title: Single-cell RNA sequencing of bladder Ewing sarcoma

status: Public on Sep 05 2024

city: Nanjing

first: Weipu

last: Mao

state: Jiangsu

address: No 87, Dingjiaqiao District

department: Urology

institute: southeast university zhongda hospital

summary: Bladder Ewing sarcoma/primitive neuroectodermal tumor (bladder ES/PNET) is a rare and highly malignant tumor associated with a poor prognosis, yet its underlying mechanisms remain poorly understood. This study employed a combination of single-cell RNA sequencing (scRNA-seq) analyses to delve into the pathogenesis of bladder ES/PNET. The investigation revealed the presence of specialized types of epithelial cells (referred to as bladder ES-Epi) and mast cells (referred to as bladder ES-Mast) within bladder ES/PNET in comparison to urothelial carcinoma. Notably, TNFRSF12A exhibited significant upregulation in bladder ES/PNET. Furthermore, mast cells possessed the ability to activate epithelial cells through the TNFSF12-TNFRSF12A ligand-receptor signaling pattern. This activation mechanism appears to contribute to the progression of bladder ES/PNET.

overall_design: Single-cell transcriptome profiling from bladder Ewing sarcoma tumor tissue and paired normal tissue, and bladder urothelial carcinoma tumor tissue and paired normal tissue.


title: Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [scRNA-Seq]

status: Public on Sep 09 2024

city: New York

first: Yang

last: Yang

state: NY

address: 417 E 68th St

country: USA

institute: Memorial Sloan Kettering Cancer Center

type: Expression profiling by high throughput sequencing

summary: Two distinct lineages, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common inner cell mass (ICM) progenitor cells in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells – in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. A dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro to embryo trajectories revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.

overall_design: Reprogramming XEN-to-iPS and ES-to-iXEN cells were assayed for gene expression using single-cell RNA-seq. Given the low proportions of cells undergoing lineage conversion (based on marker expression) from XEN to iPS cells at all timepoints assessed, and ES cells at the 9h timepoint, subpopulations were isolated using fluorescence-activated cell sorting (FACS) and reconstituted at roughly equal proportions. This serves to: (1) retain all the heterogeneity within the reprogramming population, and (2) enrich for cells undergoing key lineage marker expression changes. In addition to reprogramming stages, cells at starting and final states were also sampled.


title: Molecular mechanisms of the Xiao-chai-hu-tang on chronic stress-induced colorectal cancer growth based on an integrated network pharmacology and RNA sequencing approach with experimental validation

status: Public on Sep 11 2024

city: Shanghai

first: Yao

last: Wang

state: Shanghai

address: No. 528, Zhangheng Road

department: Department of Medical Oncology, Shuguang Hospital

country: China

institute: Shanghai University of Traditional Chinese Medicine

summary: XCHT significantly inhibited CRC growth under chronic stress in a dose-dependent manner. Mechanistically, XCHT suppressed the expression levels of glycolysis associated enzymes and inflammatory factors caused by chronic stress. Moreover, XCHT significantly mitigated the activity of the JAK2/STAT3 signaling which was activated by chronic stress induced IL-6.

overall_design: The experiment was divided into a control group (subcutaneous tumor group of colorectal cancer), a stress group (subcutaneous tumor group of colorectal cancer+chronic stress group), a low-dose group of Xiaochaihu decoction (subcutaneous tumor group of colorectal cancer+chronic stress group+low-dose intervention of Xiaochaihu decoction), and a high-dose group of Xiaochaihu decoction (subcutaneous tumor group of colorectal cancer+chronic stress group+high-dose intervention of Xiaochaihu decoction). The subcutaneous tumor tissues of each group were collected and subjected to RNA Seq detection, immunohistochemistry, WB, PCR and other analyses. And perform primary cell culture on the tissue for cell experiments.


title: Modulation of host gene expression by the zinc finger antiviral protein [RNA-seq]

status: Public on Sep 01 2024

city: London

first: Daniel

last: Goncalves-Carneiro

address: Sir Alexander Fleming Building, Imperial College Rd

country: United Kingdom

institute: Imperial College London

summary: The zinc finger antiviral protein (ZAP) depletes non-self RNAs through recognition of their elevated CpG dinucleotide content. CpG dinucleotides are sparse in most endogenous mammalian mRNAs, but a subset might potentially be modulated by ZAP. While CpG frequency alone is insufficient to predict ZAP-regulation, we developed an algorithm using experimentally determined compositional features to predict which endogenous mRNAs may be ZAP-regulated. Using ZAP-knockout mice, we demonstrate that levels of many host mRNAs that are algorithmically predicted ZAP targets are indeed increased when ZAP is absent. ZAP is interferon-inducibel and we also identify genes that are downregulated by ZAP during an innate immune response. Many ZAP-regulated gene products are extracellular matrix or of nucleosome components, whose ZAP mediated control is conserved in human cells. Overall, we provide a new tool for the prediction of ZAP target genes and reveal host mRNAs that are ZAP-regulated.

overall_design: To evaluate the effects of ZAP on endogenous gene expression, we have (1) generated ZAP-knockout mice, (2) treated ZAP+/+ and ZAP-/- mice with poly I:C, (3) extracted spleens at 6, 12, and 24h post-treatment, and (4) extracted total RNA from spleens and performed RNA sequencing.

first: Paul

last: Bieniasz


title: Radial glia promote microglial development through aVb8 -TGFb1 signaling [ChIP-seq]

status: Public on Sep 02 2024

city: San Francisco

first: Gabriel

last: McKinsey

state: CA

address: 1550 4th St. Room 545E

department: Pediatrics

institute: University of California San Francisco

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we aimed to identify 1) The relevant Itgb8 expressing cell types that mediate microglial TGFb activation; 2) The developmental timing of Itgb8-mediated TGFb signaling in microglia; 3) The cellular source and identity of the TGFb ligand relevant for microglial development and homeostasis; 4) The relationship between developmentally disrupted microglia and disease associated microglia; and 5) The role of canonical (Smad-mediated) versus non-canonical TGFb signaling in microglia.

overall_design: ChIP-seq  from Itgb8fl/fl; Emx1Cre microglia to determine genome binding by H3K9ac3.

last: Mckinsey

first: Nicolas

last: Santander

first: Xiaoming

last: Zhang

first: Kleemann

last: Kilian

first: Oleg

last: Butovsky

first: Thomas

middle: D

last: Arnold


title: Immature neutrophil subsets and emergency granulopoiesis drive sepsis immune suppression and a specific extreme response to infection [WB_ECG]

status: Public on Oct 16 2024

city: Oxford

first: Julian

last: Knight

address: Roosevelt Drive, Headington

department: Wellcome Centre for Human Genetics

institute: University of Oxford

summary: Sepsis, the dysregulated host response to infection leading to organ dysfunction, arises from diverse mechanisms that are poorly resolved by sepsis as a syndromic classification, confounding immunotherapy trials. Here we delineate neutrophil and granulopoietic disturbances underlying sepsis pathophysiology. We present a whole blood single-cell multiomic sepsis response atlas (272,993 cells, n=39 individuals), revealing multiple immature neutrophil populations that were collectively immunosuppressive, inhibiting CD4+ T cell proliferation and activation in co-culture. We traced this to altered granulopoiesis using single-cell multiomic mapping of circulating hematopoietic stem cells (HSCs) (29,366 cells, n=27). We show how these features are enriched in a subset of patients, resolving a specific poor outcome endotype (sepsis response signature SRS1). SRS1 patients have increased IL1R2+ immature neutrophils, epigenetic signatures of emergency granulopoiesis transcription factors in HSCs, and STAT3 features across infectious disease settings.  Our findings delineate an immunohematopoietic axis, therapeutic targets and stratified medicine approach to sepsis.

overall_design: Whole blood was isolated from sepsis and healthy patients, red blood cells lysed and total leukocytes were analyzed for scRNA-seq and cell surface protein sequencing (Rhapsody Abseq)

first: J

middle: C

first: A

middle: J

last: Kwok

first: E

last: Cano-Gamez

first: Alice

last: Allcock

first: Ricardo

last: Ferreira


title: Xenobot Transcriptomics: Gene Expression Changes in wild-type cells forming a synthetic biobot

status: Public on Aug 31 2024

city: Medford

first: Vaibhav

middle: P

last: Pai

state: MA

address: 200 Boston Ave suite 4600

department: Biology

institute: Tufts University

summary: The standard paradigm of developmental and synthetic biology focuses on changes in morphology driven by gene expression. Here, we investigated the reverse relationship: would transcriptomes change if cell collectives acquired a novel morphogenetic and behavioral phenotype in the absence of genomic editing, transgenes, heterologous materials, or drugs? We investigated the effects of morphology and nascent emergent life history on gene expression in Xenobots – motile, autonomous constructs that self-assemble from frog embryo epidermal progenitor cells. We compared transcriptomes of Xenobots with age-matched frog embryos, identifying at least 537 transcripts uniquely upregulated in the Xenobots. Pathway analyses indicated shifts in the categories of motility machinery, pattern formation and multicellularity, stress and immune response, metabolism, and sensory perception of sound and mechanical stimuli. Phylostratigraphic analysis showed that the majority of these shifts in Xenobots were towards evolutionarily ancient transcripts and systems. Lastly, we found enrichment of thanatotranscriptomic genes, shedding light on the distinction between death of an organism and that of its cells. These data on the relationship between genotype and phenotype may have implications for evolution, biomedicine, and synthetic morphoengineering.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Xenobots and age-matched Xenopus embryos. Xenobots and age-matched Xenopus embryo samples are in triplicates

first: Léo

last: Pio-Lopez

first: Megan

middle: M

last: Sperry

first: Patrick

last: Erickson

first: Michael

last: Levin


title: Xenobot Transcriptomics: Gene Expression Changes in wild-type cells forming one form of synthetic biobot

status: Public on Sep 20 2024

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Xenopus embryos raised in 0.1X MMR and 0.75X MMR. 0.1X MMR and 0.75X MMR Xenopus embryo embryo samples are in triplicates


title: RNA-Seq based gene expression profiling of mouse Meis1-Meis2 double KO or wild-type atria and ventricles

city: Madrid

first: Manuel

last: Gomez

state: Madrid

address: Melchor Fernández Almagro, 3

country: Spain

institute: CNIC

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

overall_design: Refer to individual Series


title: Adipose-Tumor Crosstalk contributes to CXCL5 Mediated Immune Evasion in PDAC

city: Kansas City

last: VanSaun

state: KS

address: 3901 Rainbow Blvd

institute: The University of Kansas Medical Center

summary:
BACKGROUND: CXCR1/2 inhibitors are being implemented with immunotherapies in PDAC clinical trials. CXCL ligands are a family of cytokines responsible for stimulating these receptors; while typically secreted by activated immune cells, fibroblasts, and even adipocytes, they are also secreted by immune-evasive cancer cells. CXCL ligand release is known to occur in response to inflammatory stimuli, whether pathogenic (bacterial) or endogenous (obesity). Obesity has been linked to poor patient outcome and altered anti-tumor immunity in pancreatic cancer. Importantly, adipose-derived cytokines and chemokines have been implicated as potential drivers of tumor cell immune evasion; cumulatively these findings suggest that targeting CXC ligands may be beneficial in the context of obesity.
METHODS: RNA-sequencing of human PDAC cell lines was used to assess differential influences of adipose conditioned media on the cancer cell transcriptome. In addition, the adipose-induced secretome of PDAC cells was validated with ELISA for induced CXCL5 secretion. Human tissue data from CPTAC was used to correlate IL-1β and TNF expression with both CXCL5 mRNA and protein levels. CRISPR-Cas9 was used to knock out CXCL5 from a murine PDAC cell line in order to assess orthotopic tumor studies in syngeneic, diet-induced obese mice.  Flow cytometry was used to compare the immune profiles between tumors. Mice were monitored for differences in tumor size at endpoint in combination with Anti-PD-1 immune checkpoint blockade therapy.
RESULTS: Human adipose conditioned media (hAT-CM) stimulates CXCL5 secretion from PDAC cells via either IL-1β or TNF; neutralization of both is required to significantly block release of CXCL5 from tumor cells. Ablation of CXCL5 from tumors promoted an enriched immune phenotype with an unanticipatedly increased number of exhausted CD8 T cells. Application of anti-PD-1 treatment to control tumors failed to alter tumor growth, yet treatment of CXCL5 deficient tumors showed response by significantly diminished tumor mass.
CONCLUSIONS: In summary, our findings show that both TNF and IL-1β can stimulate CXCL5 release from PDAC cells in vitro, which correlates with expression in patient data.  CXCL5 depletion in vivo alone is sufficient to promote T cell infiltration into tumors, increasing efficacy of checkpoint blockade inhibition and alleviating tumor burden.

overall_design: Human peri-pancreatic adipose was collected from pancreatic cancer patients during surgical resection. Conditioned media was made from the tissue, and used to stimulate human cell lines in tissue culture. Cells treated with serum free media or conditioned media were analyzed by RNA sequencing to assess factors from adipose tissue altering pancreatic cancer transcriptional profiles.

first: Walsh

middle: R

last: McKinnon

first: Joseph

last: Ambrose

first: Jarrid

last: Jack

first: Austin

last: Eades

first: Bailey

last: Bye

first: Mariana

last: Ruckert

first: Fanuel

last: Messaggio

first: Appolinaire

last: Olou

first: Prabhakar

last: Chalise

first: Dong

last: Pei


title: Integrator complex subunit 12 knockout overcomes a transcriptional block to HIV latency reversal

status: Public on Sep 17 2024

city: Seattle

last: Emerman

state: Washington

address: 1110 Fairview Ave N

institute: Fred Hutch Cancer Research Center

first: Carley

middle: N

last: Gray


title: Cell-type-specific genetic tools for the Drosophila central complex and their use to investigate neuropeptide expression and sleep regulation.

city: Ashburn

first: Gerald

last: Rubin

state: VA

address: 19700 Helix Drive

institute: Janelia Research Campus

summary: The central complex (CX) plays a key role in many higher order functions of the insect brain including navigation and activity regulation. Genetic tools for manipulating individual cell types, and knowledge of what neurotransmitters and neuromodulators they express, will be required to gain detailed mechanistic understanding of how these functions are executed. We have generated and characterized a large collection of split-GAL4 driver lines that express in individual or small subsets of cell types in the Drosophila CX. We survey neuropeptide expression in the central brain using fluorescent in situ hybridization and show that several CX cell types express multiple neuropeptides. We use our driver lines to identify CX cell types whose activation affects sleep, and identified other central brain cell types that link the circadian clock to the CX. The well characterized genetic tools and information on neuropeptide expression we provide should enhance studies of the CX.

overall_design: Cell-type-specific drivers were used to identify specific cell types in the Drosophlia central complex, and these cells were isolated and RNA-Seq libraries were generated from them to determine the expression of neuropeptides and neurotransmitters.

first: Tanya

last: Wolff

first: Mark

last: Eddison

last: Chen

first: Aljoscha

last: Nern

first: Preeti

last: Sundaramurthi

first: Marisa

last: Dreher

first: Divya

last: Sitaraman


title: Broad H3K4me3 controls transcription output and timing during spermatid development

status: Public on Sep 03 2024

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

summary: Male germ cells express a complex transcriptome under tight temporal regulation during their development. However, our knowledge of the epigenetic regulation of crucial stages in this process, such as meiotic onset, remains limited. Here, by dissecting a comprehensive map of the dynamic epigenomic landscape in developing mouse male germ cells, we uncover mutually exclusive shifts in the repressive histone marks H3K9me2, H3K9me3 and H3K27me3 during the mitosis-to-meiosis transition and completion of meiotic recombination. These dynamic shifts coincide with temporal changes in global transcriptional output, retrotransposon activity, and the silencing of mitotic/meiotic genes during spermatogenesis. In addition, we identify Setd1b-mediated broad H3K4me3 domains in both mouse and human spermatids. These broad H3K4me3 domains promote Pol II occupancy and transcription, resulting in high gene expression in spermatids. Setd1b ablation leads to a complete loss of broad H3K4me3, and the redistribution of Pol II from broad H3K4me3 promoters to regular H3K4me3 promoters, thereby compromising temporal gene expression and ultimately hampering spermiogenesis. These findings reveal that dynamic epigenetic changes orchestrate stage-specific gene expression in spermatogenesis, with Setd1b-mediated broad H3K4me3 serving as a crucial regulator that controls the timing of stage-specific gene expression in spermatids.

overall_design: Examination of 7 different histone modifications and gene expression levels in spermatogenetic cells during mouse spermatogenesis.

first: Zhen

last: Lin

first: Bowen

last: Rong

first: Fei

last: Lan

first: Minghan

last: Tong


title: EZH2 deletion does not impact acinar cell regeneration but restricts progression to pancreatic cancer in mice [RNA-seq]

first: Christopher

middle: L

last: Pin

state: Ontario

address: 1151 Richmond St

country: Canada

institute: University of Western Ontario

summary: Enhancer of Zeste Homologue 2 (EZH2) is part of the Polycomb Repressor Complex 2, which induces trimethylation of lysine 27 on histone 3 (H3K27me3) and promotes genes repression. EZH2 is overexpressed in many cancers including pancreatic ductal adenocarcinoma (PDAC). Previous studies in mice attributed both pro-oncogenic and tumor suppressive functions to EZH2. Deletion of the EZH2 enhancesde novoKRAS-driven neoplasia following pancreatic injury by preventing acinar cell regeneration, while increased EZH2 expression in PDAC is correlated to poor prognosis, suggesting a context-dependant effect for EZH2 in PDAC progression. In this study, we examined EZH2 function in pre- and early neoplastic stages of PDAC. Using an inducible model to generate deletion of EZH2 only in adult acinar cells (EZH2DSET), we showed loss of EZH2 activity did not prevent acinar cell regeneration in the absence of oncogenic KRAS (KRASG12D), nor lead to increased PanIN formation in the presence of KRASG12Din adult mice. However, loss of EZH2 did reduce recruitment of inflammatory cells and, when combined with a PDAC model, promoted widespread PDAC progression. Loss of EZH2 function also correlated to remodeling of the tumor microenvironment, which favors cancer cell progression. This study suggests expression of EZH2 in adult acinar cells restricts PDAC initiation and progression by affecting both the tumour microenvironment and acinar cell differentiation.

overall_design: 2-4-month-old mice of different genotypes were treated by tamoxifen (TX) gavage. Twenty-two days after initial TX treatment, mice were sacrificed and their RNA was extracted.

first: Emilie

last: Jaune-Pons

first: Xiaoyi

last: Wang

first: Fatemeh

last: Mousavi

first: Zachary

last: Klassen

first: Samad

last: Elkaoutari

first: Kurt

last: Berger

first: Charis

last: Johnson

first: Mickenzie

last: Martin

first: Saloni

last: Aggarwal

first: Sukhman

last: Brar

first: Khalid

last: Muhammad

first: Joanna

last: Ryan

first: Parisa

last: Shooshtari

first: Angela

last: Mathison

first: Nelson

last: Dusetti

first: Raul

last: Urrutia

first: Gwen

last: Lomberk


title: EZH2 deletion does not impact acinar cell regeneration but restricts progression to pancreatic cancer in mice

first: Christopher

last: Pin


title: IGF-1 activated pathways in orbital fibroblasts

status: Public on Sep 08 2024

city: Rochester

first: Collynn

last: Woeller

address: 601 Elmwood Avenue

institute: University of Rochester

summary: Orbital fibroblasts (OFs) are central to thyroid eye disease (TED) pathogenesis. Elevated insulin-like growth factor 1 receptor (IGF-1R) in TED OFs contributes to disease progression, but underlying mechanisms remain unclear. To elucidate IGF-1R-mediated signaling in OFs, we performed RNA-seq analysis after IGF-1 stimulation. Our data reveal that IGF-1 induces gene expression associated with cell proliferation, microtubule dynamics, and lipid metabolism while suppressing cell adhesion, senescence, and chromatin remodeling. Validation studies confirmed upregulation of CRABP2, a key regulator of retinoic acid signaling, and its role in IGF-1-induced OF migration. These findings uncover novel IGF-1R downstream effectors, providing insights into TED pathophysiology and potential therapeutic targets.

overall_design: To better understand the downstream effects of IGF-1 signaling in thyroid eye disease orbital fibroblasts (TED-OFs), unbiased RNA sequencing was performed on two different TED-OF strains treated with IGF-1 (50 ng/mL) or with Vehicle (V) for 24 hours. Samples are in biological replicates (1-3).

middle: F


title: Exploring the Biological Mechanisms of Severe COVID-19 in the Elderly: Insights from an Aged Mouse Model

status: Public on Aug 25 2024

city: wuhan

first: li

last: ma

state: --- Select One ---

address: 262 Jinlong Street, Jiangxia,

institute: Chinese Academy of Sciences Wuhan Institute of Virology

summary: Definitive parameters or mechanisms underlying the severity of COVID-19 in elderly people remain confused. Thus, this study seeks to elucidate the mechanism behind the increased vulnerability of elderly individuals to severe COVID-19. We employed an aged mouse model with a mouse-adapted SARS-CoV-2 strain to mimic the severe symptoms observed in elderly patients with COVID-19. Comprehensive analyses of the whole lung were performed using transcriptome and proteome sequencing, comparing data from aged and young mice. For transcriptome analysis, bulk RNA sequencing was conducted using an Illumina sequencing platform.

overall_design: Three-week-old and 18-month-old SPF C57BL/6j mice were purchased from Beijing Vital River Laboratory and Jackson Laboratory, respectively. They were then divided into four cohorts, each consisting of nine mice: young and aged groups without infection and young and aged groups with infection. Anesthesia was induced in the mice through intraperitoneal administration of tribromoethanol at a dose of 250 mg/kg body weight. Mice in the infected groups were intranasally inoculated with 2 × 105 plaque-forming units of mouse-adapted SARS-CoV-2 in 30 μL of DMEM per mouse, whereas mice in the uninfected groups were administered 30 μL of DMEM per mouse.Lung samples were collected from three mice in each group at three days post-infection for transcriptomic analyses.

first: Li

last: Ma

first: Xian

last: Lin

first: Xianliang

last: Ke

first: Quanjiao

last: Chen


title: Multidirectional effect of low-intensity neuromuscular electrical stimulation on gene expression and phenotype in thigh and calf muscles after one week of disuse

city: Moscow

first: Pavel

last: Makhnovsky

address: 76A Khoroshevskoye shosse

country: Russia

institute: Institute of Biomedical Problems of the Russian Academy of Sciences

summary:
Low-intensity neuromuscular electrical stimulation (NMES) is often used as an alternative to exercise and high-intensity electrical stimulation to prevent the loss of muscle mass, strength, and endurance in spaceflight and in patients with severe chronic diseases. This study investigated the effects of a one-week disuse, both with and without low-intensity neuromuscular electrical stimulation – a safe (non-traumatic) approach to prevent the loss of muscle mass, on the functional capacities and gene expression in thigh and calf muscles.
This study assessed the efficiency of low-intensity (~10% of maximal voluntary contraction) electrical stimulation in preventing the negative effects of 7-day disuse (dry immersion without [see a related dataset GSE271607] and with daily stimulation) on the strength and aerobic performance of the ankle plantar flexors and knee extensors, mitochondrial function in permeabilized muscle fibers, and the proteomic (quantitative mass spectrometry-based analysis) and transcriptomic (RNA-sequencing) profiles of the soleus muscle and vastus lateralis muscle.
Application of electrical stimulation during dry immersion prevented a decrease in the maximal strength and a slight reduction in aerobic performance of the knee extensors, as well as a decrease in maximal (intrinsic) ADP-stimulated mitochondrial respiration and changes in the expression of genes encoding mitochondrial, extracellular matrix, and membrane proteins in the vastus lateralis muscle. In contrast, for the ankle plantar flexors/soleus muscle, electrical stimulation had a positive effect only on maximal mitochondrial respiration, but slightly accelerated the decline in the maximal strength and muscle fiber cross-sectional area, which appears to be related to the activation of inflammatory genes.
The data obtained open up broad prospects for the use of low-intensity electrical stimulation to prevent the negative effects of disuse for “mixed” muscles, meanwhile, the optimization of the stimulation protocol is required for “slow” muscles.

overall_design:
Ten males participated in a 7-day dry immersion with NMES (DI+NMES, ages 26–39 years; height 1.74 m [1.70–1.76 m]; body mass 73 kg [70–79 kg]; and body mass index 24 kg/m² [23–26 kg/m²]).
Motor neuron firing rate plays an important role in the activation of calcium-dependent signaling and the expression of muscle-specific genes. Therefore, in our study, both low (25 Hz) and high (50 Hz) stimulation frequencies were used during DI+NMES (in the first and second NMES daily session, respectively). Every day at 11:00 (7 sessions in total), low-intensity low-frequency electrical stimulation was applied to the calf and thigh muscles for 40–45 min (bipolar symmetrical rectangular pulses [1 ms, 25 Hz] for 1 s, followed by a 2-s pause).
Every day at 17:00 (7 sessions in total), low-intensity high-frequency electrical stimulation was applied to the calf and thigh muscles for 10 min (carrier frequency of 2-kHz bipolar symmetrical pulses [10 ms separated by 10-ms pause] with bursts of 50 Hz for 10 s, followed by a 50-s pause). The burst time during high-frequency NMES was longer than that during low-frequency NMES (10 s vs. 1 s). Therefore, to increase the pain tolerance during high-frequency NMES, the carrier frequency (2-kHz) was used.
Muscle samples were taken using a Bergstrom needle with aspiration under local anesthesia (2 ml of 2% lidocaine) from the medial part of the vastus lateralis (VL) and soleus (Sol) muscles of the left leg 14 days before and 6 days after the start of disuse (DI and DI+NMES) at 10:00, 3 hours after a standardized very light breakfast (5.2 g protein, 2.7 g fat, 55 g carbohydrates, 1253 kJ). Strand-specific RNA libraries were prepared using the NEBNext Ultra II RNA kit (New England Biolabs, USA) and single-end sequencing was done by a NextSeq 550 analyzer (Illumina, USA).

first: Daniil

last: Popov

last: Makhnovskii


title: A single-cell atlas of spatial and temporal gene expression in the mouse cranial neural plate

status: Public on Aug 26 2024

city: Raleigh

first: Eric

last: Brooks

state: North Carolina

address: 1051 William Moore Dr

department: Molecular Biomedical Sciences

institute: NORTH CAROLINA STATE UNIVERSITY RALEIGH

summary: The formation of the mammalian brain requires regionalization and morphogenesis of the cranial neural plate, which transforms from an epithelial sheet into a closed tube that provides the structural foundation for neural patterning and circuit formation. Sonic hedgehog (SHH) signaling is important for cranial neural plate patterning and closure, but the transcriptional changes that give rise to the spatially regulated cell fates and behaviors that build the cranial neural tube have not been systematically analyzed. Here we used single-cell RNA sequencing to generate an atlas of gene expression at six consecutive stages of cranial neural tube closure in the mouse embryo. Ordering transcriptional profiles relative to the major axes of gene expression predicted spatially regulated expression of 870 genes along the anterior-posterior and mediolateral axes of the cranial neural plate and reproduced known expression patterns with over 85% accuracy. Single-cell RNA sequencing of embryos with activated SHH signaling revealed distinct SHH-regulated transcriptional programs in the developing forebrain, midbrain, and hindbrain, suggesting a complex interplay between anterior-posterior and mediolateral patterning systems. These results define a spatiotemporally resolved map of gene expression during cranial neural tube closure and provide a resource for investigating the transcriptional events that drive early mammalian brain development.

overall_design: Cells from manually dissected cranial regions of E7.5-E9.0 mouse embryos were isolated by enzymatic treatment and manual trituration and run through the 10X Genomics Chromium v3 single cell RNA sequencing workflow.

first: Andrew

last: Moorman

first: Bhaswati

last: Bhattacharya

first: Ian

last: Prudhomme

first: Max

last: Land

first: Heather

last: Alcorn

first: Roshan

last: Sharma

first: Dana

last: Pe'er

first: Jennifer

last: Zallen


title: Radial glia promote microglial development through aVb8 -TGFb1 signaling [ATAC-seq]

first: Gabriel

last: McKinsey

overall_design: ATAC-seq  from Itgb8fl/fl; Emx1Cre microglia to determine open chromatin regions and comparison with transcriptional expression signature.

last: Mckinsey

first: Nicolas

last: Santander

first: Xiaoming

last: Zhang

first: Kleemann

last: Kilian

first: Oleg

last: Butovsky

first: Thomas

last: Arnold


title: Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [RNA-Seq]

first: Prokopios Alexandros

last: Polyzos

address: 413 E 69th St

institute: Weill Cornell Medicine

summary: Two distinct fates, pluripotent epiblast (EPI) and primitive (extra-embryonic) endoderm (PrE), arise from common progenitor cells, the inner cell mass (ICM), in mammalian embryos. To study how these sister identities are forged, we leveraged embryonic (ES) and eXtraembryonic ENdoderm (XEN) stem cells – in vitro counterparts of the EPI and PrE. Bidirectional reprogramming between ES and XEN coupled with single-cell RNA and ATAC-seq analyses uncovered distinct rates, efficiencies and trajectories of state conversions, identifying drivers and roadblocks of reciprocal conversions. While GATA4-mediated ES-to-iXEN conversion was rapid and nearly deterministic, OCT4, KLF4 and SOX2-induced XEN-to-iPS reprogramming progressed with diminished efficiency and kinetics. The dominant PrE transcriptional program, safeguarded by Gata4, and globally elevated chromatin accessibility of EPI underscored the differential plasticities of the two states. Mapping in vitro trajectories to embryos revealed reprogramming in either direction tracked along, and toggled between, EPI and PrE in vivo states without transitioning through the ICM.

overall_design:
Expression profiling of XEN cells after KO of GATA4 of GATA6
Expression profiling of iPS and XEN cells

first: Anna-Katerina

last: Hadjantonakis

first: Effie

last: Apostolou


title: Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [CUT&Run]

overall_design: GATA4 and GATA6 binding sites in XEN identified with Cut&Run


title: Single-cell analysis of bidirectional reprogramming between early embryonic states reveals mechanisms of differential lineage plasticities [ATAC-Seq]

overall_design: ATAC-seq for wt XEN cells and XEN cells after KO of GATA4 or GATA6


title: Radial glia promote microglial development through aVb8 -TGFb1 signaling


title: FOXO1-KLF10 reinforcing loop promotes adipose lipolysis to facilitate exercise-induced anti-obesity effect in male mice

first: Jieying

last: Zhu

address: Hengren Road

institute: Shanghai University of Sport

summary: Exercise is recognized to be an effective way in the combat against obesity and related metabolic disorders, but the underlying mechanism is incompletely understood. Krüppel-like factor 10 (KLF10) is a transcription factor participating in diverse biological processes. KLF10 expression is abundant in adipose tissue, but its role in obesity is not well defined. Here, we show that exercise could facilitate adipocyte-derived KLF10 expression via the SIRT1/FOXO1 pathway. Adipocyte-specific knockout of KLF10 (KLF10AKO) blunts exercise-promoted white adipose browning, energy expenditure, fat loss, and glucose tolerance in diet-induced obese (DIO) mice. On the contrary, adipocyte-specific transgenic expression of KLF10 in mice (KLF10ATG) enhanced the abovementioned metabolic benefits induced by exercise. Mechanistically, KLF10 interacts with FOXO1 and facilitates the recruitment of KDM4A to form a ternary complex on the promoter regions of the Pnpla2 and Lipe genes to promote the expression of these key lipolytic genes, therefore facilitating lipolysis to defend against DIO in mice. As a newfound downstream effector responding to exercise, adipose KLF10 could act as a potential target in the fight against obesity

overall_design: To gain the mechanistic insight into the role of KLF10 in adipose metabolism, RNA sequencing (RNA-seq) was conducted to investigate the differentially expressed genes (DEGs) in iWAT collected from HFD-fed WT and KLF10AKO mice.


title: JAK2V617F Impairs Lymphoid Differentiation in Myeloproliferative Neoplasms

city: Bern

first: Interfaculty

last: Bioinformatics Unit

state: Bern

address: Baltzerstrasse 6

department: Interfaculty Bioinformatics Unit

country: Switzerland

institute: University of Bern

summary: Myeloproliferative neoplasms (MPNs) arise via the acquisition of a driver mutation in a single hematopoietic stem cell (HSC), often decades prior to the development of a clinical phenotype. The most common MPN driver mutation, JAK2V617F, activates aberrant JAK/STAT signaling via cytokine receptors critical for myelopoiesis. Over time, this MPN HSC clone outcompetes its normal counterparts, leading to excessive myeloid cell production and contributes to lymphopenia in patients with MPNs and leades to elevated neutrophil-to-lymphocyte ratio (NLR), which is predictive of disease-related complications including thrombosis and mortality. We conducted this study to learn how hematopoiesis from the JAK2V617F clone affects lymphopoiesis in patients with MPNs. Although myeloid proliferation via aberrant JAK2 signaling is the most apparent mechanistic link between JAK2V617F and MPN phenotypes, our findings demonstrate that impaired lymphoid differentiation is an additional feature of JAK2V617F hematopoiesis, leading to the rarity of JAK2V617F lymphocytes despite the dominance of JAK2V617F HSCs in patients with MPNs. The combination of prolific myelopoiesis and defective lymphopoiesis from the JAK2V617F clone is a potential connection between MPN pathology and the surrogate markers, including NLR and lymphopenia, which hold prognostic significance. Based on our data, we speculate that, defective JAK2V617F lymphopoiesis and the consequent increased burden of lymphopoiesis from residual normal HSC clones drives the appearance of abnormal lymphocyte subsets, lymphoproliferative disease or T cell exhaustion in MPNs. Further study of MPN lymphopoiesis provides an opportunity to define the immune deficits underlying the myriad complications that affect patients with MPNs.

overall_design: Gene expression of CLP cells from wiltype (WT_CLP) and SclCre;JAK2-V617F (VF) (SF1_CLP) mice were compared against each other

first: Tata

last: Rao


title: RNA-Seq based gene expression profiling of mouse Meis1-Meis2 double KO or wild-type atria and ventricles (Embryo).

first: Manuel

last: Gomez

summary: The goal of this study was to compare the gene expression profile, using RNA-seq technology, of mouse Meis1-Meis2 double KO or wild-type fetal.

overall_design: RNA-seq was performed in four different conditions, atria and ventricles from fetal hearts at E15.5 to compare Meis1 and Meis2 double deletion (constitutive or inducible) with control littermates. In all cases, 4 replicates were used for each condition.

first: M

last: Torres


title: Time series analysis of retinoblastoma  patient derived mesenchymal stem cells differentiated to osteogenic lineage

city: CHENNAI

first: SOWMYA

last: PARAMESWARAN

address: 41 COLLEGE ROAD

country: India

institute: VISION RESEARCH FOUNDATION

summary: The RB1 gene plays a pivotal role in the process of osteogenic differentiation.To gain insights into this role, we conducted high-throughput RNA sequencing during the invitro osteogenesis of patient-derived heterozygous RB mutant and wildtype. Our analysis involved stage-specific differential gene expression analysis and a comprehensive time series analysis of both wild-type and RB mutant cells during the osteogenic differentiation process. The findings from our study indicate that the deficiency in RB1 results in significant disruptions in cellular functions, primarily mediated by E2F1. Our results suggest compelling role for RB1 in osteogenic differentiation with its loss leading to an immature phenotype, potentially compromising the osteogenic differentiation process which might subsequently contribute to tumorigenesis.

overall_design: To investigate the whole transcriptome for gaining insights into the temporal role of RB1 in osteogenic differentiation, we performed RNA sequencing of wild type and RB1 mutant at the various stages of in vitro osteogenic differentiation.

first: Sowmya

last: Parameswaran

first: Ambily

last: Vincent


title: ChIP-seq with anti-ZBTB17 antibody in HeLa cells to find target genes

status: Public on Aug 20 2024

first: hongqin

last: liu

address: 230 Haike Road, Zhangjiang Hi-Tech Park

department: SLST

summary: ZBTB17 belongs to the ZBTB (zinc finger and BTB domain protein family) family, which contains a BTB domain at the N-terminus and multiple zinc fingers at the C-terminus. In this dataset, ChIP-seq experiment was performed with anti-ZBTB17 antibody.

overall_design: HeLa cells were prepared for ChIP-sequencing, chromatin fragments were pre-cleared and then immunoprecipitated with ZBTB17 antibody. Another sample were prepared simultaneously without antibody as the control.

first: Hongqin

last: Liu

first: Min

last: Zhuang


title: Transcriptional regulation by ZBTB17

overall_design: Refer to individual Series


title: EZH2 deletion does not impact acinar cell regeneration but restricts progression to pancreatic cancer in mice [ChIP-seq]

first: Christopher

last: Pin

first: Emilie

last: Jaune-Pons

first: Xiaoyi

last: Wang

first: Fatemeh

last: Mousavi

first: Zachary

last: Klassen

first: Samad

last: Elkaoutari

first: Kurt

last: Berger

first: Charis

last: Johnson

first: Mickenzie

last: Martin

first: Saloni

last: Aggarwal

first: Sukhman

last: Brar

first: Khalid

last: Muhammad

first: Joanna

last: Ryan

first: Parisa

last: Shooshtari

first: Angela

last: Mathison

first: Nelson

last: Dusetti

first: Raul

last: Urrutia

first: Gwen

last: Lomberk


title: Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

status: Public on Aug 19 2024

city: Madison

first: Kevin

middle: S

last: Myers

state: WI

address: 5127 WEI, 1552 University Ave

department: Great Lakes Bioenergy Research Center

institute: University of Wisconsin - Madison

summary: G-quadruplex (G4) structures can form in guanine-rich stretches of DNA or RNA and have been found to modulate a variety of cellular processes including replication, transcription, and translation. Most studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing G4s in bacteria. We utilized a chemical-genetic approach to identify genes in Escherichia coli that are important for growth in conditions that stabilize G4s. Our screens reveal translation elongation to be a key process that is impacted by G4 stabilization. Reducing levels of elongation factor Tu or slowing translation elongation with chloramphenicol suppress the effects of G4 stabilization. In contrast, downregulating the levels of certain essential translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation generally are less abundantly expressed under G4-stabilizing conditions. Taken together, the results suggest that RNA G4s present barriers to E. coli growth in G4-stabilizing conditions and reducing the rate of translation can help compensate for G4-related stress.

overall_design: To investigate the effects of stabilizing G-quadruplexes on Escherichia coli, cells were grown in the presence of the G-quadruplex stabilizing compound, NMM, and RNA-seq was performed. This was done for the control cell strain (MG1655 dtolC) as well as a strain with a decrease in a translation elongation factor (MG1655 dtolC tufA::kan). TPM values were used for differential gene expression analysis between each growth condition. All samples were grown and sequenced in triplicate.

first: Rachel

last: Cueny

first: Andrew

last: Voter

first: Aidan

last: McKenzie

first: Marcel

last: Morgenstern

first: Michael

last: Place

first: Jason

last: Peters

first: Joshua

last: Coon

first: James

last: Keck


title: The CoREST complex is a therapeutic vulnerability in malignant peripheral nerve sheath tumors (ATAC-Seq)

status: Public on Aug 17 2024

city: Boston

first: Robert

last: Fisher

address: 609 Albany St

department: Dermatology

institute: Boston University

summary: Malignant peripheral nerve sheath tumor (MPNST) is a highly aggressive sarcoma that may be seen in patients with neurofibromatosis type 1 (NF1) or occur sporadically.  While surgery is the primary treatment for localized MPNST with a 61.9% overall survival rate, metastatic disease is often fatal due to resistance to systemic therapies which underscores the urgent need for effective treatments. MPNSTs frequently harbor inactivating driver mutations in the PRC2 epigenetic repressor complex suggesting epigenetic therapies may represent a specific vulnerability in these tumors. Here, we investigate the role of the LSD1-HDAC1-CoREST (LHC) repressor complex in mediating MPNST tumor growth and progression. Our findings demonstrate that the LHC small molecule inhibitor, corin, induces apoptosis and significantly inhibits proliferation in MPNST cells. Transcriptomic analysis of corin-treated MPNST cells demonstrates specific increases in genes associated with axonogenesis and neuronal differentiation as well as altered extracellular matrix; additionally, corin treatment is shown to inhibit MPNST invasion in vitro. These results underscore the critical role of the LHC complex in facilitating MPNST growth and progression and suggest that targeting the LHC complex represents a promising therapeutic approach for this aggressive malignancy.

overall_design: 100,000 cells were seeded and treated with 1 μM Corin, HDACi, or DMSO. DNA was extracted, tagmented, purified, and adapter ligated using the ATAC-seq Kit (53150) according to the manufacturer’s instructions (Active Motif). Sequencing was done by Azenta Life Sciences and reads were trimmed using the fastp command in fastp v.0.23.4. Reads were aligned with GRCh38 reference genome using bowtie2 v.2.4.2. Sam files were filtered to retain the mapped reads only and converted to BAM files using Samtools v.1.12. Bed and Bedgraph files were created using Bedtools v.2.31.0. Peaks were called using Macs2 v.2.2.7.1 with the nomodel, and nolambda options.

first: Imad

last: Soukar

first: Sanjana

last: Bhagavatula

first: Marianne

last: Collard

first: Phillip

middle: A

last: Cole

first: Rhoda

last: Alani


title: The CoREST complex is a therapeutic vulnerability in malignant peripheral nerve sheath tumors

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


title: A co-conserved gene pair supports Caulobacter iron homeostasis and resistance to chelation stress

status: Public on Aug 14 2024

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

summary: Bacteria assimilate a diverse set of metals that enable metabolic functions essential for growth and survival, but metal homeostasis can be disrupted by natural and synthetic chelators in the environment. We have identified genes that influence fitness of the common soil and aquatic bacterium, Caulobacter crescentus, in the presence of a growth-limiting concentration of the synthetic chelator ethylenediaminetetraacetic acid (EDTA). Among the identified genes important in EDTAacclimationthere are several controlled by the metal-responsive regulators Fur, Zur, and UzcRS. However, a subset of genes in the iron-responsive Fur regulon emerged as the primary fitness determinants during EDTA challenge. EDTA treatment reduced intracellular iron levels and a syntenic gene pair, cciT and cciO, that supports Caulobacter iron homeostasis is necessary for growth in EDTA. cciT encodes one of four Fur-regulated TonB-dependent transporters (TBDTs) and – of these regulators – uniquely supports wild-type levels of growth on defined and complex lab media. The iron acquisition and EDTA resistance functions of the CciT transporter specifically require the presence of cciO, which encodes a 2-oxoglutarate-Fe(II) dioxygenase. Thus, there is a critical functional partnership between an outer membrane transporter and a cytoplasmic dioxygenase that are broadly co-conserved in the phylum Proteobacteria. cciT and cciO mutants cultivated in natural freshwater were not impacted by an equivalent EDTA treatment, demonstrating robustness of the highly redundant set of Caulobacter iron acquisition systems in an ecosystem context. This study advances our understanding of genes involved in metal acquisition and chelation stress survival, and illuminates the complex interactions between the chemical environment and the processes that regulate intracellular metal homeostasis.

overall_design: To investigate the relationship between the genes cciO (CCNA_00027), and cciT (CCINA_00028) to iron homeostasis, we grew wildtype CB15 and mutants lacking cciO or cciT in M2X broth with 10 μM FeCl3 for 2.5 hours. RNA was extracted using TRIzol (Invitrogen) ___________. RNA-sequencing libraries were prepared utilizing the Illumina TruSeq Stranded RNA Kit and sequenced on the Illumina NextSeq 500 platform at SeqCoast Genomics (Portsmouth, NH).

first: Sergio

last: Hernandez-Ortiz

first: Kiwon

last: Ok

first: Aretha

last: Fiebig

first: Thomas

last: O'Halloran


title: Single cell RNA-sequencing of 90-day old astrocyte conditioned medium treated  forebrain organoids (ACMOs) and control  forebrain organoids

status: Public on Aug 04 2024

city: Shenzhen

first: honghui

last: zheng

state: Guangdong

address: Taoyuan Street

institute: Tsinghua University

summary: The scRNA-seq analysis of 90-day old ACMOs and forebrain organoids reveals six well-defined major clusters. All cells were categorized into six distinct clusters: (1) deep layer subcortical projection neurons, (2) upper layer projection neurons, (3) intermediate progenitors, (4) radial glial cells, (5) dividing cells, (6) astrocytes. Both ACMOs and control organoids underwent a correct trajectory of cell diversification and contained a large diversity of progenitor and neuronal cell types belonging to the neuroectodermal lineage. Transcriptomic comparisons and pathway enrichment analysis were performed between control organoids and ACMOs.

overall_design: Expression profiling by high throughput sequencing

first: Honghui

last: Zheng

first: Yifan

last: Cheng


title: Comprehensive Assessment of Initial Adaptation of ESBL Positive ST131 E. coli to Carbapenem Exposure

city: Houston

first: William

middle: Charles

last: Shropshire

state: TX

address: 1901 East Road

institute: The University of Texas MD Anderson Cancer Center

summary: Background: It remains unclear how high-risk Escherichia coli lineages, like sequence type (ST) 131, initially adapt to carbapenem exposure in its progression to becoming carbapenem resistant. Methods: Carbapenem mutation frequency was measured in multiple subclades of extended-spectrum β-lactamase (ESBL) positive ST131 clinical isolates using a fluctuation assay followed by whole genome sequencing (WGS) characterization. Genomic, transcriptomic, and porin analyses of ST131 C2/H30Rx isolate, MB1860, under prolonged, increasing carbapenem exposure was performed using two distinct experimental evolutionary platforms to measure fast vs. slow adaptation. Results: All thirteen ESBL positive ST131 strains selected from a diverse (n=184) ST131 bacteremia cohort had detectable ertapenem (ETP) mutational frequencies with a statistically positive correlation between initial ESBL gene copy number and mutation frequency (r = 0.87, P<1e-5). WGS analysis of mutants showed initial response to ETP exposure resulted in significant increases in ESBL gene copy numbers or mutations in outer membrane porin (Omp) encoding genes in the absence of ESBL gene amplification with subclade specific adaptations. In both experimental evolutionary platforms, MB1860 responded to initial ETP exposure by increasing blaCTX-M-15 copy numbers via modular, insertion sequence 26 (IS26) mediated pseudocompound transposons (PCTns). Transposase activity driven by PCTn upregulation was a conserved expression signal in both experimental evolutionary platforms. Stable mutations in Omp encoding genes were detected only after prolonged increasing carbapenem exposure consistent with clinical observations. Conclusions: ESBL gene amplification is a conserved response to initial carbapenem exposure, especially within the high-risk ST131 C2 subclade. Targeting such amplification could assist with mitigating carbapenem resistance development.

overall_design: RNA-Seq of daily populations exposed to MB1860 strain 1X ertapenem (ETP) MIC (0.06 ug/mL) in standard, batch culture, flask transfer protocol (FTP) and novel, single-cell microfluidic system (MFS). Passage controls w/o ETP exposure were used for comparison. Isolates were grown up in triplicate and differential expression analysis followed by gene set enrichment analysis were performed.


title: single CD4 T cell gene expression and T cell receptor profile of human volunteers experimentally infected with malaria

city: Edinburgh

first: Wiebke

last: Nahrendorf

address: Charlotte Auerbach Rd

department: Institute for Immunology and Infection Research

institute: University of Edinburgh

summary: Human volunteers were experimentally infected with Plasmodium falciparum blood-stage malaria parasites in the context of the VAC063C experimental medicine study (ClinicalTrials.gov NCT03906474). The gene expression profile and T cell receptor alpha and beta chains of CD4 T cells were analysed at single cell resolution at baseline (before malaria infection) and six days after treatment (at the peak of the circulating T cell response). We are comparing the T cell response to the first malaria infection of life (with the highest risk of severe disease) and the third infection where disease tolerance is established. This single cell data is complemented by bulk RNAseq data of flow sorted CD4 T cell subsets (naive, memory and regulatory) available through the GEO SuperSeries GSE172481.

overall_design: CD4 T cells were flow sorted from cryopreserved PBMCs and barcoded using oligo-tagged antibodies. Six individually barcoded samples were pooled (one pool for first malaria infection and a separate pool for third infection). We then super-loaded the 10X Genomics Chromium Controller based on the workflow described by Stoeckius et al. 2018 (doi.org/10.1186/s13059-018-1603-1) to capture approx 30,000 singlets per pool across 2 wells of an A chip. We generated three libraries: i) cell surface barcode, ii) 5’ gene expression and iii) T cell receptor alpha and beta chains (after amplification of the V(D)J regions). All libraries were separately indexed and pooled at a ratio of 8% cell surface, 84% gene expression and 8% V(D)J for sequencing on a NovaSeq 6000 Illumina platform to yield at least 66,000 150 bp paired end reads per cell. In total we obtained 5931 million paired end reads (2848 and 3083 million paired end reads for first and third infection, respectively) at the expected ratios.

first: Philip

last: Spence

first: Angela

last: Minassian

first: Florian

last: Bach


title: Mutant huntingtin induces neuronal apoptosis via derepressing the non-canonical poly(A) polymerase PAPD5

status: Public on Aug 01 2024

city: Hong Kong

first: Ho Yin Edwin

last: Chan

department: School of Life Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

type: Non-coding RNA profiling by high throughput sequencing

summary: MicroRNAs (miRNAs) are small non-coding RNAs that play crucial roles in post-transcriptional gene regulation. Poly(A) RNA polymerase D5 (PAPD5) catalyzes the addition of adenosine to the 3′ end of miRNAs. In this study, we demonstrated that the Yin Yang 1 protein, a transcriptional repressor of PAPD5, was recruited to both RNA foci and protein aggregates, resulting in an upregulation of PAPD5 expression in Huntington’s disease (HD). Additionally, we identified a subset of PAPD5-regulated miRNAs with increased adenylation and reduced expression in our disease model. We focused on miR-7-5p and found that its reduction caused the activation of the TAB2-mediated TAK1–MKK4–JNK pro-apoptotic pathway. This pathway was also activated in induced pluripotent stem cell-derived striatal neurons and post-mortem striatal tissues isolated from HD patients. In addition, we discovered that a small molecule PAPD5 inhibitor, BCH001, could mitigate cell death and neurodegeneration in our disease models. This study highlights the importance of PAPD5-mediated miRNA dysfunction in HD pathogenesis and suggests a potential therapeutic direction for the disease.

overall_design: We performed small RNA-seq to investigate the 3’ adenylation levels of the miRNAs in SK-N-MC cells overexpressed with either the wild-type PAPD5 protein or a catalytic-inactive PAPD5 mutant (PAPD5 D256A & D258A).

first: Zhefan

last: Chen

first: Ho-Yin

middle: E


title: CAR-redirected natural killer T cells demonstrate superior antitumor activity to CAR-T cells through multimodal CD1d-dependent mechanisms

status: Public on Aug 21 2024

city: Chapel Hill

first: Mark

last: Woodcock

state: NC

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

summary: Compared to CAR.CD19 T cells, we found that CAR.CD19 NKTs showed superior control of tumor growth in the B16-OVA-hCD19 melanoma model without evident toxicity. To investigate whetehr   CAR.CD19 NKTs could affect the TME in the tumor. We used the single RNA seq to test the TME cell populations in the B16-OVA-hCD19 model between CAR.CD19 NKTs and CAR.CD19 Ts.

overall_design: 8-10 weeks male mice injected the  B16-OVA-hCD19 tumors and received non-transduced T cells, CAR.CD19 T cells or CAR.CD19 NKTs and 16 days later isolate the cells infiltrated the tumors. 5 mice each group.

first: Xin

last: Zhou

first: J

last: Milner

first: Gatphan

last: Atassi

first: Gianpietro

last: Dotti


title: Evaluation of bovine colostrum extracellular vesicles on NASH mouse model

city: Seoul

first: Daye

last: Mun

address: 1, Gwanak-ro, Gwanak-gu

country: South Korea

institute: Seoul National University

summary: The potential of orally administered colostrum-derived EVs to regulate gut microbiota dysbiosis and prevent non-alcoholic steatohepatitis was evaluated. The results demonstrated that colostrum-derived EVs improved steatosis, fibrosis, and inflammation. Transcriptome analysis showed decreased lipid metabolism, bacterial response, and inflammatory responses in the intestine, and reduced inflammatory and fibrosis-related pathways in the liver. Gut microbiota and metabolite analysis revealed an increased abundance of Akkermansia and elevated cholesterol excretion. Additionally, treatment with colostrum-derived EVs increased the production of tight junction proteins and mucin in the intestine. These findings suggest that increased Akkermansia due to colostrum-derived EVs improves intestinal inflammation and barrier function, preventing endotoxin translocation to the liver and thereby reducing liver inflammation and fibrosis.

overall_design: Liver and colon samples from non-alcoholic steatohepatitis mouse model were analyzed on their transcriptomic changes to investigate the effects of bovine colostrum-derived extracellular vesicles.


title: Developmental mitochondrial complex I activity determines lifespan

city: Glasgow

first: Alberto

last: Sanz

address: Davidson Building

department: School of Molecular Biosciences

institute: University of Glasgow

summary: Aberrant mitochondrial function has been associated with an increasingly large number of human disease states. Observations from in vivo models where mitochondrial function is altered suggest that adaptations to mitochondrial dysfunction may underpin disease pathology. We hypothesized that the severity of these maladaptations could be shaped by the plasticity of the system when mitochondrial dysfunction manifests. To investigate this, we have used inducible fly models of mitochondrial complex I (CI) dysfunction to reduce mitochondrial function at two stages of the fly lifecycle, from early development and adult eclosion. Here, we show that in early life (developmental) mitochondrial dysfunction results in severe reductions in survival and stress resistance in adulthood, while flies where mitochondrial function is perturbed from adulthood, are long-lived and stress resistant despite having up to an 75% reduction in CI activity. After excluding developmental defects as a cause, we went on to molecularly characterize these two populations of mitochondrially compromised flies, short- and long-lived. We find that our short-lived flies have unique transcriptomic and metabolomic responses which overlap significantly in discreet models of CI dysfunction. Our data demonstrate that early mitochondrial dysfunction via CI depletion elicits an adaptive response which severely reduces survival, while CI depletion from adulthood is not sufficient to reduce survival and stress resistance.

overall_design: RNA-seq was performed on 3-5 day old whole Drosophila melanogaster males with depleted Complex I, achieved through RNAi targeting specific subunits and controls.

first: Rhoda

last: Stefanatos


title: Cellular evolution of the hypothalamic preoptic area of behaviorally divergent deer mice

city: Cambridge

first: Jenny

address: 16 Divinity Ave

institute: Harvard

summary: Genetic variation is known to contribute to the variation of animal social behavior, but the molecular mechanisms that lead to behavioral differences are still not fully understood. Here, we investigate the cellular evolution of the hypothalamic medial preoptic area (MPOA), a brain region that plays a critical role in social behavior, across two sister species of deer mice (Peromyscus maniculatus and P. polionotus) with divergent social systems. These two species exhibit large differences in mating and parental care behavior across species and sex. Using single-nucleus RNA-sequencing, we build a molecular atlas of the MPOA for males and females of both Peromyscus species.

sample_organism:
Peromyscus maniculatus
Peromyscus polionotus

overall_design:
Nuclei from MPOA of males and females of P. maniculatus and P. polionotus were isolated and sequenced using 10x Genomics 3' V3. Each replicate contains a male and female of each species (i.e. 4 samples)

all_nuclei.seurat.rds = Seurat object of counts from all nuclei
Pman.gene_name.txt = Mapping from Pman gene ID to common gene name
Ppol.gene_name.txt = Mapping from Ppol gene ID to common gene name

first: Phoebe

last: Richardson

first: Christopher

last: Kirby

first: Sean

last: Eddy

first: Hopi

last: Hoekstra


title: Mutant huntingtin induces neuronal apoptosis via derepressing the non-canonical poly(A) polymerase PAPD5 [ChIP-Seq]

overall_design: We performed chromatin immunoprecipitation DNA-sequencing (ChIP-seq) to investigate the binding between YY1 and its DNA targets, including PAPD5, in our HD SK-N-MC cell model.

first: Ho


title: Mouse models for pancreatic ductal adenocarcinoma areaffected by the cre-driver used to promote KRASG12D activation

city: London

last: Pin

address: 1151 Richmond St

institute: University of Western Ontario

summary: The fundamental biology of pancreatic ductal adenocarcinoma has been greatly impacted by the characterization of genetically engineered mouse models that allow temporal and spatial activation of oncogenic KRAS (KRASG12D). One of the most commonly used models involves targeted insertion of a cre-recombinase into the Ptf1a gene. However, this approach disrupts the Ptf1a gene, resulting in haploinsufficiency that likely affects sensitivity to oncogenic KRAS (KRASG12D). This study aims to determine if Ptf1a haploinsufficiency affected the acinar cell response to KRASG12D before and after induction of pancreatic injury. Taken together, our results suggest Ptf1a haploinsufficiency in Ptf1acreERT mouse models promotes KRASG12D priming of genes for promotion of PDAC.

overall_design: We performed morphological and molecular analysis of three genetically engineered mouse models that express a tamoxifen-inducible cre-recombinase to activate KRASG12D in acinar cells of the pancreas. The cre-recombinase was targeted to the acinar-specific transcription factor genes, Ptf1a or Mist1/Bhlha15, or expressed within a BAC-derived Elastase transgene. Histological and RNA-seq analyses were used to delineate differences between the models

first: Fatemeh

last: Mousavi

first: Joyce

last: Thompson

first: Justine

last: Lau

first: Nur

last: Renollet

first: Mickenzie

last: Martin

first: Jake

last: McGue

first: Timothy

last: Frankel

first: Parisa

last: Shooshtari

first: Filip

last: Bednar


title: Single-Cell RNA-Sequencing facilitates the effectiveness analysis of clinical-dose arsenic trioxide (ATO) treatment in reactivating V272M in AML patient and in primary AML PBMCs

city: Shanghai

first: Huaxin

last: Song

address: Shanghai Jiao Tong University School of Medicine

summary: The goals of this study is to reveal the transcriptome of p53-V272M rescued by ATO in AML patient and in primary AML PBMCs

overall_design: The PBMCs before the first administration were isolated as the untreated sample. Then, 5 × 105 untreated PBMCs were isolated and cultured in DMEM medium with 0.2 μg/mL ATO for 24 h as the in-vitro treated sample. The in-patient treated PBMCs were collected on the day 13 after the patient received 10 mg/kg ATO for 12 consecutive days.

first: Min

last: Lu

first: Yu

last: Wu

first: Yuting

last: Dai


title: Effect of SAT1 depletion on H3K27ac alterations in the ovarian cancer cell line SKOV3 in detached conditions by chromatin immunoprecipitation and sequencing (ChIP-seq) analysis

status: Public on Jul 29 2024

city: Guangzhou

first: Chaoyun

last: Pan

address: 74 Zhongshan Er Rd.

institute: Sun Yat-sen University

summary: Ovarian cancer is an aggressive malignancy characterized by the ascitic fluid and peritoneal metastases. Cancer cells detach from the extracellular matrix and survives the loss of anchorage in the ascites to disseminate extensively in the peritoneal cavity. Metabolic reprogramming is often observed in the cancer progression, yet its role in peritoneal metastasis is largely unexplored.  Here we report that spermidine/spermine N1-acetyltransferase 1 (SAT1) promotes the anchorage-independent cell survival and potentiates metastatic dissemination. Analysis of different histone modifications in the SAT1-depleted ovarian cancer cells upon detachment revealed only a dramatic reduction in the level of H3K27ac, whereas the levels of 15 other histone lysine modifications were not reduced or slightly affected. Chromatin immunoprecipitation and sequencing (ChIP-seq) analysis of H3K27ac to map gene regions with significantly altered H3K27ac identified 1870 genes with increased and 1556 genes with reduced H3K27ac peaks in SAT1-deficient ovarian cancer cells compared to control cells upon detachment.Integrated analysis of RNA-seq and H3K27ac ChIP-seq datasets indicated that 11.05% of genes with reduced H3K27ac peaks were transcriptionally down-regulated. Remarkably, such genes were broadly associated with mitotic cell cycle process, chromosome organization, and chromosome segregation.Taking these findings together, we conclude that SAT1 increases H3K27ac mark within genes required for mitosis regulation and chromosome segregation, thereby protecting ovarian cancer cells from mitotic catastrophe upon detachment.

overall_design: To investigate effect of depletion of SAT1 on H27Kac alteration in the detached conditions, we knocked down SAT1 in ovarian cancer cell line SKOV3 by shRNA. We then perfromed comparative chromatin immunoprecipitation and sequencing (ChIP-seq) analysis of H3K27ac to map gene regions with significantly altered H3K27ac in the control (shControl) and SAT1 knockdown (shSAT1) cells.

first: Cuimiao

last: Zheng

first: Jie

last: Li


title: RNA-seq to compare gene expression profiles between WT and ZBTB17 knockdown cells

first: hongqin

last: liu

summary: ZBTB17 knockdown HeLa cells and WT HeLa cells were prepared for RNA-sequencing, 3 independent biological replicates were performed.

overall_design: HeLa cell was infected with shZBTB17 or shNT for 2 days, then treated with puromycin for 4 days for knockdown selection. The cells were then prepared for RNA-seq experiments.

first: Hongqin

last: Liu

last: Zhuang


title: A nuclear RNA degradation code is recognized by PAXT for eukaryotic transcriptome surveillance

city: Irvine

first: Yongsheng

last: Shi

state: California

address: 811 Health Sciences Road, Medical Sciences B Room 262

department: Microbiology & Molecular Genetics

institute: UC Irvine

summary: The RNA exosome is an RNA degradation machine that is critical for eukaryotic transcriptome surveillance and mutations in exosome components cause numerous human diseases. The exosome is directed to specific RNAs by adaptor protein complexes. However, it remains unclear how these adaptors specifically recognize their target RNAs. The PAXT connection is an adaptor that recruits the exosome to polyadenylated RNAs in the nucleus, especially transcripts polyadenylated at intronic poly(A) sites. Here we show that PAXT-mediated degradation is induced by the combination of a 5′ splice site and a poly(A) junction, which includes the poly(A) signal and the poly(A) tail, but not by either sequence alone. These two sequences are bound by the splicing factor U1 snRNP and pre-mRNA 3′ processing factors, which in turn cooperatively recruit PAXT. As 5′ splice sites and poly(A) junctions are typically found on unspliced precursors and processed RNAs respectively, we propose that their presence on the same RNA molecule constitutes an “RNA degradation code”. Consistent with this model, disease-associated single nucleotide polymorphisms that create novel 5′ splice sites near poly(A) sites induce aberrant RNA degradation. Our results revealed the first nuclear RNA degradation code that plays important roles in transcriptome surveillance and may also influence gene evolution.

overall_design: Examination of 16 samples by PAS-seq, a type of 3′ end mRNA-sequencing. There are 3 biological replicates of control siRNA treatment, 3 biological replicates of EXOSC3 siRNA treatment, 3 biological replicates of scramble shRNA treatment, 2 biological replicates of MTR4 shRNA treatment, 3 biological replicates of ZFC3H1 shRNA treatment, and 2 biological replicates of PABPN1 shRNA treatment. All samples were prepared from HEK293T cells.

first: Lindsey

middle: V

last: Soles


title: Effect of detachment culture condition and depletion of SAT1 on gene expression in SKOV3 ovarian cancer cell line

summary: Ovarian cancer is an aggressive malignancy characterized by the ascitic fluid and peritoneal metastases. Cancer cells detach from the extracellular matrix and survives the loss of anchorage in the ascites to disseminate extensively in the peritoneal cavity. Metabolic reprogramming is often observed in the cancer progression, yet its role in peritoneal metastasis is largely unexplored.  Here we report that spermidine/spermine N1-acetyltransferase 1 (SAT1) promotes the anchorage-independent cell survival and potentiates metastatic dissemination. We compared the detached vs attached cells with RNAseq and identified that hypoxia was among the most enriched pathways using gene set enrichment analysis.To define the underlying mechanism, we first carried out RNA-seq analysis of the detached ovarian cancer cells with or without knocking down SAT1 and identified 1,829 differentially expressed genes (P value < 0.05) in the detached SAT1 knocking down cells. Gene Ontology (GO) term enrichment analysis recognized the differentially expressed genes associated extensively with mitotic process, most likely reflecting a role of SAT1 in cell cycle control. Taken together, our data suggest that SAT1 was induced by hypoxia in the detached cell and played an important role in cell cycle control.

overall_design: To investigate effect of detachment culture condition and depletion of SAT1 on gene expression, we knocked down SAT1 in ovarian cancer cell line SKOV3 in attached and detached conditions by shRNA. We then perfromedcomparative gene expression profiling analysis of RNA-seq data for SKOV3 control  cells (pLKO) in both detached and attached conditions and its SAT1 knockdown derivative (shSAT1) in detached condition.


title: Simultaneous cyclin D1 overexpression and p27kip1 knockdown enable robust Müller glia cell cycle reactivation in uninjured mouse retina

city: Kowloon

first: Wenjun

last: XIONG

state: Hong Kong

address: Tat Chee Avenue

institute: City University of Hong Kong

summary: Müller glia (MG) stem cells are dormant retinal stem cells. While teleost fish MG re-enter the cell cycle after retinal damage and regenerate lost retinal neurons through asymmetric cell division of MG-derived progenitors, mammalian MG lack such ability. Here, we show that forced p27 downregulation and Cyclin D1 overexpression in MG using a single adeno-associated virus cell cycle activator (CCA) vector had a strong synergistic effect to induce MG proliferation. We used transcriptome profiling at single-cell level to demonstrate that CCA could induce MG proliferation and reprogram MG into neurogenic and rod-like cells. In addition, retinal injury combined with histone deacetylase inhibitor facilitates CCA to induce more rod-like cells, but not new cell types. Our study suggests new and powerful strategies for awakening the proliferative and neurogenic potential of MG in adult mammalian retinas.

overall_design: MG were labelled by Tdtomato in the Glast-CreER; Rosa26-tdTomato mice. MG proliferation was induced by the cell cycle activator (CCA) vector AAV7M8-GFAP-cyclin D1-p27sh. The CCA vector suppressed p27kip1 expression while overexpressed Cyclin D1 specifically in the MG.  After receiving the CCA treatment, some mice were further injected with NMDA and TSA (CCA+NMDA+TSA, referred to as CCANT), as NMDA induced retinal injury and histone deacetylase inhibitor have been shown to improve MG reprogramming. The control group was injected with AAV7m8-GFAP-GFP-LacZsh only to control for any non-specific effect caused by virus injection and shRNA expression. Retinas were collected at around 3 weeks post AAV injection, and Tdtomato+ MG were sorted by FACS for scRNA-Seq analysis.

first: Zhifei

last: WU

first: Virpi

last: Ahola

first: Jan

last: Keung

first: Baoshan

last: Liao

first: Zongli

last: Xiong

first: Julia

last: Ying


title: PMEL is involved in snake color pattern transition from blotches to stripes [scRNA-seq]

status: Public on Jul 26 2024

city: Geneva

first: Athanasia

last: Tzika

address: Athanasia Tzika, LANE - Sciences III, 30 quai Ernest Ansermet, 1211 Genève 4, Switzerland

institute: University of Geneva

summary: Our genomic, bulk and single-cell transcriptomic, functional, and developmental characterization of the Terrazzo corn snake color morph and the extensive comparison with wild-type snakes puts forward the dual role of PMEL in snake skin coloration, both in the differentiation of chromatophores during embryogenesis and the melanogenesis in melanophores.

overall_design: 1 X sample (single cell suspension) was harvested from 1 X E25 Pantherophis guttatus embryo

first: Pierre-Yves

last: Helleboid


title: Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with drug efficacy and adverse reactions

status: Public on Jul 24 2024

city: Setagaya-ku

first: Hideya

last: Kawaji

state: Tokyo

address: 2-1-6 Kamikitazawa

department: Research Center for Genome & Medical Sciences

country: Japan

institute: Tokyo Metropolitan Institute of Medical Science

summary: We conducted a quantitative assessment of drug-inducible cis-regulatory elements (CREs) based on transcription initiation profiling of mRNAs and noncoding RNAs, including enhancer RNAs, by using CAGE (Cap Analysis of Gene Expression). Candidate CREs were identified in a hepatocellular carcinoma HepG2 cell line with stable expression of drug-responsive transcription factor pregnane X receptor (PXR) .

overall_design: Transcription initiatin profilig by CAGE for ShP51 cells (derived from HepG2 cells, with stable expression of PXR) with and without rifampicin

first: Saki

last: Gotoh-Saito

first: Ryoko

last: Wada


title: Hemoglobin-induced Transcriptomic Changes in Human Cerebral Arteries

status: Public on Jul 15 2024

first: Shafeeque

last: Mohammedali

state: Texas

address: 6431 Fannin St.

institute: UTH Health Houston

summary: Hemoglobin (Hb) in the subarachnoid space significantly impacts cerebral vessels, leading to various pathological outcomes. The toxicity of cell-free Hb released from erythrocytes and its metabolites is suggested to cause vasoconstriction and neuronal damage, correlating with delayed ischemic neurological deficits (DIND). Here, we aim to describe the changes in the genetic profile of human cerebral arteries exposed to free Hb for 48 hours. We performed an ex vivo treatment followed by mRNA sequencing of the vessels

overall_design: Fresh human cerebral arteries were collected and processed as T0 vessel control for zero or immediate timepoint, T48 vessel control for 48 hours of culturing in media, and Hb vessels for 48 hours in culture with Hb treatment. We have isolated RNA and performed sequencing and compared the transcriptomic changes between the T0 (immediately processed), T48 vessel control and Hb (hemoglobin-treated) groups.

first: Peeyush

middle: K

last: Thankamani Pandit

first: Spiros

last: Blackburn


title: The CoREST complex is a therapeutic vulnerability in malignant peripheral nerve sheath tumors (RNA-Seq)

city: Boston

first: Robert

last: Fisher

state: MA

address: 609 Albany St

institute: Boston University

summary: Malignant peripheral nerve sheath tumor (MPNST) is a highly aggressive sarcoma that may be seen in patients with neurofibromatosis type 1 (NF1) or occur sporadically.  While surgery is the primary treatment for localized MPNST with a 61.9% overall survival rate, metastatic disease is often fatal due to resistance to systemic therapies which underscores the urgent need for effective treatments. MPNSTs frequently harbor inactivating driver mutations in the PRC2 epigenetic repressor complex suggesting epigenetic therapies may represent a specific vulnerability in these tumors. Here, we investigate the role of the LSD1-HDAC1-CoREST (LHC) repressor complex in mediating MPNST tumor growth and progression. Our findings demonstrate that the LHC small molecule inhibitor, corin, induces apoptosis and significantly inhibits proliferation in MPNST cells. Transcriptomic analysis of corin-treated MPNST cells demonstrates specific increases in genes associated with axonogenesis and neuronal differentiation as well as altered extracellular matrix; additionally, corin treatment is shown to inhibit MPNST invasion in vitro. These results underscore the critical role of the LHC complex in facilitating MPNST growth and progression and suggest that targeting the LHC complex represents a promising therapeutic approach for this aggressive malignancy.

overall_design: Library was prepared and sequenced by Azenta Life Sciences. Reads were trimmed and low-quality reads were removed using Trimmomatic v.0.36. Reads were mapped to the GRCh38 reference genome using STAR aligner v.2.5.2b. Unique gene hit counts were calculated by using featureCounts from the Subread package v.1.5.2. Counts were used for differential analysis using DESeq2. The Wald test was used to generate p-values and log2 fold changes. Genes with an adjusted p-value < 0.05 and absolute log2 fold change > 1 were called as differentially expressed genes for each comparison.

first: Imad

last: Soukar

first: Sanjana

last: Bhagavatula

first: Marianne

last: Collard

first: Phillip

last: Cole

first: Rhoda

last: Alani


title: Molecular insights in the anti-cancer potential of mesenchymal stem cells derived from the amniotic fluid and chorionic villi

status: Public on Jul 30 2024

city: Swansea

first: David

last: James

address: Swansea University, Singleton Park

department: Medical School

institute: Swansea University

summary: The environment created during embryogenesis contributes to reducing aberrations that drive structural malformations and tumorigenesis. In this study, we investigate the anti-cancer potential of mesenchymal stem cells (MSCs) derived from two different gestational tissues, the amniotic fluid (AF) and the chorionic villi (CV), with particular emphasis on the role of the paracrine signals they release. Methods: Next generation sequencing was performed on patient-derived AF- and CV-MSCs to obtain molecular insights into the molecular mechanisms driving their anti-cancer features. Secretome enrichment analysis allowed the identification of soluble moieties involved in target cell regulation, tissue homeostasis and cancer cell inhibition. Data were experimentally confirmed through in vitro assays, by evaluating the cytotoxic effect of the media conditioned (CM) by AF- and CV-MSCs and their derived exosomes (EXO) on two human ovarian cancer cell lines (OVCAR and SKOV-3), in 2D and 3D conditions. Results: The presence of molecular moieties (i.e., mRNAs, lncRNAs) released by these cells to support tissue homeostasis by inhibiting biological processes involved in the etiology of aggressive cancers, as well as to regulate immune pathways at the basis of chronic disorders. Secretome enrichment analysis showed the presence, in both cell lines, of lncRNAs with the predicted function of inhibiting cancer cell proliferation. The exposure of OVCAR and SKOV-3 cells to CM and EXOs revealed a detrimental effect in 2D (by reducing cell viability and inducing apoptosis), and to negatively interfere with spheroid formation in 3D conditions. Conclusion: Data presented here provides molecular insight on the role AF- and CV-MSCs as source of anti-tumor factors, paving the way for the development of therapeutics with the potential to create a pro-regenerative environment for tissue restoration following injury, disease, and cancer.

overall_design: To understand the difference in gene expression profiles between mesenchymal stem cells dervived from amniotic fluid vs chorionic villi

first: Salvatore

last: Vaiasicca

first: Bruna

last: Corradetti


title: dRNA-Seq data for Vibrio campbellii BB120 (ATCC BAA-1116, previously designated as Vibrio harveyi)

city: Bloomington

first: Julia

last: van Kessel

state: IN

address: 1001 E 3rd Street, Biology Building

institute: Indiana University

summary: Differential RNA-Seq data for Vibrio campbellii BB120 (ATCC BAA-1116, previously designated as Vibrio harveyi)

overall_design: RNA-Seq of cultures grown to OD600=1.0

first: Alyssa

last: Ball

first: Logan

last: Geyman

first: Kai

last: Papenfort


title: Physiologically refined cell culture conditions uncover oncogene-dependent  metabolic signatures in Ewing sarcoma spheroids

status: Public on Jul 12 2024

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

country: Germany

institute: German Cancer Research Center (DKFZ)

summary:
Ewing sarcoma (EwS) cell line culture largely relies on standard techniques, which do not
recapitulate physiological conditions. Here, we report on a physiologically improved, feasible,
and cost-efficient EwS cell culture technique employing an advanced medium composition,
reduced fetal calf serum, and spheroidal growth. Functional in vitro assays and transcriptome
profiling demonstrated that these refined conditions better recapitulate proliferation rates of
patient tumors as well as hypoxic conditions relevant for EwS pathophysiology. Moreover,
transcriptional signatures associated with the oncogenic activity of the EwS-specific FET::ETS
fusion transcription factors in the refined culture conditions were shifted from proliferative
towards metabolic gene signatures. The herein presented optimized physiological EwS cell
culture technique provides a broadly applicable approach for enhanced in vitro modeling
relevant to advancing EwS research and the validity of experimental results.

overall_design: 4 Ewing sarcoma cell lines grown in refined cell culture conditions; 3 replicates in each condition (Dox versus no Dox)

first: A

last: Ceranski

first: Anna

last: Ehlers

first: Martha

last: Carreno-Gonzales

last: Grünewald


title: Atrial fibrillation variant-to-gene prioritization through cross-ancestry eQTL and single-nucleus multiomic analyses

status: Public on Jul 09 2024

city: Montreal

first: Guillaume

last: Lettre

state: Quebec

address: 5000 Belanger

institute: Montreal Heart Institute

summary: Atrial fibrillation (AF) is the most common arrhythmia in the world, and is linked to significant morbidity and mortality. Despite advances in the treatment and management of AF, important challenges remain for patients. Human genetics can provide strong therapeutic candidates, but the identification of the causal genes and their functions is difficult. Here, we apply an AF fine-mapping strategy that leverages results from a cross-ancestry genome-wide association study (GWAS), expression quantitative trait loci (eQTLs) from left atrial appendages (LAA) obtained from two cohorts with distinct ancestry (European and East Asian), and a paired RNAseq and ATACseq LAA single-nucleus assay (sn-multiome). We found that AF-associated LAA eQTLs are largely consistent across ancestries. At ten AF loci, our co-localization and fine-mapping analyses implicated 14 genes. Furthermore, by integrating our LAA sn-multiome data and other epigenomic datasets with our fine-mapping results, we identified four primary candidate causal AF variants, including rs7612445 at GNB4 and rs242557 at MAPT, for which we propose molecular mechanisms of AF-association at the cellular level. Finally, we showed that the repression of the strongest AF-associated eQTL gene, LINC01629, in human embryonic stem cell-derived cardiomyocytes using CRISPR inhibition results in the dysregulation of pathways linked to genes involved in the development of atrial tissue and the cardiac conduction system (e.g. HCN4, PITX2 and TBX5).

overall_design: Single nuclei were extracted from left atrial appendages of patients with persistent AF and in sinus rhythm. The 10X multiome protocole was used to generate paired snATACseq and snRNAseq librairies.

first: Francis

last: Leblanc


title: Real-time quantitative PCR profiling of human miRNAs in CAG RNA-expressing cells

city: Hong Kong

first: Ho Yin Edwin

last: Chan

institute: The Chinese University of Hong Kong

summary: We examined whether PAPD5 upregulation induced by mutant CAG RNA led to any dysregulation of cellular miRNA profiling. We found that, out of the 751 miRNAs examined, the expression of 186 miRNAs was reduced in EGFPCAG78-expressing human neuroblastoma SK-N-MC cells and was restored back to normal levels upon the knockdown of PAPD5 expression.

overall_design: qPCR gene expression profiling. Equal amount of small RNAs from each sample was used for gene expression analysis. The experiments were repeated independently for three times.

first: Shaohong

middle: I

last: Peng

first: Zhefan

last: Chen

first: Ho Yin


title: Noncoding SNPs decrease expression of FABP5 during COPD exacerbations

status: Public on Jul 07 2024

city: Denver

first: Sarah

last: Sasse

state: CO

address: 1400 Jackson St., K720

department: Medicine

institute: National Jewish Health

summary: Differential susceptibility to recurrent infection and exacerbation in COPD is not well understood. Here we investigated the potential impact of genetic variation in Fatty Acid Binding Protein 5 (FABP5), a metabolic regulator we previously demonstrated to be downregulated in COPD and further downregulated in patients reporting one or more exacerbation. Through negative binomial analysis of the COPDGene SNP dataset, we identified 5 novel linked single nucleotide polymorphisms (SNPs) across the FABP5 locus that were significantly associated with severe exacerbations in a Non-Hispanic White cohort (rs4338057, rs12549270, rs202275, rs202277, and rs202279). We integrated multiple sources of previously published data to prioritize SNPs most likely to exert regulatory function. Ultimately, rs202275 emerged as the lead candidate due to unique alignment with the loading site of a bidirectional RNA Pol II signature of active enhancer utilization in our recently published patient-derived airway epithelial PRO-seq dataset, suggesting a critical regulatory role for the region harboring this variant. Using Micro-C genome-wide chromosome conformation capture, we found that the region harboring rs202275 makes three-dimensional physical contacts with the FABP5 transcription start site (TSS), suggesting the SNP region could regulate FABP5 transcription through a looping mechanism. To examine SNP function, we analyzed previously deposited gene-array data (GEO Accession #GSE42057) from peripheral blood mononuclear cell (PBMC) samples and found that COPD patients carrying the rs202275 risk allele (T) express significantly lower levels of FABP5 compared to non-carrier patients. Seahorse real-time mitochondrial respiration assays in freshly isolated PBMCs further revealed disrupted oxidative phosphorylation in cells from patients carrying the rs202275 risk allele. As macrophage polarization from pro-inflammatory toward pro-resolving phenotype is dependent on oxidative metabolism, the functional impact of the rs202275 risk allele and associated reduction in FABP5 transcription may contribute to increased or prolonged systemic inflammation, thereby increasing susceptibility to exacerbation in COPD.

overall_design: Vehicle-treated BEAS-2B airway epithelial cells were used for Micro-C to evaluate genome-wide three-dimensional chromatin conformation under basal conditions.

first: Manale

last: El Kharbili

first: Lynn

last: Sanford

first: Sean

last: Jacobson

first: Katja

last: Aviszus

first: Arnav

last: Gupta

first: Claire

last: Guo

first: Susan

last: Majka

first: Robin

middle: D

last: Dowell

first: Anthony

last: Gerber

first: Russell

last: Bowler

first: Fabienne

last: Gally


title: Macrophage containing multicellular lung organoids

city: Cheongju-si

first: Dayeon

last: Gil

state: Chungcheongbuk-do

address: 202 Osongsaengmyung 2-ro, Heungdeok-gu

department: Division of intractable disease research

institute: Korea national institute of health

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

overall_design: Refer to individual Series


title: Genome-wide DNA Methylation Patterns in Daphnia magna Reveal Targeting to 5’ Exons

status: Public on Jul 05 2024

city: Los Angeles

first: Matteo

last: Pellegrini

state: LA

address: 610 Charles E. Young Drive

institute: University of California, Los Angeles

type: Methylation profiling by high throughput sequencing

summary: Daphnia magna is a widely used model organism in ecological and evolutionary studies. DNA methylation in D. magna can influence development and adaptation to changing environments. Previous studies have demonstrated that D. magna is generally hypomethylated. In this study we confirmed these observations using whole genome bisulfite sequencing (WGBS). In line with previous studies we observe that DNA methylation is elevated in the first exons downstream of the transcription start sites (TSS). Moreover, these exons are hypermethylated compared to adjacent introns. In contrast to prior studies in Daphnia, we found no significant changes in DNA methylation with age. These observations extend our understanding of the epigenetic landscape in D. magna, and motivate further exploration of epigenetic regulation in this organism and its response to environmental factors.

overall_design: Bisulfite sequencing of whole genome WT Daphnia magna from 3 age groups (18 samples)

first: Ruoshui

last: Liu

first: Marco

last: Morselli

first: Lev

middle: Y

last: Yampolsky

first: Leonid

last: Peshkin


title: Macrophage containing multicellular lung organoids [bulkRNA-seq]

summary: Proper lung development and function maintenance depend on the cross-talk between resident immune cell populations and lung epithelial cells. However, understanding the underlying cellular and molecular mechanisms are difficult to study in human. Here, we present a method to develop macrophage-containing alveolar organoids from human pluripotent stem cells to investigate reciprocal interactions between alveolar macrophages and epithelial cells in lung development.

overall_design: Transcriptomic differences of the macrophages from the human blood monocyte, macrophages differentiated from the human embryonic stem cell and, macrophages differentiated from the human embryonic stem cells co-cultured with alveolar organoids were compared.

first: Mi

middle: O

last: Lee

first: Jung-Hyun

last: Kim


title: Npbwr1 signaling mediates fast antidepressant action

city: Jena

first: Konstantin

last: Riege

address: Beutenbergstraße 11

institute: Leibniz Institute on Aging - Fritz Lipmann Institute (FLI)

summary: Chronic stress is a major risk factor for depression, a leading cause of disability and suicide. Because current antidepressants work slowly, have common side effects, and are only effective in a minority of patients, there is an unmet need to identify the underlying molecular mechanisms. Here, we identify the receptor for neuropeptides B and W, Npbwr1, as a key regulator of depressive-like symptoms. Npbwr1 is increased in the nucleus accumbens of chronically stressed mice and postmortem in patients diagnosed with depression. Using viral-mediated gene transfer, we demonstrate a causal link between Npbwr1, dendritic spine morphology, the biomarker Bdnf, and depressive-like behaviors. Importantly, microinjection of the synthetic antagonist of Npbwr1, CYM50769, rapidly ameliorates depressive-like behavioral symptoms and alters Bdnf levels. CYM50769 is selective, well tolerated, and shows effects up to 7 days after administration of a single dose. In summary, these findings advance our understanding of mood and chronic stress and warrant further investigation of CYM50769 as a potential fast-acting antidepressant.

overall_design: Total mRNA sequenced 1) for 8 brain NAc (Nucleus accumbens) samples of 8 weeks old mice after stereotaxic surgery to infect NAc by empty Adeno-associated virus constructs (GFP control) and AAVs to overexpress (OE) Npbwr1. And 2) for 64 NAc samples at four time points in a 12L:12D light cycle and from two genotypes (C75BL/6J wild type and T75A-DARPP-32 mutant), 2 hours after injection with 7.5 mg/kg caffeine or saline at an injection volume of 10ml/kg body.

first: Gregor

last: Stein

first: Janine

last: Aly

first: Lisa

last: Lange

first: Annamaria

last: Manzolillo

first: Anna

last: Brancato

first: Christian

last: Hübner

first: Gustavo

last: Turecki

first: Steve

last: Hoffmann

first: Olivia

last: Engmann


title: Macrophage containing multicellular lung organoids [scRNA-seq]

first: Dayeon

last: Gil

overall_design: Alveolar organoids were cultured without or with macrophages and analyzed using scRNAseq.


title: Gene expression profiling in response to strigolactone signalling revealed by dexamethasone treatment to SL-insensitive version of SMXL7 tagged with glucocorticoid receptor (SMXL7d53-GR) in Arabidopsis hypocotyl.

status: Public on Jul 01 2024

first: Thomas

last: Greb

address: Im Neuenheimer Feld 360

department: Centre for Organismal Studies

institute: Heidelberg University

summary: Strigolactone (SL) signalling plays many roles in plants, however, the downstream responsive genes remain unclear. SUPPRESSOR OF MORE AXILLARY GROWTH2-LIKE 7 (SMXL7) is degraded upon SL signalling. Here, we generated Arabidopsis carrying a transgene SMXL7pro:SMXL7d53-GR, where a SL-insensitive version of SMXL7 is tagged with the ligand binding domain of the glucocorticoid receptor (GR). SMXL7d53-GR will be translocated to the nucleus upon dexamethasone (dex), and we profiled the gene expression in mock or dex treated plants and revealed the downstream responsive genes of SL signalling.

overall_design: RNA-seq analysis of mock or dex treated SMXL7pro:SMXL7d53-GR transgenic Arabidopsis. Four replicates for each mock or dex treated sample.

first: Jiao

last: Zhao

first: Dongbo

last: Shi


title: Aging Promotes Metabolic Dysfunction-Associated Steatotic Liver Disease by Inducing Ferroptotic Stress

status: Public on Jul 02 2024

city: DURHAM

first: Rajesh

middle: Kumar

last: Dutta

address: 905 S LaSalle street, GSRB1, Rm-1063

department: Gastroenterology

institute: Duke University

summary: Aging increases the risk for failure of many metabolically-stressed organs and exacerbates liver degeneration related to obesity and diabetes. We used snRNA-seq to identify the effect of metabolic disease (MASLD) on biological aging of hepatocyte.

overall_design: 12 weeks old C57BL/6J male mice were fed with either chow or CDA-HFD for 22 weeks, and nuclei were isolated from liver tissues for snRNA-seq analysis

first: Kuo

last: Du

first: Liuyang

last: Wang

first: JiHye

last: Jun

first: Raquel

last: Maeso-Díaz

first: SehHoon

last: Oh

first: Dennis

middle: C

last: Ko

last: Diehl