title: Transcriptome profiling of OCT4 positive spermatogonia in wild type and Akt1s1 null mutant mice.

first: Huayu

last: Qi

address: 190 Kaiyuan Boulevard, Science City, huangpu District

department: Center for Cell Lineage and Development

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: In order to investigate the regulatory roles of AKT1S1 during mouse spermatogenesis, we analyzed gene expression changes that caused by the deletion of Akt1s1 gene in mouse male germ cells using RNA sequencing method.  The transcriptome profiling analyses showed that OCT4+ spermatogonia from mice at different ages possess varied changes in gene expression due to the deletion of Akt1s1 gene, supporting the role of AKT1S1 plays in mediating AKT-mTORC1 signaling during mouse spermatogenesis.

overall_design: Spermatogonia expressing OCT4 were isolated from mouse testes expressing green fluorescent protein (GFP) under the control of Pou5f1 (the gene encoding OCT4) promoter in either wild type or Akt1s1 null mutant background.  OCT4+ cells were FACS isolated from enzyme-dispersed testicular cells using mice at three time points (3 days, 7 days and 2-3 months following birth) for both wild type control and Akt1s1 null mutants.  Each time point was experimentally repeated 2-3 times, generating total 15 samples for the second generation RNA sequencing via Illumina HiSeq platform.

first: Lele

last: Yang

first: Jinyue

last: Liao

last: Lee


title: Aging Induced Syntaxin 4 Deficiency Mediates Brown Adipose Tissue Pyroptosis and Thermogenic Dysfunction

status: Public on Feb 26 2024

city: Bronx

first: Kosaku

last: Shinoda

state: NY

address: 1301 Morris Park Ave

country: USA

institute: Albert Einstein College of Medicine

type: Expression profiling by high throughput sequencing

summary: Aging, chronic high fat diet feeding and housing at thermoneutrality induces brown adipose tissue (BAT) involution, a process characterized by reduction of BAT mass and function with increased lipid droplet size. Syntaxin 4 (STX4) was identified as a healthy longevity gene, in contrast endogenous STX4 protein levels in BAT declined in aged mice resulting in pyroptotic activation of caspase 1/4 signaling pathway. Single nuclei RNA sequencing of aged mice identified a specific brown adipocyte population of UCP1low cells that were Stx4 low and pyroptotic. Similarly, UCP1Stx4KO mice led to age-dependent loss of brown adipose tissue mass concomitant with increased pyroptosis whereas restoring STX4 expression protected against pyroptosis and decline in thermogenic activity. Moreover, STX4 deficiency reduced oxidative phosphorylation, glucose uptake and glycolysis leading to reduced ATP levels, a known signal for pyroptosis. All these data demonstrate a new model of rapid brown adipocyte involution and that physiologic aging and BAT involution results from pyroptotic signaling activation.

overall_design: Adipocyte nuclei were isolated from mouse interscapular BAT by fluorescence-activated cell sorting (FACS) and analyzed by 10x Genomics platform.

first: Gabrielle

last: Benitez


title: Optimization of mESC ChIP-re-ChIP workflow

city: Melbourne

first: Janith

last: Seneviratne

state: VIC

address: Peter MacCallum Cancer Centre, 305 Grattan Street

country: Australia

institute: Peter MacCallum Cancer Centre

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Epigenetics helps define current cell states, yet also shapes how cells respond to external cues such as differentiation or stress. The epigenetic plasticity of a cell describes how flexible this regulation is. Bivalent chromatin is an exemplar of epigenetic plasticity. This co-occurrence of the active-associated H3K4me3 and inactive-associated H3K27me3 histone modifications on opposite tails of the same nucleosome was first described in mouse embryonic stem cells where it is found at promoters of key developmental genes. It has been postulated that bivalent chromatin poises these promoters, keeping them free from repressive DNAmethylation, enabling them to be transcriptionally upregulated upon differentiation. Bivalent chromatin has also been reported in other cell types including somatic cells and cancer cells, however we know little of the dynamics, resolution and regulation of this chromatin state. This is partly due to the technical challenges distinguishing bone-fide bivalent chromatin, where both marks are on the same nucleosome, from sample heterogeneity where some alleles have H3K4me3 and others H3K27me3. We developed a robust and sensitive reChIP method to accurately profile bivalent chromatin in as little as 2 million mouse embryonic stem cells. We validated the sensitivity of our method to detect changes in bivalent chromatin by profiling mouse ESCs lacking the epigenetic priming factors Dppa2 and Dppa4.

overall_design: Sequential ChIPreChIP was performed on two biological replicates of E14 mouse embryonic stem cells, and two wild-type (WT) and two Dppa2/4 double knockout (DKO) clones to measure distribution of bivalent chromatin. For each sample corresponding to 2 million cells we generated in-line total H3K4me3, total H3K27me3, sequential reChIP in both orientations (H3K4me3 followed by H3K27me3 and vice versa) and IgG-IgG negative controls (one per experimental set).

first: Melanie

last: Eckersley-Maslin

first: William

last: Ho


title: Gene regulatory basis of bystander activation in CD8+ T cells (scRNA-seq)

city: Ithaca

first: Andrew

last: Grimson

address: 445 Biotech Bldg

department: Molecular Biology and Genetics

institute: Cornell University

summary: CD8+ T cells have been categorized as an adaptive lymphocyte, based on their ability to recognize specific foreign antigens and mount memory responses.  However, neonatal and adult CD8+ T cells are derived from distinct HSC progenitors, which may alter the roles they play during infection.  Here, we demonstrate that neonatal CD8+ T cells can be activated by innate cytokines alone and protect the host from a variety of unrelated pathogens in the absence of TCR signaling. Using a multi-omics approach, we found that neonatal CD8+ T cells are highly responsive to innate cytokines because they can rapidly undergo chromatin remodeling, resulting in the usage of a distinct set of enhancers that are more commonly found in innate-like T cells.  We also identified a key gene regulatory axis (Bach2/AP1) that is differentially utilized by neonatal and adult CD8+ T cells to toggle their responsiveness to innate cytokines.  Importantly, the developmental switch between innate and adaptive functions in the CD8+ T cell compartment is not mediated by a change in the maturation of individual cells along a linear axis, but rather by changes in the abundance of distinct subsets of cells. Collectively, our findings provide support for the layered immune hypothesis and indicate that the CD8+ T cell compartment is more phenotypically diverse than previously thought.

overall_design: Splenic CD8+ T cells of TCR transgenic gBT-I mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of fluorescently labeled Vβ8 and CD8. Isolated cells were then treated with IL-2 with or without co-treatment with IL-12 and IL-18 and analyzed using scRNAseq.

first: Neva

middle: B

last: Watson

first: Ravi

middle: K

last: Patel

first: Connor

middle: M

last: Kean

middle: W

first: Brian

middle: D

last: Rudd


title: Gene regulatory basis of bystander activation in CD8+ T cells (scATAC-seq)

overall_design: Splenic CD8+ T cells of TCR transgenic gBT-I mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence of fluorescently labeled Vβ8 and CD8. Isolated cells were then treated with IL-2 with or without co-treatment with IL-12 and IL-18 and analyzed using scATACseq.


title: Effect of the lack of dystrophin on the gene expression profile of hiPSC-derived cardiomyocytes

city: Krakow

first: Jacek

last: Stepniewski

address: Gronostajowa 7

department: Department of Medical Biotechnology

country: Poland

institute: Jagiellonian University

summary: Searching for the new molecular signatures of Duchenne muscular dystrophy (DMD)-associated cardiomyopathy development

overall_design: Two isogenic control and dystrophin-deficient human induced pluripotent stem cells-derived cardiomyocytes (hiPSC-CM) obtained from two differentiation runs were subjected to transcriptomic analysis .

first: Józef

last: Dulak

last: Stępniewski

first: Kalina

last: Andrysiak


title: Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration [Cut&Tag]

city: Chapel Hill

first: LI

last: QIAN

address: 111 Mason Farm Road, MBRB

department: Department of pathology

institute: UNC

summary: We applied single-cell Assay for Transposase Accessible Chromatin using sequencing (scATAC-seq) to determine the intrinsic genetic programs underlying nonCM subpopulation determination during zebrafish heart regeneration at a single cell level. A total of approximately 13,000 single non-CMs derived from zebrafish hearts isolated at different time points during heart regeneration were measured and defined into diverse cell populations, exploited for cell type-specific cis-regulatory elements and enriched motifs as control catalog of downstream cell-state-determining transcription factors.

overall_design: To assess the dynamics of chromatin lanscape of non-CMs during zebrafish heart regenration, we collected the hearts from 0, 2, 7, 14 days post amputation and lysis the nuclei to perform scATAC-seq.

first: Yanhan

last: Dong

first: Haofei

last: Wang

first: Jiandong

last: Liu


title: Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration [scATAC-seq]

first: Yuchen

last: Yang


title: Circulating microRNAs associated to cerebrospinal fluid amyloid-β and phosphorylated tau levels as potential non-invasive biomarkers for mild cognitive impairment and Alzheimer’s disease

city: Maastricht

first: Qingfeng

last: Wen

state: Limburg

address: Universiteitssingel 40

department: Department of Toxicogenomics

country: Netherlands

institute: Maastricht University

type: Non-coding RNA profiling by high throughput sequencing

summary: To identify the potential biomarkers of Alzheimer's disease (AD) based on circulating microRNAs (miRNAs), we developed a new approach using feature selection and linear mixed model. The miRNA sequencing data of 105 plasma and 112 serum samples from 112 subjects including 28 AD cases, 63 mild cognitive impairment (MCI), and 21 controls were used to identify cerebrospinal fluid biomarkers associated miRNAs. The potential of these miRNAs as biomarkers of AD or MCI was researched and validated via both internal and external dataset. Patient classification was effectuated in compliance with the NIA-AA criteria for “MCI due to AD” and “Dementia due to AD”.

overall_design: The recognition of potential biomarkers for Alzheimer’s disease based on the microRNA sequencing data of 105 plasma and 112 serum samples from 112 subjects.

first: Jacco

middle: J

last: Briedé

first: Julian

last: Krauskopf


title: Targeting CDK4/6 epigenetically impairs DNA damage repair to overcome the resistance to neoadjuvant chemotherapy in locally advanced rectal cancer II

city: Guangzhou

first: Peng

last: Deng

address: Panyu

country: China

institute: SYSUCC

summary: Resistance to neoadjuvant chemotherapy is associated tumor recurrence of locally advanced rectal cancer (LARC), which remains an unmet demand to exploit potential therapeutic strategies to improve clinical outcomes. Here we demonstrated that aberrant activation of cell cycle pathways is correlated with resistance to neoadjuvant chemotherapy in LARC. A combinatorial drug screening of 130 kinase inhibitors targeting cell cycle regulators with oxaliplatin identified that CDK4/6 inhibitors synergistically enhanced anti-tumor effects of oxaliplatin both intrinsic and acquired chemo-resistant colon cancer cells. Functional studies in both in vitro and in vivo models showed that CDK4/6 inhibitors significantly increased sensitivity to oxaliplatin. Integrative transcriptomic and chromatin profiling analysis revealed that CDK4/6 inhibitors induced DNA repair defects to enhance sensitivity of oxaliplatin through epigenetically suppression of DNA repair related genes. Mechanistically, CDK4/6 inhibition impairs DNA damage repair through a previously unrecognized RB1/TEAD4/HDAC1 co-repressor complex which contributes to the resistance to neoadjuvant chemotherapy in LARC. Together, our work revealed an important role of CDK4/6 pathway in LARC patients with neoadjuvant chemotherapy, suggesting that targeting CDK4/6 could provide a potentially effective treatment strategy for LARC.

overall_design: RNA-seq for 13 locally advanced rectal cancer (LARC) patients with neoadjuvant chemotherapy.

first: Zhaoliang

last: Yu

first: Jing

last: Tan


title: Automated generation of hiPSC-derived hepatic progeny by cost-efficient compounds

city: Leuven

first: Gert

last: Vanmarcke

address: Herestraat 49

department: Department of Development and Regeneration

country: Belgium

institute: KU Leuven

summary: Human pluripotent stem cell (hPSC)-derived hepatocyte-like cells (HLCs) hold great promise for liver disease modeling, drug discovery, drug toxicity screens, or even regenerative therapies. Yet, several hurdles still need to be overcome, including among others decrease in the cost of goods to generate HLCs and automation of the differentiation process. We here describe that use of an automated liquid handling system results in highly reproducible HLC differentiation from hPSCs. This enabled us to screen 92 chemicals to replace expensive growth factors at each step of the differentiation protocol to reduce the cost of goods of the differentiation protocol by approximately 79%. In addition, we also evaluated several recombinant extracellular matrices (ECM) to replace Matrigel. We demonstrated that differentiation of hPSCs on Laminin-521 using an optimized small molecule combination resulted in HLCs that were transcriptionally identical to HLCs generated using current growth factor combinations. In addition, the HLCs created using the optimized small molecule combination also secreted similar concentrations of albumin and urea, and relatively low concentrations of alfa-fetoprotein (AFP), displayed similar CYP3A4 functionality and a similar drug toxicity susceptibility as HLCs generated with growth factor cocktails. The broad applicability of the new differentiation protocol was demonstrated for four different hPSC lines. This allowed the creation of a scalable, xeno-free, and cost-efficient hPSC-derived HLC culture, suitable for high throughput disease modeling and drug screenings, or even for the creation of HLCs for regenerative therapies.

overall_design: RNA Samples of hiPSCs and hiPSC-derived Hepatocyte-like cells were analyzed

first: Jonathan

last: Sai-Hong Chui

first: Frederic

last: Lluis

first: Catherine

last: Verfaillie


title: Regulatory T cells converted from T helper 1 cells in tumors suppress cancer immunity via CD39

city: Beijing

first: Chen

address: Haidian District

department: Institute for Immunology and School of Medicine

institute: Tsinghua University

summary: Although Foxp3-expressing regulatory T (Treg) cells are widely believed to impede anti-tumor immunity, their regulation and functional mechanisms are not well understood. Here, through characterization of multiple cancer models, we identified substantial periphery-induced Treg cells in the tumor microenvironment, depletion of which provoked anti-tumor responses and conferred potent therapeutic effects by increasing CD8+ T cell numbers and cytolytic function. Through fate-mapping and transfer experiments, we found IFN-γ-expressing T helper (Th) 1 cells developed into Treg cells in tumors, in response to TGF-β signaling. Hence, tumor-resident Treg cells highly expressed T-bet, which was essential for their development and function. CD39, highly expressed by T-bet+ Treg cells in both mouse and human tumors, is required for Treg suppression of CD8+ T cell response. In summary, our study has elucidated a developmental pathway of intra-tumoral Treg cells and implicated new ways of targeting them in cancer patients.

overall_design: Treg cells contain several functional subsets analogous to CD4+ helper T (Th) cells. Thus, we analyzed if intra-tumoral pTreg cells were similar to any of the Th subsets in their gene expression. We performed transcriptomic analyses on intra-tumoral Treg cells derived from both Hepa1-6 and E.G7 murine tumor models by RNA sequencing. Given that intra-tumoral Treg cells were composed of a substantial proportion of pTreg cells whereas Treg cells derived from lymph nodes (LN) were mainly composed of tTreg cells, we included Treg cells purified from tumor-free LNs as a control. Intra-tumoral Treg cells were sorted from E.G7 and Hepa1-6 tumor-bearing Foxp3YFP-cre mice on day 21 and day 23, respectively. Treg cells sorted from LNs of tumor-free mice were included as a control.

first: Sang-Nee

last: Hao

first: Xiaohong

last: Zhao

first: Yazheng

first: Ni

last: Ling


title: Targeting CDK4/6 epigenetically impairs DNA damage repair to overcome the resistance to neoadjuvant chemotherapy in locally advanced rectal cancer

overall_design: 1. Chromatin immunoprecipitation sequencing (ChIP-Seq) for H3K27ac or Input was performed in DLD-1 cells. 2.RNA-seq for DLD-1 cells after  oxaliplatin, palbociclib or combinational treatment. 3. RNA-seq for 20 locally advanced rectal cancer (LARC) patients with neoadjuvant chemotherapy.


title: Single-cell chromatin landscape of non-myocytes reveals AP-1 as a key transcriptional regulator contributing to highly cooperative networks among non-myocyte subtypes during zebrafish heart regeneration

first: LI

last: QIAN

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

overall_design: Refer to individual Series


title: RNA-sequencing to idendify axon RNAs in dentate gyrus granule cells, dorsal root ganglion cells and retinal ganglion cells

city: Shenzhen

first: Zhuoxuan

state: Guangdong

address: No. 1088 Xueyuan Avenue, Nanshan District

institute: Southern University of Science and Technology

summary: To analyze axon transcriptome of dentate gyrus granule cells, dorsal root ganglion cells and retinal ganglion cells, we perfomed axon RNA sequencing.Neurons were cultured in microfluidic chambers and axons were isolated. Total RNA of axons was collected separately and subjected to library construction using M01440v2 NuGEN Trio RNA-seq kit. After sequencencing,we used TPM method to normalize RNA-seq reads.

overall_design: Three axon samples from different cells as experimental group.

first: Jun

first: Sheng-Jian

last: Ji


title: Effect of SRSF1 depletion on FANCD2 mRNA and isoform expression and effect of FANCD2 depletion or expression of SRSF1 mutants on splicing

city: NEW HAVEN

first: MANOJ

last: PILLAI

state: CT

address: 300 GEORGE STREET #786

institute: YALE UNIVERSITY

summary: To investigate the cooperative function of FANCD2/SRSF1 complex in the regulation of R-loops, we performed gene expression, isoform and splicing analysis in Hela cells depleted of SRSF1 or expressing SRSF1 mutants and FA-D2 mutant (FA-D2) and wild type (FA-D2+FANCD2) cells.

overall_design: FANCD2 gene expression and isoform analysis of RNA-seq  data for HeLa cells depleted for SRSF1. Differential splicing analysis of RNA-seq data for HeLa cells expressing  SRSF1 mutants or FA-D2 mutant (FA-D2) and wild type (FA-D2+FANCD2) cells.

first: Ane

last: Olazabal

first: Manoj

last: Pillai

first: Gary

last: Kupfer


title: ATF4-SLC7A11-GSH axis mediates the acquisition of immunosuppressive properties by activated CD4+ T cells in low arginine condition

status: Public on Feb 25 2024

city: Hangzhou

first: Meng

last: Xia

address: 866 Yuhangtang ROAD

institute: Zhejiang University

summary: The tumor microenvironment (TME) is restricted in metabolic nutrients including the semi-essential amino acid arginine. While complete arginine deprivation causes T cell dysfunction, it remains unclear how arginine levels fluctuate in the TME to shape T cell fates. Here, we found that the 20μM low arginine condition, as present in multiple TMEs, confers upon activated T cells Treg-like immunosuppressive capacities. In vivo mouse tumor models and human scRNA-Seq datasets reveal positive correlations between low arginine condition and intratumoral Treg accumulation. Mechanistically, low-arginine activated T cells engage in metabolic and transcriptional reprogramming, using the ATF4-SLC7A11-GSH axis, to preserve their suppressive function. These findings improve our understanding of the role of arginine in human T cell biology with potential applications for immunotherapy strategies.

overall_design: human CD4+ T cells activated in full arginine (FULL), 20μM low arginine (LOW) or no arginine (NA) conditions for 7 days, and the cells were collected for RNA-seq

first: Ziqi

last: ZOU

first: Qian

last: CHENG

first: Jiajie

last: ZHOU

first: Chenyao

last: GUO

first: Qingqing

last: WANG

last: XIA


title: Gene regulatory basis of bystander activation in CD8+ T cells (RNA-seq)

first: Andrew

last: Grimson

summary: The immune system is stratified into layers of specialized cells with distinct functions.  Recently, Lin28b was shown to serve as a master regulator of fetal lymphopoiesis and program the development of more innate-like lymphocytes in early life. However, it is still unclear how Lin28b alters the function of fetal-derived lymphocytes and protects the host against infection. In this report, we examined how Lin28b transcriptionally and epigenetically programs murine CD8+ T cells for innate immune defense and translated our key findings to human CD8+ T cells.  We found that Lin28b operates as a gatekeeper, opening the door to a hidden diversity of phenotypes that are unveiled upon stimulation with innate cytokines.  In particular, Lin28b promotes a transcriptionally and functionally diverse pool of cells through chromatin remodeling.  As a result, neonatal CD8+ T cells are able to deploy a bet-hedging immune strategy and protect the host against a wide range of unrelated pathogens.

overall_design: Gene expression profiling of gBT-I TCR tg adult, neonatal and Lin28b Tg adult CD8+ T cells treated with IL-2 or IL-12/18 by high-throughput sequencing, in 2 or 6 replicates, using Illumina NextSeq500.

first: Neva

last: Watson

first: Ravi

last: Patel

first: Brian

last: Rudd


title: Non-preferential, but detrimental accumulation of macrophages with clonal hematopoiesis-driver mutations in cardiovascular tissues

city: Freiburg

first: Ingo

last: Hilgendorf

address: Hugstetter Straße 55

department: Department of Cardiology and Angiology

country: Germany

institute: UNIVERSITY HOSPITAL FREIBURG University Heart Center Freiburg-Bad Krozingen

summary: To identify CHIP mutation frequency in myeloid cells in blood and in cardiovascular tissues; To compare gene expression profiles of blood or cardiovascular tissue myeloid cells from CHIP mutation carriers and non-carriers.

overall_design: Blood myeloid cells, blood lymphocytes, myeloid cells from human carotid plaque or heart tissue were isolated using fluorescence-activated cell sorting(FACS) in bulk. DNA and RNA of the same sorted cells were isolated. The DNA were used for quantifying the size of CHIP mutated clones of each cell type acquired from the CHIP mutation carriers. The RNA of myeloid cells from carriers and matched non-carriers were subjected to RNA-seq for gene expression profile comparison.

first: Tsai-sang

last: Dederichs


title: Gene regulatory basis of bystander activation in CD8+ T cells (ATAC-seq)

overall_design: Profiling chromatin landscape of gBT-I TCR tg adult, neonatal and Lin28b Tg adult CD8+ T cells treated with IL-2 or IL-12/18 by high-throughput sequencing, in 2, 3 or 6 replicates, using Illumina NextSeq500.


title: Injured Mouse Kidney

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

institute: Cedars Sinai Medical Center

summary: Mouse kidneys were harvested at either 48 hours or 10 days post injury and subjected to single-cell RNA sequencing

overall_design: We performed scRNA-seq on samples of mouse kidneys at two time points post-injury.

first: Sanjeev

last: Kumar

first: Alex

last: Rajewski


title: Determinants of chromosome organization: Loop extrusion or boundary:boundary pairing?

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

summary: Two different models have been proposed to explain how the endpoints of chromatin looped domains (“TADs”) in eukaryotic chromosomes are determined. In the first a cohesin complex extrudes a loop until it encounters a boundary element roadblock, generating a stem-loop (and an unanchored loop). In this model, boundaries are functionally autonomous: they have an intrinsic ability to halt the movement of incoming cohesin complexes that is independent of the properties of neighboring boundaries. In the second, loops are generated by boundary:boundary pairing. In this model, boundaries are functionally non-autonomous, and their ability to form a loop depends upon how well they match with their neighbors. Moreover, unlike the loop-extrusion model, pairing interactions can generate both stem-loops and circle-loops. We have used a combination of Micro-C to analyze how TADs are organized and experimental manipulations of the even-skipped TAD boundary, homie, to test the predictions of the “loop-extrusion” and the “boundary-pairing” models. Our findings are incompatible with the loop-extrusion model and instead suggest that endpoints of TADs in flies are determined by a mechanism in which boundary elements physically pair with their neighbors, either head-to-head, or head-to-tail.

overall_design: Homie transgenic cassettes have been placed at an attP target site  -142kb upstream of eve. Micro-C experiments were done in biological duplicates.

first: Xinyang

last: Bing

first: Miki

last: Fujioka

first: James

last: Jaynes


title: Single-cell technology reveals the heterogeneity of adipose tissue in human spinal canal

city: Changsha

first: Haicheng

last: Wen

state: State...

address: Hunan

institute: Central South University

summary: In order to study the heterogeneity of adipose tissue in the spinal canal, we used single-cell sequencing to sequence the subcutaneous fat and adipose tissue in the spinal canal of patients with lumbar surgery at different ages.

overall_design: We used data obtained by RNA-seq to analyze the gene expression profiles of adiposity derived from subcutaneous, intraspinal fat in the back at three different ages.

first: Yong

last: Cao


title: Uncovering the transcriptional molecular dynamics of shelf life extension and system acquired resistance induction to Fusarium pallidoroseum in melon fruits by the use of pulsed-light

city: Rio de Janeiro

first: Luis

middle: Willian

last: Pacheco Arge

state: Rio de Janeiro

address: Av. Carlos Chagas Filho, 373

department: Genetica

country: Brazil

institute: UFRJ

summary: Melon is a globally commercialized fruit, and Fusarium rot disease poses a significant threat to post-harvest losses. The conventional use of fungicides raises concerns about chemical residues, prompting exploration into alternative technologies such as Pulsed Light (PL). While PL has been effective in controlling infections in various fruits and vegetables, the precise physiological responses and molecular mechanisms in melon fruits remain incompletely understood. In this study, melon fruits infected with the Fusarium pallidoroseum were treated with different doses of PL (0, 6, 9, and 12 J cm-2), and the impact on both fungal control and fruit shelf life extension was investigated. The 9 J cm-2 dose emerged as the most effective in controlling fungal growth without causing damage, inducing beneficial responses. This optimal PL dose upregulated genes in the lignan biosynthesis pathway and the infection upregulated genes involved with systemic acquired resistance, triggered by the pipecolic acid. In this way, the PL treatment and the infection trigger a double mechanism of resistance in melon fruits. A second and third experiment focused on evaluating the extension of melon fruit shelf life and the safe manipulation window post-PL treatment. The results revealed an average shelf life extension of six days and a safe manipulation period of 24 hours. The extension in shelf life was associated with a deviation in information flux from the ethylene biosynthesis to upregulation of the polyamine biosynthesis pathway, which produces nitric oxide, a product that can inhibit ethylene biosynthesis and its action. Furthermore, the observed 24-hour safety period against fungal infection post-PL treatment was characterized as a memory response resistance caused by the upregulation of lignan biosynthesis, which is a potential and efficient alternative to chemical products like fungicides. Overall, this study provides insights into the transcriptional molecular mechanisms through which PL promotes systemic acquired resistance and extends the shelf life of melon fruits.

overall_design: Gene expression analysis of melon tissues (epicarp and mesocarp) infected and no infected with Fusarium and treated with different dosages of pulsed light (0, 6, 9, 12 J.cm-2).

last: Arge


title: Functional characterization of genetic variants associated with upper digestive cancers [ChIP-Seq]

city: Salt Lake City

first: Xiaoyang

last: Zhang

address: 1950 CIrcle of Hope

institute: University of Utah

summary: Using H3K27ac ChIP-seq assays followed by sequencing to identify regulatory elements in upper digestive cancers

overall_design: H3K27ac ChIP-seq was done to mark enhancer and promoter elements in de-identified primary tumors of gastric cancer and the adjacent normal tissues.

first: Swneke

last: Bailey


title: High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling [scRNA-seq]

city: Shanghai

first: Yuejun

last: Chen

state: Shanghai

address: 320 Yueyang Road

institute: Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences

summary: Deciphering patterns of connectivity between neurons in the mammalian brain is a critical step toward understanding brain function. Conventional imaging based neuroanatomical tracing methods identify area-to-area or sparse neuron-to-neuron connectivity patterns, but with extremely limited throughput. Recently developed barcode-based connectomics methods can efficiently map large numbers of single-neuron projections, but linking these data to single-cell transcriptomics remains a challenge. Here, we established a retro-AAV barcode-based multiplexed tracing method called MERGE-seq (Multiplexed projection neuRons retroGrade barcodE sequencing), which is capable of simultaneously characterizing the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets (AI, DMS, BLA, MD and LH). We found that projection-defined vmPFC neurons are molecularly heterogeneous, which are composed of different neuronal subtypes. We further identified transcriptional signatures of various dedicated and bifurcated vmPFC neurons, and verified Pou3f1 as the marker gene of neurons sending collateral axons to DMS and LH. Finally, we fitted our single-neuron connectome/transcriptome data into a machine learning-based model and revealed groups of genes that were predictive of certain projection pattern. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.

overall_design: Male adult C57BL/6 mice (8 weeks of age) were anesthetized intraperitoneally using pentobarbital sodium (10 mg/mL, 120 mg/kg b.w.) and unilaterally injected with rAAV-EGFP-BARCODE virus into five projection targets simultaneously. Barcode 0 sequences representing the AI target is: CTGCACCGACGCATT; barcode 1 sequences representing the DMS target is: GAAGGCACAGACTTT; barcode 2 sequences representing the MD target is: GTTGGCTGCAATCCA; barcode 3 sequences representing the BLA target is: AAGACGCCGTCGCAA; barcode 4 sequences representing the LH target is: TATTCGGAGGACGAC.  3 mice were performed scRNA-seq without FAC-sorting, cell pellets were resuspended and 48,000 cells were loaded into 3 lanes to perform 10X Genomics sequencingperformed scRNA. 3 mice with sorting and pooled together for scRNA-seq. Chromium Single Cell 3' Reagent Kits (v3) were used for transcriptome library preparation (10X Genomics). Libraries were sequenced on an Illumina Novaseq 6000 system.

first: Peibo

last: Xu

first: Jian

last: Peng

first: Tingli

last: Yuan

first: Zhaoqin

first: Ziyan

last: Wu

first: Chengyu

middle: T

last: Li

first: Zhen-Ge

last: Luo


title: Altered miRNA Expression in MSC-Derived Extracellular Vesicles Following Hydatid Antigen Stimulation

city: Urumqi

first: Zengru

last: Xie

state: Xinjiang

address: 137 Liyushan South Road

institute: The First Affiliated Hospital of Xinjiang Medical University

summary: This study investigates the impact of hydatid antigens on the miRNA expression profiles within extracellular vesicles (EVs) derived from mesenchymal stem cells (MSCs). By stimulating MSCs with echinococcus granulosus protoscoleces (ESPs), hydatid cyst fluid (HCF), and particles from the laminated layer (pLL), we aim to uncover the changes in miRNA expression and their potential roles in modulating immune responses and osteogenic differentiation. Through high-throughput sequencing, differential expression analysis, and subsequent bioinformatics analyses, we identify key miRNAs and their target genes involved in these processes. Our findings provide insights into the complex interplay between parasitic infections and host cell responses, highlighting the therapeutic potential of MSC-derived EVs in treating hydatid disease.

overall_design: 1. **Isolation and Culture:** Bone marrow-derived MSCs (BMSCs) are isolated and cultured in α-MEM medium. 2. **Stimulation:** BMSCs are treated with ESPs, HCF, or pLL at a concentration of 2 μg/ml for 48 hours. 3. **EV Isolation:** Extracellular vesicles are isolated from the cell culture supernatants using ultracentrifugation. 4. **RNA Extraction:** Total RNA is extracted from the isolated EVs using the Trizol method. 5. **Library Construction and Sequencing:** Small RNA libraries are constructed using the NEBNext Small RNA Library Prep Kit and sequenced on the Illumina NovaSeq platform. 6. **Data Analysis:** Sequencing data are processed for quality control, miRNA identification, and differential expression analysis. Bioinformatics analyses including GO and KEGG enrichment, PPI network construction, and transcription factor-miRNA network analysis are performed. 7. **Validation:** Differentially expressed miRNAs and their target genes are validated using quantitative PCR and Western blot analysis. 8. **Functional Assays:** The effects of ESPs, HCF, and pLL on MSC osteogenic differentiation and immune modulation are assessed.


title: Hi-C and Capture Hi-C maps in WT and Zfp661 knockout mESCs

status: Public on Feb 24 2024

city: Bethesda

first: Jinpu

last: Jin

address: Building 6B, Room 2B-211, 6 Center Drive

institute: NICHD

summary: In this assay, we aimed to investigate the impacts of ZFP661 on the permeability of CTCF barriers to chromatin interactions. To achieve this, we generated high-resolution Hi-C maps using WT and Zfp661 knockout (KO) mESCs. Our findings demonstrate that ZFP661 suppresses the trapping of cohesin at the CTCF barriers and modulates their permeability.

overall_design: We compared the alteration of insulation scores at CTCF barriers that are co-occupied with ZFP661 and those that are not, and also evaluated the transition between the two types of competitive interactions (being trapped at the CTCF barriers and those passing over them) after the loss of Zfp661. Each genotype was represented by two biological replicates.

first: Todd

last: Macfarlan


title: ChIP-seq data in WT and Zfp661 knockout E16.5 mouse forebrains

summary: In this assay, we aimed to investigate the occupancy of ZFP661 and CTCF at the clustered Pcdh locus during mouse brain development.

overall_design: We determined the binding signals of ZFP661 and CTCF in E16.5 mouse forebrains. Anti-HA ChIP-seq was performed in endogenously tagged ZFP661-3HA E16.5 forebrains and untagged controls. ChIP-seq for CTCF was performed in WT and Zfp661 knockout (KO) E16.5 forebrains. Each type included two biological replicates.


title: SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis II

city: London

first: James

last: Opzoomer

address: 72 Huntley Street

department: Department of Oncology

country: United Kingdom

institute: University College London

summary: We present SIGNAL-seq (Split-pool Indexing siGNalling AnaLysis by sequencing): a multiplexed split-pool combinatorial barcoding method that simultaneously measures RNA and post-translational modifications (PTMs) in fixed single cells from 3D solid-tumour models. SIGNAL-seq PTM measurements are equivalent to mass cytometry and RNA gene detection is analogous to split-pool barcoding scRNA-seq. By measuring both mRNA ligand-receptor pairs and PTMs in single cells, SIGNAL-seq simultaneously reveals both inter- and intra-cellular signalling in tumour microenvironment organoids.

overall_design: SIGNAL-seq was performed on CRC patient derived organoids (PDOs) +/- CAFs in 3D, and treated +/- SN-38 chemotherapy. This patient-derived 3D model system provides a dynamic range of cell-fates driven by both inter-cellular communication and chemotherapy. Further information on the SIGNAL-seq barcoding layout and processed data can be found at: https://github.com/TAPE-Lab/SIGNAL-seq

first: J

first: R

last: O'Sullivan

last: Sufi

last: Madsen

first: X

last: Qin

first: E

last: Basiarz

first: C

last: Tape


title: Genome-wide mapping of RNA polymerase active sites in DOT1L-depleted HCT116 cells by PRO-seq analysis

city: Seoul

first: Junyoung

last: Park

address: 84, Heukseok-ro

department: Department of Life Science

country: South Korea

institute: Chung-Ang University

summary: Precision nuclear run-on sequencing (PRO-seq) approach was adopted to evaluate the effect of DOT1L in regulating transcription and RNA polymerase active sites in HCT116 cells

overall_design: Control HCT116 cells (shNC) and DOT1L-knockdown HCT116 cells (shDOT1L) were used in this experiment

first: Yujin

first: Sang

last: Seo


title: Effects of potassium supplementation and depletion in the development of salt-sensitive hypertension in male and female rats

city: Tampa

first: Alexander

last: Starushchenko

state: FL

address: 560 Channelside Dr

department: Molecular Pharmacology & Physiology

institute: University of South Florida, College of medicine

summary: The inverse effects that dietary sodium and potassium have on blood pressure have been known for some time. High sodium consumption is detrimental, while potassium supplementation is known to be beneficial, and the ratio of sodium/potassium consumption is also very important to consider when determining how these electrolytes affect salt-induced hypertension; however, the mechanisms behind the beneficial effects of potassium are still not yet entirely established. Inwardly rectifying potassium (Kir) channels have been shown to play a major role in potassium transport and homeostasis in the kidney and might contribute to these effects. Here we aimed to examine how different variations in the sodium/potassium ratio affect the development of salt-sensitive hypertension and how channels and transporters in the kidney are altered to accommodate these changes. We hypothesize that these diets will affect the development of salt-sensitive hypertension, and that Kir channels will play a major role in the renal adaptations to varying intakes of potassium

overall_design: Both male and female animals were used for the study. At 8 weeks of age animals were implanted with a telemeter to measure chronic blood pressure. After a few days of recovery animals were switched to one of three high salt (HS, 4% NaCl) diets, potassium deficient (DK), normal potassium (NK, 0.36% K+), and high potassium (HK, 1.41% K+). After 5 weeks on the diets, animals were anesthetized with isoflurane and kidneys were collected. Kidney cortex from one kidney was snap-frozen and used for transcriptomic analysis for animals of both sexes and for each diet.

last: Staruschenko


title: Human Podocytes Develop “Names” to Practice Self-Avoidance

city: Rockville

first: David

middle: Lee

last: Gerhold

state: MD

address: 9800 Medical Center Drive

institute: NCATS/NIH

summary: Podocyte effacement and loss characterizes glomerulopathies such as diabetic nephropathy, lupus, and glomerular toxicity. Human primary podocyte-like epithelial cells cultured from urine (ECU) were characterized as a window to understand podocyte regeneration in these glomerulopathies. Cytokines TNF, and VEGF stimulated regrowth, whereas FGF-1 and IL1 inhibited growth, consistent with other podocyte or parietal epithelial cell models. Review of published micrographs indicated that podocyte foot processes in rodent kidneys interdigitated exclusively with foot processes from other cells, suggesting podocytes practice self-avoidance. In culture, ECU avoided close interactions with other cells arising from the same clone, until enough cells grew for the culture to become confluent. In contrast, ECU derived from multiple clones associated actively to form contiguous monolayers. Gene expression profiling of eight clonal ECU colonies using RNA sequencing revealed that each colony expressed a highly variable profile of the 53 Protocadherin genes. Variable combinations of the 53 Protocadherin PCDHA-, PCDHB-, and PCDHG- gene products are known to act homophilically to direct self-avoidance interactions in human neurons, so PCDH- genes are postulated to govern self-avoidance similarly in podocytes. Such protocadherin profiles could be considered cell names. Transcriptional profiles of ECUs suggest they may represent intermediate stages of Parietal Epithelial Cells (PECs) differentiating into podocytes. They further suggest that each podocyte practices self-avoidance, interdigitating selectively with other cells in the glomerulus. To enable further investigation of multi-clonal podocyte interactions, five podocyte clones were immortalized using temperature-sensitive SV40 Large T antigen.  These results suggest that non-self interdigitation of new podocytes with remnant podocytes may facilitate replacement of dying podocytes and re-establishment of a functional filtration barrier.

overall_design: Eight primary colonies were isolated, each representing a clonal epithelial cell line from human urine.  Primary ECU colonies containing approximately 50,000 – 150,000 cells were harvested 2-3 weeks after initial plating. Total RNA was isolated using Qiagen RNEasy Plus Mini kits (Qiagen, Hilden, Germany; Cat#:74106) including DNAse treatment to remove genomic DNA.  Total RNA samples were selected for polyA+ transcripts using the Qiagen Oligotex midi kit. Resulting samples were depleted of ribosomal sequences using two rounds of RiboZero Gold™, Illumina Inc. RNAseq sequencing was performed using the TruSeq® kit and Illumina HiSeq 2500 instrument by the Frederick National Laboratories Sequencing Core, (Frederick MD, USA).

first: John

last: Braisted

last: Kuo


title: Analysis of the effect of exogenous auxin on the regulatory relationship between miRNA and its target genes in rose using high-throughput sequencing [RNA-seq]

city: Beijing

first: Yi-Qing

last: Wang

address: Beijing University of Agriculture Street

institute: Beijing University of Agriculture

summary: Rose (Rosa hybrida L.) is a major cut flowers in the world. Studying the molecular mechanism of auxin regulation in growth is of great significance for enhancing the understanding of the growth and development processes of rose and informing accurate exogenous auxin application in rose production. However, the response mechanism of rose to miRNA-mediated auxin signal transduction is unclear. In this study, rose plants were treated with IAA, and 75 known miRNAs and 168 novel miRNAs were identified by small RNA sequencing. Among them, 19 known miRNAs and 42 miRNAs were differentially expressed. Many differential miRNAs demonstrated staged responses to auxin treatment. The targeted relationship between miRNA and key transcription factors regulated by auxin in rose was analyzed, and the target genes in the ARF family and AUX/IAA family were screened. By using quantitative real-time PCR(qRT-PCR) to verify the expression patterns of the miRNA regulating the auxin signal transduction pathway and its target gene, we found that miR156a, miR160a, miR164a, miR167d, miR396b-3p, novel_miR_189, novel_miR_74, novel_miR_8, and novel_miR_207 interacted negatively with the ARF family, and miR390a-3p and novel_miR_101 interacted negatively with the AUX/IAA family. These results provide a theoretical basis for further studies on the auxin regulatory mechanisms in rose.

overall_design: we comprehensively analyzed at the transcriptome and small RNA levels by using high-throughput sequencing technology. An abundance of information at the transcriptional and miRNA regulation levels was obtained, and the genes and miRNAs related to auxin transcription regulation were screened.

first: Yiqing

first: Rong

last: Ding

first: Kezhong

last: Zhang

first: Jinteng

last: Cui


title: Zbtb46 coordinates tumor angiogenesis and tumor immunity to control tumor outcome

city: Palo Alto

first: Christoph

last: Thaiss

address: 3181 Porter Dr.

department: Immunology and Pathology

institute: Arc Institute

summary: Tumor-angiogenesis and -immunity play critical roles in cancer progression and outcome. The existence of an inverse correlation hints at common regulatory mechanism(s) controlling these two processes. Here, we report that Zbtb46, a repressive transcription factor and widely accepted marker for classical dendritic cells (DCs), constitutes one such regulatory mechanism in the tumor microenvironment (TME) and is downregulated in both DCs and endothelial cells (ECs) by tumor-derived factors to facilitate robust tumor growth. This downregulation leads to the development of hallmark features of a pro-tumor environment, including dysfunctional vasculature and immunosuppressive cell accumulation. Analysis of cancer patient data revealed a similar association of a low ZBTB46 expression with an immunosuppressive TME and a worse prognosis. In contrast, upon enforced Zbtb46 expression, the hallmark TME features are mitigated, and tumor growth is restricted. Mechanistically, Zbtb46-deficient ECs were highly angiogenic, and Zbtb46-deficient bone-marrow precursors upregulated Cebpb and showed enhanced myeloid lineage output. Conversely, Zbtb46-maintenance normalizes ECs and, by suppressing Cebpb, skews the polarization of bone-marrow precursors towards more DCs and fewer macrophages, leading to an immune-hot TME. Remarkably, Zbtb46 mRNA treatment synergized with anti-PD1 immunotherapy to improve tumor management in pre-clinical models. These findings identify Zbtb46 as a common regulatory mechanism for angiogenesis and for non-hematopoietic-stem-cell-mediated myeloid lineage skewing in cancer and suggest that maintaining its expression could have therapeutic benefits.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type, Zbtb46 knockdown, and enforced Zbtb46 overexpression murine cardiac endothelial cells (MCEC).

first: Madhav

last: Subramanian

first: Kyunghee

last: Choi


title: SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis

first: James

last: Opzoomer

summary:
We present SIGNAL-seq (Split-pool Indexing siGNalling AnaLysis by sequencing): a multiplexed split-pool combinatorial barcoding method that simultaneously measures RNA and post-translational modifications (PTMs) in fixed single cells from 3D models. SIGNAL-seq PTM measurements are equivalent to mass cytometry and RNA gene detection is analogous to split-pool barcoding scRNA-seq. By measuring both mRNA ligand-receptor pairs and PTMs in single cells, SIGNAL-seq can simultaneously un- cover inter- and intra-cellular regulation of tumour microenvironment plasticity.

This SuperSeries is composed of the SubSeries listed below.

overall_design: Refer to individual Series


title: SIGNAL-seq: Multimodal Single-cell Inter- and Intra-cellular Signalling Analysis I

overall_design: HELA spheroids were grown in 96-well Eplasia plates for 48 hours in DMEM high-glucose with supplemented with 2 mM L-Glutamine and 10% FBS. Spheroids were serum starved for 4hrs and pre-treated with inhibitors 100nM Trametinib and 500nM GDC0941 Pictilisib or vehicle (DMSO) for 10 minutes prior to growth factor treatment. Spheroids were then treated for 30 minutes with 100nM Human IGF1 and 100nM Human EGF or vehicle (water) before fixation in-situ. Spheroids were fixed in-situ using an adapted SPLiT-seq protocol and dispersed by mechanical dissociation using a TissueGrinder. Single-cells were permeabilised using an adapted SPLiT-seq protocol and frozen before processing with SIGNAL-seq. The RNA and ADT libraries were sequenced separately. Further information on the SIGNAL-seq barcoding layout and processed data can be found at: https://github.com/TAPE-Lab/SIGNAL-seq

first: J

first: R

last: O'Sullivan

last: Sufi

last: Madsen

first: X

last: Qin

first: E

last: Basiarz


title: Human myofiber-enriched aging-induced lncRNA FRAIL1 promotes muscle atrophy

city: Iowa City

first: Matthew

last: Miller

state: IA

address: 375 Newton Road

institute: University of Iowa

summary: The loss of skeletal muscle mass during aging is a significant health concern linked to adverse outcomes in older individuals. Understanding the molecular basis of age-related muscle loss is crucial for developing strategies to prevent or reverse this debilitating condition. Long non-coding RNAs (lncRNAs) are a largely uncharacterized class of biomolecules that have been implicated in cellular homeostasis and dysfunction across a wide variety of tissues and cell types. To identify lncRNAs that might contribute to skeletal muscle aging we screened for lncRNAs whose expression was altered in vastus lateralis muscle from older compared to young adults. We identified FRAIL1 as an aging-induced lncRNA with high abundance in human skeletal muscle. In a cohort of healthy young and older adults, skeletal muscle FRAIL1 was most strongly expressed in older females and negatively associated with measures of muscle strength and mass. Forced expression of FRAIL1 in mouse tibialis anterior muscle elicits a dose-dependent reduction in skeletal muscle fiber size that is independent of changes in muscle fiber type. Furthermore, this reduction in muscle size is dependent on an intact region of FRAIL1 that is highly conserved across non-human primates. Unbiased transcriptional and proteomic profiling of the effects of FRAIL1 expression in mouse skeletal muscle revealed widespread changes in mRNA and protein abundance that recapitulate age-related changes in pathways and processes that are known to be altered in aging skeletal muscle. Taken together, these findings shed light on the intricate molecular mechanisms underlying skeletal muscle aging and implicate FRAIL1 in the reduction of muscle mass during this process.

overall_design: One tibialis anterior (TA) muscle per mouse (n=6) was transfected with 10 μg of empty plasmid (pcDNA3), and the contralateral TA in each mouse was transfected with 10 μg of full length human FRAIL1 lncRNA expressing plasmid. Seven days post-transfection, bilateral TAs were harvested and subjected to RNA-seq analysis.

first: Ian

middle: R

last: Lanza


title: Persistent Neurological Deficits in Mouse PASC Reveal Antiviral Drug Limitations

status: Public on Feb 23 2024

city: IOWA CITY

first: Abhishek

last: Verma

address: 3-730, Bowen Science Building, 51 Newton Road

department: Department of Microbiology and Immunology

institute: The University of Iowa

summary: PASC (Post-Acute Sequelae of COVID-19) involves many organs, including most prominently the central nervous system. Most studies of PASC in laboratory animals were performed in the context of mild disease, but higher PASC prevalence is observed in patients with severe disease.    Here, to investigate the basis of chronic neurological disease, we infected mice with mouse-adapted SARS-CoV-2 that causes severe respiratory disease but does not infect the brain. We assessed long-term effects on olfactory and substantia nigra (SN) function. While anosmia resolved within a few days, we observed long term loss of tyrosine hydroxylase (TH) expression in the olfactory bulb glomeruli, indicating chronically altered function of olfactory sensory neurons. These changes were accompanied by increased inflammation suggesting the involvement of the host immune response in anosmia-related changes. We also observed decreased neurotransmitter expression in the substantia nigra (SN) accompanied by increased levels of proinflammatory cytokines and neurobehavioral changes. Microglia have been implicated in long term changes in SARS-CoV-2 infected mice and in human neurodegenerative disease. RNAseq analysis of mouse brain microglia isolated several months after infection demonstrated key roles for these cells in ongoing pathogenesis. Finally, we showed that early treatment with antivirals (nirmatrelvir and molnupiravir) reduced virus titer and inflammation in the lung but did not prevent neurological abnormalities. Together these results show that these mice will be useful for probing the role of SARS-CoV-2 in the development of neurodegenerative disease, an aspect of disease not amenable to study in patients and that neurological PASC is not ameliorated by anti-viral therapy.

overall_design: Comparative gene analysis between Mock and 100dpi mouse brain CD11b+ cells

first: Stanley

last: Perlman

first: Juan

middle: E

last: Abrahante Lloréns


title: Cancer-associated fibroblasts rewire the estrogen receptor response in luminal breast cancer, enabling estrogen independence

city: Lund

first: Kristian

last: Pietras

address: Sheelevägen 2

department: Division of Translational Cancer Research

country: Sweden

institute: Lund University

summary: Advanced breast cancers represent a major therapeutic challenge due to their refractoriness to treatment. Cancer-associated fibroblasts (CAFs) are the most abundant constituents of the tumor microenvironment and have been linked to most hallmarks of cancer. However, the influence of CAFs on therapeutic outcome remains largely unchartered. Here, we reveal that spatial coincidence of abundant CAF infiltration with malignant cells was associated with reduced estrogen receptor (ER)-α expression in luminal breast tumors. Notably, CAFs mediated estrogen-independent tumor growth by selectively regulating ER-α signaling. Whereas most prototypical estrogen-responsive genes were suppressed, CAFs maintained gene expression related to therapeutic resistance. A high-throughput drug screen in co-cultures identified effector pathways involved in the CAF-induced regulation of ER-α signaling. Among these, the transforming growth factor-β and the janus kinase signaling cascades were validated as actionable targets to counteract the CAF-induced ER-α modulation. Finally, genes that were downregulated in cancer cells by CAFs were predictive of poor response to endocrine treatment. In conclusion, our work reveals that CAFs directly control the luminal breast cancer phenotype by selectively modulating ER-α expression and transcriptional function, and further proposes novel targets to disrupt the crosstalk between CAFs and tumor cells to reinstate treatment response to endocrine therapy in patients.

overall_design: Gene expression profiling (RNA-seq) and differentail genes expression analyses of MCF-7 cells following estrogen stimulation (after 6 and 24 hours) either alone or precultured in transwells with CAFs (for 48 hours). MCF-7 cells alone and without estrogen stimulation is the control condition. In total 24 samples divided in 6 different conditions/timepoints, each one with 4 replicates.

first: Steven

last: Reid

first: Jessica

last: Pantaleo

first: Paulina

last: Bolivar

first: Matteo

last: Bocci

first: Jonas

last: Sjölund

first: Mikkel

last: Morsing

first: Eugenia

last: Cordero

first: Sara

last: Larsson

first: Maria

last: Malmberg

first: Brinton

last: Seashore-Ludlow


title: Cholesterol 25-hydroxylase mediates neuroinflammation and neurodegeneration in a mouse model of tauopathy

city: St. Louis

first: Jinsheng

last: Yu

state: MO

address: 660 S. Euclid Ave.

department: Genetics

institute: Washington University School of Medicine

summary: Alzheimer’s disease (AD) is characterized by amyloid plaques and neurofibrillary tangles in addition to neuroinflammation and changes in brain lipid metabolism. Recent findings have demonstrated that microglia are key drivers of neurodegeneration in tauopathy mouse models. A subset of microglia referred to as disease-associated microglia (DAM) display gene signatures signifying changes in proinflammatory signaling and lipid metabolism in mouse models of amyloid and tau pathology. Ch25h is a DAM gene encoding cholesterol 25- hydroxylase that produces 25-hydroxycholesterol (25HC), a known modulator of inflammation as well as lipid metabolism. However, whether Ch25h influences tau-mediated neuroinflammation and neurodegeneration is unknown. Here, we show that in the absence of Ch25h and the resultant reduction in 25HC there is strikingly reduced age-dependent neurodegeneration and neuroinflammation in the hippocampus and entorhinal/piriform cortex of PS19 mice, which express the P301S mutant human tau transgene. Transcriptomic analyses of bulk hippocampal tissue and single nuclei revealed that Ch25h deficiency in PS19 mice strongly suppressed proinflammatory cytokine and chemokine signaling in microglia and restored sterol synthesis. Our results suggest a key role for Ch25h/25HC in potentiating proinflammatory signaling to promote tau-mediated neurodegeneration. Ch25h may represent a novel therapeutic target for primary tauopathies, AD, and other neuroinflammatory diseases.

overall_design: The PS19 transgenic mouse model overexpresses 1N4R human microtubule-associated protein tau (MAPT) driven by the PrP promoter, containing the P301S mutation that causes a familial form of frontotemporal dementia. The PS19 (T) mice were crossed to the Ch25h knockout (CKO) mice to generate wild type (WT), Ch25h KO (CKO), T and TCKO mice. Animals were perfused with PBS. Left hemisphere was fixed in 4% paraformaldehyde for immunostaining. Hippocampus from the right hemisphere was flash frozen and stored at -80˚C until RNA isolation using Zymo Research Quick-RNA MiniPrep Plus kit (Cat. #: R1058).

first: Danira

last: Toral-Rios

first: Justin

last: Long

first: Jason

last: Ulrich

first: Michel

last: Strickland

first: Xianlin

last: Han

first: David

last: Holtzman

last: Paul

first: Anil

middle: G

last: Cashikar


title: Expression of miRNAs in mice skin damaged by ultraviolet

city: Qingdao

first: Chengwen

last: Dong

address: Jiangsu road 16

institute: affiliated hospital of Qingdao University

summary: Correlated to many vulgaris and intractable skin diseases, photo damage is one of the challenges of skin caused by the ultraviolet. Modulation of miRNAs on gene expression in photo damage have attracted attentions recently. We established a photo damaged Kunming (KM) mouse skin model by UVA irradiation of 89.88 J/cm^2 in total. The skin tissues of the back of the mice were harvested, and the expression of miRNA was assayed. Difference in expression of miRNA was assayed and calculated. The target genes of the miRNA were predicted, and the gene function was speculated by the enrichment analysis. Our research has revealed miRNAs like miR-671-5p, miR-29a-3p, and miR-700-3p may play vital roles in the interaction with key genes. More evidence about interaction between genes and miRNAs and the downstream signal pathways need to be explored.

overall_design: Mice in trial group were irradiated by UVA every other day for 4 months, and the irradiation dosage is 89.88 J/cm^2 in total.


title: Characterization of caffeine response regulatory variants in vascular endothelial cells

city: Detroit

first: Roger

last: Pique-Regi

state: Michigan

address: 540 E Canfield (Scott Hall 3309)

institute: Wayne State University

summary: Genetic variants in gene regulatory sequences can modify gene expression and mediate the molecular response to environmental stimuli. In addition, genotype–environment interactions (GxE) contribute to complex traits such as cardiovascular disease. Caffeine is the most widely consumed stimulant and is known to produce a vascular response. To investigate GxE for caffeine, we treated vascular endothelial cells with caffeine and used a massively parallel reporter assay to measure allelic effects on gene regulation for over 43,000 genetic variants. We identified 665 variants with allelic effects on gene regulation and 6 variants that regulate the gene expression response to caffeine (GxE, false discovery rate [FDR] < 5%). When overlapping our GxE results with expression quantitative trait loci colocalized with coronary artery disease and hypertension, we dissected their regulatory mechanisms and showed a modulatory role for caffeine. Our results demonstrate that massively parallel reporter assay is a powerful approach to identify and molecularly characterize GxE in the specific context of caffeine consumption.

overall_design: MPRA to quantify RNA abundance for synthesized contructs transfected into HUVECs and treated with caffeine or vehicle control

first: Carly

last: Boye

first: Cynthia

last: Kalita

first: Anthony

last: Finley

first: Adnan

last: Alazizi

first: Julong

last: Wei

first: Xiaoquan

last: Wen

first: Francesca

last: Luca


title: Ploidy-specific transcriptomes shed light on the heterogeneous identity and metabolism of developing pericarp cells

city: Villenave d'Ornon

first: Pascal

middle: GP

last: Martin

address: 71 avenue Edouard Bourlaux

department: UMR1332 BFP

country: France

institute: INRAE

summary: Endoreduplication, during which cells increase their DNA content through successive rounds of full genome replication without cell division, is the major source of endopolyploidy in higher plants. Endoreduplication plays pivotal roles in plant growth and development and is associated with the activation of specific transcriptional programs that are characteristic to each cell type, thereby defining their identity. In plants, endoreduplication is found in numerous organs and cell types and especially in agronomically valuable ones, such as the fleshy fruit (pericarp) of tomato presenting high ploidy levels. We used the tomato pericarp tissue as a model system to explore the transcriptomes associated with endoreduplication progression during fruit growth. We confirmed that expression globally scales with ploidy level and identified sets of genes differentially expressed when comparing ploidy levels at a specific developmental stage. We found that non-endoreduplicated cells are defined by cell division state and cuticle synthesis while endoreduplicated cells are mainly defined by their metabolic activity changing rapidly over time. By combining this dataset with publicly available spatiotemporal pericarp expression data, we proposed a map describing the distribution of ploidy levels within the pericarp. These transcriptome-based predictions were validated by quantifying ploidy levels within the pericarp tissue. This in situ ploidy quantification revealed the dynamic progression of endoreduplication and its cell layer specificity during early fruit development. In summary, the study sheds light on the complex relationship between endoreduplication, cell differentiation, and gene expression patterns in the tomato pericarp.

overall_design: To investigate the molecular heterogeneity related to endoreduplication during tomato fruit development, we used pericarp from fruits at 6, 9 and 12 days post-anthesis (DPA). These timepoints were chosen because they correspond to an intense period of fruit enlargement, due to a high fruit growth rate, and with significant changes in ploidy levels, in particular the appearance of ploidy levels beyond 8C (16C, 32C and 64C), at the expense of 2C and 4C nuclei. We used Fluorescence Activated Nuclei Sorting (FANS) to collect nuclei from the pericarp according to their DNA content. At each timepoint, four populations of 100k nuclei, corresponding to the major ploidy classes (>85% of all nuclei), were obtained, namely 2C, 4C, 8C and 16C for 6DPA and 4C, 8C, 16C and 32C for 9 and 12DPA, their RNA was extracted and sequenced by RNA-seq

first: Edouard

last: Tourdot

first: Elie

last: Maza

first: Anis

last: Djari

first: Frédéric

last: Gévaudant

first: Christian

last: Chevalier

first: Julien

last: Pirrello

first: Nathalie

last: Gonzalez


title: Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila [hMeRIP]

city: Piscataway

first: Ruth

last: Steward

state: New Jersey

address: 190 Frelinghuysen Rd

department: Waksman Institute of Microbiology

institute: Rutgers University

summary: Modifications of mRNA, especially methylation of adenosine, have recently drawn much attention. The much rarer modification, 5-hydroxymethylation of cytosine (5hmC), is not well understood and is the subject of this study. Vertebrate Tet proteins are 5-methylcytosine (5mC) hydroxylases enzymes catalyzing the transition of 5mC to 5hmC in DNA and have recently been shown to have the same function in messenger RNAs in both vertebrates and in Drosophila. The Tet gene is essential in Drosophila because Tet knock-out animals do not reach adulthood. We describe the identification of Tet-target genes in the embryo and larval brain by determining Tet DNA-binding sites throughout the genome and by mapping the Tet-dependent 5hmrC modifications transcriptome-wide. 5hmrC-modified sites can be found along the entire transcript and are preferentially located at the promoter where they overlap with histone H3K4me3 peaks. The identified mRNAs are frequently involved in neuron and axon development and Tet knock-out led to a reduction of 5hmrC marks on specific mRNAs. Among the Tet-target genes were the robo2 receptor and its slit ligand that function in axon guidance in Drosophila and in vertebrates. Tet knock-out embryos show overlapping phenotypes with robo2 and are sensitized to reduced levels of slit. Both Robo2 and Slit protein levels were markedly reduced in Tet KO larval brains. Our results establish a role for Tet-dependent 5hmrC in facilitating the translation of modified mRNAs, primarily in developing nerve cells.

overall_design: To study the function of Tet in mRNA 5-hydroxymethyl-Cytosine modification, we did hMeRIP-seq (5-hydroxymethyl-cytosine RNA Immunoprecipitation sequencing) in Drosophila melanogaster 0-12h embryo and third instar larval brain fraction (LBF, containing larval brain and imaginal discs). The hMeRIP-seq was conducted on both wild type control and Tet deletion genotypes (Tetnull,  Delatte et.al., Science, 2016; Wang et.al. PloSONE, 2018) in larva samples. hMeRIP-seq was conducted on only 0-12h wild type embryo samples. RNA-seq was also performed at the same time with the hMeRIP-seq as input controls.

first: Badri

middle: N

last: Singh

first: Hiep

last: Tran

first: Joseph

last: Kramer

first: Elmira

last: Kirishenko

first: Neha

last: Changela

first: Fei

last: Wang

first: Yaping

last: Feng

first: Dibyendu

last: Kumar

first: Min

last: Tu

first: Jie

last: Lan

first: Martin

last: Bizet

first: François

last: Fuks


title: Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates axon guidance genes in Drosophila

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


title: Expression profiling of cartilage discs derived from Bone-marrow stromal cells.

city: Salzburg

first: Rodolphe

last: Poupardin

address: Strubergasse 22

country: Austria

summary: We analyzed the gene expression profile of chondrocytes (cartilage discs) differentiated from human bone-marrow stromal cells.

overall_design: Cartilage discs were derived from bone marrow stromal cells obtained from four different donors.


title: Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila [ChIP Embryo]

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for Tet-GFP fusion protein in Drosophila melanogaster 0-12h embryo and third instar larva brain fraction (LBF, larval brain and imaginal discs).


title: Knockdown of HSDL2 promotes the progression of cholangiocarcinoma and inhibits ferroptosis through STAT3/P53 pathway

city: Bengbu

first: Shuoshuo

last: Ma

state: Anhui

address: NO. 287, Changhuai Road, Longzihu district, Bengbu 233000, Anhui, China;

institute: The First Affiliated Hospital of Bengbu Medical College

summary: To investigate the  function of HSDL2 in the progression of cholangiocarcinom, we established RBE cell lines in which HSDL2 has been knocked down by lentiviral LV control carrying  HSDL2 knockdown interference plasmids. We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells(sh#NC and sh#HSDL2).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RBE cells（sh#NC and sh#HSDL2）.

first: ma

last: yang

first: qi

last: feiyu

first: lu

last: zheng

first: zhang

last: dengyong


title: Deciphering the determinants of recombinant protein yield across the human secretome

city: La Jolla

first: Nathan

last: Lewis

address: 9500 Gilman Dr.

institute: UCSD

summary: Mammalian cells are critical hosts for the production of most therapeutic proteins and many proteins for biomedical research. While cell line engineering and bioprocess optimization have yielded high protein titers of some recombinant proteins, many proteins remain difficult to express. Here we use systems biology methods to deciper the factors influencing yields in Chinese hamster ovary (CHO) cells as they produce proteins from the human secretome.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for a representative set of 95 samples each expressing a different human protein in CHO.

first: Johan

last: Rockberg


title: Selective effects of long-term glycolytic inhibition on B cells from autoimmune prone mice

city: Charlottesville

first: Loren

last: Erickson

state: Virginia

address: 345 Crispell Drive

department: Department of Microbiology, Immunology, and Cancer Biology

institute: University of Virginia

summary: To determine the metabolic requirements of key autoimmune populations in a spontaneous lupus-prone mouse model, we carried out RNA-seq of BXSB.Cg-Cd8atm1Mak Il15tmImx Yaa (Yaa DKO) mice following glycolytic inhibition with 2-deoxyglucose (2DG). Pre-symptomatic (6-week old) mice were used as controls for symptomatic (10-week old) mice with or without long-term (4-week) treatment with 2DG.  As a result, we found that 2DG-mediated glycolytic inhibition preferentially affected gene signatures of activated B cells and not T cells or other immune cell populations.

overall_design: Gene expression profiling by RNA-seq of spleen cells from untreated and 2DG-treated symptomatic Yaa DKO mice, and untreated pre-symptomatic Yaa DKO mice.

first: Chih-Hao

last: Chang

first: John

last: Wilson

first: Peter

last: Lipsky

first: Andrea

last: Daamen


title: Tet-dependent 5-hydroxymethyl-Cytosine modification of mRNA regulates the axon guidance genes robo2 and slit in Drosophila [ChIP LBF]

first: Ruth

last: Steward

first: Badri

last: Singh

first: Hiep

middle: H

last: Tran

first: Joseph

last: Kramer

first: Elmira

last: Kirishenko

first: Neha

last: Changela

first: Fei

last: Wang

first: Yaping

last: Feng

first: Dibyendu

last: Kumar

first: Min

last: Tu


title: Inhibition of ERK 1/2 pathway downregulates YAP1/TAZ signaling in human cardiomyocytes exposed to hyperglycemic conditions

city: Bryan

first: Irtisha

state: Texas

address: 8447 Riverside Pkwy

department: Cell Biology and Genetics

institute: Texas A&M University Health Science Center

summary: Hyperglycemia-mediated cardiac dysfunction is an acute initiator in the development of vascular complications, leading to cardiac fibrosis. To investigate the effects of hyperglycemia-mediated changes in cardiomyocytes, cells were cultured in-vitro under normoglycemic (5  mM or 25  mM D-glucose) and hyperglycemic (5 → 50  mM or 25 → 50  mM D-glucose) conditions, respectively. After 24-hours of hyperglycemic exposure, cells were collected for RNA-sequencing (RNA-seq) studies to further investigate the differentially expressed genes (DEG) related to inflammation and fibrosis in samples cultured under hyperglycemic-in comparison with normoglycemic-conditions. Western Blotting was done to evaluate the protein expression of YAP1/TAZ under hyperglycemia induced stress conditions, as it is known to be involved in fibrotic and vascular inflammatory-mediated conditions. RNA-seq revealed the DEG of multiple targets including matrix metalloproteinases and inflammatory mediators, whose expression was significantly altered in the 5 → 50  mM in comparison with the 25 → 50  mM condition. Western Blotting showed a significant upregulation of the protein expression of the YAP1/TAZ pathway under these conditions as well (5 → 50  mM). To further probe the relationship between the inflammatory extracellular-signal-regulated kinase (ERK 1/2) and its downstream effects on YAP1/TAZ expression we studied the effect of inhibition of the ERK 1/2 signaling cascade in the 5 → 50  mM condition. The application of an ERK 1/2 inhibitor inhibited the expression of the YAP1/TAZ protein in the 5 → 50  mM condition, and this strategy may be useful in preventing and improving hyperglycemia associated cardiovascular damage and inflammation.

overall_design: Analysis of differentially expressed genes in cardiomyocytes cultured in hyperglycemic conditions of 25–50 mM and 5–50 mM glucose in comparison with their respective (25 mM and 5 mM) controls. Each sample has a technical replicate.

first: Binata

last: Joddar

first: Carla

last: Loyola

first: Salma

middle: P

last: Ramirez

first: Abhinaya

last: Muruganandham


title: Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana

city: Gatersleben, Stadt Seeland, Germany

first: Hua

last: Jiang

address: Corrensstraße 3

institute: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben

summary: The nuclear matrix was identified as a nuclear fraction in eukaryotic cells that offers a supporting scaffold for chromatin. While the structure is known  in plant nuclei for decades, the distribution of regions attaching at plant nuclei, and how the nuclear matrix influences chromatin status is largely unkown. Here, we identify novel proteins, FRS7 (FAR1 RELATED SEQUENCE 7) and FRS12, attaching chromatin regions at the nuclear matrix in Arabidopsis thaliana. We found the above two proteins cooperate with AHL22 (AT-hook Motif Nuclear Localized 22) in repress hypocotyl elongation, by recruiting chromatin regions and histone deacetylases to the nuclear matrix and silence the genes. These findings shed light on understanding regulation and roles of the nuclear matrix influence in epigenetic and transcriptional regulation in Arabidopsis.

overall_design: We analyze the function of nuclear matrix attachment in transcriptional regulation by RNAseq and MARseq

first: Linhao

last: Xu

first: Shiwei

last: Zheng


title: In Chronic Kidney Disease Altered Cardiac Metabolism Precedes Cardiac Hypertrophy

first: Keith

middle: A

last: Hruska

address: 660 South Euclid Ave, Box 8208

department: Pediatrics

institute: Washington University in St. Louis

summary: Conduit arterial disease in CKD is an important cause of cardiac complications. Cardiac function in CKD has not been studied in the absence of arterial disease. In an Alport syndrome model bred not to have conduit arterial disease, mice at 225 days of life (dol) had CKD equivalent to human stage 4-5 CKD. PTH and FGF23 levels were one log order elevated, circulating sclerostin was elevated, and renal activin A was strongly induced. Aortic Ca levels were not increased and VSMC transdifferentiation was absent. The CKD mice were not hypertensive, and cardiac hypertrophy was absent. Freshly excised cardiac tissue respirometry (Oroboros) showed ADP-stimulated O2 flux was diminished from 52 to 22 pmol/mg (p=0.022). RNAseq of cardiac tissue from CKD mice revealed significantly decreased levels of cardiac mitochondrial oxidative phosphorylation genes. The data reported here show that cardiac mitochondrial respiration is impaired in CKD in the absence of conduit arterial disease. This is the first report of the direct effect of CKD on cardiac respiration.

overall_design: To investigate heart function in a murine model of chronic kidney disese, we aged collagen IV knockout and wild type animals to 225 days of life and then excised left ventricle tissue for respirometry and RNA-seq analysis. There are 8 wild type and 7 mutant CKD biological replicates.

first: MatthewJ

last: Williams

first: Sarah

last: White

first: Olga

last: Agapova

first: Yifu

last: Fang

first: Elliot

last: Klotz


title: Effect of depletion of Matn3 on  gene expression in mouse cerebral cortex after ischemia stroke

status: Public on Feb 22 2024

city: suzhou

first: Yong-Ming

last: Zhu

address: Renai Road Num 199

institute: soochow university

summary: The role of matrilin-3 in the brain, an extracellular matrix component in cartilage, is unknown. Here, we identify matrilin-3 decreased in reactive astrocytes but unchanged in neurons after ischemic stroke in animals. Importantly, it is declined in serum of patients with acute ischemic stroke. Genetic or pharmacological inhibition or supplementation of matrilin-3 aggravates or reduces brain injury, astrocytic cell death and glial scar, respectively, but has no direct effect on neuronal cell death. RNA-sequencing demonstrates that Matn3−/− mice display an increased inflammatory response profile in the ischemic brain, including the NF-κB signaling pathway. Both endogenous and exogenous matrilin-3 reduce inflammatory mediators. Mechanistically, extracellular matrilin-3 enters astrocytes via caveolin-1-mediated endocytosis. Cytoplasmic matrilin-3 translocates into the nucleus by binding to NF-κB p65, suppressing inflammatory cytokines transcription. Extracellular matrilin-3 binds to BMP-2, blocking BMP-2/Smads pathway. Thus, matrilin-3 is required for astrocytes to exert neuroprotection at least partially via suppressing astrocyte-mediated neuroinflammation.

overall_design: To investigate the mechanisms of matrilin-3 for suppressing glial scar formation, the RNA-seq analysis was performed in WT and Matn3 -/- mice. Mice were divided into 3 groups, sham_WT  group, IR_WT group, and IR_Matn3_ko group, and three mice per group. Comparative gene expression profiling analysis of RNA-seq data for IR_WT group and sham or IR_matn3_ko group .

first: Hui-Ling

last: Zhang

first: Xian-Yong

last: Zhou


title: Senescent fibroblasts and innate immune cell activation might play a role in the pathogenesis of elderly atopic dermatitis

city: Nanjing

first: Xiaokai

state: Jiangsu

address: No.12, Jiangwangmiao Street, Xuanwu District, Nanjing City, Jiangsu Province

institute: Dermatology Hospital of Chinese Academy of Medical Sciences

summary: Elderly atopic dermatitis is a subtype of AD defined by age (over 60 years), which has different clinical manifestations and distinct inflammatory patterns from AD in infants, children, and adolescents/adults. However, the molecular characteristics of elderly AD remain to be clarified.We sought to characterize the molecular features of skin lesions and peripheral blood mononuclear cells (PBMCs) in patients with AD across various age groups, focusing on elderly AD.We identified the molecular phenotypes of skin lesions and PBMCs in elderly individuals with AD. Fibroblasts, innate immune cells, and SASP might play important roles in the pathogenesis of elderly AD.

overall_design: Skin and PBMCs samples were used for RNA extraction and sequencing. Analysis of differentially expressed genes (DEGs), pathway enrichment, and gene set variation analysis (GSVA) were performed.


title: Plasma Sphingosine-1-Phosphate Orchestrates the Reverse Transendothelial Migration of Aortic Intimal Myeloid Cells

city: Toronto

first: Corey

last: Scipione

state: Ontario

address: 101 College Ave., TMDT 3-307 G,

department: Toronto General Hospital Research Institute

country: Canada

institute: University Health Network

summary: Background: Myeloid cells (MCs) reside in the aortic intima at regions predisposed to atherosclerosis. Systemic inflammation triggers reverse transendothelial migration (RTM) of intimal MCs into arterial blood, which orchestrates a protective immune response that clears intracellular pathogens from the arterial intima. Molecular pathways that regulate RTM remain poorly understood. Sphingosine-1-phosphate (S1P) is a lipid mediator that regulates immune cell trafficking by signaling via five G protein-coupled receptors (S1PRs). We investigated the role of S1P in the RTM of aortic intimal MCs.  Methods: Intravenous injection of lipopolysaccharide (LPS) was used to model a systemic inflammatory stimulus that triggers RTM. CD11c+ intimal MCs in the lesser curvature of the ascending aortic arch were enumerated by en face confocal microscopy. Local gene expression was evaluated by transcriptomic analysis of microdissected intimal cells.  Results: In wild-type C57BL/6 mice, LPS induced intimal cell expression of S1pr1, S1pr3, and sphingosine kinase 1 (Sphk1, a kinase responsible for S1P production). Pharmacological modulation of multiple S1PRs blocked LPS-induced RTM and modulation of S1PR1 and S1PR3 reduced RTM in an additive manner. Cre-mediated deletion of S1pr1 in MCs blocked LPS-induced RTM, confirming a role for myeloid-specific S1PR1 signaling. Global or hematopoietic deficiency of Sphk1 reduced plasma S1P levels, the abundance of CD11c+ MCs in the aortic intima and blunted LPS-induced RTM. In contrast, plasma S1P levels, the abundance of intimal MCs, and LPS-induced RTM were rescued in Sphk1-/- mice transplanted with Sphk1+/+ or mixed Sphk1 +/+ and -/- bone marrow. Stimulation with LPS increased endothelial permeability and intimal MC exposure to circulating factors such as S1P.  Conclusions: Functional and expression studies support a novel role for S1P signaling in the regulation of LPS-induced RTM as well as the homeostatic maintenance of aortic intimal MCs. Our data provides insight into how circulating plasma mediators help orchestrate intimal MC dynamics.

overall_design: Cells were isolated by micro-dissection of the lesser curvature aortic arch intima of C57BL/6J wildtype mice (control or injected with 30 ug ultrapure LPS i.v. 18 hours prior to harvest). Cells from 5-10 mice were pooled for each sample, and were subjected to scRNAseq.

first: Chanele

last: Polenz

first: Sharon

last: Hyduk

first: Myron

middle: I

last: Cybulsky


title: RNA sequencing of conventional 2D and 3D cultured melanoma M14 cells

city: Cardiff

first: Girish

middle: K

last: Patel

address: Maindy Road

institute: Cardiff University

summary: Background: Mutant BRAF targeted therapies remain a standard of care for the treatment of metastatic malignant melanoma (MM); however high initial response rates are tempered by the persistence of residual MM cells that eventually lead to disease recurrence and mortality. Since MM recurrence during targeted therapy can present with the simultaneous occurrence of multiple tumour nodules at the original body sites, we hypothesised the presence of an intrinsically resistant MM cell sub-population.   Objectives: Identify an MM cell subpopulation that is intrinsically resistant to targeted therapy and so may be responsible for MM recurrence.   Methods: Using melanoma cell lines, we define culture conditions for reproducible 3D growth of melanospheres to investigate putative cancer stem cell populations. We undertook RNA sequencing and bioinformatic analysis to characterise cell populations between adherent and non-adherent culture, and cells expressing or not expressing CD20. Furthermore, we define an in vitro assay to evaluate killing of melanoma cancer stem cells as a therapeutic test using combination therapies targeting driver mutation and CD20 marker.     Results: We have described culture conditions that promote MM cells to form melanospheres with a reproducible colony forming efficiency of 0.3% to 1.3%. RNA sequencing of melanosphere versus conventional MM cell cultures (n=6), irrespective of the BRAF mutation status, showed that melanosphere formation was associated with growth and differentiation transcriptional signatures resembling MM tumours. Importantly, melanosphere formation also led to the emergence of a CD20+ MM cell subpopulation, similar to that observed in primary human MM tumours. CD20+ MM cells were resistant to BRAF inhibitor therapy, and consistent with this finding demonstrated a Forkhead box protein M1 (FOXM1) transcriptomic profile (n=6). Combining BRAF inhibitor and anti-CD20 antibody treatment led to the additional killing of previously resistant CD20+ BRAF mutant MM cells.   Conclusions: In MM patients that harbour a CD20+ sub-population, combined therapy with BRAF inhibitor and anti-CD20 antibody could potentially kill residual MM cells and so prevent disease recurrence.

overall_design: Using the M14 melanoma cell line, we define culture conditions for reproducible 3D growth of melanospheres to investigate putative cancer stem cell populations. We undertook RNA sequencing to characterise cell populations between adherent and non-adherent cultures.

first: Alex

last: Gibbs

first: Huw

last: Morgan


title: The impact of HPV8 E6 on Lrig1+ hair follicle stem cell populations

summary: Despite epidermal turnover, the skin is host to a complex array of microbes including viruses, such as the human papillomavirus (HPV), which must infect and manipulate skin keratinocyte stem cells (KSC) to survive. This crosstalk between the virome and KSC populations remains largely unknown. Here, we investigated the effect of HPV8 on KSCs using various mouse models. We observed that the HPV8 early region gene E6 specifically caused Lrig1+hair follicle junctional zone KSC proliferation and expansion, which would facilitate viral transmission. Within Lrig1+KSCs specifically, HPV8 E6 bound intracellular p300 to phosphorylate the STAT3 transcriptional regulatory node. This induces a transcriptional switch from TAp63 to ΔNp63 expression, resulting in expansion of KSC into the overlying epidermis. HPV8 was associated with 70% of human actinic keratoses (AK). Together these results redefine human AK as an expansion of KSC, which lack protecting melanosomes and are thus susceptible to sun-light-induced malignant transformation.

overall_design: To determine whether HPV8 E6-driven Lrig1+ hair follicle junctional zone keratinocyte stem cell proliferation was sufficient to cause expansion into the overlying epidermis by lineage tracing we generated Lrig1CreERT2:R26RConfetti:HPV8-E6tg and Lrig1CreERT2:R26RConfetti:WT mice. Confetti labeled cells were isolated by flow-cytometry, enabling us to simultaneously identify Lrig1+ cells by antibody labeling, such that we could isolate flow-sorted Lrig1+ confetti+ and their Lrig1- confetti+ progeny. Lrig1+ confetti+ and their Lrig1- confetti+ progeny from both HPV8-E6tg and WT mice were sequenced by RNA-seq and gene expression profiling analysis was performed on the dataset.


title: Neural crest origin of sympathetic neurons at the dawn of vertebrates

city: Pasadena

first: Brittany

middle: Megan

last: Edens

state: CA

address: 1200 E California Blvd

institute: Caltech

summary: he neural crest is an embryonic stem cell population unique to vertebrates whose expansion and diversification are thought to have promoted vertebrate evolution by enabling emergence of novel cell types and structures like jaws and peripheral ganglia2. While basal vertebrates have sensory ganglia, convention has it that trunk sympathetic chain ganglia arose only in jawed vertebrates. In contrast, here we report the presence of trunk sympathetic neurons in the sea lamprey, Petromyzon marinus, an extant jawless vertebrate. These neurons arise from sympathoblasts near the dorsal aorta that undergo noradrenergic specification via a transcriptional program homologous to that described in gnathostomes. Lamprey sympathoblasts populate the extracardiac space and extend along the length of the trunk in bilateral streams, expressing the catecholamine biosynthetic pathway enzymes tyrosine hydroxylase and dopamine -hydroxylase. CM-DiI lineage tracing analysis further confirmed that these cells derive from the trunk neural crest. RNA-seq of isolated ammocete trunk sympathoblasts revealed gene profiles characteristic of sympathetic neuron function. Our findings challenge prevailing dogma which posits that sympathetic ganglia are a gnathostome innovation, instead suggesting that a late-developing rudimentary sympathetic nervous system may have been characteristic of the earliest vertebrates.

overall_design: To gain insight into the molecular identity of lamprey sympathetic neurons, we harvested bilateral tracts of cells—presumed to be the sympathetic chains—from the trunks of lamprey ammocetes. We further selected for TH+ and TH- cells and subjected them to RNA sequencing using Fixed and Recovered Intact Single Cell RNA-seq (FRISCR) followed by differential expression analysis.

middle: M

first: Marianne

last: Bronner


title: Characterisation of the melanosphere CD20 sub-population

overall_design: M14 cells were grown under non-adherent culture conditions to generate melanospheres. Melanospheres were mechanically dissociated, antibody labelled for CD20 and flow sorted to isolate CD20+ and CD20- populations. RNA was extracted from samples using an RNeasy mini kit as per manufacturers instructions. RNA was then quantified and quality assessed before being sent to Novogene (Cambridge, UK).


title: Characterisation of the melanosphere sub populations in M14 cells

overall_design: Refer to individual Series


title: Improved lung cancer classification by employing diverse molecular features of microRNAs

city: Kunming

first: Yun

last: Zheng

state: Yunnan

address: 452 Fengyuan Road

institute: Yunnan Agricultural University

summary: Lung adenocarcinoma (LUAD) is one of the most common pathological and histological subtypes of primary lung cancer, with high morbidity and mortality. MicroRNAs (miRNAs) are endogenous small non-coding RNAs that regulate the expression of genes at post-transcriptional level. It was reported that A-to-I miRNA editing was decreased in tumors, suggesting the potential value of miRNA editing in cancer classification. However, existing miRNA-based cancer classification models mainly used the frequencies of miRNAs. In order to validate the contribution of miRNA editing information in cancer classification, we extracted three types of miRNA features, including the abundances of original miRNAs, the abundances of edited miRNAs, and the editing levels of miRNA editing sites. Our results show that four classification algorithms selected, i.e., kNN, C4.5, RF and SVM, generally had better performances on all features than on the abundances of miRNAs alone. Since the number of features were large, we used three feature selection (FS) methods to further improve the classification models. One of the FS methods, the DFL algorithm, selected only three features, i.e., the frequencies of hsa-miR-135b-5p, hsa-miR-210-3p and hsa-miR-182 48u (an edited miRNA), from 316 training samples. And all of the four classification algorithms achieved 100% accuracy on these three features for 79 independent testing samples. These results indicate that the additional information of miRNA editing are useful in improving the classification of LUAD samples. And the three miRNAs selected by DFL potentially represent an effective molecular signature for LUAD diagnosis.

overall_design: Small RNA-Seq for 19 lung adenocarcinoma (LUAD) and 19 adjacent normal tissues were obtained, and put into liquid nitrogen immediately after resection. The total RNAs were retrieved and the small RNA sequencing libraries were prepared and sequenced by BGI (Shenzhen, China). Next, the mutation and editing sites of miRNAs were analyzed with the MiRME algorithm for all of these 38 sRNA-seq profiles and 357 public LUAD and normal samples. Then, abundance of original and edited miRNAs, editing levels of identified miRNA editing sites were obtained for these 395 samples. Four machine learning algorithms were used to classify these samples as LUAD or normal samples. Three Feature Selection algorithms were used to select molecular features that were accurate in predicting the samples.


title: Thalamocortical organoids reveal axonogenesis phenotypes of 22q11.2 microdeletion [scRNA-seq]

city: San Francisco

first: David

last: Shin

address: 1651 4th Street Room 521A

department: Neurosurgery

institute: University of California, San Francisco

summary: Dysfunction of the thalamocortical pathway has been implicated in multiple psychiatric disorders, but mechanisms by which these defects emerge remain poorly understood. We explored this question in the context of the 22q11.2 microdeletion, which represents a significant genetic risk for schizophrenia, leveraging emerging technologies of in vitro brain organogenesis using chimeric brain organoids derived from human induced pluripotent stem cells. Here we show that the 22q11.2 microdeletion leads to transcriptional dysregulation in thalamic organoids that is enriched for psychiatric disease risk genes, including elevated expression of FOXP2, which represents the most significantly dysregulated transcription factor in glutamatergic neurons and astroctyes. In a co-culture model fusing thalamic and cortical organoids, we demonstrate that the 22q11.2 deletion mediates an overgrowth of thalamic axons via overexpression of FOXP2, which then subsequently mediates the overgrowth of reciprocal corticothalamic axons. Dysregulation of FOXP2 leads to downregulation of ROBO2, an axon repulsive receptor important for thalamocortical axon pathfinding, and knockdown of ROBO2 in control organoids phenocopies excessive outgrowth of thalamic axons. Together, our study suggests that early steps in thalamocortical pathway development may be dysregulated in a model of genetic risk for schizophrenia, and contribute to neural phenotypes in 22q11.2 microdeletion syndrome.

overall_design: Thalamic and cortical organoids derived from iPS cells carrying the 22q11 deletion or karyotypically normal controls were cultured for 10 weeks and then dissociated to perform single cell RNA-sequencing (either 10X v2 or v3 platform)


title: Microarray data of lenses with glutamate

city: Fukui

first: Masaru

last: Takashima

address: 3-9-1 Bunkyo

country: Japan

institute: University of Fukui

summary:
The addition of Glutamate to the lens induced by galactose eliminated the white clouding formed and showed a therapeutic effect.
Genes regulated by Glutamate addition were identified by microarray analysis. A total of seven samples were used in this analysis: two samples without galactose (control), three samples with galactose (galactose) and two samples with Glutamate (Glutamate).

overall_design: Genes that increased in galactose-treated lenses and reverted with Glutamate were extracted.

first: Shunki

last: Yamamura

first: Chie

last: Tamiya

first: Mayumi

last: Inami

first: Yoshihiro

last: Takamura

last: Inatani

first: Masaya

last: Oki


title: Dynamic regulation of miRNA accumulation during C. elegans larval development

city: Basel

first: Dimos

last: Gaidatzis

address: Maulbeerstrasse 66

department: Computational Biology

country: Switzerland

institute: Friedrich Miescher Institute for Biomedical Research

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

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans