title: Cell types activated in mouse muscle by TLR7/8 stimulation

status: Public on Sep 02 2024

city: Billerica

first: Nicholas

last: Geraci

state: MA

address: 45 Middlesex Turnpike 01821

department: Neuroscience & Immunology

institute: EMD Serono

summary: ScRNA-seq analysis of 11,450 cells from mouse muscle tissue sections following R848 injection identified 19 cell clusters, including four fibroblast, two endothelial cell, two macrophage, and two T cell subpopulations. To identify which cell populations were activated downstream of TLR7/8, interferon gene signature (IFN-GS) and NF-κB-gene signature (NF-κB-GS) scores were calculated and heat maps generated. There was a noticeable IFN response in most cell populations, with the greatest IFN-GS induction in neutrophils, endothelial cells and macrophages, and some response in T cells. However, IFN induction was not observed in any muscle cell type after R848 injection. The NF-κB-GS was expressed under basal conditions in many cell populations and was induced by R848 most in macrophages and neutrophils, with some increase also seen in endothelial cells.

overall_design:
Healthy C57BL/6 mice were injected intramuscularly with R848 or PBS. Post injection time points were collected at 1 or 2 hours where the whole tibialis anterior muscle tissue was excised and a single-cell suspension was made. The cells were analyzed by single-cell RNA sequencing using the 10X Genomics platform.

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first: Fatima

last: Strand

first: Andrew

last: Bender


title: CircRNAs expression profile in Mus musculus pre-metastatic lungs

status: Public on Sep 01 2024

city: Rizhao

first: Huifang

last: Shi

address: No. 126 Taian Road

country: China

institute: The Rizhao People’s Hospital Affiliated to Jining Medical University

type: Expression profiling by high throughput sequencing

summary: Our research aims to chart the circRNA expression profile and assess their impact on the lung PMN. We developed a lung PMN model and employed comprehensive RNA sequencing to analyze the differences in circRNA expression between normal and pre-metastatic lungs.Overall, our study highlights the crucial role of circRNAs in the formation of lung PMNs, supporting their potential as diagnostic or therapeutic targets for lung metastasis.


title: Effects of PSF inhibitors in castration-resistant prostate cancer cells

city: Itabashi-ku

first: Ken-ichi

last: Takayama

address: Sakaecho

country: Japan

institute: Tokyo Metropolitan Institute of Gerontology

summary:
Prostate cancer is the most common cancer in men and AR downstream signalings promote prostate cancer cell proliferation. Although initially hormone-deprovation therapy is effective to inhibit cancer progression, most of cancers relapse as castration-resistant prostate cancer (CRPC). RNA binding protein PSF is upregulated in CRPC tissues comparedd with hormone-sensitive prostate cancer. Therefore, we examined the effect of newly developed small molecules targeting PSF in CRPC cells.
In order to investigate the effect of PSF inhibiton in CRPC cells, we performed gene expression analysis in AR-negative CRPC cell line, DU145. We treated cells with vehicle, No.10-3, or C-30, which are supposed to inhibit PSF function.

overall_design: Observation of gene expression changes in CRPC after treatmet with PSF inhibitors No.10-3 oe C-30 using microarray.


title: Serial mRNA profiling of peripheral blood monocytes from PAH patients treated with phosphodiesterase 5 inhibitors (PDE5i) and PDE5i+macitentan

city: Pittsburgh

first: Satoshi

last: Okawa

state: PA

address: 200 Lothrop Street

country: USA

institute: University of Pittsburgh

summary:
Purpose: We performed single cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) from non-diseased control individuals (N=3) as well as from individuals with PAH, naïve to treatment (N=4), 3 months after phosphodiesterase 5 inhibitor (PDE5i) treatment (N=5), and 3 months after treatment with PDE5i plus an endothelin receptor antagonist, macitentan (N=5). We performed complementary analyses of differential gene expression and differential gene network dependency.
Method: Blood samples collected in EDTA purple top vacutainer were centrifuged at 2000 RPM for 15 minutes and plasma was removed for banking. Buffy coats were collected and used for Ficoll gradient to isolate PBMC which are used for the single cell RNA sequencing analysis. RNA libraries were prepared using Chromium Single Cell 3’ Reagent Kits V2 per manufacturer’s guidelines (10x Genomics manual CG00052, cat# PN-12237). Single cell RNA-sequencing was performed using the GemCodeTM Single Cell Instrument (Chromium, 10X Genomics) which included at least 800 cells (~50K reads per cell) per N=3 non-PAH control samples, N=4 PAH no treatment samples, N=8 PDE5i treated samples, and N=6 PDE5i+Macitentan treated samples.

overall_design: B cells, CD8+ T cells, CD4+ T cells, and NK cell RNA profile from non-PAH control, PAH no treatment, PDE5i treated, and PDE5i+macitentan treated samples

first: Stephen

middle: Y

last: Chan

first: Anna

last: Kirillova

first: Seungchan

last: Kim


title: Cellular senescence in hyperoxic neonatal rat lung

city: Milwaukee

first: Ru-Jeng

last: Teng

state: WI

address: 9200 W. Wisconsin Ave.

department: Pediatrics

institute: Medical College of Wisconsin

summary: Sprague-Dawley (SD) rat pups exposed to room air (NOX) or 95% O2 (HOX) from P1-P10 to study the role of cellular senescence in bronchopulmonary dysplasia (BPD). Markers of cellular senescence in the lungs were obtained at P10 and P21. ScRNAseq of the lungs were obtained at P10 to study cell type-specific cellular senescence.

overall_design: Cells isolated from the lungs of SD rat pups exposed to NOX and HOX were prepared for sc-RNAseq run through the Chromium platform.

first: Xigang

last: Jing

first: Shuang

last: Jia

first: Maggie

first: Chien-Wei

last: Lin

first: Martin

middle: J

last: Hessner

first: Kirwood

middle: A

last: Pritchard Jr

last: Naylor


title: The Human Milk Oligosaccharide 3’Sialyllactose Promotes Inflammation Resolution and Reduces Atherosclerosis Development in Mice

city: San Diego

first: Nathan

middle: E.

last: Lewis

state: CA

address: 9500 Gilman Dr.

institute: University of California, San Diego

summary: Macrophages contribute to the induction and resolution of inflammation and play a central role in the chronic low-grade inflammation in cardiovascular diseases caused by atherosclerosis. Human milk oligosaccharides (HMOs) are complex unconjugated glycans unique to human milk that benefit infant health and act as innate immune modulators. Here we identify the HMO 3’sialyllactose (3’SL) as a natural inhibitor of TLR4-induced low-grade inflammation in macrophages and endothelium. Transcriptome analysis in macrophages revealed that 3’SL attenuates a selected set of inflammatory gene expression and promotes activity of LXR and SREBP. Surprisingly, the acute anti-inflammatory effects of 3’SL were associated with reduced histone H3K27 acetylation at a subset of LPS-inducible enhancers distinguished by preferential enrichment for CTCF, IRF2, BCL6 and other transcription factor recognition motifs.  In a murine atherosclerosis model, the subcutaneous administration of 3’SL significantly reduced atherosclerosis development and macrophage content in atherosclerotic lesions. This study provides evidence that 3’SL attenuates inflammation by a transcriptional mechanism to reduce atherosclerosis development in the context of cardiovascular disease.

overall_design: We designed four different intervention groups (PBS, HMO, LPS, and LPS+HMO), each in triplicate  for a total of 12 different samples.

middle: E

first: Lars

last: Bode

first: Philip

middle: L

last: Gordts


title: Single-cell sequencing of diaphragms from both control and knockout mice at postnatal day 1

status: Public on Sep 05 2024

city: Shanghai

first: Zhen

middle: zhen

last: Wang

address: 320 Yueyang Road

institute: Shanghai Insititute of Nutrition and Health, University of Chinese Academy of Sciences

summary: Single-cell sequencing of diaphragms from control, SRSF1 knock-out, and SRSF2 knock-out mice revealed distinct cell types and highlighted the different roles of SRSF1 and SRSF2 in the development and function of skeletal muscle satellite cells.

overall_design: The diaphragms were isolated from one-day-old control, SRSF1 KO, and SRSF2 KO mice. The knockout of SRSF1 or SRSF2 was driven by Cre recombinase under the control of the MyoD1 promoter. To obtain a single-cell suspension, the diaphragms were fully digested with Dispase I and Collagenase type XI. The resulting single cells were then used for single-cell sequencing.

first: Rula

last: Sha

first: Zhenzhen

first: Ying

last: Feng


title: Cancer-cell-secreted miR-9-5p regulates cholesterol homeostasis to promote tumor metastasis [PBS, MCF-10A EV and MDA-MB-231 EV]

status: Public on Aug 31 2024

city: Wuhan

first: Li

last: Mei-Xin

address: College of Life Science, Wuhan University, Luojiashan Road, Wuchang District, Wuhan City, Hubei Province, China

institute: Wuhan University

summary:
To investigate the effects of breast cancer derived EVs on liver metabolism, NSG mice had received 5 weeks of i.v. injections of MCF-10A EVs, MDA-MB-231 EVs or PBS.
We then performed gene expression profiling analysis using data obtained from RNA-seq of liver from mice received 5 weeks of i.v. injections of MCF-10A EVs, MDA-MB-231 EVs or PBS.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver (PBS, MCF-10A EV and MDA-MB-231 EV ).

first: Mei-Xin

last: Li

first: Wei

last: Yan


title: Cancer-cell-secreted miR-9-5p regulates cholesterol homeostasis to promote tumor metastasis [TF TB Rab27AKD miR-9KO]

summary:
To investigate the effects of breast cancer derived EVs on liver metabolism,we inoculated MDA-MB-231,231 /Rab27A KD and 231 /miR-9 KO cells into subcutaneous tumor in NSG mice.
We then performed gene expression profiling analysis using data obtained from RNA-seq of liver from mice xenografted MDA-MB-231 cells (tumor bearing) or MDA-MB-231/Rab27A KD cells (231/Rab27A KD) or MDA-MB-231 /miR-9 KO (231/miR-9 KO) and tumor free mice.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for liver (tumor free, MDA-MB-231 cells (tumor bearing), MDA-MB-231/Rab27A KD cells (231/Rab27A KD) and MDA-MB-231/miR-9 KO cells (231 /miR-9 KO)).


title: Cancer-cell-secreted miR-9-5p regulates cholesterol homeostasis to promote tumor metastasis [vehicle and 25-HC]

summary:
To investigate the effects of 25-HC on the polarization of macrophage RAW264.7,RAW264.7 cells treated with 25-HC and untreated control were collected for RNA sequencing
We then performed gene expression profiling analysis using data obtained from RNA-seq of RAW264.7 cell treated with 25-HC and untreated control

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RAW264.7 (vehicle and 25-HC ).


title: Tumor-derived miR-9-5p-loaded EVs regulate cholesterol homeostasis to promote breast cancer liver metastasis in mice.

summary: Cancer cells secrete extracellular vesicles (EV) encapsulating bioactive cargoes to facilitate inter-organ communication in vivo and are emerging as critical mediators of tumor progression and metastasis, a condition which is often accompanied by a dysregulated cholesterol metabolism. Whether EVs are involved in the control of cholesterol homeostasis during tumor metastasis is still undefined and warrant further investigation. Here, we find that breast cancer-derived exosomal miR-9-5p induces the expression of HMGCR and CH25H, two enzymes involved in cholesterol synthesis and the conversion of 25-hydroxycholesterol from cholesterol by targeting INSIG1, INSIG2 and ATF3 genes in the liver. Notably, in vivo miR-9-5p antagomir treatment and genetic CH25H ablation prevents tumor metastasis in a mouse model of breast cancer. Thus, our findings reveal the regulatory mechanism of tumor-derived miR-9-5p in liver metastasis by linking oxysterol metabolism and Kupffer cell polarization, shedding light on future applications for cancer diagnosis and treatment.


title: Inactivation of the conserved protease LonA increases production of xylanase and amylase in Bacillus subtilis

status: Public on Aug 30 2024

city: Amsterdam

first: Biwen

address: Work, Science Park 904,1098 XH,Amsterdam,The Netherlands

department: Swammerdam Institute for Life Science

country: Netherlands

institute: University of Amsterdam

summary: In a previous study we used RNA-seq to identify cellular stresses related to the overexpression of xylanase XynA, and found that upregulation of the CtsR regulon improves the yield of XynA production in B. subtilis. In this study, we compared the transcriptomes of B. subtilis cells overexpressing either the xylanase XynA or the heterologous amylase AmyM, to identify general and enzyme-specific stress responses. In addition, we further compared the translational profiles of cells overexpressing XynA and AmyM using ribosome profiling.

overall_design: Overexpression of XynA and AmyM was achieved by cloning xynA and amyM respectively in the multicopy expression plasmid pUB110 behind the strong amyQ promoter. As a negative control, we transformed cells with an empty plasmid (Emp). The strains were grown in nutrient-rich LB medium at 37 °C in the presence of 50 μg/ml kanamycin to maintain the plasmids. We sampled cells  at 3 h (OD600~0.8) and 6h growth (OD~4) and performed RNA-seq and Ribome profiling. We compared the transcriptomes and translation profiles between XynA and AmyM overproducing cells. Two independent biological replicates were performed.

first: Mariah

middle: B

last: Kes

first: Anna

middle: C

last: van den Berg van Saparoea

first: Gaurav

last: Dugar

first: Joen

last: Luirink

first: Leendert

middle: W

last: Hamoen


title: Spatiotemporal Single-Cell Roadmap of Human Skin Wound Healing (Spatial)

status: Public on Sep 04 2024

city: Stockholm

first: Ning

last: Xu Landén

address: K2 Medicin, Solna, K2 Derm o Ven Xu Landén N

country: Sweden

institute: Karolinska Institutet

summary: The process of wound healing in humans is poorly understood. To identify spatiotemporal gene expression patterns during human wound healing, we performed spatial transcriptomics profiling of human in vivo wound samples.

overall_design:
We obtained the human skin wound tissues by recruiting healthy volunteers and we collected wound tissues at different time points to reflect different healing stages (intact skin, wound day1, day 7, and day 30). Samples from different wound healing stage were anaylsed by Spatial transcriptomics sequencing.

*** The raw sequencing data are available for controlled access in European Genome–phenome Archive (EGA) under the accession code EGAS50000000571 ***


title: Characterization of co-transcriptional splicing in acute lymphoblastic leukemia

status: Public on Sep 09 2024

city: Memphis

first: Rashid

last: Mehmood

state: Tennessee

address: 324 NIGHT SAIL DR N APT 112, UNIT # 04-112

department: Hematology

institute: St Jude Children's Research Hospital

type: Genome binding/occupancy profiling by high throughput sequencing

summary:
Alternative splicing is a promising therapeutic target in acute lymphoblastic leukemia. Here, we report the alternative splicing changes in B-ALL cell lines including NALM6 cells and MUTZ-5 cells treated with DYRK1 inhibitor, EHT 1610 and GNF 2133.
Dysregulation of co-transcriptional splicing is a therapeutic target in acute lymphoblastic leukemia (ALL). Here, we detected the alternative splicing in NALM6 cells or MUTZ-5 cells treated with EHT 1610 or GNF2133. We detected the alternative splicing in NALM6 cells cells treated with THAL-SNS-032. We also determined the alternative splicing in MEF2D-BCL9 ALL and MEF2D-HNRNPUL1 ALL patient xenografted samples treated with E7820, a anticancer sulfamide, or DMSO. Furthermore, ChIP-seq for RNA polymerase II (Pol II), p-Ser2 Pol II, and p-Ser5 Pol II were performed after DMSO or EHT 1610 treatment in NALM6 cells. ChIP-seq for p-Ser2 Pol II, and p-Ser5 Pol II were performed after DMSO or THAL-SNS-032 treatment in NALM6 cells.PRO-seq in NALM6 cells treated with DMSO, EHT 1610, and THAL-SNS-032 were performed.

overall_design:
NALM6 and MUTZ-5 cells were treated with 5 μM of EHT 1610 or GNF 2133 following by RNA-seq
NALM6 cells were treated with 5 microM of EHT 1610 or DMSO followed by eCLIP-seq for SF3B1
NALM6 cells were treated with 5 microM of EHT 1610 or DMSO followed by ChIP-seq for RNA polymerase II (Pol II), p-Ser2 Pol II, and p-Ser5 Pol II
MEF2D-BCL9 and MEF2D-HNRNPUL1 PDX samples were treated with 1 microM of E7820 or DMSO followed by RNA-seq
NALM6 cells were treated with, DMSO, 5 microM of EHT 1610, 500 nM of THAL-SNS-032 followed by PRO-seq
THAL-SNS-032 treatment (500 nM) in NALM6 cells followed by RNA-seq.
NALM6 cells were treated with 500 nM of THAL-SNS-032 or DMSO followed by ChIP-seq for p-Ser2 Pol II and p-Ser5 Pol II.

first: Qi

last: Jin

first: Rashd


title: Plekhg5 regulates the unconventional secretion of Sod1 by presynaptic secretory autophagy

status: Public on Aug 28 2024

city: Wuerzburg

first: Patrick

last: Lüningschrör

address: Versbacher Str. 5

department: Institute of Clinical Neurobiology

country: Germany

institute: University Hospital Wuerzburg

summary: Increasing evidence suggests an essential function for autophagy in unconventional protein secretion (UPS). However, despite its relevance for the secretion of aggregate-prone proteins, the mechanisms of secretory autophagy in neurons have remained elusive. Here we show that the lower motoneuron disease-associated protein Plekhg5 drives the UPS of Sod1. Mechanistically, Sod1 is sequestered into the intermembrane space of autophagosomes which fuse with secretory lysosomal-related organelles (LROs). Deletion of Plekhg5 in mice disrupts the secretion of these LROs causing Sod1 accumulation at swollen presynaptic sites. A reduced secretion of toxic ALS-linked SOD1G93A following deletion of Plekhg5 in SOD1G93A mice accelerated disease onset while prolonging survival due to an attenuated microglia activation. Using human isogenic iPSC-derived motoneurons we show an impaired secretion of ALS-linked SOD1D90A, which coincided with a reduced PLEKHG5 expression. Our findings highlight an unexpected pathophysiological mechanism that converges two motoneuron disease-associated proteins into a common pathway.

overall_design: To investigate the impact of Plekhg5 on the phenotype of SOD1-G93A mice, we crossed Plekhg5-deficient mice with SOD1-G93A expressing mice. Total RNA was isolated from spinal cord tissues of 7 months-old mice and we performed gene expression profiling analysis with RNAseq data from wildtype (control) mice, Plekhg5-deficient mice, SOD1-G93A mice, and Plekhg5-deficient SOD1-G93A mice.

first: Amy-Jayne

last: Hutchings

first: Thorsten

last: Bischler


title: Identifying key regulatory networks and predicting targets of orphan box C/D SNORD116 snoRNAs in Prader-Willi Syndrome

status: Public on Aug 29 2024

city: Heidelberg

first: Rachel

last: Gilmore

state: BW

address: Im Neuenheimer Feld 366

department: Institute for Human Genetics

institute: Heidelberg University

summary: To identify the targets and functions of SNORD116 snoRNAs, we engineered two different deletions mimicking those seen in Prader-Willi Syndrome (PWS) patients into two distinct human embryonic stem cell lines to control for effects of genetic background. We also introduced an inducible Neurogenin-2 cassette into the safe-harbor AAVS1 locus to enable quick and reproducible differentiation into neurons. We verified wild type and deletion genotypes across both genetic background generated comparable neruons at a gene expression level by comparing them to wild type hESCs. We then performed differential gene expression analysis using data obtained from bulk RNA-sequencing to compare the two distinct deletion types to their isogenic wild type pair and each other.

overall_design: Comparative differential gene expression analysis of bulk RNA-seq data for 4-6 biological replicates of wild type H9 and CT2 inducible neurons and their PWS-like deletion derivatives.

first: Gilmore

last: Rachel B.

first: Liu

last: Yaling

first: Carmichael

last: Gordon

first: Cotney

last: Justin L.


title: Tumor cell-based liquid biopsy using high-throughput microfluidic enrichment of entire leukapheresis product

status: Public on Aug 27 2024

city: Boston

first: Ben

middle: S.

last: Wittner

address: 149 13th Street

department: Center for Cancer Research

institute: Massachusetts General Hospital

summary: Circulating Tumor Cells (CTCs) encompass multiple analytes, interrogated by sampling blood from patients with cancer. However, the clinical utility of tumor cell-based liquid biopsy has proven to be limited since CTCs are rare, and current technologies cannot process larger blood volumes required to isolate a sufficient number of tumor cells. We have described a high-throughput microfluidic prototype utilizing high-flow channels and amplification of cell sorting forces through magnetic lenses. Here, we apply this technology to analyze patient-derived leukapheresis products, interrogating a mean blood volume of 5.83 liters from patients with metastatic cancer and achieving a median of 2,799 CTCs per patient. Isolation of many CTCs from individual patients enables characterization of their morphological and molecular heterogeneity, including cell and nuclear size and RNA expression. It also allows robust detection of gene copy number variation (CNV), a definitive cancer marker with potential diagnostic applications. High-volume microfluidic enrichment of CTCs constitutes a new dimension in liquid biopsies.

overall_design: We performed single-cell RNA-seq for cells displaying CNV isolated from leukapheresis product [PMID: 32641515] from two metastatic castration resistant prostate cancer patients, GU-1 and GU-2. Of the 30 cells from GU-1, 27 were EpCAM+ and/or PSMA+ using a SONY sorter SH800, and three were EpCAM- and PSMA-. For GU-2 63 were EpCAM+ and/or PSMA+ using the SONY sorter and 11 were EpCAM- and PSMA-. We also performed single-cell RNA-seq for three cells isolated from the BRx68 cultured circulating tumor cells [PMID: 25013076] and for three white blood cells from a healthy donor.

first: Avanish

last: Mishra

first: Shih-Bo

last: Huang

middle: S

first: Daniel

last: Haber

first: Mehmet

last: Toner


title: Mapping cells through time and space with moscot - pancreatic endocrinogenesis multiome

status: Public on Aug 26 2024

city: Neuherberg

first: Heiko

last: Lickert

address: Ingolstaedter Landstraße 1

department: Institute of Diabetes and Regeneration Research

institute: Helmholtz Zentrum München German Research Center for Environmental Health

summary: This dataset consists of single-nucleus RNA-seq and single-cell ATAC-seq (10X multiome) data from 3 embryonic stages (E14.5-16.5) of pancreatic epithelial cells from Neurogenin3 (Ngn3)-Venus fusion (NVF) homozygous mice. Endocrine progenitor cells (NVF+) were enriched by FACS cell sorting.

overall_design: 4 single cell RNA seq experiments were performed (E14.5, E15.5 (1), E15.5 (2), E16.5) using 10X Genomics technology to generate single cell transcriptomic and ATAC-seq profiles of embryonic pancreatic epithelial cells from a Neurogenin3 (Ngn3)-Venus fusion (NVF) reporter mouse line. Cells were sorted and NVF+ and NVF- cells mixed (2/3, 1/3) to enrich for endocrine Ngn3+ progenitors. Cells were sampled from pancreata of E14.5,E15.5 and E16.5 embryos.

first: Dominik

last: Klein

first: Giovanni

last: Palla

first: Marius

last: Lange

first: Michal

first: Zoe

last: Piran

first: Manuel

last: Gander

first: Laetitia

last: Meng-Papaxanthos

first: Michael

last: Sterr

first: Lama

last: Saber

first: Changying

last: Jing

first: Aimée

last: Bastidas-Ponce

first: Marta

last: Tarquis-Medina

first: Shrey

last: Parikh

first: Ilan

last: Gold

first: Mostafa

last: Bakhti

first: Mor

last: Nitzan

first: Marco

last: Cuturi

first: Fabian

last: Theis


title: Inhibition of the Wnt/β-catenin signaling pathway and SOX9 by XAV939 does not alleviate inflammation in a dextran sulfate sodium-induced ulcerative colitis model

status: Public on Aug 23 2024

city: Foshan

first: Shaojie

last: Liang

address: No.3 Baojian road

institute: Shunde Maternal and Children’s Hospital, Guangdong Medical University

summary: The Wnt/β-catenin signaling pathway is known to be hyperactivated during the pathogenesis of ulcerative colitis (UC). The present study aimed to explore the therapeutic efficacy of the Wnt/β-catenin signaling inhibitor XAV939 in mitigating UC symptoms. Utilizing a dextran sulfate sodium (DSS)-induced UC mouse model, the present study aimed to evaluate the impact of XAV939 on intestinal morphology through H&E staining and to measure the expression levels of critical proteins in the Wnt/β-catenin signaling cascade. XAV939 did not exert a significant influence on the morphological features and inflammatory status of the intestinal epithelium. However, XAV939 was found to effectively suppress the Wnt/β-catenin signaling pathway and its downstream target SOX9. This suppression implies a reduction in the differentiation of intestinal stem cells into secretory cell progenitor cells. Additionally, XAV939 was ineffective in reversing the DSS-induced derease in Villin and peroxisome proliferator-activated receptor γ, suggesting that it did not facilitate the differentiation of intestinal absorptive cells. The present findings indicated that the Wnt/β-catenin signaling pathway may not be the predominant mechanism in the pathogenesis of DSS-induced UC.

overall_design: For RNA-sequencing (RNA-seq) experiment, a total of 6 healthy male C57BL/6 mice (18-22 g; 8 weeks of age) were randomly divided into two groups (n=3). The control group received distilled water, while the treatment group received 3.5% DSS for 7 days.

first: Kun

last: Wang

first: Dabin

last: Mao

first: Qianqian

last: Ouyang


title: 12-Lipoxygenase Inhibition Suppresses Islet Immune and Inflammatory Responses and Delays Autoimmune Diabetes in Human Gene Replacement Mice

city: Chicago

first: Sarah

last: Tersey

state: IL

department: Medicine

institute: University of Chicago

summary: Type 1 diabetes (T1D) is characterized by the autoimmune destruction of insulin-producing β cells and involves an interplay between β cells and cells of the innate and adaptive immune systems. We investigated the therapeutic potential of targeting 12-lipoxygenase (12-LOX), an enzyme implicated in inflammatory pathways in β cells and macrophages, using a mouse model in which the endogenous mouse Alox15 gene is replaced by the human ALOX12gene. Our findings demonstrate that VLX-1005, a potent 12-LOX inhibitor, effectively delays the onset of autoimmune diabetes in human gene replacement non-obese diabetic (NOD) mice. By spatial proteomics analysis, VLX-1005 treatment resulted in marked reductions in infiltrating T and B cells and macrophages with accompanying increases in immune checkpoint molecules PD-L1 and PD-1, suggesting a shift towards an immune-suppressive microenvironment. RNA sequencing analysis of isolated islets from inhibitor-treated mice revealed significant alteration of cytokine-responsive pathways. RNA sequencing of polarized proinflammatory macrophages showed that VLX-1005 significantly reduced the interferon response. This study highlights a functional equivalence of human ALOX12 and mouse Alox15 in T1D pathogenesis. Our studies provide a platform for the preclinical evaluation of LOX inhibitors and supports the development of 12-LOX inhibitors as a therapeutic strategy for T1D and other inflammatory diseases.

overall_design: To investigate the inhibition of 12-lipoxygenase in islets, NOD.hALOX12 mice were treated for 4 weeks with VLX-1005 or vehicle. After 4 weeks of treatment, islets were isolated using standard protocols. RNA was isolated and processed for RNA-sequencing.

first: Raghavendra

middle: G

last: Mirmira

first: Titli

last: Nargis

first: David

last: Maloney


title: 12-Lipoxygenase Inhibition Suppresses Islet Immune and Inflammatory Responses and Delays Autoimmune Diabetes in Human Gene Replacement Mice.

overall_design: To investigate the inhibition of 12-lipoxygenase in macrophages, bone marrow was harvested from NOD.hALOX12 mice and bone marrow devired macrophages were isolated to M0 macrophages. M0 macrophages were treated with vehicle or VLX-1005. M0 macrophages were stimulated to M1 macrophages with LPS and IFN-γ in the presence of vehicle or VLX-1005 were treated for 4 weeks with VLX-1005 or vehicle. RNA was isolated and processed for RNA-sequencing.


title: Single-cell view and a novel protective macrophage subset in perivascular adipose tissue (PVAT) in T2DM

city: Jinan

first: Zhenyu

last: Tian

state: Shandong

address: No. 107, Wenhua west road

institute: Qilu Hospital of Shandong University

summary: Reveal the single-cell landscape of the stromal vascular fraction (SVF) of perivascular adipose tissue (PVAT) and show its tremendous heterogeneity and significant alterations in type 2 diabetes.

overall_design: We performed single-cell RNA sequencing of the SVF of thoracic aorta PVAT from two groups (NC and T2DM) of rat

first: Jiaxuan

last: Li

first: Zhe

first: Qunye

last: Zhang


title: Genome concentration limits cell growth and modulates proteome composition in Escherichia coli

city: Stanford

first: Georgi

middle: Kolev

last: Marinov

state: California

address: 279 Campus Drive West, Beckman Center, B-257A/259

department: Genetics

institute: STANFORD UNIVERSITY

summary: Defining the cellular factors that drive growth rate and proteome composition is essential for understanding and manipulating cellular systems. In bacteria, ribosome concentration is known to be a constraining factor of cell growth rate, while gene concentration is usually assumed not to be limiting. Here, using single-molecule tracking, quantitative single-cell microscopy, and modeling, we show that genome dilution in Escherichia coli cells arrested for DNA replication results in a decrease in the concentration of active RNA polymerases and ribosomes. The resulting sub-linear scaling of total active RNA polymerases and ribosomes with cell size leads to sub-exponential growth, even within physiological cell sizes. Cell growth rate scales proportionally with the total number of active ribosomes in a DNA concentration-dependent manner. Tandem-mass-tag mass spectrometry experiments further revealed that a decrease in DNA-to-cell-volume ratio also incrementally remodels proteome composition with cell size. Altogether, our findings indicate that genome concentration is an important driver of exponential cell growth and a global modulator of proteome composition in E. coli. Comparison with studies on eukaryotic cells suggests DNA concentration-dependent scaling principles of gene expression across domains of life.

sample_organism:
Escherichia coli K-12
Caulobacter vibrioides

overall_design: RNA-seq libraries associated with the project; CRISPRi oriC strain (SJ_XTL676) was grown in M9glyCAAT at 37°C and cells were collected 60, 120, 200, and 240 min after addition of 0.2% L-arabinose. For each timepoint, the aliquot was spun down, the supernatant was removed, and the pellet was flash-frozen. E. coli pellets were resuspended in ice cold phosphate buffer saline solution (PBS) and mixed with C. crescentus cells in approximately a 1-to-1 ratio based on OD600, with the intent of using the latter as a spike-in reference.

first: Jarno

last: Mäkelä

first: Alexandros

last: Papagiannakis

first: Wei

middle: H

last: Lin

first: Skye

last: Glenn

first: Michael

last: Lanz

first: Matthew

last: Swaffer

middle: K

first: Jan

middle: M

last: Skotheim

first: Christine

last: Jacobs-Wagner


title: Identification and genetic dissection of convergent persister cell states

status: Public on Aug 22 2024

city: New York

first: Sydney

last: Blattman

state: NY

address: 1150 St. Nicholas Ave

institute: Columbia University

summary:
We generated a high-resolution single-cell RNA atlas of E. coli growth transitions, which revealed that a distinct persister state. We then used ultra-dense CRISPR-interference to determine how every E. coli gene contributes to persister formation across genetic models.

***Download data version 2 whenever present***

overall_design: scRNA-seq of E. coli cells using PETRI-seq method; CRISPRi screen of E. coli cells

first: Wenyan

last: Jiang

first: E. Riley

last: McGarrigle

first: Menghan

last: Liu

first: Panos

last: Oikonomou

first: Saeed

last: Tavazoie


title: Nuclear speckles regulate functional programs in cancer

city: Cold Spring Harbor

first: Katherine

middle: Ann

last: Alexander

address: 1 Bungtown Road

institute: Cold Spring Harbor Laboratory

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

overall_design: Refer to individual Series


title: Dendritic cell effector mechanisms and tumor immune microenvironment infiltration define TLR8 modulation and PD-1 blockade

status: Public on Aug 14 2024

city: Newport

first: Jillian

middle: F

last: Wise

state: Rhode Island

address: 100 Ochre Point Ave

department: Biology and Biomedical Sciences

institute: Salve Regina University

summary: The potent immunostimulatory effects of toll-like receptor 8 (TLR8) agonism in combination with PD-1 blockade has resulted in a variety of preclinical investigations, yet the mechanism of action in humans remains unknown. We used scRNAsequencing and multi-spectral spatial imaging to elucidate the tumor immune microenvironment and correlates to response to a a unique open-label phase 1b pre-operative window of opportunity clinical trial (NCT03906526) in head and neck squamous cell carcinoma (HNSCC)

overall_design: scRNAseq was performed on three head and neck squamous cell carcinoma patient samples treated with a TLR8 agonist (Motolimod) and anti-PD1 therapy (Nivolumab) pre and post therapy.

first: Daniel

last: Ruiz-Torres

first: Brian

middle: Y

last: Zhao

first: Joao

middle: P

last: Oliveira-Costa

first: Sara

last: Cavallaro

first: Peter

last: Sadow

first: Jacy

last: Fang

first: Osman

last: Yilmaz

first: Amar

last: Patel

first: Christopher

last: Loosbrock

first: Moshe

last: Sade-Feldman

last: Faden

first: Shannon

last: Stott


title: Studies on the International Space Station to assess the effects of microgravity on iPSC-derived neural organoids

first: Scott

middle: Allen

last: Noggle

address: 619 West 54th Street

institute: NYSCF

summary: Exposure to microgravity in low-Earth orbit (LEO) has been shown to affect human health. Post-flight brain imaging and studies of astronauts and mouse models suggest that microgravity may cause intracranial fluid shifts and possibly alter white and gray matter of the brain. To focus on the effects of microgravity on brain cells, we used induced pluripotent stem cells (iPSCs) to produce three-dimensional (3D) human neural organoids as models of the nervous system. We studied iPSC-derived organoids from four individuals, including people with the neurological diseases primary progressive multiple sclerosis (PPMS) and Parkinson’s disease (PD) and non-symptomatic controls. We patterned the organoids toward cortical and dopaminergic fates representing regions of the brain affected by MS and PD, respectively. Microglia were generated from the same cell lines and integrated into a portion of the organoids. The organoids were maintained for a month in a novel static culture system on the International Space Station (ISS) and live samples were returned to Earth. The post-flight samples were evaluated using transcriptome analysis. Microglia-specific genes were detectable in the microglia-containing organoid cultures. Differential gene expression analyses of individual organoids cultured in LEO and on Earth suggest that cell proliferation was lower and neural cells were more mature in samples that were cultured in LEO. These experiments lay the groundwork for further studies, including long term studies to investigate the effects of microgravity on the brain.

overall_design: Three dimensional aggregates created from iPSC-derived cortical neurons or dopaminergic neurons were exposed to microgravity for 38 days on the ISS with ground control samples cultured in parallel under normal gravity conditions on earth.  Additional experimental variabiles incuded samples with or without iPSC-derived microglia added to the organoids at the start of the experiment. Bulk RNAseq analysis was performed on individual organoids in replicates for each condition.

middle: A

first: Valentina

last: Fossati

first: Jeanne

last: Loring

first: Paula

last: Grisanti

first: Davide

last: Marotta

first: Laraib

last: Ijaz

first: Madjura

last: Nijsure

first: Jason

last: Stein

first: Twyman

last: Clements

first: Jana

last: Stoudemire


title: Generation of megakaryocytes and functional platelets from human embryonic stem cells

city: Guangzhou

first: Chuxin

last: Chen

address: Xiaoguwei Street

institute: South China University of Technology

summary: We developed a novel differentiation system that directionally induces hESCs into megakaryocytes and functional platelet in vitro by highly mimicking the in vivo developmental process of megakaryocytes and platelets. We then performed gene expression profiling analysis using data obtained by RNA-seq at different stages of differentiation during the differentiation of hESCs into megakaryocyte lineages.

overall_design: Cell spheres or suspension cells were collected for RNA-seq on days 0, 2, 6, 9, 9+0, 9+2, and 9+6 of differentiation during the directed differentiation of hESCs towards megakaryocytes.


title: LncRNA SNHG26 facilitates inflammatory to proliferative state transition of keratinocyte progenitors during wound healing

first: Ning

last: Xu Landén

summary: The epidermal stem cell transition from inflammation to proliferation is a crucial process in tissue repair. However, the molecular mechanism underlying this process is poorly understood. Combined with lncRNA expression profiling of human acute wounds and functional screening, we identified SNHG26 as a pivotal regulator of inflammatory to proliferative state transition of keratinocyte progenitor cells. Snhg26-deficient mice showed impaired wound healing characterized by increased inflammatory response and decreased reepithelization in the wound. Consistently, single-cell transcriptomic analysis of the wound-edge tissue identified proliferative, migratory, and proinflammatory basal progenitors, which were dramatically changed in Snhg26 deficient mice. Mechanically, SNHG26 binds with ILF2 to relocate this transcription factor from the inflammatory gene loci (such as JUN) to the LAMB3 genomic loci. Collectively, this work identified a conserved lncRNA SNHG26 as a master regulator of epidermal stem cell state transition from inflammation to proliferation, highlighting the importance of lncRNAs in tissue repair and regeneration.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design:
The epidermal stem cell transition from inflammation to proliferation is a crucial process in tissue repair. However, the molecular mechanism underlying this process is poorly understood. We identified SNHG26 as a pivotal regulator of inflammatory to proliferative state transition of keratinocyte progenitor cells. The Snhg26-deficient mice showed impaired wound healing. We collected mice skin and acute wound edge (Day3) samples and performed 10x single cell sequencing according to the manufacture instruction.
Mechanically, SNHG26 binds with ILF2. To study the effect of silencing of SNHG26 on ILF2 interaction with genome, we knockdown SNHG26 followed by TNFa stimulation. Then we performed ILF2 CHIP sequencing.
To study which genomic loci the SNHG26 interact with, we performed SNHG26 ChIRP assay by using antisense oligoes targeting SNHG26. The chromatin associated with SNHG26 antisense oligoes was purified and subjected to deep DNA sequencing.

middle: X

last: Landén

first: Dongqing

last: Li


title: Disruption of C5a/C5aR1 axis confers protection against hookworm infection in lung

first: Markus

last: Bosmann

address: 72 E Concord Street

department: Pulmonary Centre, Department of Medicine

institute: Boston University

summary: Hookworms are soil-transmitted parasitic nematodes that penetrate the host skin before migrating to the lungs. With an estimated 500-700 million people infected worldwide, hookworm infections are a neglected tropical disease and a significant cause of morbidity, particularly in children, pregnant women, and immunocompromised individuals. Although there is ample evidence that complement activation is pivotal to elicit a protective host immune response against invasive pathogens, its role in hookworm infection remains insufficiently explored. Here, we investigated the complement anaphylatoxin, C5a, during the early lung stage of infection with Nippostrongylus brasiliensis in C57BL/6J wild type and C5aR1-/- mice. Despite the previously reported ability of lung larvae to evade complement activation, C5a was detectable locally in lung tissue and broncho-alveolar lavages. Surprisingly, C5aR1 presence directly contributed to the pathogenicity of hookworm infection. The burden of viable parasites in the lungs was mitigated in C5aR1-/- mice, compared to C57BL/6J mice 48 hours post-infection. Additionally, C5aR1-/- mice showed significantly reduced lung injury, lower cytokine release, attenuated alveolar hemorrhage, and limited alveolar-capillary barrier disruption. Neutrophils were the most abundant and highest C5aR1-expressing cell type in the alveolar space after infection. Deficiency of C5aR1 reduced the influx of neutrophils, monocytes, and eosinophils to the pulmonary airways. RNA sequencing of alveolar neutrophils revealed C5aR1-dependent regulation of the novel nuclear protein, DEDD2. In conclusion, our findings highlight the impact of C5aR1 signaling in neutrophils during hookworm infection uncovering an unexpected downside of complement activation in parasitic infection.

overall_design: Wild type (WT) and  C5aR1-/- male mice (10-12 weeks of age) were injected sub-cutaneously in the flank with 500 Nippostrongylus brasiliensis L3 larvae in 0.1 mL of sterile phosphate buffered saline. Bronchoalveolar lavages were collected 48 h after infection, neutrophils isolated and bulk RNA-sequencing was performed.

first: Sarah

last: Walachowski

first: Lucien

last: Garo

first: Arjun

last: Sharma

first: Archana

last: Jayarman


title: Structural variant allelic heterogeneity in MECP2 Duplication Syndrome provides insight into clinical severity and variability of disease expression

status: Public on Aug 12 2024

city: Seattle

first: Jesse

last: Bengtsson

state: WA

address: 720 Broadway

institute: Pacific Northwest Research Institute

summary: MECP2 Duplication Syndrome, also known as X-linked intellectual developmental disorder Lubs type (MRXSL; MIM: 300260), is a neurodevelopmental disorder caused by copy number gains spanning MECP2. Despite varying genomic rearrangement structures, including duplications and triplications, and a wide range of duplication sizes, no clear correlation exists between DNA rearrangement and clinical features. We had previously demonstrated that up to 38% of MRXLS families are characterized by complex genomic rearrangements (CGRs) of intermediate complexity (2 ≤ CNV breakpoints < 5), yet the impact of these genomic structures on regulation of gene expression and phenotypic manifestations have not been investigated. To study the role of the genomic rearrangement structures on an individual’s clinical phenotypic variability, we employed a comprehensive genomics, transcriptomics, and deep phenotyping analysis approach on 137 individuals affected by MRXSL. Genomic structural information was correlated with transcriptomic and quantitative phenotypic analysis using Human Phenotype Ontology (HPO) semantic similarity scores. Duplication sizes in the cohort ranging from 64 kb to 16.5 Mb were classified into four categories comprising of tandem duplications (47%), terminal duplications (23%), inverted triplication structures (23%), and other CGRs (7%). A majority of the terminal duplication structures consist of translocations (65%) followed by recombinant chromosomes (23%). Notably, 67% of de novo events occurred in the terminal duplication group in contrast with 17% observed in tandem duplications. RNAseq data from lymphoblastoid cell lines indicated that the MECP2 transcript quantity in MECP2 triplications is statistically different from all duplications, but not between other classes of genomic structures. We also observed a significant (p < 0.05) correlation (Pearson R = 0.6, Spearman = 0.63) between the log-transformed MECP2 RNA levels and MeCP2 protein levels, demonstrating that genomic aberrations spanning MECP2 lead to altered MECP2 RNA and MeCP2 protein levels. Genotype-phenotype analyses indicated a gradual worsening of phenotypic features, including overall survival, developmental levels, microcephaly, epilepsy, and genitourinary/eye abnormalities in the following order: tandem duplications, other CGRs, terminal duplications/translocations, and triplications encompassing MECP2. In aggregate, this combined analysis uncovers an interplay between MECP2 dosage, genomic rearrangement structure and phenotypic traits. Whereas the level of MeCP2 is a key determinant of the phenotype, the DNA rearrangement structure can contribute to clinical severity and disease expression variability. Employing this type of analytical approach will advance our understanding of the impact of genomic rearrangements on genomic disorders and may help guide more targeted therapeutic approaches.

overall_design: This work was designed to determine the structure of copy number variants in the Xq28 region in MECP2 duplication syndrome patients

first: Ming

last: Lun

first: Claudia

last: Carvalho


title: Thyroid hormone receptor beta (THRB) dependent regulation of diurnal hepatic lipid metabolism in adult male mice

status: Public on Aug 13 2024

city: Lübeck

first: Leonardo

last: de Assis

address: Marie Curie

institute: University of Lübeck

summary: Thyroid hormones (THs) are critical regulators of systemic energy metabolism and homeostasis. In the liver, high TH action protects against steatosis by enhancing cholesterol and triglyceride turnover, with thyroid hormone receptor beta (THRB) signaling playing a pivotal role. This study probed the potential interaction between THRB action and another critical regulator of liver energy metabolism, the circadian clock. Liver transcriptome analysis of THRB deficient (THRBKO) mice under normal chow conditions revealed a markedly modest impact of THRB deletion. Temporal transcriptome and lipidome profiling uncovered significant alterations in diurnal metabolic rhythms attributable to THRB deficiency pointing to a pro-steatotic state with elevated levels of cholesterol, tri- and diacylglycerides, and fatty acids. These findings were confirmed by THRB agonization in hepatocytes under steatosis-promoting conditions in vitro. Integration of transcriptome profiles from THRBKO mice and mice with induced high or low TH action identified a subset of TH responsive but THRB insensitive genes implicated in immune processes. In summary, our study reveals a complex time-of-day dependent interaction of different TH-related signals in the regulation of liver physiology indicating an opportunity for chronopharmacological approaches to TH/THR(B) manipulation in fatty liver diseases.

overall_design: Two to three-months-old male wild type (THRB+/-) and knockout (THRB-/-) were group-housed under 12h/12h light/dark conditions (LD, 200 – 400 lux) at 22 ± 2°C with food and water provided ad libitum (normal chow, 5 % fat, 1314, Altromin, Germany). Mice were culled by cervical dislocation at 4-hour intervals, tissues were kept in dry ice, and stored at -80°C

first: Henrik

last: Oster


title: Role of nuclear p38 in the transcriptional response to oxidative stress in Drosophila (RNA-Seq)

status: Public on Aug 09 2024

city: Barcelona

first: Montserrat

last: Corominas

state: Catalonia

address: Diagonal 643

department: Genètica, Microbiologia i estadística

country: Spain

institute: University of Barcelona

summary: p38 mitogen-activated protein kinases play fundamental roles in the regulation of the cellular response to environmental stress. p38 is known to regulate translation, mRNA processing and stability, and transcription. The transcriptional response mediated by phosphorylated p38 (P-p38) to extracellular stimuli, such as growth factors, cytokines and different environmental agents, has been thoroughly analysed in a variety of tissues and organisms. However, the genomic localisation of P-p38 is poorly understood. Here, we analysed the chromatin binding of activated P-p38 and the transcriptional response triggered by reactive oxygen species (ROS) in Drosophila S2 cells. We found that P-p38 is already bound to chromatin in basal conditions and relocates in the genome after exposure to high levels of ROS. The distribution pattern of P-p38 suggests that it is involved in the activation and repression of transcription in S2 cells, mainly regulating house-keeping functions.

overall_design: Gene expression profiling analysis of Drosophila S2 cells.

first: Paula

last: Climent-Cantó

first: Palmira

last: Llorens-Giralt

first: Cecilia

last: Klein

first: Florenci

last: Serras


title: RNA binding properties of NONO and NONO-delta-ER in testis;

status: Public on Aug 08 2024

city: nanjing

first: huicong

last: zhai

address: 101 Longmian Avenue, Jiangning District (or 818 Tianyuan East Road)

institute: Nanjing Medical University

summary:
To investigate the RNA binding proterties of NONO and NONO-delta-ER in testis;  we collected adult NONO and NONO-delta-ER mice  testis
We then performed eCLIP-seq respectively and convey subsequent bioinformatic analysis.

overall_design: Comparative RNA binding specificity and affinity analysis analysis of eCLIP-seq data for NONO and NONO-delta-ER in testis;

first: Yang

first: Yuanyuan

last: Wang


title: Centrophilic retrotransposon integration via targeting CENH3 chromatin in Arabidopsis [TED-seq]

city: Bunkyo-ku

first: Sayuri

last: Tsukahara

state: Tokyo

address: Hongo 7-3-1

institute: The University of Tokyo

summary: In organisms ranging from vertebrates to plants, major components of centromeres are rapidly-evolving repeat sequences, such as tandem repeats (TRs) and transposable elements (TEs). These repeats harbor centromere-specific histone H3 (CENH3), which also evolves rapidly. Complete centromere structures recently determined in human and Arabidopsis suggest frequent integration and purging of retrotransposons within the TR regions of centromeres. Despite the high impact of “centrophilic” retrotransposons on the paradox of rapid centromere evolution, the mechanisms involved in centromere targeting remain poorly understood in any organism. Here we show that both Ty3 and Ty1/Copia LTR elements rapidly turnover within the centromeric TRs of Arabidopsis species. We demonstrate that the Ty1/Copia element Tal1 (Transposon of Arabidopsis lyrata 1) integrates de novo into regions occupied by CENH3 in A. thaliana, and that ectopic expansion of the CENH3 region results in spread of Tal1 integration regions. The integration spectra of chimeric TEs revealed the key structural variations responsible for the contrasting chromatin targeting specificities to centromeres versus gene-rich regions, which have recurrently converted during the evolution of these TEs. Our findings reveal the impact of centromeric chromatin on TE-mediated rapid centromere evolution, with relevance across eukaryotic genomes.

overall_design: Arabidopsis seedlings grown on plates of MS medium were used for TEd(Transposable Element display)-seq.

first: Sota

last: Yamaguchi


title: Dissociation of mitochondrial and ribosomal biogenesis during thallium administration in rat kidney

status: Public on Aug 07 2024

city: Tokyo

first: Toshihiko

last: Aki

address: 1-5-45 Yushima

department: Forensic medicine

institute: Tokyo Medical and Dental University

summary:
Total RNAs from the control and thallium groups were subjected to DNA microarray analysis.
Transcriptome analysis showed that many of the genes were upregulated by Tl administration.

overall_design: We analyzed kidney from rats administered thallium (30 mg/kg, daily for 2 or 5 days) using the ClariomS platform.

first: Kana

last: Unuma

first: Koichi

last: Uemura

first: Sho

last: Sugahara

first: Shuheng

last: Wen

first: Takeshi

last: Funakoshi

first: Moeka

last: Nomura


title: Non-canonical Telomerase Reverse Transcriptase Controls Osteogenic Reprogramming of Aortic Valve Cells Through STAT5

city: Pittsburgh

first: Rolando

last: Cuevas

address: 200 LOTHROP ST

institute: University of Pittsburgh

summary: Background: Calcific aortic valve disease (CAVD) is the pathological remodeling of valve leaflets. The initial steps in the osteogenic reprogramming of the leaflet are not fully understood. Studies have shown that TERT overexpression primes mesenchymal stem cells to differentiate into osteoblasts, and we investigated whether TERT contributes to the osteogenic reprogramming of valve interstitial cells (VICs).  Methods: Human control and CAVD aortic valve leaflets and patient-specific hVICs were used in in vivo and in vitro calcification assays. Loss of function experiments in hVICs and cells isolated from Tert-/- and Terc-/- mice were used for mechanistic studies. In silico modeling, proximity ligation and co-immunoprecipitation assays defined novel TERT interacting partners. Chromatin immunoprecipitation and CUT&TAG sequencing defined protein-DNA interactions. Results: TERT protein was highly expressed in calcified valve leaflets without changes in telomere length, DNA damage, or senescence markers, and these features were retained in isolated primary hVICs. TERT expression increased with osteogenic stimuli, while knock-down or genetic deletion of TERT prevented calcification. Mechanistically, TERT was required to initiate osteogenic reprogramming independent of its canonical telomere-extending activity and the lncRNA TERC. TERT’s osteogenic functions via binding with Signal Transducer and Activator of Transcription 5 (STAT5). Depletion and inhibition of STAT5 prevented calcification. STAT5 was found to bind the promoter region of Runt-Related Transcription Factor 2 (RUNX2), the master regulator of osteogenic reprogramming. Finally, we demonstrate that TERT and STAT5 are upregulated and colocalized in CAVD tissue. Conclusions: TERT's non-canonical activity is required to initiate VIC calcification. TERT partners with STAT5 to bind the RUNX2 gene promoter. These data identify a novel mechanism and potential therapeutic target to decrease vascular calcification.

overall_design: Cleavage Under Targets and Tagmentation (CUT&Tag) coupled with DNA sequencing for the transcription factor Stat5 in mouse valve interstitial cells after seven days of osteogenic treatment in vitro

first: Cynthia

last: St. Hilaire


title: Analysis of microisolated frontal cortex excitatory layer III and V pyramidal neurons reveals a neurodegenerative phenotype in individuals with Down syndrome

city: Orangeburg

first: Stephen

middle: D.

last: Ginsberg

state: New York

address: 140 Old Orangeburg Road

department: Centre for Dementia Research

institute: Research Foundation for Mental Hygiene

summary: Down syndrome (DS) is the most prevalent genetic abnormality, occurring in ~1/700 live births caused by triplication of human chromosome 21 (HSA21). DS individuals have a multitude of phenotypic changes in peripheral systems and most notably, are cognitively impaired, with deficits in learning, language and memory acquisition and consolidation. Further, individuals with DS develop Alzheimer’s disease (AD) pathology during early middle-age (mid-30’s), although the underlying mechanism(s) driving this pathology onset are not well understood. Contributing to cognitive impairment in DS, morphological deficits are present in cortical lamination and distribution, with Layer III (L3) and Layer V (L5) pyramidal neurons showing reduced proliferation and a disorganized laminar structure. As such, examining cortical L3 and L5 pyramidal neurons in DS individuals with AD pathology may elucidate alternate driver mechanisms of disease onset. We examined DS and age-matched control (CTR) brains from individuals without intellectual disabilities or dementia using postmortem frontal cortex (BA9) via single population low input RNA-sequencing. We specifically targeted L3 and L5 pyramidal neurons to understand circuitry-based alterations in DS/AD individuals to elucidate mechanistic drivers of disease pathology. We show convergent and divergent gene expression changes in L3 and L5 pyramidal neurons which may underlie cognitive deficits and degenerative pathology associated with aging in the DS brain. We pinpoint alterations in HSA21 gene expression as well as a multitude of convergent differentially expressed genes (DEGs) and relevant pathways via bioinformatic inquiry in the DS brains that underlie mechanisms of degeneration. Distinctly, convergent gene expression reveals a neurotoxic phenotype, with multiple canonical pathways of dysregulation and disease functions linked to the convergent DEGs, including downregulation of the CLEAR signaling pathway and significantly increased activation of the neuroinflammation signaling pathway. We identify several target genes including mitogen activated protein kinase 1 and 3 (MAPK1/3), calcium voltage-gated channel subunit alpha1 A (CACNA1A) and superoxide dismutase 1 (SOD1), which exhibit overlap in multiple pathways and disease functions and/or display dysfunctional protein-protein network interactions for further examination. Novel targets identified by our single population approach in L3 and L5 pyramidal neurons may be drivers of the disease mechanism and therefore may be therapeutic candidates for amelioration of degenerative pathology that targets memory and executive function circuits in DS/AD.

overall_design:
To determine gene expression changes in L3 and L5 pyramidal neurons from Down Syndrome compared to control brains, we isolated via LCM and purified RNA from single populations of pyramidal neurons spatially and morphologically identified before LCM.  RNA was purified from ~500 neurons for single population assays of L3 and L5 individual populations from the each brain specimen.  A total of n=12 DS (6M/6F) and n= 19 CTR (9M/8F) brains were captured via LCM for RNA-sequencing analysis of differentially expressed genes in age (42-67 yrs old), sex  and PMI matched cohorts. We purified RNA from LCM captured neurons.  RNA was split to perform library preparation on two techical replicates per layer per brain.  Sequencing was performed using New York University's Genome Technology Center with Illimina's NovaSeq 6000 platform.
We compare the DS brains compared to controls in to determine gene expression differences due to genotype within each specific cortical layer.  We further analyzed the data to determine convergent and divergent gene expression between L3 and L5 pyramidal neurons due to the DS phenotype, to examine circuitry differences and overall alterations in cortical pyramidal neuron gene expression due to disease in aged samples (age range 42-67 yrs old).

first: Melissa

middle: J

last: Alldred

first: Harshitha

last: Pidikiti

first: Kyrillos

last: Ibrahim

first: Adriana

last: Heguy

first: Gabriel

last: Hoffmann

first: Panos

last: Roussos

middle: D


title: Role of nuclear p38 in the transcriptional response to oxidative stress in Drosophila (ChIP-Seq)

first: Montserrat

last: Corominas

overall_design: Chromatin immunoprecipitation for P-p38 in Drosophila S2 cells.

first: Paula

last: Climent-Cantó

first: Palmira

last: Llorens-Giralt

first: Cecilia

middle: C

last: Klein

first: Florenci

last: Serras


title: TSSC4 inhibits tumor cell growth by modulating the alternative splicing and expression of tumor-associated genes

status: Public on Aug 06 2024

city: Shanghai

first: Haiping

last: Zhao

address: 131 DongAn Road

institute: Fudan University

summary: Post-transcriptional regulation encompasses the regulation of gene expression at the RNA level following transcription. This regulation involves a series of modifications and processing events that occur to the gene transcripts in eukaryotic cells. These processes include splicing, editing, stabilization and degradation of RNA, which collectively ensure the precise control of gene expression. TSSC4 (tumor suppressing subtransferable candidate 4) is a component of U5 snRNP, which associates with U5 snRNP and the PRPF19 complex. It has been reported that TSSC4 inhibits cancer cell proliferation and tumor growth. Here, our findings indicate that TSSC4 deficiency results in widespread alterations in gene expression and splicing patterns. Knockout of TSSC4 is found to enhance the proliferation of cancer cells driven by oncogene. In conclusion, our results provided evidence that the potential importance of TSSC4 in mediating cancer progression, highlighting its role as a critical mediator of gene expression and splicing in tumor biology

overall_design:
To further investigate how TSSC4 affects  tumor cell growth, we utilized CRISPR/Cas9  to knock out TSSC4 in HeLa cells. Infect cells with lentiCRISPR-Cas9 lentivirus. After 48 hours, add 2 μg/ml puromycin to select for transduced cells, and select and expand single-cell clones.
Comparative gene expression and alternative splicing profiling analysis of RNA-seq data for TSSC4 knockout and WT HeLa cells.


title: Epigenetic Mechanisms Regulating The Transcription of BBB Genes: Role of Wnt/β-catenin signaling

status: Public on Aug 02 2024

city: Houston

first: Peeyush Kumar

last: Thankamani Pandit

state: TEXAS

address: 6431 Fannin St,

department: Neurosurgery

institute: University of Texas Health Science Center Houston

summary:
To identify CNS endothelial cell (EC) the gene cohorts that participate in blood brain barrier (BBB) formation versus maintenance. We investigated mechanism behind the reduced Wnt/β-catenin signaling observed in adult CNS ECs
We also investigated whether the adult endothelial cells  can re express the EC gene cohorts required for the BBB formation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for E-13.5 cortical ECs vs Adult Cortical ECs, vs Wnt3a (200nM) treated Adult cortical Ecs, Adult cortical ECs versus MS-275 (10uM) treated cortical Ecs.

first: Peeyush


title: Dual Role of Neuroplastin in Pancreatic β Cells: Regulating Insulin Secretion and Promoting Islet Inflammation

status: Public on Aug 04 2024

city: Saint Louis

first: Fumihiko

last: Urano

state: Missouri

address: 660 South Euclid Ave

institute: Washington University School of Medicine

summary: Mesencephalic astrocyte-derived neurotrophic factor (MANF) is an endoplasmic reticulum (ER)-resident secretory protein that reduces inflammation and promotes proliferation in pancreatic β cells. Numerous studies have highlighted the potential of MANF as a therapeutic agent for diabetes mellitus (DM), making it essential to understand the mechanisms underlying MANF's functions. In our previous search for a molecule that mediates MANF signaling, we identified Neuroplastin (NPTN) as a binding partner of MANF that localizes on the cell surface. However, the roles of NPTN in pancreatic β cells remain unclear. In this study, we generated β cell-specific Nptn knockout (KO) mice and conducted metabolic characterization. NPTN deficiency improved glucose tolerance by increasing insulin secretion and β cell mass in the pancreas. Moreover, proliferation and mitochondrial numbers in β cells increased in Nptn KO islets. These phenotypes resulted from elevated cytosolic Ca2+ levels and subsequent activation of downstream molecules. Simultaneously, we demonstrated that NPTN induces the expression of proinflammatory cytokines via the TRAF6-NF-κB axis in β cells. Additionally, NPTN deficiency conferred resistance to STZ-induced diabetic phenotypes. Finally, exogenous MANF treatment in islets or β cells led to similar phenotypes as those observed in NPTN-deficient models. These results indicate that NPTN plays important roles in the regulation of insulin secretion, proliferation, and mitochondrial quantity, as well as pro-inflammatory responses, which are antagonized by MANF treatment. Thus, targeting the MANF-NPTN interaction may lead to a novel treatment for improving β cell functions in diabetes mellitus.

overall_design: To better understand the impact of Nptn knockout in b cells, bulk RNA-sequencing (RNA-seq) with islets isolated from Nptnf/f and Nptnf/f; Ins1Cre mice at 7 weeks old was performed.


title: CWF19L1 promotes T-cell cytotoxicity through the regulation of alternative splicing

status: Public on Aug 05 2024

city: shanghai

first: YI

last: JINGJING

state: shanghai

address: fenglin compus

institute: FuDan university

summary: Enhancing host anti-tumor immunity is paramount for advancing cancer immunotherapy. Here, we identify CWF19-like cell cycle control factor 1 (CWF19L1) as a promising immunotherapeutic target that functions as a splicing factor to enhance T cell-mediated cytotoxicity. CWF19L1 interacts prominently with key splicing factors and regulators, including U5 small nuclear ribonucleoprotein (snRNP) and the pre-mRNA processing factor 19 (PRPF19) complex. Deficiency of CWF19L1 leads to aberrant alternative splicing of immune-related genes and repression of cytotoxic molecule expression. Furthermore, CWF19L1 plays a pivotal role in promoting T cell-mediated anti-tumor immunity by upregulating effector cytokine expression. Our findings unveil previously undocumented functions of CWF19L1 in alternative splicing and its crucial involvement in anti-tumor immunity. These insights underscore the potential of targeting CWF19L1 for the development of novel cancer immunotherapies.

overall_design: To examine the possible role of CWF19L1 in mRNA splicing, we performed RNA sequencing on control Jurkat cells (shCtrl) and CWF19L1 knockdown Jurkat cells (shCWF19L1).


title: Single nuclear RNA sequencing and 10X spatial transcriptomic profiling of murine tumors initiated by transplantation of engineered prostate organoids [snRNA-seq]

first: Rodrigo

last: Romero

address: 1275 York Avenue

institute: Memorial Sloan Kettering

summary: Single-nuclear RNA-sequencing of murine organoid transplant-derived prostate tumors.  Purpose: To identify differences in cell composition in murine prostatic tumors and to generate a reference dataset of all major cell types present in mouse prostate tumors Results: We recovered 4,872 cells with a median of 7055.5 UMIs per cell. Conclusions: snRNASeq reveals heterogeneity within neuroendocrine prostate cancer compartment, dominated by an Ascl1+ expression profile with mixed luminal lineage marker genes. snRNASeq recovers all the major epithelial, immune, and stromal cell types in prostate tumors.  Spatial transcriptomic profiling of murine prostate tumors. Purpose: To spatially map the major cell types in the mouse prostatic tumors and identify spatially distinct neuroendocrine tumor compartments. Distinct tumor microenvironments were also used for identification of cell:cell signaling axes distributed between the histological subtypes. Conclusions: Spatial transcriptomic profiling of the mouse prostate reveals all major cell types and allows for cell:cell signaling analyses upon integration with our matching snRNA-Seq data

overall_design: One RPM tumor was isolated from a mouse at 10 weeks post transplantation, when the neuroendocrine transition was expected to be fully penetrant. This tumor (RR1818) was flash frozen and processed for single nuclear RNA sequencing to capture all cell types within tumors and generate a reference dataset. For Visium: 4 biologically independent RPM tumors (primary mouse prostate tumor and metastatic lymph node) at different stages of the adeno-to-neuroendocrine transdifferentiation process were used for this analysis. RPM tumors isolated from 2 weeks (RR1104), 3 weeks (RR1105 and RR1107), 4weeks (RR1109), 6 weeks (RR1117 and RR1118), and 10 weeks (RR1123, RR1132, RR1124, and RR1128) were isolated and processed for 10X Visium in technical replicates. No treatments applicable.

first: Tinyi

last: Chu

first: Dana

last: Pe'er

first: Charles

middle: L

last: Sawyers


title: Single nuclear RNA sequencing and 10X spatial transcriptomic profiling of murine tumors initiated by transplantation of engineered prostate organoids [visium]


title: Bendamustine combined with rituximab induces pyroptosis to shape an "immunologically hot" tumor microenvironment  in DLBCL cells via the STING pathway

status: Public on Aug 01 2024

first: Xiao

last: Ruipei

address: Guangzhou North Stress

institute: Southern Medical University

summary: Bendamustine plus rituximab (BR) therapy has demonstrated favorable clinical outcomes in the treatment of DLBCL patients who are intolerant to R-CHOP therapy. In vitro, BR therapy exhibits a synergistic cytotoxic effect on DLBCL cell lines. Mechanistically, BR induces pyroptosis in DLBCL cells by activating the cGAS-STING pathway, leading to the release of inflammatory factors and the formation of an "immunologically hot" microenvironment. Additionally, BR therapy upregulates MHC molecules on the tumor cell surface, thereby augmenting T cell activation and function.

overall_design: OCI-LY1 cells were planted in 48-well culture plates and treated in four conditions. B (Bendamustine) group was treated the same as control group for 1 day before exposed to 200uM Bendamustine for 1.5 days. R (Rituximab) group exposed to 10uM Rituximab for 2.5 days. BR (Bendamustine+Rituximab) group exposed to 10uM Rituximab for 1 days before exposed to 200uM Bendamustine and 10uM Rituximab for 1.5 days. The control group was grown in the same culture conditions for 2.5 days without the addition of any drugs.

first: Ruipei

last: Xiao

first: Wei

last: Lin

first: Yudian

first: Enguang

last: Bi

first: Ling

last: Jiang


title: Expression data from control and PRRG1 (Vitamin K-dependent Gamma-carboxyglutamic acid protein 1) knockdown cells

first: zheng

last: wu

address: 800 Dongchuan Road

institute: School of Medicine, Shanghai Jiao Tong University

summary: In order to uncover biological function of PRRG1 and its underlying molecular mechanism, we used high throughput sequencing to determine the expression profile of control and PRRG1 konckdown cells.

overall_design: To investigate the role of PRRG, we used shRNA to knock down PRRG1 in Patu8988 cells. Subsequently, RNA-seq analysis was conducted on three sets of control and PRRG1-knockdown Patu8988 cells to profile gene expression.

first: Zheng

last: Wu

first: Xiaomei

last: Yang

first: Zhigang

last: Zhang


title: Thrombopoietin mimetic reduces mouse lung inflammation and fibrosis after radiation by attenuating activated endothelial phenotypes

city: Bronx

first: Jeb

last: English

address: 1300 Morris Park Ave

institute: Albert Einstein College of Medicine

summary: Radiation-induced lung injury (RILI) initiates radiation pneumonitis and progresses to fibrosis as the main side effect of lung cancer patients treated with radiotherapy. There is no effective drug for RILI. Sustained vascular activation is a major contributor to the establishment of chronic disease. Here, using a whole thoracic irradiation (WTI) mouse model, we investigated the mechanisms and effectiveness of thrombopoietin mimetic (TPOm) for preventing RILI. We demonstrated that administering TPOm 24 hours before irradiation decreased histologic lung injury score, apoptosis, vascular permeability, expression of pro-inflammatory cytokines, and neutrophil infiltration in the lung of mice 2 weeks after WTI. We described the expression of c-MPL, a TPO receptor, in mouse primary pulmonary microvascular endothelial cells, showing TPOm reduced endothelial cell-neutrophil adhesion by inhibiting ICAM-1 expression. Seven months after WTI, TPOm-treated lung exhibited less collagen deposition, expression of MMP-9, TIMP-1, IL-6, TGF-b, and p21. Moreover, TPOm improved lung vascular structure, lung density, and respiration rate, leading to a prolonged survival time after WTI. Single-cell RNA sequencing analysis of lungs 2 weeks after WTI revealed that TPOm shifted populations of capillary endothelial cells towards a less activated and more homeostatic phenotype. Taken together, TPOm is protective for RILI by inhibiting endothelial cell activation.

overall_design: C57BL/6 male mice underwent whole thoracic irradiation with 16.0 Gy  delivered by x-ray irradiator (300 kv and 10 mA, 1mm Cu filtration). Fourteen days post-IR, lungs were collected, and processed into a single-cell suspension after sacrificing mice.

first: Weng-Lang


title: Identifying hand2 downstream targets in cardiomyocyte during early cardiogenesis

city: Bad Nauheim

first: Mario

last: Looso

address: Ludwigstrasse 43

institute: Max Planck Institute for Heart and Lung Research

summary: hand2 reporter-expressing cardiac cells fail to migrate to the midline.  To investigate the underlying molecular changes, we sequenced mRNA from 3900 and 3836 hand2 reporter-expressing single cells from 24 hpf hand2 FLD-/- and hand2 FLD+/? sibling embryos, respectively.  Furthermore, hand2 is broadly expressed within the LPM, which gives rise to various cell lineages and tissues including the cardiovascular system, blood, kidneys, mesothelium, and limb connective tissue.  To further investigate the requirement of Hand2 in the early events of cardiac lineage specification in zebrafish, we aim to characterize the early hand2 expressing cardiac precursors by using embryonic CM H3K27ac ChIP-seq and ATAC-seq data.

overall_design: scRNA-seq: WT: hand2 reporter-expressing single cells from 24 hpf  hand2 FLD+/?  Embryos; mutants: hand2 reporter-expressing single cells from 24 hpf hand2 FLD-/- sibling embryos.  ATAC-seq and CGIP-seq: Comparing myl7:GFP+ CMs with  myl7:GFP- cells

first: Yanli

last: Xu

first: Scott

last: Lacadie


title: Profiling of murine tumors initiated by transplantation of engineered prostate organoids

city: New York

first: Rodrigo

last: Romero

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

overall_design: Refer to individual Series


title: Role of nuclear p38 in the transcriptional response to oxidative stress in Drosophila

first: Montserrat

last: Corominas


title: TRIM7 ubiquitinates SARS-CoV-2 membrane protein to limit apoptosis and viral replication

status: Public on Jul 31 2024

city: Galveston

first: Maria

middle: De jesus

last: Gonzalez Orozco

state: Texas

address: 301 University Blvd

department: Microbiology and Immunology

institute: UTMB

summary: SARS-CoV-2 is a highly transmissible virus that causes COVID-19 disease. Mechanisms of viral pathogenesis include excessive inflammation and viral-induced cell death, resulting in tissue damage. We identified the host E3-ubiquitin ligase TRIM7 as an inhibitor of apoptosis and SARS-CoV-2 replication via ubiquitination of the viral membrane (M) protein. Trim7-/- mice exhibited increased pathology and virus titers associated with epithelial apoptosis and dysregulated immune responses. Mechanistically, TRIM7 ubiquitinates M on K14, which protects cells from cell death. Longitudinal SARS-CoV-2 sequence analysis from infected patients revealed that mutations on M-K14 appeared in circulating variants during the pandemic. The relevance of these mutations was tested in a mouse model. A recombinant M-K14/K15R virus showed reduced viral replication, consistent with the role of K15 in virus assembly, and increased levels of apoptosis associated with the loss of ubiquitination on K14. TRIM7 antiviral activity requires caspase-6 inhibition, linking apoptosis with viral replication and pathology.

overall_design: Next generation sequencing of Lung from mice WT and TRIM7 knockout infected with SARS-CoV-2 CMA3p20 at day 3 post-infection

last: Gonzalez-Orozco

first: Hsiang-chi

last: Tseng

first: Adam

last: Hage

first: Hongjie

last: Xia

first: Padmanava

last: Behera

first: Kazi

last: Afreen

first: Yoatzin

last: Peñaflor-Tellez

middle: I

last: Giraldo

first: Matthew

last: Huante

first: Lucinda

last: Puebla-Clark

first: Sarah

last: van Tol

first: Abby

last: Odle

last: Crown

first: Natalia

last: Teruel

first: Thomas

middle: R

last: Shelite

first: Vineet

last: Menachery

first: Mark

last: Endsley

first: Janice

first: Rafael

last: Najmanovich

last: Bashton

first: Robin

last: Stephens

first: Pei-Yong

last: Shi

first: Xuping

last: Xie

first: Alexander

middle: N

last: Freiberg

first: Ricardo

last: Rajsbaum


title: EZH2 directly methylates PARP1 and regulates its activity in cancer

city: CHICAGO

first: Qingshu

last: Meng

state: Illinois

address: 303 E. Superior Street

institute: Northwestern University

summary: DNA repair dysregulation is a key driver of cancer development. Understanding the molecular mechanisms underlying DNA repair pathways and their dysregulation in cancer cells is crucial for cancer development and therapies. Here, we report that enhancer of zeste homolog 2 (EZH2) directly methylates poly (ADP-ribose) polymerase-1 (PARP-1), an essential enzyme involved in DNA repair, at lysine 607 and regulates its activity. Functionally, EZH2-catalyzed methylation represses PARP1 catalytic activity, inhibits the recruitment of X-ray repair cross-complementing group-1 (XRCC1) recruitment to DNA lesions and hence impairs DNA damage repair. Meanwhile, EZH2-mediated methylation regulates PARP1 transcriptional and oncogenic activity, at least in part, through impairing PARP1-E2F1 interaction and E2F1 transcription factor activity. Collectively, our findings uncover a novel insight of EZH2 functions in DNA damage repair and cancer progression, which provides a new rationale for combinational targeting EZH2 and PARP1 in cancer.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PARP1-KD C4-2 cells stably expressing PAPR1-WT or -K607A.

first: Yanan

last: Ren

first: Rendong

last: Yang

first: Qi

last: Cao


title: Gene expression profile at single cell level of testicular cells from the adult NONO and NONO△ER mice testis

city: Nanjing

first: Yan

last: Yitong

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the diversity  and gene expression of testis cells in the adult NONO and NONO△ER mice testis

overall_design: NONO and NONO△ER mice testis were collected and separated into single cell mixture by enzyme digestion and analyzed using scRNAseq.

first: Yang

last: Li

first: Yuanyuan

last: Wang

first: Yitong

last: Yan

first: Yiqiang

last: Cui


title: MYT1L deficiency impairs excitatory neuron trajectory during cortical development [P1]

city: St. Louis

first: Joseph

last: Dougherty

state: MO

address: 4370 Duncan Ave

institute: Washington University in St. Louis

summary: Mutations that reduce the function of MYT1L, a neuron-specific transcription factor, are associated with a syndromic neurodevelopmental disorder. Furthermore, MYT1L is routinely used as a pro-neural factor in fibroblast-to-neuron transdifferentiation. MYT1L has been hypothesized to play a role in the trajectory of neuronal specification and subtype specific maturation, but this hypothesis has not been directly tested, nor is it clear which neuron types are most impacted by MYT1L loss. In this study, we profiled 412,132 nuclei from the forebrains of wild-type and MYT1L-deficient mice at three developmental stages: E14 at the peak of neurogenesis, P1 when neurons in the six cortical layers have been born, and P21 when neurogenesis is complete and neurons are maturing, to examine the role of MYT1L levels in the trajectory of neuronal development. We found that MYT1L deficiency significantly disrupted the relative proportions of cortical excitatory neurons. Changes in gene expression were concentrated in excitatory neurons, suggesting that transcriptional effects of MYT1L deficiency are largely due to disruption of neuronal maturation programs. Most effects on gene expression were cell autonomous and persistent through development. In addition, while MYT1L can both activate and repress gene expression, the repressive effects were most sensitive to haploinsufficiency, and thus more likely mediate MYT1L syndrome. These findings illuminate the intricate role of MYT1L in orchestrating gene expression dynamics during neuronal development, providing insights into the molecular underpinnings of MYT1L syndrome.

overall_design: Samples for snRNAseq were collected at three key developmental timepoints: E14, P1, and P21. At E14, forebrains were dissected from MYT1L WT, Het, and KO mice, with three replicates per genotype. These E14 samples included a mix of males and females for each genotype. For P1 samples, forebrains were harvested from 8 WT mice (5 male, 3 female) and 4 Het mice (3 male, 1 female). At P21, cortices were colleced from 6 WT animals (3 male, 3 female) and 6 Het animals (3 male, 3 female). Across all time points, nuclei were isolated from the dissected tissues. Library preparation was carried out using the Scale Biosciences Single Cell RNA Kit, with samples batched by age.

first: Allen

last: Yen

first: Simona

last: Sarafinovska

first: Xuhua

last: Chen

first: Dominic

last: Skinner

first: Fatjon

last: Leti

first: MariaLynn

last: Crosby

first: Jessica

last: Hoisington-Lopez

first: Yizhe

last: Wu

first: Jiayang

first: Zipeng

first: Kevin

middle: K

last: Noguchi

first: Robi

last: Mitra


title: RNA binding properties of PDHA2, TEX30 in testis; RNA binding properties of HA-NONO and HA-NONO△ER in 3T3L1 cell line.

first: huicong

last: zhai

address: 101 Longmian Avenue, Jiangning District (or 818 Tianyuan East Road)

institute: Nanjing Medical University

summary:
To investigate the RNA binding proterties of PDHA2, TEX30 in testis; RNA binding properties of HA-NONO and HA-NONO△ER in 3T3L1 cell line, we collected wildtype testis and HA-NONO/HA-NONO△ER overexpressed 3T3L1 cells.
We then performed eCLIP-seq respectively and convey subsequent bioinformatic analysis.

overall_design: RBP_eCLIP-seq; RNA substrate analysis of eCLIP-seq data for TEX30 and PDHA2 in testis; Comparative RNA binding specificity and affinity analysis of eCLIP-seq data for HA-NONO and HA-NONO△ER in 3T3L1 cell line

first: Yang

first: Ruoyu

last: yan

first: Xin

first: Qiushi

last: Xu


title: DNA Methylome Analysis of Human Cancer Cells with STELLA Protein Overexpression and the Xenograft Tumor Tissues from the Mice Treated by the Indicated LNP Formulations

status: Public on Jul 28 2024

city: Guangzhou

first: Wenbin

last: Gu

address: 190 Kaiyuan Avenue, Huangpu District, Guangzhou

department: Chinese Academy of Sciences

institute: Guangzhou Institutes of Biomedicine and Health

type: Methylation profiling by genome tiling array

summary: Genome-wide DNA methylation profiling of non-small cell lung cancer (NSCLC) cell line A549 and breast cancer cell line MDA-MB-231 stably expressing hSTELLA and mSTELLA, as well as the HCT116 xenograft tumor tissues from the mice treated by the indicated LNP formulations. The Infinium MethylationEPIC v2.0 array was used to obtain DNA methylation profiles across more than 935,000 CpGs in 15 samples. Samples included 3 stable NSCLC cells and 3 stable breast cancer cells expressing the STELLA orthologs, and 9 xenograft tumors from the mice with the indicated treatments.

overall_design: Bisulphite converted DNA from the 15 samples were hybridised to the Infinium MethylationEPIC v2.0 Beadchip

first: W

last: Bai

first: Y

first: H

last: Guo

first: C

last: Xia

first: S

middle: B

last: Baylin

first: X

last: Kong


title: RNA Sequencing of six pairs of gastric cancer

city: Shijiazhuang

first: Ping'an

last: Ding

state: None Selected

address: Shijiazhuang 050011, China

institute: the Fourth Hospital of Hebei Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: Stomach cancer (GC) remains one of the most prevalent tumors globally, ranking third in terms of cancer-related mortality worldwide. Currently, the prognosis for gastric cancer following radical resection is still suboptimal, primarily due to metastasis. Therefore, it is crucial to explore target therapy as a means to address this issue. Circular RNAs (circRNAs) have emerged as pivotal regulators in the development and progression of cancer and hold promise as biomarkers for diagnosing and prognosticating various cancers. However, the precise mechanism by which circular RNA contributes to metastasis in gastric cancer remains unclear. Our objective is to validate the expression profile of circRNA in gastric cancer and investigate its functional role in metastasis within this context.

overall_design: To investigate the expression patterns of circRNA transcripts in gastric cancer tissues and adjacent normal tissues, we conducted RNA-sequencing (RNA-seq) analyses on ribosomal RNA-depleted total RNA extracted from six paired samples of gastric cancer tissues and their corresponding adjacent normal tissues.


title: Systematic surveillance of SARS-CoV-2 reveals dynamics of variant mutagenesis and transmission in a large urban population I

status: Public on Jul 30 2024

city: Toronto

first: Jeff

last: Wrana

state: Ontario

address: 600 University Avenue

country: Canada

institute: Lunenfeld-Tanenbaum Research Institute

summary: Highly mutable pathogens generate viral diversity that impacts virulence, transmissibility, treatment, and thwarts acquired immunity.  We previously described C19-SPAR-Seq, a high-throughput, next-generation sequencing platform to detect SARS-CoV-2 that we deployed to systematically profile variant dynamics of SARS-CoV-2 for over 3 years in a large, North American urban environment (Toronto, Canada). Sequencing of the ACE2 receptor binding motif and polybasic furin cleavage site of Spike in over 70,000 patients revealed that population sweeps of canonical variants of concern (VOCs) occurred in repeating wavelets. Furthermore, we found that subvariants and putative quasi-species with alterations characteristic of future VOCs and/or predicted to be functionally important arose frequently, but always extinguished. Systematic screening of functionally relevant domains in pathogens could thus provide a powerful tool for monitoring spread and mutational trajectories, particularly those with zoonotic potential.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design:
RNAseq and sequence variant analysis for 63036 human  nasopharyngeal swabs for SARS-CoV-2, with 1928 negative swabs and 2886 synthetic controls.
(part2)  Additional RNAseq and sequence variant analysis for 3129 human nasopharyngeal swabs for SARS-CoV-2, with 283 negative swabs and 259 synthetic controls.

Please note that the 'sparseq_sample_data_GEOver_v3.txt' and 'sparseq_sample_data_GEOver_part2_v3.txt' files were replaced with the 'sparseq_sample_data_GEOver_v4.txt' and 'sparseq_sample_data_GEOver_part2_v4.txt', respectively, on Oct 10, 2024 (only to fix some typos in text fields, no change to the number of samples).

Please note that the records have been updated with 10 additional sample records and the updated 'sparseq_sample_data_GEOver_part2_v5.txt', 'sparseq_sample_data_GEOver_v5.txt'files on Nov 5, 2024.

first: Marie-Ming

last: Aynaud

first: Lauren

last: Caldwell

first: Khalid

last: Al-Zahrani

first: Seda

last: Barutcu

first: Kin

last: Chan

first: Andreea

last: Obersterescu

first: Abiodun

last: Ogunjimi

first: Min

last: Jin

first: Kathleen-Rose

last: Zakoor

first: Shyam

last: Patel

first: Ron

last: Padilla

first: Mark

last: Jen

first: Princess Mae

last: Veniegas

first: Nursrin

last: Dewsi

first: Filiam

last: Yonathan

first: Lucy

last: Zhang

first: Amelia

last: Ayson-Fortunato

first: Analiza

last: Aquino

first: Paul

last: Krzyzanowski

first: Jared

last: Simpson

first: John

last: Bartlett

first: Ilinca

last: Lungu

first: Bradley

middle: G

last: Wouters

first: James

middle: M

last: Rini

first: Michael

last: Gekas

first: Susan

last: Poutanen

first: Laurence

last: Pelletier

first: Tony

last: Mazzulli

first: Jeffrey


title: Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy [RNAseq_Eso]

status: Public on Jul 26 2024

first: Dimitris

last: Karagiannis

institute: Columbia University

summary: While cell fate determination and maintenance are important in establishing and preserving tissue identity and function during development, aberrant cell fate transition leads to cancer cell heterogeneity and resistance to treatment. Here, we report an unexpected role for the transcription factor p63 (Trp63/TP63) in the fate choice of squamous versus neuroendocrine lineage in esophageal development and malignancy. Deletion of p63 results in extensive neuroendocrine differentiation in the developing mouse esophagus and esophageal progenitors derived from human embryonic stem cells. In human esophageal neuroendocrine carcinoma (eNEC) cells, p63 is transcriptionally silenced by EZH2-mediated H3K27 trimethylation (H3K27me3). Upregulation of the major p63 isoform ΔNp63α, through either ectopic expression or EZH2 inhibition, promotes squamous transdifferentiation of eNEC cells. Together these findings uncover p63 as a rheostat in coordinating the transition between squamous and neuroendocrine cell fates during esophageal development and tumor progression.

overall_design: We performed RNA-sequencing of E12.5 mouse p63 KO and WT esophageal epithelium.

first: Yongchun

first: Jianwen

last: Que


title: Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy [RNAseq_Ezh2i]

overall_design: We performed RNA sequencing of TYUC-1 cells treated with EPZ-6438 for 0 (D0), 3(D3) or 6 (D6) days. We assesed 3 biological replicates.

first: Helu

last: Liu

first: Chao

last: Lu


title: Epigenetic regulation of p63 blocks squamous-to-neuroendocrine transdifferentiation in esophageal development and malignancy [CUTnTag_Ezh2i]

overall_design: CUT&Tag of H3K27me3, H3K27ac and BRD4 in EPZ-6438-treated TYUC-1 cells for 0 (D0), 3 (D3) and 6 (D6) days.


title: Differential content of circRNA in human induced pluripotent stem cells (hiPSCs) and their extracellular vesicles (EVs).

status: Public on Aug 03 2024

city: Milano

first: Valeria

last: Peli

address: via Francesco Sforza, 35

country: Italy

institute: IRCCS Ca' Granda Ospedale Maggiore Policlinico di Milano

summary: Circular RNAs (circRNAs) are an emergent class of non-coding RNAs commonly generated by back-splicing events, resulting in a highly stable RNA structure, devoid of free 5’ and 3’ ends. circRNAs display the main mechanism of action as miRNA sponges, resulting in the modulation of their regulatory activity. Current knowledge suggests that they could play a relevant role in cellular biology and pathophysiology. In this study, for the first time, we detected circRNAs as a new component of the induced pluripotent stem cell (hiPSC)-derived extracellular vesicles (EV) cargo. We further compared the circRNA profile of hiPSC-EV with that of their parental cells (hiPSCs).

overall_design: Two samples:  Parental hiPSC versus hiPSC-derived EVs. Parental hiPSC was submitted previously in GSE144629  (reference parental cell).

first: M

last: Barilani

first: P

last: Valeria

first: L

last: Lazzari


title: Estrogen-triggered Monkey Multi-Organ Cell Atlas [scRNA-Seq]

status: Public on Jul 25 2024

city: Nan Jing

first: Fang

last: Wen

address: Xianlin street

institute: Nanjing University

summary: Awareness of estrogen's effects on health is broadening rapidly. The effects of long-term high levels of estrogen on the body involve multiple organs. Here we use both single cell chromatin accessibility and RNA sequencing data to analyze the potential effect of estrogen on major organ at single cell levels.

overall_design: A total of 10 scRNA-seq data and 10 paired scATAC-seq data for different organs and groups were available

first: Yang

last: Sun

first: Jiao

last: Qu

first: Wen

last: Fang

first: Wanjun

last: Zhao

first: Xinran

last: Cao


title: RNA profiling of CSF resident macrophages and monocyte-macrophages from leptomeningeal metastasis mice

status: Public on Jul 24 2024

first: Yudan

last: Chi

address: 131 Dongan Road

institute: Fudan University

summary: We investigated the functional effect of dura-derived leptomeningeal matastasis (LM)-associated macrophages (dLAMs) on the cerebrospinal fluid (CSF) niche during LM outgrowth. Using lung cancer leptomeningeal metastasis models of Cx3cr1CreER:mTmG mice with tamoxifen administration, we achieved dLAMs and monocyte-macrophages via fluorescence-activated cell sorting (FACS). Then we performed bulk RNAseq analysis for these two cell populations.

overall_design: At day12 of LLC-LeptoM cell inoculation for LM models in Cx3cr1CreER:mTmG mice, CSF cells were collected and sorted for dLAMs and monocyte-macrophages (mono-MΦs). During FACS, dLAMs were sorted by CD45+CD11b+F4/80+Ly6C-GFP+, and mono-MΦs were sorted by CD45+CD11b+F4/80+GFP- and CD45+CD11b+F4/80lowLy6C+GFP-. We then performed gene expression profiling analysis using data obtained from bulk RNAseq of dLAMs and mono-MΦs.Total 10 samples were analyzed using RNAseq, including three dLAMs samples and three mono-MΦs samples.

first: Jiaxu

first: Rui

last: Zeng


title: Estrogen-triggered Monkey Multi-Organ Cell Atlas


title: An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [STARR-seq]

status: Public on Jul 22 2024

city: 津南区

first: An

last: Jiang

state: 天津市

address: 南开大学津南校区综合实验楼D413

institute: 南开大学

summary: Previous Genome-wide association studies (GWASs) have identified susceptibility loci of primary angle closure glaucoma (PACG), but applicating these findings is difficult. Although shallow anterior chamber depth (ACD) and short axial length (AL) are characteristic phenotypes of PACG, current GWAS variants do not show any correlation with these features, calling for the identification of more risk factors . Here, thicker and enlarged iris was identified as a significant independent risk factors. By employing allelic-specific STARR-seq and assay for transposase-accessible chromatin using sequencing (ATAC-seq), we screened disease-related variants in linkage disequilibrium and identified 2 causative variants in iris. Alterations in these variants may contribute to the pathogenic iris phenotype by upregulating the expression of PLEKHA7 and C10orf53, potentially regulating PACG development and progression. Our efforts nominate the important role of iris and identify pathogenic SNP-target gene interactions for PACG, providing a potentially powerful approach for interpreting noncoding variation of diseases.

overall_design: We conducted allelic-specific STARR-seq for PACG candidate variants and ATAC-seq for ARPE-19 cell lines and human iris.

first: Jiaying

last: Li

first: Yun

last: Chen

first: Wenbin

last: Wang

first: Guangsong

last: Su

first: Yuanyuan

last: Zhang

first: Yilong

last: Yao

first: Wange

first: Chunyan

last: Qiao

first: Kunlin

first: Ye

first: Yuwen

first: Ningli


title: An integrated clinical morphology and functional genomics approach reveals upregulation of PLEKHA7 and C10orf53 in iris contributes to primary angle closure glaucoma [ATAC-seq]

address: 南开大学津南校区综合实验楼D413

last: Lu

last: Liu


title: NK receptors replace CD28 as the dominant source of signal 2 for cognate recognition of cancer cells by TAA-specific effector CD8+ T cells

status: Public on Jul 19 2024

city: Buffalo

first: Henry

middle: G.

last: Withers

address: Elm and Carlton Streets

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Center

summary: CD28-driven “signal 2” is critical for naïve CD8+ T cell responses to dendritic cell (DC)-presented weak antigens, including non-mutated tumor-associated antigens (TAAs). However, it is unclear how DC-primed cytotoxic T lymphocytes (CTLs) respond to the same TAAs presented by cancer cells which lack CD28 ligands. Here, we show that NK receptors (NKRs) DNAM-1 and NKG2D replace CD28 during CTL re-activation by cancer cells presenting low levels of MHC I/TAA complexes, leading to enhanced proximal TCR signaling, immune synapse formation, CTL polyfunctionality, release of cytolytic granules and antigen-specific cancer cell killing. Double-transduction of T cells with recombinant TCR and NKR constructs or upregulation of NKR-ligand expression on cancer cells by chemotherapy enabled effective recognition and killing of poorly immunogenic tumor cells by CTLs. Operational synergy between TCR and NKRs in CTL recognition explains the ability of cancer-expressed self-antigens to serve as tumor rejection antigens, helping to develop more effective therapies.

overall_design:
Dynabead-induced CTLs from 3 human donors were stimulated by anti-human CD3 (OKT3) with or without anti-human DNAM-1 (OKT3 + anti-DNAM1), anti-human NKG2D (OKT3 + anti-NKG2D), or anti-human CD28 (OKT3 + anti-CD28)for 4 hours.

Raw RNA-sequencing read files are not currently provided to ensure confidentiality and protect participant’s privacy under New York State law. Researchers interested in accessing the data for replication or further analysis may request access through the Institutional Review Board (IRB) of Roswell Park Comprehensive Center, subject to approval and compliance with ethical guidelines.

first: Bowen

last: Dong

first: Pawel

last: Kalinski