title: The master transcription factor of the Plasmodium merozoite formation. [RNA-Seq]

first: masao

last: yuda

summary: Plasmodium berghei transcriptomes of pbsip2cKO, a parasite line in which pbsip2 is disrupted by DiCre-mediated recombination in the presence of rapamycin, were analyzed at the schizont stage.

overall_design: pbsip2cKO parasites treated with 10 nM rapamycin or DMSO were synchronized and harvested at 26 h post-injection. Total RNA was extracted from the parasites. Libraries were constructed from the total RNA and then sequenced by the Next Generation Sequencing.

first: Tsubasa

last: Nishi

first: Izumi

last: Kaneko

first: Masao

last: Yuda


title: Exosomal miR-302b rejuvenates aging mice by reversing cell cycle arrest

status: Public on Nov 01 2024

city: Chaoyang District

first: Youkun

last: Bi

state: Beijing

address: NO.15, Datun Road

department: Institute of Biophysics

country: China

institute: Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Exosomal miR-302b rejuvenates aging mice by reversing cell cycle arrest [LO2 scRNA-Seq]

summary: Cellular senescence is a hallmark of aging characterized by a stable exit from the cell cycle in response to cellular damage and stress. Senescent cells (SnCs) are closely associated with aging and aging-related disorders, making them a potential target for slowing aging. In this study, we developed a tool for dynamically monitoring the p21 signaling to determine the degree of cellular senescence, named p21-YFP LO2. The senescent cells were prepared by FCM sorting targeting p21-YFP LO2 treated with 50 nM Dox for 48 h based on the YFP signaling. The single-cell RNA sequencing (scRN-seq) analysis was performed to observe the effects of human embryonic stem cell-derived exosomes (hESC-Exos) on the transcriptional profiles of SnCs. We specifically demonstrated that hESC-Exos enable SnCs to reverse the cell cycle arrest and restore their proliferative capacity in vitro.

overall_design: A senescence reporter cell line was generated by inserting the YFP gene downstream of the Cdkn1a (code p21) stop codon and subsequently transfecting LO2 cells, named p21-YFP LO2. Temporal fluctuations in p21 expression were visualized using the YFP signal. A senescent cell model was established by treating the p21-YFP LO2 with 50 nM Dox for 48 h. To observe the effects of hESC-Exos on the transcriptional profiles of SnCs, we performed single-cell RNA sequencing (scRN-seq) on SnCs sorted by FCM and then treated with hESC-Exos or PBS, termed as Dox-pbs and Dox-Exos group, respectively.

first: Xinlong

last: Qiao

first: Yuanchao

last: Xue

first: Guangju

last: Ji


title: Exosomal miR-302b rejuvenates aging mice by reversing cell cycle arrest [scRNA-Seq]

summary: Senescent cells (SnCs) are considered the driving force of aging; therefore, restoring the normal function of SnCs or reversing the senescence-associated secretory phenotype (SASP) may have anti-aging effects. Current anti-aging strategies include destroying, or reprogramming, SnCs and inhibiting SASP. However, significant challenges persist, such as the progressive loss of tissue function and risk of tumorigenesis. Herein, we report a Senoreviver strategy that breaks cell cycle arrest and reverses SASP simultaneously via human embryonic stem cell exosome (hESC-Exo)-mediated delivery of miR-302b. miRNA-seq analysis revealed that hESC-Exos enriches miR-302 family members. Ago2 CLIP-seq mapping revealed that miR-302b could repress the cell cycle inhibitors Cdkn1a and Ccng2, which collectively restored the proliferative capacity of SnCs and reversed SASP. Our study provides a Senoreviver strategy to rejuvenate SnCs in vitro and in vivo, rather than eliminate or reprogram them, thus holding great promise for maintaining tissue homeostasis, extending the health span, and countering age-related diseases.

overall_design: At the age of 20 months, mice were randomly divided into Aging-pbs (n = 30) and Aging-Exos (n = 30) groups and transferred to the Institute of Biophysics, Chinese Academy of Sciences, in an SPF-grade facility with individually ventilated cages. Mice in the Aging-Exos group received a weekly tail vein injection of hESC-Exos (2 × 1010 particles in 200 μL PBS), while those in the Aging-pbs group were administered 200 μL PBS via tail vein injection. The 30th month was selected as the test point. Three mice were chosen randomly from each of the two groups, and their skin and liver tissues were collected for single-cell sequencing.


title: Transcriptomic changes in HCT116 cells after KAT2A knockout

city: Dresden

first: Alexander

middle: Arthur

last: Wurm

address: Fetscherstrasse 74

country: Germany

institute: NCT Dresden

summary: We were interested in transcriptional changes after depletion of histone acetyltransferase KAT2A in human colorectal cancer. Therefore, we utilized HCT116 cells as model, and analyzed global alterations of gene expression.

overall_design: RNA-Sequencing from HCT116 cells stably expressing Cas9-GFP after transduction with either a sgRNA targeting Luciferase (control) or human KAT2A. Experiment was performed in biologically independent triplicates.

middle: A


title: Differential transcriptome analysis of mid-logarithmic and early stationary growth phases of hyperacidophilic archaea Cuniculiplasma divulgatum S5

city: Bangor

first: Rafael María

last: Bargiela Bargiela

state: Gwynedd

address: Deniol Road

department: Center for Environmental Biotechnology

country: United Kingdom

institute: Bangor University

summary: Comparative gene expression analysis was employed for deciphering the major metabolic pathways in actively growing and stationary-phase cultures of Cuniculiplasma divulgatum S5. The analysis of data revealed differences in expression profiles that could not be investigated otherwise, e.g. through the shotgun proteome studies. This transcriptome study accompanies physiological and metabolic studies to pinpoint the key  niche adaptation mechanisms and disentangle evolutionary trajectories within Thermoplasmata.

overall_design: After cultivation of Cuniculiplasma divulgatum and samples have been collected after 3 days, corresponding to its mid-log growing phase, and afer 5 days, corresponding to its early stationary phase. The goal is to compare both samples and check when and which proteins are expressed regarding its surface (archeaellum, pili, etc), production of carotenoids and metabolism. RNA-seq experiments were performed to compare the differential expresion of genes among the two growing phases.

first: Olga

last: Golyshina

first: Peter

last: Golyshin

first: Rafael

last: Bargiela


title: DCHP targets lipid associated macrophages to disrupt lipid metabolism via crosstalk with adipocyte precursor cells

city: Beijing

first: Hui

last: Yang

address: 7 Panjiayuan Nanli, Room314

department: Department of Toxicology

institute: China National Center for Food Safety Risk Assessment (CFSA)

summary: The role of lipid associated macrophages (LAMs) in metabolic homeostasis remains an important yet understudied aspect of adipose tissue. Here, we report a potential new regulatory mechanism by which LAM control adipose tissue homeostasis, involving the endocrine disrupting chemical (EDC) dicyclohexyl phthalate (DCHP) and resulting in altered metabolic regulation. Prepubertal DCHP exposure decreased adipose tissue mass and increased plasma triglycerides in mice. Mechanistically, DCHP facilitated the formation of LAMs. And LAMs communicated with adipocyte precursors, especially adipose progenitor cells, via ApoE-APP interaction, leading to abnormal adipogenesis. Blocking LAMs formation via macrophage-specific PPARγ knockout enabled adaptive adipogenesis, ameliorating DCHP-induced metabolic disorder. Our data highlight the essential role of LAMs in inhibiting adaptive adipogenesis, providing a scientific basis for EDC-induced metabolic dysfunction and phthalates toxicity.

overall_design: To investigate the mechanistic regulation of macrophages polarization by Monocyclohexyl phthalate (MCHP), PPRE-eGEP-THP-1 cell line from our previous study was used. Cells were treated with MCHP (100 μM) or corresponding solvent for 24 hours during the polarization of M1 or M2 macrophages. Then, total RNA were extracted with TRIzol for transcriptome sequencing. Biological replicates (n=3/per treat) were used.

first: Miao

last: Xu

first: Xudong

last: Jia

first: Yongning

last: Li

first: Yi

last: Wang

first: Yaru

last: Tian

first: Lijuan

last: You


title: Detoxification of wastewater treatment plant effluents by enhanced soil aquifer treatment

city: Barcelona

first: Claudia

middle: Sanz

last: Lanzas

address: Jordi Girona 18-26

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

summary: Soil Aquifer Treatment (SAT) is recognized as a cost-effective approach to reduce contaminants of emerging concern (CECs) from Wastewater Treatment Plant (WWTP) effluents. However, its efficiency in removing the associated biological effects is still poorly understood. Here, we evaluated the efficiency of three pilot SAT systems, two of them enhanced with reactive barriers containing different proportions of sand and organic materials, in removing toxicity associated to CECs. SATs were fed with secondary effluents from the Palamós WWTP (N.E. Spain) during two consecutive campaigns scheduled before and after the summer of 2020. Fifteen water samples were collected from the WWTP effluent, below the barriers and 15 m into the aquifer. Transcriptomic analyses of zebrafish embryos exposed to the corresponding water extracts revealed a wide range of toxic activities in the WWTP effluents. Results demonstrated that the associated responses were reduced by more than 70% by SAT, achieving control levels in some cases. Similar results were obtained when human HepG2 hepatic cells were tested for cytotoxic and dioxin-like responses. Toxicity reduction appeared to be partially determined by the reactive barrier composition and/or SAT managing and was correlated with the removal of CECs by SAT. In conclusion, SAT appears to be a very promising approach for efficiently reducing the effects of recalcitrant pollutants from WWTP secondary effluents on the environment and human health.

overall_design: Whole embryo (5 dpf; wild type zebrafish) mRNA profiles of 4 groups (CTRL larvae and larvae exposed to WWTP's secondary effluent extract (SEC) from "JUN20" sampling campaign; CTRL larvae and larvae exposed to WWTP's secondary effluent extract (SEC) from "OCT20" sampling campaign) were generated by deep sequencing.

last: Sanz

first: Adrià

last: Sunyer-Caldú

first: Marta

last: Casado

first: Sylvia

last: Mansilla

first: Lurdes

last: Martinez-Landa

first: Cristina

last: Valhondo

first: Ruben

last: Gil-Solsona

first: Pablo

last: Gago-Ferrero

first: Jose

last: Portugal

first: M.

last: Silvia Diaz-Cruz

first: Jesús

last: Carrera

first: Benjamin

last: Piña

first: Laia

last: Navarro-Martín


title: Differential transcriptome analysis of mid-logarithmic and early stationary growth phases of hyperacidophilic archaea Oxiplasma meridianum M1

first: Rafael María

last: Bargiela Bargiela

summary: Comparative gene expression analysis was employed for deciphering the major metabolic pathways in actively growing and stationary-phase cultures of Oxiplasma meridianum M1. The analysis of data revealed differences in expression profiles that could not be investigated otherwise, e.g. through the shotgun proteome studies. This transcriptome study accompanies physiological and metabolic studies to pinpoint the key  niche adaptation mechanisms and disentangle evolutionary trajectories within Thermoplasmata.

overall_design: After cultivation of Oxiplasma meridianum M1 and samples have been collected after 3 days, corresponding to its mid-log growing phase, and afer 5 days, corresponding to its early stationary phase. The goal is to compare both samples and check when and which proteins are expressed regarding its surface (archeaellum, pili, etc), production of carotenoids and metabolism. RNA-seq experiments were performed to compare the differential expresion of genes among the two growing phases.

first: Olga

last: Golyshina

first: Peter

last: Golyshin

first: Rafael

last: Bargiela


title: Nucleosome intermediate preference of SMARCAD1 chromatin remodeler, and the structural insights

first: Youyang

last: Sia

address: Haidian district

institute: Tsinghua University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Examination of the repositioning of nucleosome and hexasome-sized particles induced by the SMARCAD1 family proteins in cells support the hexasome-binding mode. Our findings reveal a new mode of chromatin regulation, wherein the nucleosome intermediates are specially remodeled through an ATP-dependent process.

overall_design: MNase-seq in Saccharomyces cerevisiae. Compare nucleosome shift between WT-mutant(dFun30). Two biological replicates were sampled.

first: Pengjing

last: Hu

first: Xian

last: Xia

first: Kangjing

last: Chen

first: Zhucheng


title: Comprehensive analysis of  molecular expression differences in NALM6 cells before and after use of  verteporfin

city: Fuzhou

first: feng

last: zhang

address: 29 Xinquan Road

institute: Fujian Medical University

summary:
Aims:This study used cell line models and patient datasets to investigate the role of YAP1 in B- ALL.
Methods: We used RNA-Seq to compare the gene expression levels of the Hippo pathway-related molecules before and after verteporfin (VP) treatment to identify important Hippo pathway-related genes in the NALM6 cell line.
Results:we identified a total of 2002 differentially expressed genes in VP and DMSO treatment groups (FC ≥ 1.5, p ≤ 0.05), including 1042 upregulated and 960 downregulated genes, of which 146 were associated with the Hippo signaling pathway. Further screening resulted in 29 identified genes comprising 12 upregulated and 17 downregulated genes, which were associated with VP-treated NALM6 cells.
Conclusion:Pre- and post-VP  treatment, the upstream gene LATS1 was upregulated, and its overexpression increased YAP1 Ser127  site phosphorylation further studies.

first: Feng

last: Zhang

first: Mohammed

last: Issah

first: Haiying

last: Fu

first: Huarong

last: Zhou

first: Tingbo

last: Liu

first: Jianzhen

last: Shen


title: Drosophila TRAP soma vs germline

city: clermont ferrand

first: yoan

last: renaud

address: place henri dunand

country: France

institute: igred

summary: mRNA seq after IP of RPL10-GFP specfically expressed in follilce cells or germ cells

overall_design: RPL10-GFP expression was driven by tj:Gal4 or Nos:Gal4VP16: Gal4 before standard TRAP protocol

first: Vincent

last: Mirouse

first: Yoan

last: Renaud


title: Dopamine inhibits type 2 innate lymphoid cell-driven allergic lung inflammation via dampening mitochondrial activity

city: Tianjin

first: Jie

address: No22.Qixiangtai Rd.,Heping Dist,Tianjin P.R. China

institute: Tianjin Medical University

summary: Neuroimmune interactions are critical regulators of tissue homeostasis and allergic inflammation, and group 2 innate lymphoid cells (ILC2s) have emerged as an important cell type for mediating these interactions. Here, we identified that the abundance of dopamine (DA) was negatively correlated with the number of circulating ILC2s and lung function in human. Dopamine potently suppressed lung ILC2 responses in mice, which was dependent on the expression of dopamine receptor DRD1. Correspondingly, the local ablation of dopaminergic neurons further augmented ILC2 responses and aggravated allergic lung inflammation. Transcriptome and metabolic analyses revealed that dopamine impaired oxidative phosphorylation (OXPHOS) pathway in ILC2s. Augmentation of OXPHOS activity with oltipraz antagonized the inhibitory effects of dopamine. Finally, the local administration of dopamine dramatically alleviated allergen-induced ILC2 responses and airway inflammation. Our work highlights a model where dopamine is critical for suppressing ILC2 responses and maintaining homeostasis of type 2 immune machinery in lung.

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq and scRNA-seq data for ILC2s isolated from wild type mice treated with IL-33 plus dopamine or PBS.

first: Yingjiao

last: Cao

first: Yu

last: Li

first: Shaorui

first: Heping

last: Xu


title: Screening radiation-differentially expressed circular RNAs and establishing dose classification models in the human lymphoblastoid cell line AHH-1

city: BEIJING

first: XUELEI

last: TIAN

address: 2 Xinkang Street, Deshengmenwai, Beijing

institute: National Institute for Radiological Protection, Chinese Center for Disease Control and Prevention

summary: To investigate whether circRNAs have the potential for being radiation biomarker,we screened the radiation-induced differential expressed circRNAs in the AHH-1 cell line exposed to 60Co γ rays. And we established 4 expression models for radiation dose estimation by use of the validated radiation-induced differential expressed circRNAs.

overall_design: radiation-induced differential expressed circRNAs were screened through transcriptome sequencing with human lymphoblastoid cell line AHH-1 at 4 h after irradiated with 0, 2, and 5 Gy 60Co γ-rays.

first: Xuelei

last: Tian

first: Tingting

first: Tianjing

last: Cai

first: Mei

first: Qingjie


title: Single cell transcriptomic analysis of female mice after rhabdomyolysis-induced nephrotoxic injury

city: Firenze

first: Roberto

last: Semeraro

address: Viale Pieraccini, 6

department: Medicina Sperimentale e Clinica

country: Italy

institute: Università degli studi di Firenze

summary: We found that PTC undergo polyploidization immediately after glycerol-induced rhabdomyolysis (nephrotoxic-AKI). Polyploidization of PTC is controlled by YAP1. Block of YAP1 related polyploidization of TC employing a specific inhibitor of YAP1 transcriptional activity (CA3) after the acute phase of damage prevented CKD progression after AKI. To identify novel pathways and potential targets involved in AKI response and subsequent CKD development, we generated single-cell RNA sequencing (scRNAseq) datasets from nephrotoxic-AKI female mice treated with vehicle or CA3 starting from 4 days after AKI. Mice were sacrificed two weeks after AKI, when blood urea nitrogen levels, that reflect kidney functionality, were found to start diverging between treated and control mice, but before CKD development.

overall_design: To identify novel pathways and potential targets involved in the response to AKI and subsequent CKD development.

first: Letizia

last: De Chiara

first: Elena

last: Lazzeri

first: Paola

last: Romagnani


title: High-Throughput Sequencing Analysis of Differential MicroRNA Expression in the  Process of Blocking the Progression of Chronic Atrophic Gastritis to Gastric Cancer by Xianglianhuazhuo Formula

city: shijiazhaung

first: yuxi

last: guo

state: china

address: Hebei Hospital of Traditional Chinese Medicine, 389 Zhongshan East Road, Chang 'an District, Shijiazhuang City, Hebei Province, China

institute: Hebei Province Traditional Chinese Medicine Hospital

summary: To investigate the potential mechanism of action of Xianglianhuazhuo formula (XLHZ) in blocking the progression of chronic atrophic gastritis (CAG) to gastric cancer (GC) . The microRNA (miRNA) expression profiles of gastric mucosal tissues were analyzed by high-throughput sequencing.

overall_design: We used the gastric mucosa tissues of 3 groups of rats for gene expression profiling analysis using the data obtained from miRNA-SEQ.

first: Yuxi

last: Guo

first: Ze

last: Cheng

first: Xuemei

last: Jia


title: ALK effection analysis on T-lymphocyte cells

city: Philadelphia

first: Wasik

last: Mariusz

state: Pennsylvania

address: 422 Curie Blvd

country: USA

institute: University of Pennsylvania

summary: In this study we compared the effects of ALK inhibitor on the gene expression, activation of cell signaling pathways, and functional properties of cells derived from a patient with Anaplastic Large Cell Lymphoma. we used microarrays to map the genome-wide gene expression patterns in ALK+TCL cells in response to ALK inhibition.

overall_design: The ALK+TCL 4 cell line were treated in triplicates with the ALK inhibitor, CEP-14083, or the compound's solvent for 6 h. The isolated RNA was reverse-transcribed, biotin-labeled, and hybridized to the human gene 2.0 ST array (Affymetrix). Microarray data were normalized using the MAS5 algorithm and analyzed using Partek GS (Partek).

first: Qian

last: Zhang

first: XIaobin

last: Liu

first: Hong

middle: Y

last: Wang

first: Baldwin

last: Donald

first: Mariusz

last: Wasik


title: Expression analysis of radio-resistant and -sensitive head and neck cancer cells

city: Leuven

first: Peihua

last: Zhao

address: Herestraat 49

country: Belgium

institute: KU Leuven

summary: Head and Neck Squamous Cell Carcinoma (HNSCC) is a common cause of cancer death. Despite enormous technical advances in surgery and radiotherapy in the recent decade, survival of HNSCC patients has not markedly improved, with only 30% of patients diagnosed with advanced HNSCC that will survive for 5 years. This highlights the need to look into molecular processes leading to mechanisms of HNSCC radioresistance in HNSCC and identify novel radiosensitizers. To identify the lncRNAs associated with radiotherapy resistance in HNSCC, we performed RNA-seq analysis of radiation resistant and sensitive HNSCC cells.

overall_design: We performed RNA-seq analysis of the isogenic SCC61 and RTR61 cell pair, as well as in two radioresistant single clones RTR61-1 and RTR61-4 derived from the total RTR61 cell population. We also used another isogenic pair, radiosensitive SCC154 cells and radioresistant RTR154 cells, and two radioresistant single clones RTR154-1 and RTR154-4 isolated from the RTR154 total population. Finally, we determined the lncRNA expression profiles of 4 radioresistant and 5 radiosensitive HNSCC cell lines

first: Anna

last: Sablina


title: Effect of SNHG6 depletion on gene expression in radioresistant RTR61 cells

summary: Head and Neck Squamous Cell Carcinoma (HNSCC) is a common cause of cancer death. Despite enormous technical advances in surgery and radiotherapy in the recent decade, survival of HNSCC patients has not markedly improved, with only 30% of patients diagnosed with advanced HNSCC that will survive for 5 years. This highlights the need to look into molecular processes leading to mechanisms of HNSCC radioresistance in HNSCC and identify novel radiosensitizers. Up-regulation of the SNHG6 micropeptide is associated with radioresistance of HNSCC cells. To assess the mechanism SNHG6-mediated radioresistance, we performed transcriptome analyses of RTR61 cells expressing either siScramble, or siSNHG6.

overall_design: We performed RNA-seq analysis of the cytoplasmic and total RNA isolated from RTR61 cells 72 hours after  transfection with siScramble or siSNHG6. siPOOL SNHG6 or Scramble control, each containing a mixture of 30 different siRNAs (BioTech).


title: POH1 regulates MYC in pancreatic cancer cells [CUT&TAG]

city: Shanghai

first: Boshi

address: No.800 Dongchuan Road

institute: Shanghai Cancer Institute

summary: CUT&Tag experiments were used to analyze DNA-binding of MYC protein in the vector or POH1-Flag expressed mouse pancreatic cancer cells.

overall_design: The Pan02 cells stably expressing POH1-Flag were constructed. The CUT&Tag assays were performed using anti-Flag antibody and anti-MYC antibody.

first: Tiantian

last: Jing


title: Botrytis cinerea genes activated in infection process

first: Daoxin

last: Xie

address: School of Life Sciences, Room 407, Renhuan Building, Tsinghua University

summary: To screen Botrytis genes activated in infection process, we performed gene expression profiling analysis using data obtained from RNA-seq of Botrytis cinerea cultured in vitro or infecting Arabidopsis leaves.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Botrytis cinerea cultured in vitro or with infection on Arabidopsis leaves.

first: Jiaojiao

first: Dewei

last: Wu


title: Ribosome profiling of lncRNA-derived sORFs in radiosensitive and radioresistant HNSCCs

summary: Head and Neck Squamous Cell Carcinoma (HNSCC) is a common cause of cancer death. Despite enormous technical advances in surgery and radiotherapy in the recent decade, survival of HNSCC patients has not markedly improved, with only 30% of patients diagnosed with advanced HNSCC that will survive for 5 years. This highlights the need to look into molecular processes leading to mechanisms of HNSCC radioresistance in HNSCC and identify novel radiosensitizers. A growing body of evidence suggests that long non-coding RNAs (lncRNA) containing small open reading frames (sORFs) produce biologically active micropeptides. We performed ribosome profilming of  radiosensitive and radioresistant HNSCC cells to identify the lncRNA-encoded micropeptides differentially expressed in radioresistance cellls.

overall_design: Ribosome profiling of parental radiosensitive SCC61 and radioresistant RTR61 cells


title: Retinoic acid induced meiosis initiation of female germline stem cells by remodeling three-dimensional chromatin structure [RNA-seq]

first: Ji

address: No.800, Dongchuan Road, Minhang District

institute: Shanghai Jiao Tong University

summary: We use RNA-sequencing to report the transcriptomic differences between FGSCs with stra8-positive germ cells induced by retinoic acid

overall_design: Examination of the transcriptomic differences in 6 cell types.

first: Yabin


title: Retinoic acid induced meiosis initiation of female germline stem cells by remodeling three-dimensional chromatin structure [HiC]

summary: We use Hi-C to report the three-dimensional chromatin organization between FGSCs with stra8-positive germ cells induced by retinoic acid

overall_design: Examination of the chromatin architecture in female germline stem cells


title: Retinoic acid induced meiosis initiation of female germline stem cells by remodeling three-dimensional chromatin structure

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

overall_design: Refer to individual Series


title: The underlying mechanism by which DAZAP1 exerted carcinogenesis and its potential targets in MM

city: nanjing

first: zhou

middle: yan

last: yan

address: xianlin road

institute: nanjing univercity of China medicine

summary: An RIP experiment was performed in CAG cells using FLAG antibody as bait. The position of peak summit around transcript start sites of genes can predict the interaction sites of protein and gene. We compared the peak summit of  CAG EV and CAG DAZAP1 OE cells to find the differences between CAG EV cells and CAG DAZAP1 OE cells.

overall_design: Examination in CAG cells.

first: Yanyan

last: Zhou


title: Uncovering the mechanisms-based quality control of traditional Chinese medicine against essential hypertension by network analysis and experimental validation

first: Xiaochen

last: Yang

address: Beixiange 5#, Xicheng District

department: Cardiology

institute: Guangan men Hospital

type:
Expression profiling by array
Non-coding RNA profiling by array

summary: A total of 4276 lncRNAs (1426 upregulated and 2850 down-regulated) and 9230 mRNAs (5187 upregulated and 4043 down-regulated) were differently expressed in SHR-C compared with WKY, whereas 265 lncRNAs (65 up-regulated and 200 down-regulated) and 267 mRNAs (132 upregulated and 135 down-regulated) were differently expressed after BSJY treatment (fold change >2. 0 and P value< 0. 05).  Taking the intersection of the two sets, the analysis found that 8 lncRNAs and 35 mRNAs were upregulated, whereas 11 lncRNAs and 15 mRNAs were downregulated in the WKY vs.  SHR-C group and SHR-Bh group (fold change > 2. 0 and P value < 0. 05).  It showed the heatmap that were constructed using fold change, It showed the Volcano plots that were constructed using fold change values and P values and revealed the relationship between fold change and statistical significance.

overall_design: We applied microarray analysis to examine lncRNA and mRNA expression profiles in thoracic aorta tissues of SHRs with (SHR-Bh or Ca) or without treatment (SHR-C) and wistar rats (WKY).

first: Cheng

last: Kang


title: Recognition of m6A RNA by the non-canonical reader IMP1

city: London

first: Pierre

last: Klein

address: Gower Street

department: Institute of Structural and Molecular Biology

institute: University College London

summary: m6A methylation is the prevalent post-transcriptional modification in eukaryotic mRNAs and provides an essential layer of regulation in organismal development and in disease. The information encoded by m6A methylation is integrated into existing RNA regulatory networks by the binding of an expanding list of m6A readers. An important question is how protein readers that do not contain a canonical m6A-specific YTH domain recognize methylated RNA. Here, we show that the non-canonical reader IMP1 directly recognises the m6A group using a dedicated hydrophobic platform in the KH4 domain, creating a stable and high affinity interaction with the methylated RNA targets. Notably, the recognition of the m6A group is independent from the underlying sequence context, but is layered upon IMP1 strong sequence specificity for GGAC RNA. Together, our data indicate that, contrarily to the well-characterised YTH readers, IMP1 recognises and binds both m6A-methylated and non-methylated RNA targets with high affinity. This suggests that m6A methylation does not provide a general layer of control of IMP1 function, but rather plays a directed role in specific regulatory pathways.

overall_design: iCLIP in HeLa for IMP1

first: Giuseppe

last: Nicastro

first: Giancarlo

last: Abis

first: Sofia

last: Esteban-Serna

first: Christopher

last: Gallagher

first: Belen

last: Chaves-Arquero

first: Yuyang

last: Cai

first: Angelo Miguel

last: Figueiredo

first: Stephen

middle: R

last: Martin

first: Rickie

last: Patani

first: Ian

last: Taylor

first: Andres

last: Ramos


title: Expression data from U251-shCtrl and U251-shCPVL cells

city: Wuhu

first: xiao

middle: long

last: zhu

state: Anhui

address: 2 Zheshan western road

institute: Yijishan Hospital

summary: we performed microarray expression profiling to analyze the differentially expressed genes between U251-shCtrl and U251-shCPVL cells.

overall_design: U251-shCtrl and U251-shCPVL cells were constructed for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain differently expressed gene.

first: Hui


title: Enterococcus faecalis-derived lactate mediated suppression of NF-κB and ERK pathways in macrophages to promote polymicrobial wound infection

city: Singapore

first: Brenda

last: Tien

address: 60 Nanyang Drive

country: Singapore

institute: NTU

summary: Enterococcus faecalis, a member of the human gastrointestinal microbiota, is a Gram-positive, opportunistic pathogen associated with hospital-acquired wound, bloodstream, and urinary tract infections. E. faecalis can suppress or evade immune-mediated clearance by macrophages to promote persistent infection, although the exact mechanisms and bacterial factor(s) involved are not well-defined. In this study, we examined E. faecalis factor(s) involved in suppressing macrophage activation, as well the macrophage pathways modulated by E. faecalis to suppress activation. We observed that E. faecalis prevents ERK and p65 phosphorylation and reduces MyD88 expression leading to a reduction in NF-κB activity. We identified E. faecalis lactate dehydrogenase, which is important for lactic acid production by E. faecalis, to be necessary for macrophage suppression and demonstrated that E. faecalis lactate dehydrogenase-mediated immune suppression promotes E. coli survival during polymicrobial wound infection. Taken together, these results suggest that that E. faecalis-derived lactic acid is involved in macrophage subversion and may help to promote the virulence of co-infecting bacteria.

overall_design: We aim to identify genes that are differentially expressed by macrophages during E. faecalis infection at different multiplicity of infection with or without LPS co-stimulation.

first: Kimberly

last: Kline


title: CRISPR-Cas9 Whole-Genome Screen Identify Critical Genes Regulating Cholesterol Metabolism in Macrophages

city: Brookings

first: Natalie

middle: W

last: Thiex

state: SD

address: 1390 College Ave

department: Biology & Microbiology

institute: South Dakota State University

summary: We designed CRISPR-Cas9 whole genome screens to identify and rank critical genes for cholesterol metabolism in modified LDL treated BMDMs

overall_design: Identify and rank critical genes for cholesterol metabolism in bone marrow-derived macrophages (BMDM) by CRISPR/Cas9 whole genome screen. The screens assayed cellular neutral lipid amounts following exposure of BMDM to  low-density lipoprotein. Here, we have screens with change in neutral lipid content following 1) 24-h exposure to AcLDL or OxLDL (24h LDL) 2) 24-h exposure followed by 36-48 h post AcLDL or OxLDL removal culture (post-LDL 48h)

first: Kevin

last: Wanniarachchi

first: Rifat

last: Sultana

first: Jared

last: Wollman

first: Lu

last: Huang

first: Xijin

last: Ge


title: RNA sequencing data of intestinal tissue from wild-type C57BL/6 mice and ITGB6-overexpressing transgenic mice

city: Hangzhou

first: Haiting

last: Xie

state: Zhejiang

address: 88 Jiefang Road

institute: The Second Affiliated Hospital of Zhejiang University School of Medicine

summary: To acquire a better understanding of the role of ITGB6 in the development of  inflammatory bowel disease (IBD), we performed mRNA-Req  to compare gene expression in two kinds of mice (wild-type C57BL/6 mice and ITGB6-overexpressing transgenic mice)  in DSS-induced intestinal fibrosis model.

overall_design: First, intestinal tissue samples were collected from wild-type C57BL/6 mice and ITGB6-overexpressing transgenic mice for RNA extraction and analysis. Then, intestinal fibrosis model based on the oral administration of 2.5% DSS was estabished with the two kinds of mice, and intestinal tissue samples were collected form these models for RNA extraction and analysis.

first: Jian

last: Wang


title: Time-resolved and multi-tissue RNAseq provided new insights on the immune responses of European eels following infection with Aeromonas hydrophila

city: Wuhan

first: cao

last: lu

state: Hubei

address: 7 Donghu South Road

department: Chinese Academy   of Sciences

institute: Institute of Hydrobiology

summary: No studies systematically compared time-resolved and multi-tissue innate immune responses for European eels (Anguilla anguilla) with Aeromonas hydrophila infection through a high throughput method. Here, we challenged European eels with A. hydrophila (infected) or PBS (control). A low fatality rate (16.1%) was observed for infected group at 2 days post-infection (dpi). Then we examined transcriptional profiles of intestines, livers and spleens from 12 European eels with/without the infection of A. hydrophila at 6, 18 and 36 hours post-infection (hpi). The results showed that the most differentially expressed genes (DEGs) were found in the spleens at 6 hpi (7569 DEGs), followed by the intestines at 6 hpi (3129 DEGs) and the livers at 18 hpi (2722 DEGs). Only a few DEGs were found in three tissues at 36 hpi. The comparisons for DEGs numbers and KEGG enrichments suggested a consistent time-course immune responses among these three tissues. A similar enrichment of PRRs-related pathways including TLRs, NLRs and RLRs was revealed in the livers and spleens, but not in the intestines. Among immune-related DEGs, 62 paralogues pairs were found, and the expression trends of most paralogues pairs were consistent. Some paralogues of immune-related DEGs had unique domains. Furthermore, a larger clusters representing the similar tissue were revealed for the intestines and spleens. The distinct cytokine signal transduction and interaction existed between the livers and spleens. Altogether, the present study provides time-resolved and multi-tissue transcriptome characteristics of A. anguilla in response to A. hydrophila infection.

first: Fan

last: Xiong

last: Cao

first: Jing

first: Ya

middle: F

last: Wu

first: Wen

middle: S

first: Ming

middle: X

last: Chang


title: Single cell analysis of SW620/SW620-TET2CD with long time clone culturing

city: Guangzhou

first: Hao

last: Sun

address: 190 Kaiyuan Avenue

institute: Chinese Academy of Sciences

summary: In order to understand the single cell nature of SW620/SW620-TET2CD, we used the SW620/SW620-TET2CD clone from Day6/Day9/Day12/Day15 to start our single cell sequencing and analysis the diffference of single cell gene expression from different samples.

overall_design: SW620/SW620-TET2CD clones were cultred with different time,ie 6 days, 9 days, 12 days and 15 days. Clones were dissociated to single cell and sequneced. Gene expression difference were analyized between diffferent time points.

first: Zheng

last: Hui

first: Sun

last: Hao

first: Li

last: Changpeng


title: Expression data of multple drug resistant bladder cancer cell model constructed by repeated exposure to pirarubicin treatment

city: Shenyang

first: Chuize

last: Kong

state: Liaoning

address: 155 Nanjing North Street, Heping District

department: Department of Urology

institute: The First Hospital of China Medical University

summary:
Bladder cancer has a high incidence worldwide accompanies by high recurrent rate after treatment. The emergence of primary or acquired chemotherapy resistance leads to poor efficacy in many cases. Therefore, there is an urgent need to elucidate the mechanism underlying drug resistance and enhance the sensitivity of cancer cells to chemotherapy.
To explore the underlying mechanisms of drug resistance, we firstly established a drug-resistant cell model T24/THP by repeated exposure of T24 cells to pirarubicin (THP) whose concentration increases gradually. After a stable mode of drug resistance of cancer cell had been repeatedly tested, we performed a gene expression profiling by microarray.

overall_design: The human bladder cancer cell line T24 were bought from the Type Culture Collection of the Chinese Academy of Sciences (Shanghai, China) and cultured in RPMI-1640 supplemented with 10% fetal bovine serum (FBS) under environment where the temperature is 37°C and CO2 concentration in the air is 5%. In order to establish the multiple drug resistance (MDR) bladder cancer cell line, T24 was initially cultured in the medium containing 5ng/ml pirarubicin for 24 hours and then replaced with normal culture medium without drug. Once the cells returned to an optimal state, the exposure to pirarubicin as described above was repeated with a gradually increasing concentration gradient containing 5, 10, 20, 50, 100, 200, 500 to 1000 ng/ml. In order to maintain the resistance, we added drugs at regular interval (every 2-3 weeks depends on cell state and counts). Parent cell line T24 were also cultured during the process of resistance cell establishment so that we can measure and compare IC50 continuously to ensure the development of resistance. The whole process lasted for over 6 months and finally we obtained the MDR bladder cell line T24/THP after a series of drug resistance tests were carried out. Afterwards, total RNA of both T24 and T24/THP (3 independent samples for each cell line) was firstly extracted, purified, amplified, and labeled in order to obtain biotin labeled cDNA for microarray test and analysis in order to obtain the different expressed genes between drug sensitive and resistant cell lines.

first: Yiming

last: Zhu

first: Chiyuan

last: Piao

first: Zhe

last: Zhang

first: Yuanjun

last: Jiang


title: Next generation sequencing for quantitative analysis of double-negative (DN) thymocyte transcriptomes from Toxf/f and Toxf/fCd4Cre mice.

city: Nanjing

first: qifeng

last: he

state: JIANGSU

address: zhongshan Road

department: general surgery

institute: nanjing university

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare the difference of NGS-derived transcriptome profiling between DN thymocytes from Toxf/f and Toxf/fCd4Cre mice.
Methods: mRNA profiles of DN thymocytes sorted by FACS from 3-4-week-old Toxf/f and Toxf/fCd4Cre mice were generated by deep sequencing, in triplicate, using Illumina Novaseq6000. The sequence reads that passed quality filters were analyzed at the transcript level with qRT–PCR using TaqMan and SYBR Green assays.
Results: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to the mouse genome (Build Ensembl_release100) and identified 19,045 transcripts in the DN thymocytes of Toxf/f and Toxf/fCd4Cre mice with BWA workflow. RNA-seq data showed approximately 1.1% of the transcripts which were differentially expressed between the DN thymocytes from Toxf/f and Toxf/fCd4Cre mice, with the parameter of false discovery rate (FDR) < 0.05 and absolute fold change ≥ 2.
Conclusions: Our study exhibits the detailed analysis of DN thymocyte transcriptomes with biologic replicates, generated by RNA-seq technology. The optimized data analysis here provides a framework for comparative investigations of expression profiles. The RNA-seq data allow researchers to identify the transcripts affected by TOX and to better understand the role of TOX in the development of thymocytes.

overall_design: mRNA profiles of DN thymocytes from 3-4-week-old Toxf/f and Toxf/fCd4Cre mice

first: Qifeng

last: He

first: Yijun

last: Lu

first: Runqiu

first: Beicheng


title: AMTB, a TRPM8 Antagonist, Suppresses Growth and Metastasis of Osteosarcoma through Repressing the TGFβ Signaling Pathway

city: shanghhai

first: yujie

last: liu

address: fengyang road 415

institute: 上海长征医院

summary: Since its first identification in prostate cancers and prostate tissues, transient receptor potential melastatin-subfamily member 8 (TRPM8) is subsequently found to be overexpressed in a wide range of cancers and is shown to be implicated in tumorigenesis and tumor progression. Here, we used N-(3-aminopropyl)-2-[(3-methylphenyl) methoxy] -N-(2-thienylmethyl) benzamide hydrochloride (AMTB), a specific TRPM8 antagonist, to explore its antitumoral effect on osteosarcoma. We find that AMTB suppress osteosarcoma cell proliferation, metastasis and induce cellular apoptosis. Xenograft model in nude mice experiments also define that AMTB can increase the sensitivity of tumor cells to cisplatin, the cytotoxic chemotherapeutic regimens in treating osteosarcoma. Molecularly, AMTB specific antagonizes TRPM8 which is upregulated in osteosarcoma and its expression level in osteosarcoma tissues is negatively related to patients’ prognosis. Finally, RNA sequencing analysis was performed to explore the mechanism underlying the antitumoral effect of AMTB on osteosarcoma cells and the results prove that AMTB suppresses the Transforming Growth Factor β (TGFβ) signaling pathway. Our study provides evidence that TRPM8 could be a potential therapeutic target and AMTB can suppress growth and metastasis of osteosarcoma cells through repressing the TGFβ signaling pathway and increase the sensitivity of tumor cells to cisplatin.

overall_design: mRNA profiles of U2OS cells  (control),  U2OS cells  (AMTB=30μM),

first: Y

last: Liu

first: J

last: Xiao


title: Whole blood gene expression from infliximab treated Crohn's disease patients at three time points: pre-treatment, two weeks and fourteen weeks post first treatment

city: Haifa

first: Shai

last: Shen-Orr

address: 1st Efron Street

department: Immunology

country: Israel

institute: Rappaport Institute of Medical Research, Faculty of Medicine and Faculty of Biology, Technion

summary: Personalized treatment of complex diseases is an unmet medical need pushing towards drug biomarker identification of one drug-disease combination at a time. Here, we used a novel computational approach for modeling cell-centered individual-level network dynamics from high-dimensional blood data to predict infliximab response and uncover individual variation of non-response. We identified and validated that the RAC1-PAK1 axis is predictive of infliximab response in inflammatory bowel disease. Intermediate monocytes, which closely correlated with inflammation state, play a key role in the RAC1-PAK1 responses, supporting their modulation as a therapeutic target. This axis also predicts response in Rheumatoid arthritis, validated in three public cohorts. Our findings support pan-disease drug response diagnostics from blood, implicating common mechanisms of drug response or failure across diseases.

overall_design: Whole blood samples from anti-TNF responding (n=15) and non-responding (n=9) IBD patients at three time points: pre-treatment, two weeks and fourteen weeks post first treatment

first: Shiran

last: Gerassy-Vainberg

first: Elina

last: Starosvetsky

first: Renaud

last: Gaujoux

first: Alexandra

last: Blatt

first: Naama

last: Maimon

first: Yuri

last: Gorelik

first: Sigal

last: Pressman

first: Ayelet

last: Alpert

first: Haggai

last: Bar-Yoseph

first: Tania

last: Dubovik

first: Benny

last: Perets

first: Adir

last: Katz

first: Neta

last: Milman

first: Yehuda

last: Chowers


title: RNAseq of mRNA from whole mouse liver

city: München

first: sainitin

last: donakonda

state: Bavaria

address: Ismaningerstr. 22

department: Institute of Immunology

institute: TUM

summary: In this study we want to map the gene expression profile of hepatic myeloid cells, either Ly6C+CD40+ and Ly6C+CD40 neg cells after CpG application, to Kupffer cells out of livers treated with non-CpG. This comparison will reveal transcriptional signature that is induced by the application of CpG.

overall_design: NUMBER of three to four biological replicates were used for analysis

first: Kim

last: Pawelka

first: Sainitin

last: Donakonda

first: Rupert

last: Oellinger

first: Thomas

last: Engleitner

first: Percy

last: Knolle


title: Oxytocin Signaling Regulates the Homeostatic Response to Cold Stress in Ectothermic Vertebrate

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Homeothermic vertebrates exposed to low temperature challenge activate multiple central and physiological pathways in order to regain homeostatic balance within the new environmental constrains. Such homeostatic responses include shivering and non-shivering thermogenesis, altered carbohydrate and lipid metabolism and protein catabolism synchronized by neuroendocrine responses. Pending their evolutionary life history, some of these physiological responses were also identified in poikilothermic vertebrates, yet a conception of heat seeking behavior and lack of cold-related metabolic regulation prevails. Using various physiological parameters and hypothalamic transcriptome analysis in the tropical poikilotherm Nile tilapia, we now demonstrate that cold stress in a poikilotherm induce complex central and physiological homeostatic responses. We further show that oxytocin which is a known thermoregulator in homeotherms, actively regulates temperature related homeostasis in poikilotherms. Moreover, we show that pharmacological or genetic blockage of oxytocin signaling affects oxygen-dependent metabolic rate in two cold exposed poikilothermic models. Therefore, our study identifies oxytocin as an adaptive and evolutionarily conserved metabolic regulator and show that poikilotherms brain actively respond to cold temperature stress by regulating metabolic physiology.

overall_design: RNAseq of midbrains from cold exposed (N=4) and normothermy-maintained Nile tilapia (N=4).

first: Jakob

last: Biran


title: Identifying the molecular mechanisms that underlie impaired kidney development due to maternal diabetes.

city: Pittsburgh

first: Dennis

last: Kostka

state: PA

department: Developmental Biology

institute: University of Pittsburgh

summary: The prevalence of diabetes has significantly increased among women of childbearing age worldwide, and it is known that infants who are exposed to maternal diabetes in utero are at increased risk of congenital anomalies of the kidney and urinary tract. The primary role of the kidney is to filter blood through the nephrons. These anomalies can result in a reduction in the number of nephrons that are formed during kidney development, or decreased congenital nephron endowment, which is linked to hypertension and chronic kidney disease. It is unknown how exposure to maternal diabetes in utero results in abnormal kidney development and the long-term health consequences of this exposure remain ill-defined. In this study, we profiled gene expression in the developing mouse kidney from C57BL/6J control and maternal diabetes exposed (DM_Exp) mice at single cell resolution. Consistent with previous studies, clusters with distinct transcriptional signatures clearly identify major compartments and cell types of the developing kidney.

overall_design: Single cell RNA sequencing pooled cells from 1 kidney from postnatal day 2 (P2) C57BL/6J control and 1 kidney from postnatal day 2 (P2) DM_Exp male mice.

first: Debora

last: Cerqueira

first: Andrew

last: Clugston

first: Jacqueline

last: Ho


title: Genome-wide mapping of Notch2 target sites in the embryonic kidney.

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: During kidney development, Notch signaling plays multiple roles including promoting differentiation of nephron progenitors that give rise to all of the epithelial cells found in the nephron. Little is known about what genes Notch signaling regulates and how Notch signaling interacts with other transcription factors. To address this, we carried out genome-wide mapping of Notch2, a major Notch receptor required for differentiation of nephron progenitors, in the embryonic kidney.

overall_design: Embryonic kidneys at E16.5 were crosslinked with 1% PFA and Notch2 ChIP was performed. Sequencing libraries were generated using NEBNext ChIP-seq library prep master mix set for Illumina and sequencing was performed using the Illumina HiSeq 2000.

first: Eunah

last: Chung


status: Public on Oct 31 2024

city: ST LOUIS

first: KIAN

middle: HUAT

last: LIM

state: MO

address: 660 S. Euclid Avenue  Campus Box 8069, St. Louis

department: internal Medicine

institute: WashU

summary: We make Pa01c cells stable expressing a scramble or shRNA against MAP3K8 and performed bulk RNASeq to assess transcriptomic changes Pa01c cells

overall_design: Bulk RNAseq analysis of Pa01c cells stable expressing a scramble or shRNA against MAP3K8.

first: Kian-Huat

last: Lim

first: Sapana

last: Bansod

first: Paarth

last: Dodhiawala


title: T Cell Receptor-mimic STAR Conveys Superior Sensitivity over CAR in Targeting Tumors with Low-density Neoantigens

city: Beijing

first: Xin

last: Lin

state: Beijng

address: chengfu road, Haidian

institute: Tsinghua University

summary: Targeting tumor-specific neoantigens is promising for cancer immunotherapy, yet their ultra-low expression on tumor cells poses significant challenges for T cell therapies. Here, we found that chimeric antigen receptors (CARs) exhibited 10-100 times lower sensitivity compared to T cell receptors (TCRs) when targeting p53R175H common neoantigen. To enhance CAR functionality, we introduce T cell receptor fusion construct (TRuC) and synthetic TCR and antigen receptor (STAR).  Our data demonstrate that STAR, which incorporates TCR-mimic antibody fragments and complete TCR signaling machinery, optimally reproduces antigen sensitivity of TCRs. STAR outperforms both CAR and TRuC in redirecting both CD8+ and CD4+ T cells to recognize HLA class I neoantigens. In vitro, human primary T cells engineered with STAR kill multiple cancer cell lines with low neoantigen density better than CAR-T and TRuC-T cells.  In tumor mouse models, STAR-T cells outperform CAR-T and TRuC-T cells in controlling neoantigen-low breast cancer and leukemia. Taken together, our findings highlight severe defects in CAR sensitivity and introduce STAR as a more sensitive synthetic receptor, providing a new framework for T cell-based immunotherapy targeting tumors with low neoantigen density.

overall_design: To characterize transcriptional and chromatin accessibility changes in T cells expressing different antigen receptors, we performed RNA-Seq and ATAC-Seq on CD8+ and CD4+ CAR, TCR-1, and STAR-T cells, respectively, following coculture with T2 cells at three different neoantigen densities (0, 10, 100nM and 1μM) for 24 hours.

first: Keyong

last: Sun

first: Daosheng

last: Huang


title: HeLa input control in high salt condition

city: Charlottesville

first: Chongzhi

last: Zang

state: VA

institute: University of Virginia

first: Chunyuan

last: Jin

first: Gang

last: Wei

first: Cairong

last: Cui

first: Weiqun

last: Peng

first: Keji

last: Zhao

first: Gary

last: Felsenfeld


title: Bisulfite sequencing of medaka egg methylomes

city: Columbia

first: Ramji

middle: Kumar

last: Bhandari

address: 1200 University Avenue Lefevre Hall 114

department: Biological Sciences

institute: University of Missouri

type: Methylation profiling by high throughput sequencing

summary: Medaka egg methylomes were sequenced using whole genome bisulfite sequencing (WGBS)

overall_design: Three biological replicates, and two technical replicates for each samples

middle: K


title: Single-cell sequencing of E12.5 mouse placenta

first: WENLI

last: FAN

state: Jiangsu

address: Hankou road 22

institute: Nanjing university

summary: In our study, we performed single-cell sequencing of the E12.5 mouse placenta to explore the cellular diversity and gene expression dynamics during placental development. This approach allowed us to delineate the complex landscape of cell types and states present at this critical stage of gestation. By analyzing the transcriptomic data, we identified several distinct trophoblast subpopulations, each characterized by unique gene expression patterns that suggest different functional roles in placental structure and function. Additionally, our data provided insights into the potential regulatory pathways involved in cell differentiation.

overall_design: We utilize placental samples from E12.5 mice, specifically choosing two distinct genotypes: wild-type (control group) and Elf5-Cre; Slc25a1f/f (experimental group). Wild-type placentas serve as control samples to evaluate the impact of Slc25a1 deletion on placental development.

first: Wenli

last: Fan

first: Zhongzhou

last: Yang


title: Inhibition of RNA splicing triggers CHMP7 nuclear entry impacting TDP-43 function and leading to onset of ALS

city: La Jolla

first: Brian

last: Yee

state: CA

address: 9500 Gilman Dr

department: Health

institute: UCSD

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

overall_design: Refer to individual Series


title: Single cell transcriptome sequencing of diabetic mouse heart

city: Xi'an

first: Yan

last: Zhang

address: 127 Changle West Road

institute: Xijing Hospital

summary: Cardiovascular disease is the leading cause of mortality in individuals with diabetes. However, the specific mechanisms and cell heterogeneity underlying cardiac injury in diabetes are still unclear, making it difficult to effectively manage diabetic cardiovascular damage. Our study used leptin receptor knockout (db/db) mice as diabetic models and sequenced their hearts at different pathological stages. Our findings provide important insights for preventing and treating diabetic heart damage.

first: Yang

last: Cao

first: Dongdong


title: ChIP-seq Profiling of RXRα in Proliferating C2C12 Myoblasts

city: Ottawa

first: Qiao

last: Li

state: Ontario

address: 451 smyth road

department: Cellular and Molecular Medicine

country: Canada

institute: University of Ottawa

summary: In this dataset, we present ChIP-seq profiling of RXRα in proliferating C2C12 myoblasts, which serves as an extension of Series GSE94558. The overall data provides genome-wide occupancy of RXRα in normal myoblast proliferation.

overall_design:
We profiled the genome-wide enrichment of RXRα, a binding partner of different nuclear receptors, in proliferating C2C12 myoblasts. High-throughput ChIP-seq analysis was performed to assess RXRα binding, with input chromatin DNA serving as control (GSE94558).

***************************************************************
The table below lists GEO accessions reused/reanalyzed for this study.
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title: The immune checkpoint TIGIT is upregulated on T cells during bacterial infection and is a potential target for immunotherapy

city: Woolloongabba

first: Timothy

middle: Ryan

last: McCulloch

state: QLD

address: 37 Kent St

department: Frazer Institute

country: Australia

institute: University of Queensland

summary:
Antibiotic resistance is a major public health threat, and alternatives to antibiotic therapy are urgently needed. Immunotherapy, particularly the blockade of inhibitory immune checkpoints, is a leading treatment option in cancer and autoimmunity. In this study, we used a murine model of Salmonella Typhimurium infection to investigate whether immune checkpoint blockade could be applied to bacterial infection. We found that the immune checkpoint T-cell immunoglobulin and ITIM domain (TIGIT) was significantly upregulated on lymphocytes during infection, particularly on CD4+ T cells, drastically limiting their proinflammatory function. Blockade of TIGIT in vivo using monoclonal antibodies was able to enhance immunity and improve bacterial clearance. The efficacy of anti-TIGIT was dependent on the capacity of the antibody to bind to Fc (fragment crystallizable) receptors, giving important insights into the mechanism of anti-TIGIT therapy. This research suggests that targeting immune checkpoints, such as TIGIT, has the potential to enhance immune responses toward bacteria and restore antibacterial treatment options in the face of antibiotic resistance.

In this experiment, we investigated the effect of TIGIT on CD4+ T cells by performing bulk RNA-sequencing on WT or TIGIT-/- CD4+ T cells in the context of S. Typhimurium infection.

overall_design: Four-week-old recipient CD45.1 mice were sublethally irradiated with two doses of 550 cGy 3 h apart. Four hours after the second dose of irradiation, mice were injected intravenously with a 50:50 mix of bone marrow cells from WT CD45.1.2 and Tigit−/− (CD45.2) mice. Mice were maintained on neomycin water for at least 3 weeks and used for experimentation 8–10 weeks after reconstitution. Mice were challenged with an attenuated aroA mutant strain of Salmonella enterica subspecies Typhimurium, SL3261, using a dose of 1e6 CFU in 200 μL by intraperitoneal injection. After 10 days, CD4+ T cells were sorted by flow cytometry and RNA was isolated using the Maxwell RSC simplyRNA Cells RNA Extraction Kit (Promega, Madison, WI, USA) as per the manufacturer's instructions. Libraries were prepped using an Illumina Stranded mRNA prep Kit (Illumina, San Diego, CA, USA) and sequenced on a NovaSeq6000 platform (single end, 100 bp).

first: Fernando

last: Souza-Fonseca-Guimaraes


title: Multiomics approaches disclose very-early molecular and cellular switches during insect-venom allergen-specific immunotherapy: an observational study

status: Public on Oct 30 2024

city: Esch-sur-Alzette

first: Feng

middle: Q.

last: Hefeng

address: 29, rue Henri Koch

department: Department of Infection and Immunity

country: Luxembourg

institute: Luxembourg Institute of Health

summary: Allergen-specific immunotherapy (AIT) induces immune tolerance, showing the highest success rate (>95%) for insect venom while a much lower chance for pollen allergy. However, the molecular switches leading to successful durable tolerance restoration remain elusive. Here we applied a multilayer-omics approach to reveal dynamic peripheral immune landscapes during AIT-initiation phase in venom allergy patients (VAP) versus pollen-allergic and healthy controls. Already at baseline, VAP exhibited altered abundances of several cell types, including classical monocytes (cMono) and CD4/CD8 type 1-type 17 hybrids. At 8-24h following AIT launch in VAP, we identified a uniform AIT-elicited pulse of late-transitional/IL-10-producing B cells, IL-6 signaling within Th2 cells and non-inflammatory serum-IL-6 levels. Sequential induction of activation and survival protein markers also immediately occurred. A disequilibrium between serum IL-6 and cMono in VAP baseline was restored at day seven following AIT launch. Our longitudinal analysis discovers molecular switches during initiation-phase insect-venom AIT that secure long-term outcomes. Trial number: NCT02931955.

overall_design: Here we administered allergen-specific immunotherapy (AIT) in two groups of patients allergic to insect venom or pollen. For 18 Venome allergy patients (VAP), we implemented an ultra-rush (only within eight hours) up-dosing protocol while we administered a conventional (within six weeks) up-dosing AIT in 16 PAP. For the ultra-rush protocol, the physcians injected 14 times within 8 hours with the following dose (0.003, 0.006, 0.015, 0.030, 0.060, 0.150, 0.30, 0.60, 1.50, 3.00, 6.00, 15.00, 30.00, 55.00) ug. Although the exact sampling periods are different between VAP and pollen allergy patients (PAP), our sampling schemes allowed us to cover comparable periods, essentially the build-up phase, until the achievement of the expected cumulative maintenance dose for both types of AIT. We performed time-series sampling of peripheral blood during the first seven days (0h, 8h, 24h and D7) in VAP. As for PAP, we measured at 0h, 24h and extended our sampling period to two weeks (2W), six weeks (6W) and 12 weeks (12W). To benchmark with the natural immune fluctuations, we also recruited 10 healthy controls (HC), who did not receive any AIT or other immunotherapy, and sampled seven times (0h, 8h, 24h, D7, 2W, 6W and 12W) within 12 weeks to match various time points of both patient groups. For the samples collected at each time point, we performed a multi-layer cellular and molecular omics (multi-omics) analysis, including single-cell mass cytometry (CyTOF) for deep immunophenotyping of 77 immune subsets, FACS-sorting-enabled Th2-cell-type-specific whole-genome RNA sequencing (RNA-seq), kinome analysis of ~350 different kinases, multiplexing analysis of 10 serological cytokines and conventional 17-parameter whole-blood-count analysis. Our multi-omics analysis was accompanied by a detailed clinical workup in all the patients. For details of various immunological datasets from each participant at each time point, please visit our interactive resource website 'i3Dare' (https://public.tableau.com/app/profile/lihpublicdata/viz/i3Dare_SYSTACT_Database/SYSTACTHome) that allows investigators to explore the datasets and figures in an interactive and interlinked manner. While the age of the PAP was comparable to that of HC (median, ∼37 and ∼35 years, respectively), VAP were older (median, ∼49 years). In the study design, we did not consider the sex ratio as the recruitment criteria for this real-world observational study. While both patient groups included male and female participants at a comparable ratio (PAP: 8 males, 8 females; VAP: 11 males, 7 females), the HC group was predominantly female (9 of 10). For demographic details, please refer to the manuscript.

first: Dimitrii

last: Pogorelov

first: Sebastian

last: Nepomuk Bode

first: Murilo

middle: L

last: Bazon

first: Xin

last: He

first: Javier

last: Ramiro-Garcia

first: Fanny

last: Hedin

first: Wim

last: Ammerlaan

first: Maria

last: Konstantinou

first: Christophe

middle: M

last: Capelle

first: Ni

last: Zeng

first: Aurélie

last: Poli

first: Olivia

last: Domingues

first: Guillem

last: Montamat

first: Oliver

last: Hunewald

first: Séverine

last: Ciré

first: Alexandre

last: Baron

first: Joseph

last: Longworth

first: Lorie

last: Neuberger-Castillo

first: Dominique

last: Revets

first: Lea

last: Guyonnet

first: Agnieszka

last: Demczuk

first: Sylvie

last: Delhalle

first: Jacques

last: Zimmer

first: Vladimir

last: Benes

first: Françoise

last: Codreanu-Morel

first: Christiane

last: Lehners-Weber

first: Ilse

last: Weets

first: Pinar

last: Alper

first: Dirk

last: Brenner

first: Jan

last: Gutermuth

first: Coralie

last: Guerin

first: Martine

last: Morisset

first: François

last: Hentges

first: Reinhard

last: Schneider

first: Mohamed

middle: H

last: Shamji

first: Fay

last: Betsou

first: Paul

last: Wilmes

first: Enrico

last: Glaab

first: Antonio

last: Cosma

first: Jorge

last: Goncalves

middle: Q

first: Markus

last: Ollert

first: Ingrid

last: Casper


title: Fenebrutinib, a Bruton’s tyrosine kinase inhibitor, blocks distinct human microglial signaling pathways

status: Public on Oct 28 2024

city: Basel

first: Roland

last: Schmucki

address: Grenzacherstrase

country: Switzerland

institute: F. Hoffmann - La Roche AG

summary: Bruton’s tyrosine kinase (BTK) is an intracellular signaling enzyme that regulates B cell and myeloid cell functions. Due to its involvement in both innate and adaptive immune compartments, inhibitors of BTK have emerged as a therapeutic option in autoimmune disorders such as multiple sclerosis (MS). Brain penetrant small molecule BTK inhibitors may also help to address compartmentalized neuroinflammation which is proposed to underlie MS disease progression. BTK is expressed by microglia, the resident innate immune cells of the brain, however the precise roles of microglial BTK and the impact of BTK inhibitors on microglial functions is still being elucidated. Much research to date has also focused on the effects of BTK inhibitors using rodent disease models. Here we characterize the pharmacological and functional properties of fenebrutinib (FEN), a potent, highly selective, noncovalent, reversible BTK inhibitor, in human microglia and complex human brain cell systems including brain organoids. We find that FEN blocks the effects of microglial FcγR activation including cytokine and chemokine release, microglial clustering and neurite damage in diverse human brain cell systems. Gene expression analyses identified pathways linked to inflammation, matrix metalloproteinase production and cholesterol metabolism that were modulated by FEN treatment. In contrast, FEN had no significant impact on human microglial pathways linked to TLR4 or NLRP3 signaling nor myelin phagocytosis. Our study increases the understanding of BTK functions in human microglial signaling relevant to MS pathogenesis and suggests that FEN could attenuate detrimental microglial activity associated with FcγR activation in MS patients.

overall_design: Bulk RNA sequencing of iPSC-derived brain tricultures (neurons, astrocytes, microglia) and immunocompetent human brain organoids

first: Simona

last: Lange

first: James

last: Keaney

first: Martin

last: Ebeling


title: Inhibition of EZH2 restores normal expression of genes associated with cysteine metabolism and ferroptosis in hepatocellular carcinoma [CUT&Tag]

status: Public on Oct 25 2024

city: Cheongju-si

first: Jaehyun

last: Lee

state: Chungcheongbuk-do

address: 1, Chungdae-ro, Seowon-gu

department: Biological Science and Biotechnology

country: South Korea

institute: Chungbuk National University

summary: Epigenetic dysregulation is closely associated with the pathogenesis of hepatocellular carcinoma (HCC). Enhancer of zeste homolog 2 (EZH2) is a key protein involved in the exacerbation of various cancers, including HCC. Despite several clinical trials of epigenetic therapies targeting EZH2, the mechanisms underlying EZH2-mediated gene suppression in HCC are not fully understood. In this study, we investigated EZH2-mediated transcriptional programs under EZH2-selective inhibition through an integrative analysis of epigenomic (ATAC-seq) and transcriptomic (RNA-seq) approaches. To determine the impact of EZH2 dysfunction, we measured the levels of H3K27me3 and EZH2 expression using flow cytometry and reverse transcription quantitative real-time PCR (RT-qPCR), respectively. Notably, we found that higher expression of EZH2 was significantly correlated with poorer survival among HCC patients by reanalyzing transcriptomes in the cancer genome atlas (TCGA). Inhibition of EZH2 with Tazemetostat (EPZ-6438), a selective inhibitor of EZH2, showed that EZH2 regulates genes involved in lipid homeostasis, and cysteine-methionine metabolism. Among the 13 EZH2 target genes identified by transcriptomic and epigenomic profiling, we selected BHMT and CDO1, which were significantly associated with poor survival in HCC patients. When HCC cells were treated with Tazemetostat, the expression levels of the BHMT and CDO1 genes increased, while the expression levels of ferroptosis marker genes, such as FSP1, NFS1, and SLC7A11, decreased. This suggests that inhibiting EZH2 may have potential therapeutic benefits in HCC by regulating the expression of genes involved in important biological processes. Our study suggests that EZH2 epigenetically regulates ferroptosis by controlling cysteine metabolism in HCC.

overall_design: To investigate regulation of H3K27me3 levels under EZH2 inhibition and EZH2 knockdown in liver cancer cell line, we performed Cleavage under Targets and Tagmentation (CUT&Tag) with Tazemetostat treatment compared with untreated and with EZH2 knockdown compared with siNC in HepG2.

first: Geunho

last: Kwon

first: Keunsoo

last: Kang

first: Kyuho


title: Integrated single-cell analysis reveals distinct epigenetic-regulated cancer cell states and a heterogeneity-guided core signature in tamoxifen-resistant breast cancer

status: Public on Oct 26 2024

city: Milwaukee

first: Victor

last: Jin

state: WI

address: 8701 Watertown Plank Rd

department: IHE

institute: Medical college of Wisconsin

summary: Inter- and intra-tumour heterogeneity of breast cancer might be one of the reasons that develops endocrine therapy resistance. Here, we conduct an integrated scRNA-seq and scATAC-seq analysis of ~80K breast tissue cells from two normal (NTs), three primary (PTs) and three tamoxifen-treated recurrent tumour tissues (RTs). We identify distinct cell types among breast tumour tissues and observe a striking level of cell-to-cell heterogeneity among six tumuor tissues and delineates the primary to recurrent tumour progression, underscoring the significance of these single-cell level tumour cell clusters classified from scRNA-seq data. We then define nine cancer cell states (CSs), including five PT-specific, three RT-specific and one PT-RT-shared CSs and identify a heterogeneity-guided core signature. We further identify distinct open chromatin regions and specific transcription factors (TFs) associated with cancer cell states as well as novel biological pathways that mediate their communications with the tumour microenvironment. We finally in silico characterize the core signature and in vitro functionally examine the role of one of core signature, BMP7 suggesting that it plays an oncogenic role in tamoxifen-resistant breast cancer cells, and could be a promising therapeutic target in treating endocrine resistant breast cancer. We envision this integrated single-cell epigenomic and transcriptomic measure will become a powerful approach to unravel how epigenetic factors and tumour microenvironment govern the development of tumour heterogeneity and to uncover potential therapeutic targets that circumvent heterogeneity-related failures.

overall_design: We conducted scRNA-seq and scATAC on 8 breast tumor tissues, including 2 normal tissues, 3 primary tumor tissues and 3 recurrent (tamoxifen) tumor tissues

first: Kun

last: Fang

first: Aigbe

middle: G

last: Ohihoin

first: Tianxiang

last: Liu

first: Lavanya

last: Choppavarapu


title: Metabolic dysfunction-associated steatohepatitis reduces interferon and macrophage liver gene signatures in chronic HBV patients

city: Rotterdam

first: Andre

last: Boonstra

address: Dr. Molewaterplein 40

department: Dept. of Gastroenterology and Hepatology

country: Netherlands

institute: Erasmus MC

summary:
Background & Aims: Chronic HBV patients with concomitant metabolic dysfunction-associated steatohepatitis (MASH) have been shown to develop more advanced fibrosis faster with more severe liver disease as compared to patients with chronic HBV alone. However, our understanding of the underlying mechanisms is limited.  Here we study how MASH co-morbidity impact immune activity in the liver of patients with chronic HBV infection.

Methods: Bulk RNA sequencing was performed on liver biopsies from patients with only MASH (n=10), only HBeAg-negative chronic HBV (ENEG; n=11), combined MASH/ENEG (n=9) and healthy controls (n=9). Biopsies with no or minimal fibrosis (≤F2) were selected to avoid confounding effects of fibrosis. We compared whole transcriptome data from patients with MASH/ENEG to those with ENEG alone to determine the impact of MASH co-morbidity on chronic hepatitis B.

Results: There is a high degree of overlap of liver gene expression profiles in patients with only ENEG versus those with only MASH compared to healthy controls, suggesting a largely shared mechanism of liver dysfunction and immune activity for these distinct conditions. In patients with ENEG, MASH co-morbidity significantly reduced interferon pathway activity (NES=2.03, p.adj=0.0251), the expression of ISGs (e.g., IFIT2, IFI27, IFITM1, IFI6), and macrophage gene signatures (e.g., MARCO, CD163, CD5L, CD63), when compared to patients with ENEG alone.

Conclusions: Transcriptomic profiling of the liver suggests that MASH negatively impacts ISGs expression in the liver of patients with ENEG, which may affect antiviral immune pathways, viral replication and inflammatory responses resulting in an increased risk of advanced fibrosis in patients with chronic hepatitis B. Our study provides valuable insights for guiding future research aimed at developing effective, tailored strategies for managing patients with both conditions.

overall_design: Formalin-fixed paraffin-embedded (FFPE) core liver biopsies, archived as part of routine diagnostics at Erasmus MC, were selected from patients at the outpatient clinic of the Erasmus MC Rotterdam. HBeAg-negative chronic hepatitis B (ENEG) patients with high viral loads and ALT levels were selected in this study. In addition, two cohorts of patients with biopsy-proven metabolic dysfunction-associated steatohepatitis (MASH) with and without concomitant ENEG were selected in this study. Liver fibrosis was determined by histology and transient elastography. Patients had no or minimal liver fibrosis at the time of inclusion (maximum of ≤F2, <7.0 kPa). Patients were not pregnant and received neither antiviral treatment prior to biopsy, nor had any co-existing primary liver disease, nor were they co-infected with HCV, HEV, HDV or HIV. Liver biopsies of healthy individuals were collected to determine their eligibility as altruistic liver donors. Total RNA isolation of FFPE liver biopsies and library preparation were performed as described previously (Montanari NR et al. Multi-parametric analysis of human livers reveals variation in intrahepatic inflammation across phases of chronic hepatitis B infection. J Hepatol. 2022 Aug;77(2):332-343. PMID: 35218813).

first: Zgjim

last: Osmani


title: Inhibition of EZH2 restores normal expression of genes associated with cysteine metabolism and ferroptosis in hepatocellular carcinoma [ATAC-seq]

overall_design: To investigate regulation of chromatin accessibility under EZH2 inhibition in liver cancer cell line, we performed Omni-Assay for Transposase-Accessible Chromatin sequencing (ATAC-seq) with Tazemetostat treatment compared with untreated in HepG2.

first: Chaelin

last: You


title: CHARTING AND PROBING THE ACTIVITY OF ADARS IN HUMAN DEVELOPMENT AND CELL-FATE SPECIFICATION

status: Public on Oct 24 2024

first: Prashant

last: Mali

state: California

address: 9500 Gilman Drive

department: Bioengineering

summary: Adenosine deaminases acting on RNA (ADARs) impact diverse cellular processes and pathological conditions. While we possess important insights into their roles in adult tissues, their functions in early cell fate specification remain less understood. To address this, we devised a comprehensive framework to investigate ADARs in human development. We began by charting time-course RNA editing profiles in human organs from fetal to adult stages, enabling broad insights into RNA editing trends across diverse tissues. Next, we utilized hPSC differentiation to experimentally probe ADARs across specific tissue-types, harnessing brain organoids as neural specific, and teratomas as pan-tissue developmental models. We found that time-series teratomas faithfully recapitulated developmental trends observed in fetal tissue. Motivated by this, we conducted pan-tissue, single-cell CRISPR-KO screens of ADARs in teratomas to assess their role in cell-fate specification. Knocking out ADAR1 led to a global decrease in RNA editing across all germ-layers. Intriguingly, we observed a significant fitness defect in mesodermal tissues, and an enrichment of adipogenic cells, revealing a novel role for ADAR1 in mesenchymal differentiation. Collectively, we developed a multi-pronged framework charting time-resolved RNA editing profiles in fetal and fetal-like organ tissues, thereby shedding light on the role of ADARs in development and cell fate-specification.

overall_design: We generated teratoma from H1 stem cells and harvested 2 replicates at 2 week intervals from week 4 to week 10. One teratoma from each time point was split into 2 or more replicates. We also ran a CRISPR-KO screen targeting ADAR family genes. 4 replicate teratomas generated from PGP1 iPSCs were generated for the screen.

first: Amir

last: Dailamy

first: Weiqi

last: Lyu

first: Sami

last: Nourreddine

first: Michael

last: Tong

first: Joseph

last: Rainaldi

first: Daniella

last: McDonald

first: Rebecca

last: Panwala

first: Alysson

last: Muotri

last: Breen

last: Zhang


title: A pattern to rule them all: tracing a human brain map of shared molecular aspects across aging, Alzheimer’s disease and dementia with Lewy bodies

city: Abbiategrasso

first: Riccardo Rocco

last: Ferrari

address: Corso San Martino, 10

institute: Golgi Cenci Foundation

summary: Aging is often characterized by a progressive loss of cognitive abilities due to the onset of different forms of dementia. Among these, Alzheimer’s Disease (AD) and dementia with Lewy bodies (LBD) are the most widespread ones. However, little is known about the common aspects between these conditions and how these aspects can be linked to aging itself. With this work, we aim to identify a molecular fil rouge that could link aging and different dementias in order to possibly highlight strategic targets for novel therapeutical approaches. A whole transcriptome analysis and a Gene Set Enrichment Analysis (GSEA) have been carried out on brain samples from hippocampus (HI), temporal and parietal cortex (TC, PC), cingulate cortex (CG), and substantia nigra (SN) from the Abbiategrasso Brain Bank (ABB) of subjects with a neuropathological diagnosis of AD and LBD (6 per pathology) and 3 age-matched controls with no dementia (CTRLs). Clinical and neuropsychological profile were obtained through serial evaluations, made at the baseline and in the following years. According to the ABB protocol, the neuropathological diagnosis was based on a complete histological characterization, including all the main proteinopathies and vascular scoring. Transcriptomic results showed some major differences in the number of differentially expressed genes (DEGs) between the two pathologies and in particular that AD brains gene expression is more affected compared to LBD’s one (DEGsAD=3156; DEGsLBD=278). Furthermore, the GSEA showed that in AD it is possible to cluster the analysed regions by biological processes (HI and TC: DEGs primarily related to synaptic transmission; PC, CG and SN: DEGs primarily related to proper protein folding and inflammation) while in LBD there is only a strong and peculiar involvement of SN (DEGs primarily related to proper protein folding and inflammation) and PC (DEGs primarily related to myelination and glial system activation). AD and LBD are different forms of dementia characterized by a definite time and severity-related pattern. Therefore, it is possible to draw a molecular map of pathology spreading in the brain that could unveil unexplored roads and possible shortcuts leading to a better understanding of AD and LBD pathogenesis. This could help to discover novel biological targets in order to develop effective and well-timed therapeutical approaches.

overall_design: We performed RNA-seq profiling of 5 brain regions (hippocampus, temporal cortex, parietal cortex, cingulate gyrus , and substantia nigra) from 6 AD patients, 6 LBD patients, and 3 healthy controls in duplicate. We used RNA extracted from brain tissue.

first: Valentina

last: Fantini

first: Maria

last: Garofalo

first: Rosalinda

last: Di Gerlando

first: Francesca

last: Dragoni

first: Bartolo

last: Rizzo

first: Erica

last: Spina

first: Elisa

last: Pellegrini

first: Chiara

last: Calatozzolo

first: Mauro

last: Ceroni

first: Antonio

last: Guaita

first: Annalisa

last: Davin

first: Stella

last: Gagliardi

first: Tino Emanuele

last: Poloni


title: Hematopoietic aging promotes cancer by fueling IL-1⍺-driven emergency myelopoiesis

status: Public on Oct 23 2024

city: New York

first: MATTHEW

middle: Dae-Young

last: PARK

state: NY

address: 50 East 98th Street, 6A-1

institute: Icahn School of Medicine at Mount Sinai

summary: Age is a major risk factor for cancer, but how aging impacts tumor control remains unclear. Here, we establish that aging of the immune system, regardless of the age of the stroma and tumor, impacts lung cancer progression. Hematopoietic aging enhances emergency myelopoiesis, resulting in the local accumulation of myeloid progenitor-like cells in lung tumors. These cells are a major source of IL-1⍺ that drives the enhanced myeloid response. The age-associated decline of DNMT3A enhances IL-1⍺ production, and disrupting IL-1R1 signaling early during tumor development normalized myelopoiesis and slowed the growth of lung, colonic, and pancreatic tumors. In human tumors, we identified an enrichment for IL-1⍺-expressing monocyte-derived macrophages linked to age, poorer survival, and recurrence, unraveling how aging impacts cancer.

overall_design: Sample preparation: Single-cell suspensions from lung tissues were obtained, as described above. Samples were broadly enriched for myeloid and lymphoid cells by fluorescence-activated cell sorting, and these cells were suspended in PBS supplemented with 0.5% BSA. Samples were loaded onto the 10x Genomics Next GEM 5’ assay, as per the manufacturer’s instructions, for a target cell recovery of 10,000 cells per lane. Libraries were constructed, according to manufacturer’s instructions. All libraries were quantified via Agilent 2100 hsDNA Bioanalyzer and KAPA library quantification kit (Roche, Cat. #0797014001). Libraries were sequenced at a targeted depth of 25,000 reads per cell; all libraries were sequenced using the Illumina NovaSeq S2 100 cycle kit.  scRNAseq analysis: Gene expression reads were aligned to the mm10 reference transcriptome and count matrices were generated using the default CellRanger 2.1 workflow, using the ‘raw’ matrix output. Following alignment, barcodes matching cells that contained > 500 unique molecular identifiers (UMIs) were extracted. From these cells, those with transcripts > 25% mitochondrial genes were filtered from downstream analyses. Matrix scaling, logarithmic normalization, and batch correction via data alignment through canonical correlation analysis, and unsupervised clustering using a K-nn graph partitioning approach were performed as previously described. Differentially expressed genes were identified using the FindMarkers function (Seurat). Mean UMI were imputed to determine logarithmic fold changes in expression between cell states to further the analysis of markers of interest.

first: Matthew

middle: D

last: Park

first: Miriam

last: Merad


title: Integration of epigenomic and transcriptomic profiling uncovers EZH2 target genes linked to cysteine metabolism in hepatocellular carcinoma

first: Jaehyun

last: Lee


title: FOXA2 and ASCL1 Cooperate in Driving Neuronal Lineage Commitment in Prostate Cancer [ChIP-seq]

city: Vancouver

first: Amina

last: Zoubeidi

state: BC

address: 2660 Oak Street

institute: Vancouver Prostate Centre

summary: In castration-resistant prostate cancer, lineage plasticity mediates resistance to androgen receptor pathway inhibitors (ARPIs) and progression from adenocarcinoma to neuroendocrine prostate cancer (NEPC), a highly aggressive and poorly understood subtype. ASCL1 has emerged as a central regulator of the NEPC phenotype, driving neuroendocrine differentiation. However, ASCL1’s influence on neuronal lineage switching and maturation, as well as its partners in NEPC, remain largely unknown. Here, we provided insights into ASCL1’s cistrome reprogramming in ARPI-induced NEPC versus terminal NEPC and showed that ASCL1 binding pattern tailors the subsequent expression of transcription factor combinations that underlie discrete terminal NEPC identity. We identified FOXA2 as a major co-factor of ASCL1 in terminal NEPC that it is highly expressed  in ASCL1-driven NEPC. FOXA2 and ASCL1  interact and work in concert to orchestrate terminal neuronal differentiation in prostate cancer, and regulate key neuroendocrine-associated genes including PROX1. Our findings provide insights into the molecular conduit underlying the interplay between different lineage determinant transcription factors to support the neuroendocrine identity in prostate cancer.

overall_design: Chromatin Immunoprecipitation DNA sequencing (ChIPseq) for FOXA2 in NCI-H660.

first: Shaghayegh

last: Nouruzi

first: Takeshi

last: Namekawa

first: Nakisa

last: Tabrizian

first: Maxim

last: Kobelev

first: Dwaipayan

last: Ganguli


title: Inhibition of EZH2 restores normal expression of genes associated with cysteine metabolism and ferroptosis in hepatocellular carcinoma [RNA-seq]

overall_design:
To investigate gene regulation under EZH2 inhibition in liver cancer cell line, we performed gene expression profiling analysis using data obtained from RNA-seq of Tazemetostat treatment compared with untreated in HepG2.
To investigate gene regulation under EZH2 inhibition in liver cancer cell line, we performed gene expression profiling analysis using data obtained from RNA-seq of EZH2 knockdown compared with siNC(non-targeting control) treatment in HepG2.

first: Chaelin

last: You

first: Keunsoo

last: Kang

first: Kyuho


title: Loc1 RIP-chip; Niedner et al.

city: Guildford

first: André

middle: P.

last: Gerber

state: Surrey

address: Stag Hill Campus

department: Microbial Sciences

institute: University of Surrey

summary:
Loc1 RIP-chip

Experimental procedure: C-terminally TAP-tagged Loc1p from yeast S. cerevisiae was purified from 1 L of cells grown in YPD medium as previously described (Gerber et al. 2004, PLoS Biol. 2, E79). Untagged control cells (BY4741) cells served as a negative control. cDNA was synthesized from 3 μg of total RNA derived from the extract and 500 ng of affinity-isolated RNA and labeled with Cy3 and Cy5 fluorescent dyes, respectively. Samples were mixed and hybridized to cDNA microarrays.

Publication: Niedner-Boblenz A. et al. 2024, Nucleic Acids Res, in press.
Title: Intrinsically disordered RNA-binding motifs cooperate to catalyze RNA folding and drive phase separation

Abstract:
RNA-binding proteins are essential for gene regulation and the spatial organization of cells. Here, we report that the yeast ribosome biogenesis factor Loc1p is an intrinsically disordered RNA-binding protein with eight repeating positively charged, unstructured nucleic acid binding (PUN) motifs. While a single of these previously undefined motifs stabilizes folded RNAs, multiple copies strongly cooperate to catalyze RNA folding. In the presence of RNA, these multivalent PUN motifs drive phase separation. Proteome-wide searches in pro- and eukaryotes for proteins with similar arrays of PUN motifs reveal a strong enrichment in RNA-mediated processes and DNA remodeling. Thus, PUN motifs are potentially involved in a large variety of RNA- and DNA-related processes by concentrating them in membrane-less organelles. The general function and wide distribution of PUN motifs across species suggests that in an ancient “RNA world” PUN-like motifs may have supported the correct folding of early ribozymes.

first: John

last: Matese

first: Andre


title: A multiplex single-cell RNA-seq pharmacotranscriptomics pipeline for drug discovery

status: Public on Oct 21 2024

city: Oulu

first: Alice

last: Dini

address: Aapistie 5A

department: Faculty of Biochemistry and Molecular Medicine

country: Finland

institute: University of Oulu

summary: We report a pipeline for high-throughput pharmacotranscriptomic profiling via 96-plexed single-cell RNA-sequencing (scRNA-Seq) using Cell Hashing. We show the potential of this approach by exploring the heterogeneous transcriptional landscape of primary high-grade serous ovarian cancer (HGSOC) cells after treatment with 45 drugs, with 13 distinct classes of mechanisms of action. A subset of PI3K/AKT/mTOR inhibitors induced the activation of receptor tyrosine kinases, such as the epithelial growth factor receptor (EGFR), and this is mediated by the upregulation of caveolin-1 (CAV1). This drug resistance feedback loop could be mitigated by the synergistic action of PI3K/AKT/mTOR- and EGFR-targeting agents for HGSOC with CAV1/EGFR expression.

overall_design:
JHOS2, PDC2, and PDC3 cells were treated for 24 hours with 45 drugs (and DMSO as control) in duplicates using a drug concentration above EC50 based on DSRT screens, which was likely able to elicit a transcriptional response across all drugs. Following drug treatments, cells in each well were labeled with a unique pair of β2microglobulin (B2M) and CD298 antibody-oligo conjugates from a set of 20 (12 for the columns and 8 for the rows of a 96-well plate) before samples pooling for multiplexed scRNA-Seq. Drug name (concentration in µM): AR-42 (10 µM); AT 101 (100 µM); AT9283 (1 µM); AZD-8055 (1 µM); AZD-8186 (1 µM); Belinostat (10 µM); BI 2536 (0.1 µM); Birabresib (10 µM); Birinapant (0.1 µM); BMS-754807 (10 µM); Buparlisib (10 µM); Cobimetinib (1 µM); Copanlisib (1 µM); Dactolisib (1 µM); Danusertib (10 µM); Dasatinib (1 µM); Dinaciclib (0.1 µM); ENMD-2076 (10 µM); Fedratinib (10 µM); Gedatolisib (0.1 µM); I-BET151 (10 µM); Ipatasertib (10 µM); JQ1 (10 µM); LY3009120 (2.5 µM); Milciclib (10 µM); Niraparib (10 µM); NVP-BGT226 (0.1 µM); NVP-LCL161 (2.5 µM); OTS167 (0.1 µM); Pacritinib (10 µM); PD0325901 (1 µM); PF-00477736 (10 µM); PF-03758309 (10 µM); Pictilisib (10 µM); Pracinostat (10 µM); Quisinostat (1 µM): Ralimetinib (10 µM); SCH772984 (10 µM);  Selinexor (10 µM);  SNS-032 (1 µM); Talazoparib (1 µM); TGX-221 (10 µM); UCN-01 (1 µM); Volasertib (1 µM); ZSTK474 (10 µM).

JHOS2 raw sequencing data are provided with this record. For the patient-derived cells raw sequencing data, please contact the corresponding author.

first: Harlan

last: Barker

first: Daniela

last: Ungureanu


title: Epigenome mapping in quiescent cells reveals a key role for H3K4me3 in regulation of RNA polymerase II activity

city: Huddinge

first: Shengyuan

last: Zeng

state: Stockholm

address: Blickagången 16

department: Department of Medicine, Huddinge

country: Sweden

institute: Karolinska Institutet

summary: (1) Background: Quiescent cells have stopped dividing and show strongly reduced levels of gene expression during dormancy. In response to appropriate signals the cells can wake up and start growing again.  Many histone modifications are regulated in quiescence, but their exact functions remain to be determined. (2) Methods: Here we map the different histone modifications: H3K4me3, H3K9ac, H3K9me2, H3K9me3, and the histone variant H2A.Z, comparing vegetative and quiescent fission yeast (S. pombe) cells. We also map histone H3 as a control and RNA polymerase II (phosphorylated at S2 and S5) to enable comparisons of their occupancies within genes. We use ChIP-seq methodology and several different bioinformatics tools. (3) Results: The histone modification mapping data show that H3K4me3 changes stand out as being the most significant. Changes in occupancy of histone variant H2A.Z was also significant consistent with earlier studies. Regarding gene expression changes in quiescence, we found that changes in mRNA levels were associated with changes in occupancy of RNA polymerase II (S2 and S5). Analysis of quiescence genes showed that increased H3K4me3 levels and RNA polymerase II occupancy was super-significant at a small set of core quiescence genes which are continuously upregulated during dormancy. We demonstrate that several of these genes were require Set1C/COMPASS activity for their strong induction during quiescence. (4) Conclusions: Our results imply that regulation of gene expression in quiescent cells involves epigenome changes with a key role for H3K4me3 in regulation of RNA polymerase II activity, and that different gene activation mechanisms are controlling early and core quiescence genes.  Thus, our data give further insights into important epigenome changes in quiescence using fission yeast as experimental model.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) was performed for histone modifications H3K9ac, H3K4me3, H3K9me2, H3K9me3, H3, H2A.Z, and RNA Pol II S2 and RNA Pol II S5 in wild-type fission yeast cells (Hu3112 strain) at both vegetative and quiescent stages. The same amounts of sheared chromatin, spike-in chromatin, and final system volumes were maintained for comparison.

first: Karl

last: Ekwall


title: Impact of Hydroxycarbamide Treatment on the Whole Blood Transcriptome in Sickle Cell Disease

status: Public on Oct 20 2024

city: Atlanta

first: Varsha

last: Bhat

state: Georgia

address: 950 Atlantic Drive, EBB1

institute: Georgia Institute of Technology

summary: Hydroxycarbamide (HC, also known as hydroxyurea) is the most widely used therapeutic for individuals with sickle cell disease (SCD). HC’s clinical benefits are primarily associated with its ability to induce fetal hemoglobin (HbF). However, much remains unknown about the non-HbF related impact of HC on genes and pathways relevant to SCD pathophysiology. In this study, we performed bulk RNA-Seq on whole blood samples collected from a cohort of 25 pediatric patients with SCD to identify genes and pathways that are affected by treatment with HC. The results illustrate the range of effects exerted by HC during therapy for SCD and pave the way for an improved understanding of the HbF induction-independent benefits of HC.

overall_design: Whole blood samples were collected at pre-HC (pre-HU) and at the maximum tolerated dose of HC (HU MTD). Gene expression profiling was performed with RNA-Seq.

first: Alka

middle: A

last: Potdar

first: G

last: Yu

first: Greg

last: Gibson

first: Vivien

last: Sheehan


title: The CIC::DUX4 oncoprotein maintains DNA integrity through direct regulation of the catalytic subunit of DNA polymerase epsilon (POLE).

status: Public on Oct 16 2024

city: San Francisco

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

summary: Transcription factor (TF) fusion oncoproteins represent cancer specific alterations that arise from chromosomal rearrangements.  Through target gene recognition, TF fusions can disseminate transcriptional responses that collectively work to drive tumorigenesis. Thus, identifying the molecular targets that operate as a disease driving network can potentially uncover key actionable dependencies. We have taken this strategy to dissect the underlying biological mechanism by which CIC::DUX4, a fusion oncoprotein associated with dismal outcomes, drives sarcomagenesis. We and others have defined a CIC::DUX4 fusion mediated network that dysregulates cell-cycle and DNA replication checkpoints. Specifically, CIC::DUX4-mediated CCNE1 upregulation compromises the G1/S transition leading to high DNA replication stress and conferring a dependence on the G2/M checkpoint kinase, WEE1. Thus, WEE1 provides a molecular brake to enable effective DNA repair prior to mitotic entry. Importantly, the mechanism by which CIC::DUX4 regulates DNA repair remains unknown. Here we show that the catalytic subunit of DNA polymerase epsilon (POLE) is essential for DNA integrity and cellular division in CIC::DUX4 sarcoma. Mechanistically, POLE loss increases DNA damage and induces p21-mediated cellular senescence to limit CIC:DUX4 mediated tumor growth in vitro and tumor formation in vivo. Altogether, we credential POLE as a CIC::DUX4 target and further characterize a functional network through which CIC::DUX4 operates to drive tumor progression and survival.

overall_design: To examine the regulatory role of CIC::DUX4 on POLE expression, we performed RNA interference (RNAi) to silence POLE in NCC-CDS1_X1_C1 patient-derived sarcoma cells. To understand how POLE regulates cellular senescence in CIC::DUX4 sarcoma cells, we conducted transcriptional profiling via RNA-Seq in POLE-deficient and POLE replete NCC_CDS1_X1_C1 cells.

first: Zeinab

last: Kosibaty

first: Cuyler

last: Luck