address: Pujian Road, NO. 160, Pudong New Area

institute: Renji Hospital, School of Medicine, Shanghai Jiaotong University

summary: The tumor ecosystem heterogeneity of papillary thyroid carcinoma (PTC) is poorly characterized especially in children and young adult patients (CAYA-PTC). Here, we used single-cell RNA sequencing to profile transcriptomes map from eleven patients’ paratumors and localized tumors, covering comprehensive clinical courses of PTC. Compared with adult-PTC, CD4T_Tfh and CD8T_Tex cells were significantly higher in CAYA-PTC patients which closely related to metastasis. Along the differentiation trajectory, we discover three phenotypes of thyrocytes population (normal, BRAF-like, Fusion-like), whose composition shapes bulk molecular subtypes and tumor characteristics. Furthermore, our data identifies CAYA-PTC patients lack a “mild-state (BRAF-like)” malignant thyrocyte population. This different differentiation states indicates PTC cells quickly develop into invasion and metastasis in CAYA patients, while they gradually progress over a long time in adult patients. In addition, extracellular matrix cancer-associated fibroblasts(emCAFs_LAMP5) interact with endothelial cells and thyrocytes, ultimately promoting tumor angiogenesis and metastasis, which plays a more evident role in CAYA patients. FAP was highly expressed in emCAF_LAMP5 and positive correlated with LAMP5 in CAYA-PTC tissues. Therefore, ⁶⁸Ga-FAPI-PET have the potential to be used as a promising diagnostic method for CAYA patients with failed by traditional 18F-FDG-PET/CT. Together, our findings provide insight into the CAYA-PTC ecosystem that suggests distinct diagnostic, prognostic and therapeutic implications compared to adults.

overall_design: Six patients (including five CAYA specimens and one adult specimen) diagnosed with PTC was enrolled from Shanghai Jiao Tong University School of Medicine Affiliated Renji Hospital and Children's Hospital of Shanghai, Shanghai Jiao Tong University. The thyroid tumor (T), adjacent normal thyroid (P) were collected and digested into single-cell suspensions for 10×Genomics single cell sequencing (scRNA-seq).

first: Kai

last: Guo

first: Lingyi

last: Yang

first: Zirui

last: Huang

last: Qian

last: Shi

first: Mengjia

last: Fei

last: Feng

first: Zixian

last: Chen

first: Ming

last: Qiu

first: Linglin

last: Tang

first: Anqi

first: Zhibao

last: Lv

first: Jiangbin

last: Liu

first: Zhou

first: Kuiran

last: Dong

first: Zhuoying

last: Wang


title: Codon Specific Readthrough as a Mechanism of BRCA2 Restoration in Acquired PARP Inhibitor and Chemotherapy Resistance

status: Public on Sep 01 2024

city: Rochester

first: Cristina

last: Correia

state: Minnesota

address: Kellen Bld 3 th Floor, 200 1st street SW

institute: Mayo Clinic

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

overall_design: Refer to individual Series


title: Evolutionarily conserved role of Telomerase reverse transcriptase (TERT) in programming the microenvironment via regulation of cGAS/STING pathway

status: Public on Jul 22 2024

city: Singapore

first: Vinay

last: Tergaonkar

address: 61 Biopolis Drive, Proteos

department: Institute of Molecular and Cell Biology (IMCB)

country: Singapore

institute: Agency for Science, Technology and Research (A*STAR)

summary: Telomerase holoenzyme plays a critical role in maintaining telomere length, and thus in regulating inflammation caused by telomeric DNA damage. However, beyond its role in telomere maintenance, the molecular function of telomerase in directly regulating inflammation remains unclear. Here, we show that the reverse transcriptase component of telomerase, TERT, has a cell-type-specific role in directly regulating inflammation via the cytoplasmic cGAS-STING nucleic acid-sensing pathway. Analyses of murine and zebrafish models of gut inflammation and human colitis/Crohn’s patients document that this function of TERT is evolutionarily conserved. Using our novel knock-in TERTVAA mouse model where reverse-transcriptase-inactive TERT is driven by its endogenous loci, and molecular, pharmacological and single-cell approaches we identify the myeloid subpopulation, termed T-MAC, wherein TERT enhances STING activation and initiates type-1 interferon responses independent of reverse transcriptase activity or telomere length. We highlight a hitherto unappreciated role of TERT in directly regulating inflammation and provide a therapeutic rationale for targeting TERT beyond cancers.

overall_design:
To understand the canonical and non-canonical role of TERT in programming the microenvironment, we have generated an enzymatically inactive TERT mouse model (TERT-VAA). Additionally, we utilized TERT WT and  TERT KO mouse models. We employed an experimental colitis model using Dextran Sulfate Sodium (DSS). Mice were treated with 3% DSS for 4 days, followed by 4 days of normal water. Colon tissues were harvested on day 8. RNA was isolated by Trizol and column purification.
Bulk RNA Sequencing was performed for DSS untreated and treated mice of TERT WT, TERT VAA and TERT KO. The library was prepared using the Illumina Truseq Total RNA sequencing kit according to the manufacturer's guidelines. Paired-end sequencing was performed using Illumina Nextseq 2x76bp.

first: Semih

middle: C

last: Akincilar

first: Kerem

last: Fidan


title: 3D chromatin architecture of drug-tolerant cancer cells at single-cell resolution (Reference dataset of population cells)

status: Public on Aug 14 2024

city: San Antonio

first: Yufan

last: Zhou

address: 7703 Floyd Curl Dr

institute: UT health Science Center at San Antonio

summary: Anticancer drug therapy generally elicits the drug tolerance after long-term treatment. Recent studies suggested that 3D chromatin structures of cancer cells were intimately linked to drug resistance. However, 3D chromatin structures in drug-tolerant cancer cells at single-cell resolution haven’t been elucidated. Here we performed single-cell Hi-C (scHi-C) analysis to examine the 3D chromatin structures in three stages of breast cancer cells. Population cells Hi-C data as the reference.

overall_design: To fully understand the 3D chromatin structures of drug-tolerant cancer cells at single-cell resolution, we designed scHi-C approach for analyzing a breast cancer cell model system, MCF7, MCF7M1 and MCF7TR cells. A total of 293 cells (89 MCF7 cells, 91 MCF7M1 cells, 113 MCF7TR cells) were used for scHi-C profiling. Population cells Hi-C data as the reference. This is the dataset stored for population cells. During in situ Hi-C profiling MCF7 was treated with HindIII, MCF7M1 was treated with DpnII, and MCF7TR was treated with DpnII.

first: Victor

last: Jin


title: Distinct roles of keratinocyte- and myeloid- MCPIP1 in maintaining skin homeostasis

status: Public on Jul 09 2024

city: Warsaw

first: Michal

last: Mikula

address: Roentgena 5

department: Experimental Oncology

institute: Maria Skłodowska-Curie National Research Institute of Oncology

summary: The morphology of the skin changes upon depletion of MCPIP1 in cells of myeloid origin as well as in keratinocytes. The thicknesses of epidermal and hypodermal layers are significantly increased in mice with loss of epidermal MCPIP1, whereas loss of myeloid MCPIP1 exerts completely opposite effect. Both types of mice show contrary response to the stimulation with 12-O-tetradecanoylphorbol-13-acetate. Skin morphology and inflammatory phenotype of keratinocyte- and myeloid- double MCPIP1 knockout mice is similar to that of the single keratinocyte knockout of MCPIP1. In all, myeloid and epidermal MCPIP1 play significant but distinct roles in the modulation of skin-related processes. This study was funded by National Science Centre grant numbers 2020/37/N/NZ5/00575 (to Weronika Szukala) and 2021/41/B/NZ5/03601 (to Jolanta Jura)."

overall_design: RNA-seq was performed to analyse transcriptomes of the whole skin lysates of 12-week Mcpip1EKO (keratinocyte-specific knockout), Mcpip1MKO (myeloid-specific knockout), Mcpip1EMdKO (keratinocyte and myeloid-specific knockout)  and control mice.

first: Weronika

last: Szukala

first: Agata

last: Lichawska-Cieslar

first: Roza

last: Zawada

first: Izabela

last: Rumienczyk

first: Krzysztof

last: Goryca

first: Jolanta

last: Jura


title: Deficiency of gut-enriched Lipase H promotes gut aging and reduces lifespan in Drosophila

status: Public on Jun 28 2024

first: ying

last: sun

address: 2005 Songhu road

institute: Fudan University

summary: Liph, a gut-enriched Lipase H encoding gene, shows decreased expression during gut aging in both fruit fly and mouse. However, whether such evolutionary conserved Liph plays a protective role in gut aging remains unknown. In this study, RNA-seq was performed on gut tissue from fly model to identify changes in gene expression produced in whole guts after knocking down CG6295, the Drosophila ortholog of the mammalian Liph. In addition, we performed RNA-seq analysis on rat intestinal epithelial IEC-6 cells with Liph knockdown to investigate the role of Liph in mammalian intestinal aging.

sample_organism:
Drosophila melanogaster
Rattus norvegicus

overall_design: To perform RNA-sequencing of the whole gut, flies from CG6295 RNAi-1 and control flies at 5 days after eclosion were prepared. The whole guts (30 per sample) were carefully dissected from each genotype by removing trachea and Malpighian tubules. We performed RNA-seq analysis on rat IEC-6 cells with Liph knockdown by two short hairpin RNAs (Liph_sh1, Liph_sh2). Three biological replicates for each sample.

first: Ying

last: Sun

first: Ting

last: Ni


title: A chromatin-driven mechanism of transcription in ammonia-oxidizing archaea under environmental stress [MNase-seq]

status: Public on Jun 30 2024

city: Cheongju

first: Kyunghwan

last: Kim

address: Rm #202a, Bldg. S1-5, 1 chungdae-ro

country: South Korea

institute: Chungbuk National University

summary: Ammonia-oxidizing archaea (AOA) play a significant role in global nitrogen and carbon cycling. AOA can survive under fluctuating environmental conditions by modulating gene expression. Little is known about how AOA regulate gene expression to adapt environmental stress. Here, we report a chromatin-driven mechanism of transcription in Nitrososphaera Viennensis (EN76) to adapt to temperature stress. Using computational and biochemical assays, we found EN76 contains an archaeasome structure. We found that several residues, including G20, K57, and T58 of histone, are important to form archaea chromatin structures. In vitro transcription assays revealed that AOA chromatin efficiently controls gene expression, similar to eukaryote chromatin. Furthermore, we identified AOA histone acetylation, which activates gene expression. Moreover, by integrating chromatin-based gene expression analyses, we revealed that AOA differentially regulate gene expression in response to temperature stress by altering archaeasome occupancy. Our study provides unprecedented documentation that AOA fine-tunes gene expression through a chromatin-driven epigenetic mechanism.

overall_design: Cells were collected by centrifugation and washed twice with MNase digestion buffer. The pellet was resuspended in MNase buffer and incubated with 50 mU of micrococcal nuclease (MNase) at 37 °C for 15 min to partially digest chromatin. The reaction was quenched with 10 mM EDTA, and DNA was extracted using phenol:chloroform:isoamyl alcohol, followed by ethanol precipitation. Purified DNA was quantified, and sequencing libraries were prepared and subjected to high-throughput sequencing on an Illumina platform (single read 75bp sequencing using HigSeq 2500).


title: Comprehensive DNA methylation analysis of human neuroblastoma cells treated with blonanserin and perospirone

status: Public on Dec 26 2024

city: Kumamoto

first: Kazuya

last: Iwamoto

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

department: Faculty of Life Sciences

country: Japan

institute: Kumamoto University

summary: This work reveals the effect of antipsychotics on DNA methylation using the cell model. After the treatment of antipsychotics, blonanserin and perospirone, DNA methylation profiles obtained by Illumina HumanMethylation450 beadchip were examined.

overall_design: We conducted a comprehensive DNA methylation analysis of human neuroblastoma cells (SK-N-SH) cultured with antipsychotics. The cells were cultured with low and high concentrations of blonanserin and perospirone based on their effective blood concentrations for 8 days. DNA methylation assay was performed with the Illumina HumanMethylation450 BeadChip. Three independent samples were prepared for each experimental group (n=15 in total).

first: Jianbin

last: Du

first: Yutaka

last: Nakachi

first: Ayaka

last: Fujii

first: Shinya

first: Kiyoto

last: Kasai

first: Miki

last: Bundo


title: The Ednrb–Aim2–AKT axis regulates neural crest-derived melanoblast proliferation during early development

status: Public on Nov 06 2024

first: yu

last: chen

address: 270 West Xueyuan Road

institute: Wenzhou Medical University

summary: Ednrb is specifically required to develop neural crest (NC) stem cell-derived lineages. However, it is still unknown why Ednrb signaling is only needed for the early development of melanoblasts in the skin and eye. We show that Ednrb is required for the proliferation of melanoblasts during early mouse development. To understand the mechanism of melanoblast proliferation, we found that the gene absent in melanoma 2 (Aim2) is upregulated in Ednrb-deficient NC cells by RNA-sequencing analysis. Consequently, the knockdown or knockout of Aim2 partially rescued the proliferation of Ednrb-deficient melanoblasts. Conversely, the overexpression of Aim2 in melanoblasts suppressed their proliferation. We further show that Ednrb signaling could act through the microRNA miR-196b to block the suppression of melanoblast proliferation by Aim2 in primary NC cell cultures. These results reveal the Ednrb–Aim2–AKT axis in regulating melanocyte development and suggest that Ednrb signaling functions as a negative regulator of Aim2, which inhibits the proliferation of melanoblasts in early development. These findings uncover a previously unreported role for Aim2 outside the inflammasome, showing that it is a significant regulator controlling NC stem cell-derived lineage development.

overall_design: To understand the mechanism of melanoblast proliferation,WT and Ednrb-/- NT explants from E9.5 embryos containing neural crest cells were isolated. After culture for 4 days, RNAs (5 biological replicates for each group)  were extracted .

first: Yu

last: Chen

first: Huirong

last: Li

first: Jing

last: Wang

first: Ling

last: Hou


title: 1) Lipid-orchestrated paracrine circuit coordinates mast cell maturation and anaphylaxis through functional interaction with fibroblasts & 2) Epidermal ABHD12B-driven atypical acylceramide safeguards against scleroderma [skin scRNA-seq]

status: Public on Nov 12 2024

city: Tokyo

first: Yoshitaka

last: Taketomi

address: 7-3-1 Hongo, Bunkyo-ku,

department: CDBIM, Graduate School of Medicine,

institute: The University of Tokyo

summary:
1) Interaction of mast cells (MCs) with fibroblasts is essential for MC maturation within tissue microenvironments, although the underlying mechanism is incompletely understood. Through a phenotypic screening of >30 mouse lines deficient in lipid-related genes, we found that deletion of the lysophosphatidic acid (LPA) receptor LPA1, like that of the phospholipase PLA2G3, the prostaglandin D2 (PGD2) synthase L-PGDS, or the PGD2 receptor DP1, impairs MC maturation and thereby anaphylaxis. Mechanistically, MC-secreted PLA2G3 acts on extracellular vesicles (EVs) to supply lysophospholipids, which are converted by fibroblast-derived autotaxin (ATX) to LPA. Fibroblast LPA1 then integrates multiple pathways required for MC maturation by facilitating integrin-mediated MC-fibroblast adhesion, IL-33-ST2 signaling, L-PGDS-driven PGD2 generation, and feedforward ATX-LPA1 amplification. Defective MC maturation resulting from PLA2G3 deficiency is restored by supplementation with LPA1 agonists or PLA2G3-modified EVs. Thus, the lipid-orchestrated paracrine circuit involving PLA2G3-driven lysophospholipid, eicosanoid, integrin, and cytokine signaling fine-tunes MC-fibroblast communication, ensuring MC maturation.
2) Systemic scleroderma (SSc) is a devastating fibrotic disease with poor prognosis, yet its underlying mechanisms remain poorly understood. Given that lipid dysregulation is often associated with skin disorders, we screened cutaneous expression of various lipid hydrolases in SSc patients and found that ABHD12B, a putative hydrolase expressed in terminally differentiated epidermal keratinocytes, was most robustly downregulated in the affected skin. ABHD12B deficiency disturbed skin barrier and exaggerated skin fibrosis in mouse scleroderma models. Single-cell RNA-sequencing and untargeted lipidomic analyses of the skin revealed that ABHD12B deficiency facilitated epidermal- and endothelial-to-mesenchymal transitions and selectively reduced the levels of 1-O-acylceramides with very-long-chain fatty acids. Topical application of 1-O-acylceramide to ABHD12B-deficient mice reversed skin barrier abnormality and fibrosis. Thus, our results reveal a functional connection of ABHD12B with 1-O-acylceramide biosynthesis, highlight an unexplored anti-fibrotic role of this unique lipid, and point to this lipid-driven pathway as a potential drug target for SSc.

overall_design: Whole cells and CD326-negative cells isolated by AutoMACS from ear skin of Abhd12b deficient (Abhd12b-/-) and wild-type (Abhd12b+/+) developing control or hypochrorite (HClO)-induced SSc model and analyzed using scRNA-seq. Preparation of the scRNA-seq library was performed as described previously (Shichino et al. Commun Biol 2022). In brief, cells prepared from mouse skin were stained with BD Ms Single-Cell Multiplexing Kit (anti-mouse CD45, 30-F11) and Custom BD Single-Cell Multiplexing Set (anti-mouse MHC-H2 class I, M1/42) (BD Biosciences). Obtained single-cell suspensions were subjected to a BD Rhapsody system with Targeted mRNA and AbSeq Amplification Kit (BD Biosciences) following the manufacture’s instructions. Resultant beads were reverse transcribed, treated with exonuclease I, and subjected to TAS-Seq workflow for cDNA and hashtag library amplification. Illumina cDNA libraries were constructed from amplified cDNA libraries by using NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs). Ligand products were purified and performed barcording PCR. Size distribution of amplified products was analyzed by a MultiNA system (MCE-202; Shimadzu). Resultant libraries and barcorded hastag libraries were quantified using KAPA Library Quantification Kit (Roche). Pooled libraries were sequenced on an Illumina NovaSeq 6000 sequencer with an Illumina NovaSeq 6000 S4 Reagent Kit v1.5 (both from Illumina). Two billion clusters, equivalent to 400 Gb/analysis, were obtained by pair-ended analysis of 100 bp of sequencing data. Fastq data preprocessing and generation of the single-cell gene-expression matrix was performed as described previously (Shichino et al. Commun Biol 2022). The resultant dataset was analyzed using R software package Seurat v4.0.4120 in R 4.1.3.

first: Takayoshi

last: Higashi

first: Shigeyuki

last: Shichino

first: Satoshi

last: Ueha

first: Kouji

last: Matsushima

first: Makoto

last: Murakami


title: PD-1 Mediated Regulation of Unique Activated CD8+ T Cells by NK Cells in the Submandibular Gland

status: Public on Dec 11 2024

city: Boston

first: Liang

last: Yang

address: 77 Avenue Louis Pasteur

institute: Harvard Medical School

summary: The increasing use of anti-PD-1 immune checkpoint blockade has led to the emergence of immune-related adverse events (irAEs), including dysfunction of the submandibular gland (SMG). In this study, we investigated the immunoregulatory mechanism contributing to the susceptibility of the SMG to irAEs. Here, we found that the SMG of PD-1 deficient mice and anti-PD-L1 treated mice harbor an expanded population of CD8+ T cells. We demonstrate that NK cells expressing PD-L1 tightly regulate CD8+ T cells in the SMG. When this immunoregulation is disrupted, CD8+ T cells clonally expand and acquire a unique transcriptional profile consistent with TCR activation. These clonally expanded cells phenotypically overlapped with cytotoxic GzmK+ CD8+ T autoimmune cells identified in primary Sjögren’s syndrome patients. Understanding how NK cells modulate CD8+ T cell activity in the SMG opens new avenues for preventing irAEs in patients undergoing checkpoint blockade therapies.

overall_design:
T cells were extracted from the submandibular glands of WT and PD-1KO mice, and the spleen of WT mice for transcriptomic, proteomic, and TCR repertoire analysis
On August 15, 2025, the Series was reorganized in order to include tissue-specific samples.

first: Sam

last: Borys

first: Shanelle

last: Reilly

first: Ian

last: Magill

first: David

last: Zemmour

first: Laurent

last: Brossay


title: Predictive prioritization of enhancers associated with pancreatic disease risk

status: Public on Oct 15 2024

city: bethesda

first: Efsun

last: Arda

address: 41 medlars drive

institute: National Institutes of Health

first: H

first: Li

first: Songjoon

last: Baek


title: DNA mutagenesis driven by transcription factor competition with mismatch repair

status: Public on Mar 31 2025

city: Durham

first: Raluca

last: Gordan

state: NC

address: 101 Science Dr, CIEMAS 2179

department: Center for Genomic and Computational Biology

institute: Duke University

summary: The distribution of somatic mutations across the genome is not uniform. Recently, an unexpected pattern of hyper-mutation was reported at binding sites of transcriptional regulatory factors (TFs). In some human cells, a decrease in DNA repair activity was also observed at TF binding sites, leading to the hypothesis that TFs may increase mutagenesis by interfering with the recognition of DNA lesions by repair enzymes, and thus inhibiting repair. However, direct proof of this surprising TF-induced mutagenesis mechanism is lacking. Here, we show that TF binding to DNA mismatch lesions leads to increased mutation rates at TF binding sites by reducing the efficiency of lesion recognition by MutSα, the main enzyme that initiates mismatch repair in eukaryotic cells. We developed a yeast mutagenesis assay to directly observe the accumulation of mutations in a TF binding site. Upon TF overexpression, the binding site exhibited an increased mutation rate, specifically for mutations resulting from mismatches where the TF strongly reduced MutSα binding in vitro. This trend was amplified in cells with an increased rate of misincorporation errors, and it was not observed in mismatch repair-deficient cells. Analyses of human cancer somatic mutation data revealed a pattern similar to that observed in yeast, with mutations resulting from TF-bound mismatches being specifically enriched in mismatch repair-proficient tumors. Taken together, our results demonstrate that in addition to their well-known roles in gene regulation, TFs also play a role in DNA mutagenesis, by directly interfering with the repair of replication errors. Since a majority of cancer mutations originate from unrepaired replication errors, most commonly mismatches, our results suggest that TF interference with mismatch repair will shape the mutation landscape of regulatory DNA in cancer genomes.

sample_organism:
Saccharomyces cerevisiae
Homo sapiens

overall_design: Competition DNA-binding experiments were performed for yeast MutS⍺ and human TFs MYC:MAX, MAX:MAX, EGR1, and CREB1. The competition experiment was also perfomed for human MutS⍺ and human TF EGR1. Briefly, we designed DNA sequences to form a stem-loop structure that incorporates mismatched base pairs in the stem, and the DNA molecules were synthesized on an Agilent microarray. Then we measured the binding of MutS⍺ to the DNA, either by itself or under direct competition from TFs. Each genomic DNA sequence represented on the array is present in 10 replicate spots. We report the PBM signal intensity of MutS⍺ and each TF respectively for each spot.


title: Functional maps of a genomic locus reveal confinement of an enhancer by its target gene

status: Public on Aug 21 2024

city: Amsterdam

first: Christina

last: Moene

address: Plesmanlaan 121

institute: Netherlands Cancer Institute


title: Transcriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells

status: Public on Sep 11 2023

city: La Jolla

first: Gene

last: Yeo

address: 2880 Torrey Pines Scenic Dr. Room 3805/Yeo Lab

institute: UCSD


title: Pro‐inflammatory activation of microglia in the cerebellum hyperexcites Purkinje cells to trigger ataxia

status: Public on Jul 01 2023

city: Nanjing

first: Xiaoyang

last: Ma

address: No.163, Xianlin Avenue, Qixia District

department: School of life sciecne

institute: Nanjing University

summary: Specific medications to combat cerebellar ataxias, a group of debilitating movement disorders characterized by difficulty with walking, balance and coordination. Notably, cerebellar microglial activation appears to be a common feature in different types of ataxic patients and rodent models. However, the causal link between the activation of microglia in the cerebellum and ataxias remains inconclusive. In the present study, using a classic mouse model of cerebellar ataxia induced by 3-acetylpyridine (3-AP), we find a early-onset and long-lasting microglial activation accompanied by neuronal loss and dysfunction in the cerebellum. Transcriptome and behavior analyses indicate that microglial depletion in 3-AP ataxic mice decreases neuroinflammatory response in the cerebellum and rescues the ataxic motor symptoms including motor incoordination, gait abnormality, and locomotor dysfunction. Moreover, specific chemogenetic activation of cerebellar microglia in the vermis by M3D(Gq), a designer receptor exclusively activated by designer drugs (DREADDs), directly induces an expression of pro-inflammatory cytokines and aggravates ataxic motor deficits of 3-AP mice. On the contrary, inhibition of cerebellar microglial activation by M4D(Gi) or minocycline reduces the production of pro-inflammatory cytokines including TNF-α and alleviates motor deficits. Furthermore, blockage of TNF-α signaling attenuates the microglial-triggered hyperactivity of Purkinje cells (PCs). These results suggest that cerebellar microglial activation aggravates neuroinflammatory response, and subsequently induces dysfunction of PCs, which in turn triggers ataxic motor deficits. Our findings thus reveal a causal relationship between pro-inflammatory activation of cerebellar microglia and the ataxic motor symptoms, which may offer novel evidence for therapeutic intervention for cerebellar ataxias by targeting microglia and microglia-derived inflammatory mediators.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in  cerebellums for the vehicle and PLX3397 treated mice after 3-AP induced damage .

first: Xiao-Yang

first: Shu-Tao

last: Xie

first: Fa

last: Zhang

first: Jing-Ning

last: Zhu


title: Cholesin Receptor Signalling is Active in Cardiovascular System-Associated Adipose Tissue and Correlates with SGLT2i Treatment in Patients with Diabetes

status: Public on Jun 20 2024

city: Łódź

first: Jędrzej

last: Chrzanowski

state: łódzkie

address: Mazowiecka 15

department: Department of Biostatistics and Translational Medicine

institute: Medical University of Lodz

summary:
Objective: To identify the cholesin receptor-associated genes and clinical factors linked with their expression in cardiovascular system and associated adipose tissues.
Research Design and Methods: Right cardiac auricle, aortic wall, saphenous vein and adipose tissue (periaortic-PAT, epicardial-EAT, thymic-TAT) samples were collected during coronary-artery bypass grafting.
Results: We included 46 participants [37 male, 23 with type 2 diabetes, median age 68.50 (Q1-Q3: 63.00-72.00) years, BMI 28.39 (26.06-31.49) kg/m2]. GPR146 expression in adipose tissues significantly correlated with BMI, c-peptide, total cholesterol and LDL concentrations. Selected metabolic pathways were significantly and positively enriched in GPR146-dependent manner. GPR146-coexpressed genes contained key regulators of lipid metabolism, and correlated positively with LDL, HDL and total cholesterol concentrations. SGLT2i treatment mirrored GPR146-associated signature in EAT, suggesting potential impact of SGLTi on  cholesin-GPR146 network.
Conclusions: GPR146 expression is associated with serum lipids and metabolically-relevant transcriptomic changes in adipose tissue, in EAT similar to  iSGLT2-associated ones.

Funding: The scientific work was funded by the National Science Center Grant Number 2022/45/N/NZ4/01206 awarded to AR, and a grant of Diabetes Poland awarded to AR and co-financed from the state budget funds as part of the Minister of Education and Science program named “Perły Nauki” Project Number PN/01/0025/2022.

overall_design: RNAseq data from tissue samples (athymic adipose tissue, epicardial adipose tissue) collected during coronary bypass grafting (CABG) procedure from patients with type 2 diabetes mellitus (T2DM) or patients without diabetes (control group) with present coronary artery disease (CAD) and significant coronary artery stenosis or multi-vessel disease.

first: Aleksandra

last: Ryk

first: Anna

last: Marcinkiewicz

first: Arkadiusz

last: Michalak

first: Izabela

last: Dróżdż

first: Jacek

last: Burzyński

first: Maciej

last: Krajca

first: Wojciech

last: Fendler


title: Droplet-based high-throughput 3D genome structure mapping of single cells with simultaneous transcriptomics

status: Public on Jan 08 2025

city: Beijing

first: Xiaoliang

address: No.5 Yiheyuan Road, Haidian District

institute: Peking University

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Semaglutide Exacerbates Stunting in Growth-Impaired Juvenile Male Mice via Reduced Energy Metabolism

status: Public on May 07 2024

city: Lyon

first: Filipe

last: De Vadder

address: 32-34 Avenue Tony Garnier

country: France

institute: Institut de Génomique Fonctionnelle, ENS de Lyon, CNRS UMR5242, Université Claude Bernard Lyon 1

summary: Animals rely on linear growth to attain their full adult size. The regulators of this multifactorial process, including environmental and endocrine cues, are still incompletely understood. Notably, GLP-1, glucagon-like peptide 1 (GLP-1) has emerged as a potential player in this process. Here, we employ semaglutide, a pharmaceutical GLP-1R agonist as a tool to mechanistically dissect the interplay between GLP-1 receptor activation, energy metabolism, and linear growth during the juvenile period, independent of its clinical applications. Using a juvenile mouse model, we show that chronic semaglutide treatment lowers blood glucose without affecting food intake or weight gain in juveniles with a normal growth pattern. However, in growth-stunted juveniles, semaglutide treatment exacerbates linear growth impairment through at least 2 concomitant mechanisms: a moderate reduction in food intake, and a decreased catabolic activity incompatible with tissue growth. These data suggest a complex interplay between GLP-1 signaling, energy metabolism, and growth during juvenile development. Overall, these findings highlight the value of semaglutide as a mechanistic tool for understanding how GLP-1 receptor activation modulates growth and metabolism in juveniles, emphasizing the importance of developmental context for interpreting its effects.

overall_design: To investigate the effect of semaglutide treatment on undernourished juveniles males, we analyzed the liver of those mice at 8 weeks (after a 5 weeks dietary challenge with low-protein diet, 5% in kcal). Bulk RNA sequencing was performed after RNA isolation from the tissue. We used vehicle-treated animals as the reference (5 mice), and semaglutide-treated animal as the experimental condition (5 mice).

first: Amélie

last: Joly

first: Lucas

last: Rebiffé

first: Yves

last: Dusabyinema

first: Julien

last: Dellinger

first: François

last: Leulier

first: Karine

last: Gauthier

first: Estelle

last: Caillon


title: Oxidized 5-methylcytosine modulates synthetic lethality to poly-ADP-ribose polymerase inhibitors in acute myeloid leukemia [cell line RNA-seq]

status: Public on Nov 12 2022

city: Miami

first: Luisa

last: Cimmino

state: Florida

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

summary: TET2 haploinsufficiency is a driving event in myeloid cancers and is associated with a worse prognosis in patients with AML. Enhancing residual TET2 activity using vitamin C increases oxidized 5-methylcytosine (mC) formation and promotes active DNA demethylation via BER that slows leukemia progression. We utilized genetic and compound library screening approaches to identify rational combination treatment strategies to improve the use of vitamin C as an adjuvant therapy for AML. In addition to increasing the efficacy of several FDA approved drugs, vitamin C treatment with PARPi elicited a strong synergistic effect at blocking AML self-renewal in murine and human AML models. Vitamin C-mediated TET activation combined with PARPi caused an enrichment of chromatin-bound PARP1 at oxidized mCs, and H2AX accumulation during mid-S phase leading to cell-cycle stalling and differentiation. Given most AML subtypes maintain residual TET2 expression, vitamin C could elicit broad efficacy as a PARPi therapeutic adjuvant.

overall_design: Comparison of differentially expressed genes of LAA, Olaparib, or LAA+Olaparib treatment to vehicle control in MLL-AF9+ acute leukemia cell lines MOLM-13 and THP-1.

first: John

last: Brabson


title: Functional CRISPR-Cas9 knockout screening of the genetic determinants of human fibroblast migration propensity

status: Public on May 01 2024

city: Bologna

first: Camilla

last: Luni

address: Via Terracini 28

department: DICAM

institute: University of Bologna

summary: Directional cell migration plays a central role in a wide range of physiological and pathological conditions, such as inflammation and cancer. Steps involved in cell migration include cell polarization, formation of membrane protrusions at the cell front side and adhesion disassembly at the rear side, and a general cytoskeletal rearrangement. However, there are cell-specific and context-specific molecular events acting in the process. Here, we show how to screen for genes and miRNAs involved in migration by the direct integration of a high-throughput gene editing method, the CRISPR-Cas9 knockout pool screening, and a well-established functional assay, the transwell migration assay. We applied this methodology to human fibroblasts migrating in the presence of a biochemical gradient. The results confirm known genes involved in migration, but also highlight new candidates, like the ectopically expressed family of olfactory receptors. This work establishes a methodological advancement in the use of CRISPR technology for functional screening, and represents a resource for candidate genes and miRNA playing a role in human fibroblast directional migration.

overall_design: We sequenced the plasmid library amplified from Human CRISPR Knockout Pooled Library (GeCKO v2 library). Then, human fibroblasts were transduced with this library, cells were expanded for 14 days under puromycin selection conditions, before starting the migration selective pressure in tranwells. Three rounds of selection were performed collecting separately the cells attached to the top and the bottom of the transwell membrane. Control culture was performed in parallel in conventional flasks.

first: Antonio

last: Mazzei

first: Sebastian

last: Martewicz

first: Ramin

last: Amiri

first: Meihua

last: Cui

first: Nicola

last: Elvassore


title: Glut1 inhibitor BAY-876 and TNF treated LLC cells

status: Public on Jan 18 2023

first: Lijian

last: Wu

address: 30 Shuangqing Rd, Haidian District, Beijing

department: School of Medicine

institute: 清华大学

summary: To investigate the mechanisms by which Glut1 inactivation synergized with TNFa to induce cell death, LLC cells were either pretreated or left untreated for 200nM BAY-876 for 24 hours, followed by treatment with 20ng/ml TNF or left untreated for 32 hours.To compare the expression of glucose transporters in tumor and tumor-reactive immune T cells, we analyzed the expression levels ofperformed RNAseq on adoptively transferred adoptively transferred OT-I T cells and LLC-OVA cells, respectively.

overall_design: Comparative gene expression profiling analysis of RNA-seq data of LLC cells treated with TNFand BAY-876 alone or in combination. Compare the expression of glucose transporters in tumor and tumor-reactive immune T cells.

first: Yiteng

last: Jin

first: Deng

last: Pan


title: Spermine Synthase Engages in Macrophages M2 polarization to Sabotage Antitumor Immunity in Hepatocellular Carcinoma (Hepa 1-6 cell)

status: Public on Nov 11 2024

city: Guangzhou

first: Yining

last: Sun

address: No. 1023-1063, Shatai South Road, Baiyun District, Guangzhou

institute: Nanfang hospital, Southern medical university

summary: Disturbances in tumor cell metabolism reshape the tumor microenvironment (TME) and impair antitumor immunity, but the implicit mechanisms remain elusive. Here, we found that spermine synthase (SMS) was significantly upregulated in tumor cells, which correlated positively with immunosuppressive microenvironments and predicted poor survival in hepatocellular carcinoma (HCC) patients. Via “subcutaneous” and “orthotopic” HCC syngeneic mouse models and a series of in vitro coculture experiments, we identified elevated SMS level in HCC cells played a role in immune escape mainly through its metabolic product spermine, which induced tumor-associated macrophage (TAM) reprogramming and subsequently corresponded with a decreased antitumor functionality of CD8+ T cells. Mechanistically, we discovered that spermine reprogrammed TAM mainly by activating the PI3K-Akt-mTOR-S6K signaling pathway. Spermine inhibition in combination with immune checkpoint blockade effectively diminishes tumor burden in vivo. Our results expand the understanding of the critical role of metabolites in regulating cancer progression and anti-tumor immunity, and open new avenues for developing novel therapeutic strategies against HCC.

overall_design: To investigate how SMS regulated the tumor microenviroment, we estsblished overexpressed Sms (Sms-OE) cells by lentivirus and used them to construct orthotopic liver tumor model.

first: Yuan

last: Fan

first: Peitao

last: Zhou

first: Dehua


title: A time course of sea anemone development

status: Public on Sep 09 2022

city: Vienna

first: Alison

last: Cole

address: Djerassiplatz 1

department: Neurosciences and Developmental Biology

country: Austria

institute: University of Vienna

summary: A diversity of life cycle stages processed into single-cell RNA-seq libraries in order to characterize cell type diversity and relationships

overall_design: Embryos/animals were dissociated and cell suspensions were processed with a 10X Genomics Chromium Controller

first: Ulrich

last: Technau

first: Julia

last: Steger


title: MATRIN3 deficiency leads to cGAS-STING activation

status: Public on May 15 2024

city: Bethesda

first: Stefan

last: Muljo

state: MD

address: 10 Center Drive

institute: NIH, NIAID

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

overall_design: Refer to individual Series


title: Identification of genes responsive to hypoxia in human cervical epithelial adenocarcinoma HeLa cells

status: Public on Nov 13 2020

city: Toyama

first: Yoshiaki

last: Tabuchi

state: Toyama

address: 2630 Sugitani

department: Life Science Research Center

institute: University of Toyama

summary:
It has been well-known that cancer cells acquire approximately three-fold radioresistance under hypoxia than under normoxia due to both radiation chemical and radiation biological mechanisms, causing a negative impact on the outcome of radiation therapy.
In the present study, to identify genes responsive to hypoxia in human cervical epithelial adenocarcinoma HeLa cells, global-scale gene expression analysis was carried out using a GeneChip® system.

overall_design: Human cervical carcinoma cell line HeLa cells were used. Cells were cultured at 37°C in Dulbecco’s modified Eagle medium (DMEM) containing 10% FBS, 100 U/mL penicillin, and 100 μg/mL streptomycin. Cells were incubated in a well-humidified 5% CO2 and 95% air for the normoxic culture, or in a RUSKINN INVIVO2 500 for hypoxic culture at < 0.1% O2. Total RNA samples were prepared from the cells. Gene expression was analyzed by an Affymetrix GeneChip® system with a Human Genome U133-plus 2.0 array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Hiroshi

last: Harada


title: spatiotemporal single-cell transcriptomics in mouse and human to investigate TAM evolution during GBM progression

status: Public on Sep 06 2023

city: Houston

first: Ailiang

last: Zeng

address: 12515 stoney creek dr

department: Cancer Biology

institute: MD Anderson Cancer Center

summary: Glioblastoma (GBM) is the most common and malignant primary brain tumor. Although immunotherapy has shown promise in certain cancer types, it has not been effective against GBM, largely due to its highly immunosuppressive tumor microenvironment (TMEs), which is rich in tumor-associated macrophages/microglia (TAMs). TAMs in late-stage GBM contribute to T-cell exhaustion and worsen prognosis, but the role of TAMs in earlier stages of tumor development is unclear. By employing genetically engineered mouse models and human samples, we used spatiotemporal single-cell transcriptomics to investigate TAM evolution during GBM progression.

overall_design:
1,Single immune cell sequencing of spatial sampling (paired Periphery, Border and Core) in 5 implanted QPP#7 mouse GBMs, and in 4 human GBM masses. 2,Single immune cell sequencing of longitudinal sampling of 6 spontaneous QPP Mouse GBM 3,Single immune cell sequencing of Vehicle- or KD3010-treated GL261 mouse GBMs.
1,Single immune cell (CD45+) sequencing of spatial sampling (paired Periphery, Border and Core) in 3 implanted QPP#7 mouse GBMs,  and in 3 human GBM masses (Emory Cohort). 2,Single immune cell sequencing of Mg-TAMs and Mo-TAMs

first: Jian

last: Hu

first: Mingxin

last: Li

first: Kristin

last: Huntoon

first: Chen

last: Ju

first: Bo

last: Zhao


title: Unsaturated fat alters clock phosphorylation to align rhythms to the season in mice

status: Public on Jan 29 2024

city: San Francisco

first: Louis

last: Ptacek

institute: University of California San Francisco

summary: The circadian clock maintains synchrony between biological processes and light/dark cycles by integrating environmental cues. How the clock adapts to seasonal variations in the environment is incompletely understood. We found that a high-fat diet increased phosphorylation of the clock protein PERIOD2 (PER2) on serine 662 (S662), which was necessary and sufficient for regulating phase shifting of daily locomotor activity to entrain to seasonal light cycles. PER2-S662 phosphorylation correlated with genome-wide expression pathways that regulate polyunsaturated fatty acid (PUFA) conversion into oxylipins in the hypothalamus. Partial hydrogenation of dietary PUFAs increased hypothalamic PER2-S662 phosphorylation and entrainment to a summer photoperiod in control mice, but not in mice for which PER2-S662 could not be phosphorylated. PER2-S662 phosphorylation is influenced by, and alters the regulation of, unsaturated fat to control circadian phase shifting across the seasons.

overall_design: RNA-seq was performed from hypothalamic extracts of ad libitum fed and 16-hour fasted, wild type, Per2 knockout, and PER2-S662D mutant mice.

first: Daniel

last: Levine

first: Rasmus

last: Reeh

first: Thomas

last: McMahon

last: Mandrup-Poulson

first: Ying-Hui

last: Fu


title: RNAseq of malignant peripheral nerve sheath tumors from Nf1 flox/flox Arf flox/flox PostnCre+ mice

status: Public on Dec 12 2023

city: Indianapolis

first: Steven

middle: P

last: Angus

state: IN

address: 1044 W Walnut St

department: Pediatrics

institute: Indiana University School of Medicine

summary: Malignant peripheral nerve sheath tumors (MPNSTs) are the leading cause of premature death for patients with Neurofibromatosis type 1 and no approved targeted therapies are available. Transformation from Nf1-null benign plexiform neurofibromas is driven by the loss of the Cdkn2a (Arf) locus. Here, genetically engineered mouse models with combined Nf1 flox/flox and Arf flox/flox alleles were used (crossed with Postn-Cre+ mice). Tissue from MPNSTs that form in the Nf1-/-;Arf-/- setting were used for mRNA sequencing and compared to benign plexiform neurofibroma tissue (Nf1-/- from Nf1 flox/flox; Postn-Cre+ mice, GSE213789) to identify transcriptome signatures from MPNST and compare them to benign plexiform neurofibroma.

overall_design: 6 experimental samples (malignant peripheral nerve sheath tumors from 6 Nf1 flox/flox Arf flox/flox, Postn-Cre+ mice, used to compare to plexiform neurofibromas from GSE213789)

middle: D

last: Rhodes


title: Novosphingobium sp. HR1a modifies the clover-root architecture through the alteration of the jasmonic acid levels in clover plants

status: Public on Nov 16 2022

city: Little Rock

first: Zulema

last: Udaondo

state: AR

address: 501 Jack Stephens Drive

department: Biomedical Informatics

institute: UAMS


title: Single cell atlas of the human retina

status: Public on Apr 25 2024

city: Palo Alto

first: Lattice

last: Data Coordination

address: 3165 Porter Drive

department: Genetics

institute: Stanford University

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

As the light sensing part of the visual system, the human retina is composed of five classes of neuron, including photoreceptors, horizontal cells, amacrine, bipolar, and retinal ganglion cells. Each class of neuron can be further classified into subgroups with the abundance varying three orders of magnitude. Therefore, to capture all cell types in the retina and generate a complete single cell reference atlas, it is essential to scale up from currently published single cell profiling studies to improve the sensitivity. In addition, to gain a better understanding of gene regulation at single cell level, it is important to include sufficient scATAC-seq data in the reference. To fill the gap, we performed snRNA-seq and snATAC-seq for the retina from healthy donors. To further increase the size of the dataset, we then collected and incorporated publicly available datasets. All data underwent a unified preprocessing pipeline and data integration. Multiple integration methods were benchmarked by scIB, and scVI was chosen. To harness the power of multiomics, snATAC-seq datasets were also preprocessed, and scGlue was used to generate co-embeddings between snRNA-seq and snATAC-seq cells. To facilitate the public use of references, we employ CELLxGENE and UCSC Cell Browser for visualization. By combining previously published and newly generated datasets, a single cell atlas of the human retina that is composed of 2.5 million single cells from 48 donors has been generated. As a result, over 90 distinct cell types are identified based on the transcriptomics profile with the rarest cell type accounting for about 0.01% of the cell population. In addition, open chromatin profiling has been generated for over 400K nuclei via single nuclei ATAC-seq, allowing systematic characterization of cis-regulatory elements for individual cell type. Integrative analysis reveals intriguing differences in the transcriptome, chromatin landscape, and gene regulatory network among cell class, subgroup, and type. In addition, changes in cell proportion, gene expression and chromatin openness have been observed between different gender and over age. Accessible through interactive browsers, this study represents the most comprehensive reference cell atlas of the human retina to date. As part of the human cell atlas project, this resource lays the foundation for further research in understanding retina biology and diseases.


title: Nucleoporin Seh1 controls murine neocortical development via transcriptional repression of p21 in neural stem cells

status: Public on Jun 09 2022

city: xiamen

first: Liu

last: Zhixiong

state: Fujian

address: Xiangan Nanlu 4221-120

department: School of Life Sciences

institute: Xiamen University

summary: Nucleoporin Seh1 has been involved in gene regulation. To dissect nucleoporin's direct regulated genes, we performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for nucleoporin Seh1 in neural stem cells.

overall_design: We performed ChIP-seq using neural stem cells at proliferation stage.

first: Liang

last: Zhang

first: Zhixiong

last: Liu

first: Wenxiu

last: Dai


title: Acute IL-1beta exposure in rat insulinoma cells and human islets

status: Public on May 26 2022

city: Baton Rouge

first: James

middle: Jason

last: Collier

state: LA

address: 6400 Perkins Road

department: Islet Biology

institute: Pennington Biomedical

summary: Comparison of acute cytokine signaling in rat insulinoma cells versus human islets

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Untreated versus IL-1 treated (3 hour exposure) in rat insulinoma cells and human islets

first: J

first: Susan

last: Burke

first: Richard

last: Carmouche

middle: S

last: Newman


title: Genetic and epigenetic determinants of reactivation of Mecp2 and the inactive X chromosome in neural stem cells [RNA-seq]

status: Public on Jan 24 2022

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

institute: Erasmus MC

summary: Rett Syndrome is a neurodevelopmental disorder in girls that is caused by heterozygous inactivation of the chromatin remodeler gene MECP2. Rett Syndrome may therefore be treated by reactivation of the wild type copy of MECP2 from the inactive X chromosome. Most studies that model Mecp2 reactivation have used mouse fibroblasts rather than neural cells, which would be critical for phenotypic reversal, and rely on fluorescent reporters that lack adequate sensitivity. Here, we present a mouse model system for monitoring Mecp2 reactivation that is more sensitive and versatile than any bioluminescent and fluorescent system currently available. The model consists of neural stem cells derived from female mice with a dual reporter system where MECP2 is fused to NanoLuciferase and TdTomato on the inactive X chromosome. We show by bioluminescence and fluorescence that Mecp2 is synergistically reactivated by 5-Aza treatment and Xist knockdown. As expected, other genes on the inactive X chromosome are also reactivated, the majority of which overlaps with genes reactivated early during reprogramming of mouse embryonic fibroblasts to iPSCs. Genetic and epigenetic features such as CpG density, SINE elements, distance to escapees and CTCF binding are consistent indicators of reactivation, whereas different higher order chromatin areas are either particularly prone or resistant to reactivation. Our MeCP2 reactivation monitoring system thereby suggests that genetic and epigenetic features on the inactive X chromosome affect reactivation of its genes, irrespective of cell type or procedure of reactivation.

overall_design: We performed RNA-seq on Xist-/+ Mecp2+/NLucTom NSCs which were either untreated or treated with 5-AZA and Xist knockdown and then FACS-sorted into low-, medium- and high-Tomato populations (three biological replicates per condition).

first: Hegias

last: Mira-Bontenbal

first: Wilfred

middle: F

last: van IJcken

first: Joost

last: Gribnau


title: Chromatin structure dynamics during human cardiomyocyte differention

status: Public on Nov 01 2021

city: La Jolla

first: Bing

last: Ren

address: 9500 Gilman Drive

institute: University of California, San Diego

sample_organism:
Callithrix jacchus
Pan paniscus
Pan troglodytes
Homo sapiens


title: H3K4me3, mRNA and lncRNA profiling of hypoxic human pulmonary artery endothelial cells treated with KMT2E-AS1 siRNA

status: Public on Nov 09 2023

city: Pittsburgh

first: Satoshi

last: Okawa

state: PA

address: 200 Lothrop Street

institute: University of Pittsburgh


title: Inactivation of branched-chain amino acid uptake halts Staphylococcus aureus growth and induces bacterial quiescence within macrophages

status: Public on Jun 28 2023

city: Wuerzburg

first: Martin

middle: J

last: Fraunholz

address: Theodor-Boveri-Weg

department: Chair of Microbiolgy

country: Germany

institute: University of Wuerzburg

summary: Staphylococcus aureus is a notorious human pathogen that thrives in macrophages. It resides in mature phagolysosomes, where a subset of the bacteria eventually begin to proliferate. How S. aureus acquires essential nutrients, such as amino acids, for growth in this niche is poorly understood. Using a long-term primary human macrophage infection model, we show that branched-chain amino acid (BCAA) uptake mediated by the major transporter BrnQ1 is required by S. aureus for intracellular replication in macrophages and we provide mechanistic insight into the role of BCAAs in the success of intracellular S. aureus. Loss of BrnQ1 function renders intracellular S. aureus non-replicative and non-cytotoxic. The defective intracellular growth of S. aureus brnQ1 mutants can be rescued by supplementation with BCAAs or by overexpression of the BCAA transporters BrnQ1 or BcaP. Inactivation of the CodY repressor rescues the ability of S. aureus brnQ1 mutants to proliferate intracellularly independent of endogenous BCAA synthesis but dependent on BcaP expression. Non-replicating brnQ1 mutants in primary human macrophages become metabolically quiescent and display aberrant gene expression marked by failure to respond to intraphagosomal iron starvation. The bacteria remain, however, viable for an inordinate length of time. This dormant, yet viable bacterial state is distinct from classical persisters and small colony variants.

sample_organism:
Staphylococcus aureus
Homo sapiens

platform_organism:
Staphylococcus aureus
Homo sapiens

overall_design: S. aureus JE2 wild-type or its isogenic brnQ1 mutant were either used to infect human macrophages or were grown in the infection medium (RPMI1640+10% [v/v] fetal bovine serum [heat-inactivated at 56 degrees C for 30 minutes]). RNA of both, pathogen and host cells were isolated together (dual RNA-Seq of infected macrophages) or was isolated from planktonic bacteria (grown in infection medium and were labelled "RPMI").

first: Adriana

last: Moldovan

first: Mugdha

last: Srivastava


title: Isoform switching events in Barrett's Esophagus and esophageal adenocarcinoma

status: Public on Aug 17 2022

city: Ann Arbor

first: Laura

last: Kresty

state: MI

address: 1500 E Medical Center Dr

department: Surgery

institute: University of Michigan

summary: Global isoform switching in esophageal adenocarcinoma (EAC) has not been previously characterized. This form of alternative splicing has recently been recognized as highly prevalent in multiple other cancers. In this study, isoform switch analysis was performed using next generation sequencing of RNA isolated from patient tissues across a continuum of histopathologies, ranging from low risk Barrett’s esophagus (BE) to BE with dysplasia and EAC. Patients were stratified based on histopathology.

overall_design: Isoform switching analysis was performed between two histopathology subtypes of Barrett's esophagus (BE), including BE with metaplasia or low-grade dysplaisa combined and referred to as BE.LGD (n = 25) and BE with high-grade dysplasia based on >40% HGD in the sample referred to as BE.HGD (n = 21). In addition, isoform switching analysis was performed between BE.LGD and BE.HGD+EAC.

first: Andrew

last: Chang


title: Single-cell transcriptomics reveals subtype-specific molecular profiles in Nrf2-deficient macrophages from murine atherosclerotic aortas

status: Public on Oct 22 2023

city: Kraków

first: Monika

middle: Marta

last: Stefanska

state: malopolska

address: Medical College, Wielicka 265

department: Department of Clinical Immunology

institute: Jagiellonian University

summary:
The aim of this study was to analyze the transcriptome of diverse Nrf2-deficient macrophage subpopulations from murine atherosclerotic aortas. Mice with transcriptionally inactive Nrf2 in Cdh5-expressing cells (Nrf2Cdh5tKO) were used in the experiments. These mice lack transcriptional Nrf2 activity in endothelial cells, but also in a proportion of leukocytes. We confirmed that the bone marrow-derived and tissue-resident macrophages isolated from Nrf2Cdh5tKO mice exhibit a significant decline in Nrf2 activity. Atherosclerosis was induced in Nrf2Cdh5tKO and appropriate control mice via adeno-associated viral vector (AAV)-mediated overexpression of murine proprotein convertase subtilisin/kexin type 9 (Pcsk9) in the liver and high-fat diet feeding. After 21 weeks, live aortic cells were sorted on FACS and single-cell RNA sequencing (scRNA-seq) was performed.  Our findings indicate that Nrf2 deficiency in aortic macrophages leads to subtype-specific transcriptomic changes associated with inflammation, iron homeostasis, cell injury or death pathways. This may help understanding the role of aging-associated decline of Nrf2 activity and the function of specific macrophage subtypes in atherosclerotic lesion development.
This work was supported by grant ERA-CVD/MEND-AGE/6/2019 from the National Centre for Research and Development and project No. 2021/43/B/NZ5/03336 financed from the funds of the National Science Center, Poland.

overall_design: single cell RNA sequencing from murine atherosclerotic aortas, Mice with transcriptionally inactive Nrf2 in Cdh5-expressing cells (Nrf2Cdh5tKO) were used in the experiments as well as appropriate lox Control animals.

first: Katarzyna

last: Sarad

first: Izabela

last: Kraszewska

first: Krzysztof

last: Szade

first: Judith

last: Sluimer

first: Przemyslaw

last: Blyszczuk

first: Jozek

last: Dulak

first: Agnieszka

last: Jazwa-Kusior


title: Effects of polycyclic aromatic hydrocarbons on osteoclasts and osteoblasts in the scales of zebrafish

status: Public on Nov 12 2020

first: Yoshiaki

last: Tabuchi

summary:
It has been reported that polycyclic aromatic hydrocarbons (PAHs) act on calcified tissue and suppress osteoblastic activity in the scales of teleost fish.
In the present study, the differentially-expressed genes in the zebrafish scales treated with benzo[c]phenanthrene (BcP), a kind of PAH, or its metabolite 3-hydroxybenzo[c]phenanthrene (3-OHBcP) were investigated using GeneChip® oligonucleotide microarrays.

overall_design: Zebrafish scales were used. The scales were incubated at 15 °C for 6 h in Leibovitz's L-15 medium (Invitrogen, Grand Island, NY, USA) with benzo[c]phenanthrene (BcP: 1 nM) or 3-hydroxybenzo[c]phenanthrene (3-OHBcP: 1 nM). Total RNA samples were prepared from the scales, and quality of the RNA was analyzed using a Bioanalyzer 2100. Gene expression was analyzed by an Affymetrix GeneChip® system with a GeneChip Zebrafish Genome array. Sample preparation for array hybridization was carried out as described in the manufacturer’s instructions.

first: Nobuo

last: Suzuki


title: Oxidized 5-methylcytosine modulates synthetic lethality to poly-ADP-ribose polymerase inhibitors in acute myeloid leukemia [murine AE9a RNA-seq]

status: Public on Nov 12 2022

city: Miami

first: Luisa

last: Cimmino

address: 1501 NW 10th Ave, BRB 711

institute: University of Miami

summary: TET2 haploinsufficiency is a driving event in myeloid cancers and is associated with a worse prognosis in patients with AML. Enhancing residual TET2 activity using vitamin C increases oxidized 5-methylcytosine (mC) formation and promotes active DNA demethylation via BER that slows leukemia progression. We utilized genetic and compound library screening approaches to identify rational combination treatment strategies to improve the use of vitamin C as an adjuvant therapy for AML. In addition to increasing the efficacy of several FDA approved drugs, vitamin C treatment with PARPi elicited a strong synergistic effect at blocking AML self-renewal in murine and human AML models. Vitamin C-mediated TET activation combined with PARPi caused an enrichment of chromatin-bound PARP1 at oxidized mCs, and H2AX accumulation during mid-S phase leading to cell-cycle stalling and differentiation. Given most AML subtypes maintain residual TET2 expression, vitamin C could elicit broad efficacy as a PARPi therapeutic adjuvant.

overall_design: Comparison of differentially expressed genes in AE9a+ leukemic cells from terminal mice treated with ascorbate and sustained Tet2 knockdown, or PBS-treated with Tet2 restoration, to PBS-treated Tet2 knockdown mice.

first: John

last: Brabson

first: Igor

last: Dolgalev