title: Early Transcriptional Responses to Human Paratyphoid Challenge

city: Oxford

first: Henderson

last: Zhu

address: Oxford Vaccine Group, Old Road, Headington, Old Road, Headington

department: Oxford Vaccine Group, Department of Paediatrics

institute: University of Oxford

summary: The whole blood transcriptome 12 hours after challenge with S. Paratyphi A. Samples were collected in a study aiming to find the challenge dose giving a 60-75% attack rate, published in Dobinson et al. PMID: 28158395. Participants were challenged with S. Paratyphi A NVGH308 strain suspended in sodium bicarbonate. Enteric fever was diagnosed based on oral temperature or positive blood culture. Participants were treated with antibiotics either following diagnosis or 14 days without diagnosis. Paired baseline samples are available under Series GSE114033.

overall_design: Outpatient dose-finding challenge study in healthy human volunteers. Peripheral blood was collected 12 hours post-challenge in Tempus Blood RNA tubes. RNA was extracted using a Tempus Spin RNA Isolation kit and poly-A selected.

first: Amber

last: Barton

first: Christoph

last: Blohmke

first: Andrew

last: Pollard


title: Computational map of colon polyps

status: Public on Jan 01 2025

city: La Jolla

first: Daniella

last: Vo

state: CA

address: 9500 Gilman Dr

department: Pediatrics

country: USA

institute: UC San Diego

type: Expression profiling by high throughput sequencing

summary: We compared the transcriptional profiles of colon tissues and patient derived organoids (PDOs) in  genetic polyposis syndromes (FAP, LYNCH, JPS, and PJS)

overall_design: We developed organoids from genetically predisposed CRC pediatric and compared the transcriptome changes between the PDOs of different diseases and also in the original tissue

first: Debashis

last: Sahoo

first: Soumita

last: Das

first: Pradipta

last: Ghosh


title: MiR-125b regulates the occurrence and development of atherosclerosis through pyropyosis.

city: nanjing

first: Rui

last: Li

address: 138 Xianlin Avenue

country: China

institute: Nanjing University of Traditional Chinese Medicine

summary: To investigate the cooperative function miR-125b in the regulation of AS, we established  cell lines in which each target mirna has been overexpression by mirna mimics.

overall_design: Comparativemirna expression profiling analysis of RNA-seq data for RAW cells and its NC derivatives .

first: Ning

last: GU

first: Bingqian

last: WANG

first: Xinyi

last: Cai


title: Erucic acid improves the pregnancy complicated with systemic lupus erythematosus by inhibiting the effector function of CD8+ T cell

city: Shanghai

first: Yanling

last: Chang

address: Pujian road 160

institute: renji hospital

summary: Pathogenic CD8+ T cells are closely related to the development of systemic lupus erythematosus. Erucic acid (EA) has been proved to have anti-inflammatory activity. However, whether EA can regulate pathogenic CD8+ T cells function in pregnancy complicated with systemic lupus erythematosus (pSLE) has not been investigated. In our study, we detected enhanced CD8+ T cell effector function and decreased EA levels in patients with pSLE compared to healthy pregnancy control. Plasma EA levels were negatively correlated with the severity complications of pSLE. In blood from patients with pSLE, EA inhibited the effector function of CD8+ T cells and the maintenance of stem cell-like memory CD8+ T cells. Mechanically, EA inhibited STAT3 phosphorylation and promoted ferroptosis, which contributed directly to the attenuated effector function of CD8+ T cells in pSLE. Moreover, EA supplementation in pregnant MRL/lpr mice inhibited the effector function of uterine CD8+ T cells and alleviated placental pathological damage. Our findings reveal the modulatory effects of EA on pathogenic CD8+ T cells from an immune response perspective, thus providing new insights into therapeutic strategy for patients with pSLE.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for EA treated versus untreated CD8+T cell from patients with pSLE

first: Meng

last: Jiang

first: You

last: Wang

first: Qing

last: Fu

first: Sihan

last: Lin

first: Jiayue

last: Wu

first: Wen

last: Di


title: Tire-wear particle leachate toxicity to Americamysis bahia: analysis of sublethal and molecular effects

city: Saskatoon

first: Markus

last: Hecker

state: Saskatchewan

address: 44 Campus Drive

department: Toxicology

country: Canada

institute: University of Saskatchewan

summary: Tire-wear particles (TWPs) are considered among the largest contributors of microplastics to the environment. They are subject to break-down due to environmental weathering, which allows for potentially toxic chemicals to be leached from and sorbed onto the particles.  In this study, leachate generated from “weathered” and “un-weathered” TWPs were used for sublethal toxicity tests with Americamysis bahia.

overall_design: Organisms were exposed for 2, 4, and 6 days and the effects endpoints included changes in respiration rate and molecular responses (i.e., changes in the abundance of transcripts after 4 days of exposure).

first: Karrin

middle: N

last: Leazer

first: Alper

middle: J

last: Alcaraz

first: Ruth

last: Sofield


title: Dynamic of intrauterine crosstalk promotes embryo implantation in early pregnancy

city: Guangzhou

first: Xupeng

last: Zang

address: No. 483, Wushan Road, Tianhe District

institute: South China Agricultural University

summary: The success of early pregnancy depends largely on the successful implantation of the embryo. Dynamic crosstalk between embryo and mother plays a crucial role in this process, but our understanding is still limited. Here, using the pig as a model, we first comprehensively profile the single-cell transcriptome of early free embryos and corresponding maternal endometrium, identifying embryonic and matched endometrial cells with heterogeneity. We developed a novel tool, ExtraCellTalk, to predict crosstalk between the early embryo and the maternal uterus using uterine luminal proteins as bridges, generating an overall dynamic map of maternal-fetal crosstalk. Through cross-species comparisons, we identified a conserved RBP4/STRA6 pathway in which embryonic-derived RBP4 targets the STRA6 receptor on stromal cells in the endometrium, thereby interacting with endothelial and perivascular cells to regulate their interconversion to promote endometrial remodeling. These maternal-fetal crosstalks and corresponding endometrial changes that we uncovered are essential for subsequent embryo implantation and are the basis for further studies to improve embryo implantation.

overall_design: Pig embryos and endometrium on days 9 and 12 of pregnancy.


title: Nuclear IDH1 regulates human erythropoiesis by eliciting chromatin state reprogramming

city: zhengzhou

first: li

last: mengjia

address: 河南省郑州市高新技术开发区科学大道100号郑州大学新校区

institute: zhengzhou university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Although, IDH1 has been recognized to play critical roles in the regulation of dynamic chromatin states, the mechanism remained largely unknown. Here, using the human erythropoiesis system, we presented an innovative perspective of metabolism independent role of nuclear IDH1. We discovered that IDH1 acted as a nuclear located chromatin-binding protein. Knockdown of IDH1 induced chromatin reorganization and subsequently aroused aberrant biological events germination on erythroid precursors in a metabolism independent manner. IDH1 knockdown induced genome-wide coordinate changes in the distribution and intensity of multiple histone marks, among which H3K79me3 was identified to be the decisive factor in chromatin state reprogramming. Integrating ChIP-seq, ATAC-seq and RNA-seq recognized SIRT1 to be the key gene affected by IDH1 deficiency. Taken together, these findings provided a novel insight for further clarifying the fundamental biological function of IDH1 which had substantial implications for an in-depth understanding of the pathogenesis of diseases with IDH1 dysfunction and accordingly the development of therapeutic strategies.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K79me3, H3K9me3 and H3K27me2 in erythroid cells

first: Mengjia

first: Lixiang

last: Chen


title: Iso-seq analysis of hepatocellular carcinoma (HCC), in which HBV-KMT2B integration was identified. The tumor region and nontumorous region were extracted from the HCC surgical specimen.

city: bunkyo-ku

first: Masato

last: Miyoshi

address: yushima

department: Gastroenterology

country: Japan

institute: Tokyo Medical and Dental University

summary: To investigate the transcriptomic analysis of HBV-KMT2B integrated HCC, RNA-seq analysis of tumor tissue of HBV-KMT2B integrated HCC was performed. To further analyze KMT2B integrations, we identified full-length complementary DNA by long-read RNA-seq (Iso-seq).

overall_design: We investigated the transcriptomic analysis of HBV-KMT2B integrated HCC. To investigate HBV integration, we detected HBV-human junctions by next-generation sequencing. Three HBV-KMT2B integration were identified in 45 HBV-related HCC. the tumor tissue from one of the identified HCCs were obtained and extracted total RNA. For Iso-seq, tumor tissue from HBV-KMT2B integrated HCC were used.

first: Jun

last: Tsuchiya

first: Sei

last: Kakinuma


summary: To investigate the global analysis of H3K4me3 of HBV-KMT2B integrated HPCs, CUT＆Tag analysis of HBV-KMT2B integrated HPCs and KMT2B heterozygous knockout HPCs was performed.

overall_design: We investigated the function of HBV-KMT2B integration in HCC development.To investigate HBV integration, we detected HBV-human junctions by next-generation sequencing. Then we reproduce a HBV integraiton on induced pluripotent stem cells. Established HBV integrated iPSCs were differentiated into hepatic progenitor cells (HPCs), subsquently analyzed phenotype. Further,we investigated the global analysis of H3K4me3 of HBV-KMT2B integrated HPCs(HPC-Int). KMT2B heterozygous knockout HPCs (HPC-HT) were used for control of HBV-KMT2B integrated HPCs.  For CUT＆Tag analysis, 2 x 10^5 cells of each cell line were used.


city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary:
HBV-KMT2B integrated human induced pluripotent stem cell-derived hepatic progenitor cells (KMT2B-Int HPCs) vs heterozygous mutated KMT2B human induced pluripotent stem cell-derived hepatic progenitor cells (KMT2B-HT HPCs) vs original human induced pluripotent stem cell-derived hepatic progenitor cells (KMT2B-WT HPCs)
Transcriptional profiling of all KMT2B-WT, HT, and Int HPCs. KMT2B-HT and Int iPSCs were generated by gene editing using CRISPR/Cas9 and Cre recombinase technologies. iPSCs were differentiated into a hepatic lineage. On Day14 of hepatic differentiation, CD13 high and C133 high hepatic cells were sorted by fluorescence-activated cell sorter (FACS) on feeder mouse embryonic fibroblasts (MEFs). HPCs forms colony on MEFs and were stably cultured with maintaining their hepatic phenotype.

overall_design: Transcriptional profiling of all KMT2B-WT, HT, KO, Int iPSCs. As the KMT2B-Wand T iPSCs, P11025 iPSCs were used, which were reprogrammed by the episomal vector from normal skin. KMT2B-HT, KO, and Int iPSCs were generated by gene editing using CRISPR/Cas9 and Cre recombinase technologies. KMT2B-HT iPSCs were used as control cell lines of KMT2B-Int iPSCs because KMT2B Int iPSCs were heterozygous KMT2B due to HBV integration. DNA sequences as results of gene editing such as integration of HBV sequences were determined by direct sequencing. Knockout of KMT2B also was confirmed by immunoblotting. All iPSCs were differentiated into hepatic lineages. At day14 of hepatic differentiation, CD13 high and CD133 high hepatic cells were sorted on MEFs After 2week cultivation, colonies of HPCs were cultured and then passaged. These HPCs maintained hepatic phenotype and proliferative potential. All HPCs were passaged on MEFs and cultured for about 14 days, and the HPCs were harvested and analyzed.


title: Gene expression signatures of melatonin-treated dental papilla cells during odontoblastic differentiation

city: GuangZhou

first: Jia

last: Shilin

address: No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou

institute: Institute of Stomatological Research, Sun Yat-sen University

summary: To further reveal the regulatory mechanism of melatoin-mediated odontoblastic differentiation during tooth development, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to modulate melatonin-induced odontoblastic differentiation. Rat dental papilla cells were primary cultured from PN1-3 tooth germ tissue, and treated with melatonin at the concentration of 10-8M for 3 days along with odontoblastic differentiation induction medium (OS). Current microarray analysis generally profiled a total of 181 upregulated genes and 580 downregulated genes between two groups.

overall_design: Cultured with odontogenic differentiation induction medium(OS), rat dental papilla cells were treated with 0 or 10-8M melatonin, gene expression was measured at day 3.

first: Fuping

last: Zhang

first: Shengyan

last: Yang

first: Shilin

last: Jia


title: RNA-seq analysis of hepatocellular carcinoma (HCC), in which HBV-KMT2B integration was identified. The tumor region and nontumorous region were extracted from the HCC surgical specimen.

overall_design: We investigated the transcriptomic analysis of HBV-KMT2B integrated HCC. To investigate HBV integration, we detected HBV-human junctions by next-generation sequencing. Three HBV-KMT2B integration were identified in 45 HBV-related HCC. the tumor and nontumorous tissues from one of the identified HCCs were obtained and extracted total RNA. For RNA-seq, tumor tissue from HBV-KMT2B integrated HCC were used.


title: Nonclinical in-vitro evaluation of the transcriptomic and metabolic effects of immune checkpoint inhibitors on sunitinib-resistant renal cell carcinoma

city: Rockville

first: Alexis

middle: L

last: Norris

state: MD

address: 7500 Standish Place

institute: US FDA

summary: Recently, immune checkpoint inhibitors (ICIs) have been approved as first line and second-line therapies for individuals with advanced renal cell carcinoma (RCC) who developed a resistance to anti-angiogenic therapies. It remains unknown how ICIs efficacy is affected by the development of resistance to anti-angiogenic inhibitors. Thus, our goal is to evaluate transcriptomic and metabolic effects after ICI therapy of sunitinib-resistant RCC and compare the efficacy of ICIs between naïve and sunitinib-resistant RCC.

overall_design: Two Sunitinib-resistant human advanced renal cell carcinoma cell lines A498-Su and 786-O Su were developed from parental A498 and 786-O, respectively. Sunitinib resistant cells were then treated separately with three ICIs like Atezolizumab (At), Avelumab (Av), and Durvalumab (Dur) with a concentration of 10mg/mL for 24 hours and undergone in vitro metabolomics and transcriptomics analyses to investigate metabolic and transcriptomic rewiring, if any.

first: Ghosh

last: Susmita

first: Carole

last: Sourbier


title: Depletion of BamA activates the RSI circuit in S. meliloti

city: Stanford

first: Sharon

middle: R

last: Long

address: 371 Jane Stanford Way

department: Biology

institute: Stanford University

summary: The symbiotic relationship between the alpha-proteobacterium S. meliloti and the legume M. truncatula has been extensively studied. However, stress response mechanisms vital to bacterial survival and adaptation are as yet poorly understood. In this study, we sought to characterize the response of S. meliloti to depletion of essential outer membrane protein BamA, which is predicted to cause a loss of outer membrane integrity and an accumulation of unfolded proteins in the periplasm. A total of 132 differentially expressed genes were detected, with 74 genes up-regulated and 58 genes down-regulated. The transcriptomic response to BamA depletion shares similarities to those observed during activation of the RSI circuit, which plays a role in mitigating loss of viability in response to this stress. Induction of genes in the RSI regulon is likely due to a loss of negative regulator ExoR during BamA depletion. The two-component stress response system CpxRA and regulator CpxP also were found to affect the response to BamA depletion.

platform_organism:
Sinorhizobium meliloti
Medicago truncatula

overall_design: To identify genes whose expression changes upon depletion of BamA, we used custom affymetrix stSmel_Mtra GeneChips to compare CL150 ΔbamA with bamA on lac-inducible vector pSRKKm (Khan et al 2008; Applied and Environmental Microbiology) grown with and without 1mM IPTG for 4 hours. Three replicates were performed for each condition.

first: Aaron

last: Duthoy


title: Machine-learning detects non-invasive 5-hydroxymeythylcytosine biomarkers for predicting response to chemotherapy in patients with metastatic colorectal cancer

first: Yixiang

last: Shi

address: Room 303, Building #1, 928 Shenhong Road

institute: Accrete Covenant (AC) (Shanghai) Medical Technology Co., Ltd.

summary: Background: For the majority of patients of metastatic colorectal cancer (mCRC), systematic chemotherapy has been a choice for palliative treatment. When first-line chemotherapies do not work, targeted therapies are administered. Because of inter-individual genetic and epigenetic variations, patients with mCRC who are treated with these therapies may respond differently. It is of great clinical interest to elucidate response mechanisms that could be utilized in predicting individual response to these treatments.   Methods: A highly sensitive technique, the 5hmC-Seal was applied to profile genome-wide 5-hydroxymethylcytosines (5hmC) in 155 cfDNA samples from patients with mCRC recruited for two clinical trials at Zhongshan Hospital, Fudan University in China. Response to systematic chemotherapy and targeted therapy (becacizumab or cetuximab) (CR, complete response; PR, partial response; SD, stable disease; PD, progressive disease) was measured and a 5hmC-based predictive model in cfDNA was developed using a machine learning approach in the PROVE Study (NCT03679039) (n = 100), followed by validation in the METHOD Study (NCT03599947) (n = 55).  Results: Genome-wide mapping of 5hmC in patient-derived cfDNA suggested a distinct 5hmC landscape showing tissue origin and gene regulatory relevance. A eleven-gene model involving relevant pathways such as Rap1 signaling pathway, cAMP signaling pathway, Phospholipase D signaling pathway and cGMP-PKG signaling pathway, distinguished patients with mCRC who responded to chemotherapy, regardless of targeted therapy, resectability, or mutation status in the validation samples (AUC=0.77; 95% CI, 0.64-0.90), outperforming RAS mutation status (AUC=0.70; 95% CI, 0.57-0.83). In addition, the 5hmC model also showed a trend of capacity for predicting progression-free survival (PFS) for mCRC.   Conclusions: Genome-wide mapping reflected relevant pathways and functional interaction networks implicated in the determination of treatment response for patients with mCRC. The 5hmC-Seal model in cfDNA provided a promising non-invasive method for predicting response to systematic chemotherapy in patients with mCRC, who will be essential for personalized medicine.

first: Tianyu

last: Liu

first: Wenju

last: Chang

first: Bowen

last: Wang

first: Chang

last: Zeng

first: Wei


title: Satellite cell – specific deletion of CIPC alleviates myopathy in mdx mice.

city: suzhou

first: zheng

middle: ji

last: qing

address: renairoad

institute: szdx

summary: The regeneration of skeletal muscle relies on satellite cells which can proliferate, differentiate and form new myofibers upon injury. Emerging evidence suggests that misregulations of satellite cell fate and function influence the severity of Duchenne Muscular Dystrophy (DMD). The myogenic identity and maintenance of the pool of satellite cells is determined by the transcription factor PAX7. Satellite cell proliferation and self-renewal is regulated by the circadian clock. Here, we show that the CLOCK-interacting protein, Circadian (CIPC), a negative-feedback regulator of the circadian clock, is up-regulated during myoblast differentiation. Specific deletion of CIPC in satellite cells alleviated myopathy, improved muscle function and reduced fibrosis in mdx mice. CIPC deficiency led to activation of the ERK1/2 and JNK1/2 signaling pathways, which in turn activated the transcription factor SP1 to trigger the transcription of PAX7. Therefore, CIPC is a negative regulator of satellite cell function and loss of CIPC in satellite cells promotes muscle regeneration.

overall_design: Total RNA from 8-week old CIPC-flox mouse and CIPC-scko mouse.

first: Yao-Hua

last: Song

first: Jiqing

last: Zheng


title: Single-Cell RNA-Seq Analysis of cells from different outcome populations of membranous nephropathy

last: Zuo

state: Shanghai

address: No. 500 Zhennan Road, Putuo District, Shanghai

institute: University

summary: Urine passes through the entire kidney and urinary tract system starting from the glomerulus and ending to the urethra. Cells in the kidney and urinary tract could be exfoliated from the epithelium into the urine, while leukocyte could infiltrate from the local tissue into the urine, which makes the urine a useful subject for clinical evaluation of relevant diseases. We performed scRNA-seq on voided urine samples. 50–100 mL middle stream urine samples were collected from 12 Chinese healthy adults and combined for droplet-based single-cell RNA sequencing after flow cytometric sorting of live cells. We presented the first single-cell atlas of adult human urine and identified multiple previously unrecognized cell types. Based on our scRNA-seq analysis data, a SOX9+ cell population was identified in adult human urine which we speculated to have progenitor potential.

overall_design: For scRNA-seq analysis, urine samples were collected from healthy adult volunteers. Midstream of voided urine specimen was collected for each donor. Samples were centrifuged immediately at the speed of 390 ×g and combined for droplet-based single-cell RNA sequencing after flow cytometric sorting of live cells.

first: Yu

last: Zhao


title: STK40 regulates T cell development and effector function through COP1-depenendent degradation of c-Jun transcription factor

city: South San Francisco

first: Rohit

last: Reja

address: 1 DNA Way

institute: Genentech

summary: To examine the effect of Stk40 deletion specifically in T cells during chronic LCMV infection, we have generated a T cell specific knockout mouse line (CD4CreER; Stk40loxp/loxp). We found that mice lacking Stk40 exhibited improved viral clearance and T cell function compared to WT counterparts. To gain a broader understanding of how Stk40 regulates T cell response to chronic LCMV infection, we performed single cell transcriptome analysis on magnetically enriched LCMV-specific dextramer+ CD8 T cells isolated from spleens of Stk40 KO or WT mice at days 15 and 22 after infection with LCMV clone 13.

overall_design: Single cell transcriptome analysis on magnetically enriched LCMV-specific dextramer+ CD8 T cells isolated from spleens of Stk40 KO or WT mice at days 15 and 22 after infection with LCMV clone 13.


title: TTFields plus TMZ treatment effects on newly diagnosed Glioblastoma patients in peripheral blood

city: SOUTH PASADENA

first: SON

middle: B

last: LE

address: 1645 Amberwood Drive, Unit 11

institute: University of Southern California

summary: We report the application of single-cell-RNA-based sequencing technology for high-throughput profiling of peripheral blood mononuclear cells. By sequencing in total of 193,760 PBMCs in 12 GBM patients, we generated an overview of patient peripheral immune status with 38 biologically recongnized cell subtypes. By paired comparing pre- and post- treatment samples, we find a robust post-TTFields activation of adaptive immunity via the T1IFN trajectory anchored by plasmacytoid DCs. This study provides a framework for the application of scRNAseq towards characterization of peripheral immune activation status.

overall_design: Examination of TTFields plus TMZ treatment effects in peripheral blood mononuclear cells. We collected PBMCs from 12 adult patients with newly diagnosed GBM after they have completed radiotherapy with concurrent TMZ. The first time point is  at least 2 weeks after completion of chemoradiation and within 2 weeks before initiation of TTFields and TMZ.  The second time point is approximately 4 weeks after initiation of TTFields and TMZ.

first: David

middle: D

last: Tran

first: Son

last: Le

first: Dongjiang

last: Chen


title: MicroRNA-150 controls experimental autoimmune encephalomyelitis by regulating CD4 T cell differentiation and function [RNA-seq I]

city: Stockholm

first: Ewoud

last: Ewing

address: CMM L8:05, Karolinska University Hospital

department: Clinical Neuroscience

country: Sweden

institute: Karolinska Institutet

summary: MicroRNAs are small non-coding RNA molecules that have an important role in the fine tuning of all biological processes and are often found to be dysregulated in diseases, such as multiple sclerosis (MS). MS is an immune-mediated disease of the central nervous system characterized by demyelination, axonal loss and neurodegeneration. We have previously shown microRNA-150 (miR-150) levels to be elevated in cell-free cerebrospinal fluid (CSF) of MS patients compared to controls. The aim of this study is to further understand the physiopathological function of miR-150 using experimental autoimmune encephalomyelitis (EAE), a mouse model for MS. To establish its role in-vivo, we generated miR-150 knock-out (KO) and knock-in (KI) mice using CRISPR/Cas9. After induction of EAE, miR-150 KO mice showed ameliorated disease compared to WT littermate controls while miR-150 KI mice presented with exacerbated disease. An ameliorated disease in miR-150 KO was accompanied by a decreased infiltration of CD4 T cells compared to WT and KI. At priming stage of EAE we found that miR-150 KO had an increase in regulatory CD4 T cells (TREGS). Furthermore, after reconstitution of T cell deficient animals, CD4 T cells from miR-150 KO mice could protect against EAE and also showed an increased FOXP3 expression. A role of miR-150 in regulating TREG cells was further substantiated by transcriptome profiling, where miR-150 KO CD4 T cells suggested an enhancement of TREG phenotype as well as a diminished translation in miR-150 KO CD4 T cells. Moreover the results implicated miR-150 with mechanisms such as translation, autophagy and metabolism as well T cell proliferation and differentiation. In conclusion, miR-150 deficiency favored a more anti-inflammatory environment while miR-150 expression promoted pathogenic CD4 T cells subsets, potentially associated with metabolic mechanisms.

overall_design: mRNA profiles of sorted CD4 T cells from miR-150 knock-out, wildtype and knock-in mice at naive stage and 7 days (D7) after EAE induction.

first: Eliane

last: Piket

first: Maja

last: Jagodic


title: Genome-wide maps of transcription in GART overexpression(OE) and wildtype(WT) cells in Multiple Myeloma

city: China

first: Mengying

last: Ke

state: Jiangsu

institute: Nanjing University of Chinese Medicine

summary: We found different genes change between WT and OE cells.

overall_design: Examination of different genes changes in 2 cell types.

first: Chao

last: Tang


title: Interspecies comparison reveals Hmga1 as a key determinator of cardiac regenerative potential

city: Jena

first: Dennis

middle: de

last: de Bakker

address: Beutenbergstraße 11

country: Germany

institute: FLI

summary: Myocardial infarction causes a massive loss of cardiomyocytes, leading to the formation of a fibrotic scar resulting in impaired cardiac function. In contrast to mammals, zebrafish display robust cardiac regeneration following injury due to the proliferation of pre-existing cardiomyocytes in the injury border zone. Here, we aim to identify transcriptomic differences that will help explain the differential cardiac regenerative capacity observed between the injured zebrafish and mammalian heart. First, we transcriptionally profiled the border zone of the injured mouse heart, which does not support regeneration. Then, we bioinformatically compared the transcriptome of the mouse border zone with the zebrafish border zone, identifying many genes and processes overlapping or diverging between the two species. Interestingly, we identified the architectural chromatin remodeller hmga1a to be expressed in the zebrafish, but not the mouse border zone. Using a loss-of-function hmga1a mutant we show that hmga1a is required for border zone cardiomyocyte proliferation and zebrafish heart regeneration. Using single-cell RNA-sequencing, we identify the near absence of proliferative cardiomyocyte sub-populations in hmga1a mutant border zones. Furthermore, we show that overexpression of hmga1a can induce cardiomyocyte proliferation in uninjured zebrafish hearts. Using a combination of RNA- and ATAC-sequencing, we show that hmga1a overexpression leads to the induction of a broad border zone-like gene program, including robust chromatin remodelling. Last, we provide evidence suggesting that overexpression of Hmga1 can stimulate mammalian cardiomyocyte proliferation and functional recovery post myocardial infarction. Taken together, through transcriptional comparison of the zebrafish and mouse border zone we have identified hmga1a as a key determinator of cardiac regenerative potential.

overall_design: Tg(nppa:mCitrine)  positive cells showing high mCitrine expression were isolated from cyoinjured zebrafish hearts (7 days post injury). From 12 hmga1a-/- mutants hearts, 768 cells were isolated. From 12 hmga1a+/+ wild-type hearts, 768 cells were isolated. All cells were sent for single cell RNA sequencing, but one wild-type plate failed during sequencing and was not used for further analysis.

middle: M

first: Phong

last: Nguyen

first: Daniel

last: Colquhoun

first: Vincent

last: Christoffels

first: Jan

last: Kaslin

first: Eva

last: van Rooij

first: Jeroen

last: Bakkers


title: Distinct effects of glucose and fructose on gut and liver transcriptome in mice

city: Groningen

first: vincent

last: bloks

country: Netherlands

institute: UMCG

summary: The metabolic syndrome, in which insulin resistance, obesity, atherogenic dyslipidemia and/or hypertension co-occur, is an increasing health problem and can result in various metabolic diseases. A high-sugar consumption, including glucose and fructose, is especially linked to an accelerated development of the metabolic syndrome. Recently the role of the gut has been highlighted in fructose metabolism. Here we studied the effects of a 2-weeks high-fructose diet as compared to a high-dextrose diet and a cornstarch diet, in the small intestine and liver transcriptome of mice. There were no differences in weight gain and food intake between all groups. Liver weight was solely increased in fructose-fed mice. Surprisingly, the glucose-fed mice displayed increased hepatic cholesterol and triglycerides (TGs) content. Overall, we found major effects in the small intestine and only limited changes in the liver transcriptome. The transcriptome of fructose-fed mice was distinct from the dextrose and cornstarch fed mice in both gut and liver, while dextrose and cornstarch feeding only caused differences in the gut transcriptome. Taken together, we underscore the importance of the small intestine in fructose metabolism and this study can provide cues about the harmful effects of dietary fructose and glucose.

overall_design: Here we studied the effects of a 2-weeks high-fructose diet as compared to a high-dextrose diet and a corn starch diet, in the small intestine and liver transcriptome of  3groups of 5 mice

first: V

middle: W

last: Bloks

first: I

last: Zwarts

first: J

last: Jonker

middle: K

last: Kruit


title: Differential gene expression in male mouse macrophages from BAL

city: Ann Arbor

first: Bioinformatics

last: Core

state: MI

address: BRCF Bioinformatics Core, 2800 Plymouth Rd

institute: University of Michigan

summary: The goal of this study is to investigate the gene expression in mouse macrophages following bacterial pneumonia.  To address whether TLR3 deletion leads to deregulation of specific molecular pathways relevant to apoptosis and investigated transcriptional differences between TLR3 (+/+) and TLR3 (-/-) naïve macrophages or injured macrophages (following pneumonia).

overall_design: Four groups: WT.Control, WT.Injured, TLR3.control, TLR3.injured. With 3 or 4 replicates each, for 15 samples total

first: Suresh

middle: V

last: Madathilparambil

first: Krishnan

last: Raghavendran


title: Analysis of hepatocellular carcinoma (HCC), in which HBV-KMT2B integration was identified

first: Masato

last: Miyoshi

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

overall_design: Refer to individual Series


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1 [scRNA-seq]

status: Public on Dec 31 2024

city: Tianjin

first: Ke

last: Zhao

address: Qixiangtai Road, No.22

institute: Tianjin Medical University

summary: The majority of genetic loci linked to polygenic complex traits are found in non-coding regions of the human genome. These loci often exhibit complex gene regulatory relationships and linkage disequilibrium (LD) configurations, making it challenging to accurately identify causal variants and their target genes. We used multiplexed single-cell CRISPR interference and activation perturbations to investigate cis-regulatory element (CRE) and target gene expression relationships within tight LD in the endogenous chromatin context. We demonstrated the prevalence of multiple causality in perfect LD (pLD) for independent expression quantitative trait locus (eQTL) and uncovered fine-grained genetic effects on gene expression within pLD, which are difficult to decipher using traditional eQTL fine-mapping or existing computational methods. We found that over one third of the causal CREs lack classical epigenetic markers, and we functionally validated one of these hidden regulatory mechanisms. Leveraging Multiome single-cell epigenetic and sequence perturbations, we highlighted the regulatory plasticity of the human genome. Our study will guide the exploration of missing causal mechanisms in molecular trait formation and disease development.

overall_design: Nine scRNA-seq datasets under varying multiplicity-of-infection (MOI) conditions, three single-cell multiome datasets (ATAC + Gene Expression) from modified HAP1 clones(dCas9-KRAB-blast, dCAS9-VP64-blast and Cas9-blast stably expressed HAP1 clones), four ATAC-seq datasets from wild-type and CRISPR-edited HAP1 cells(64bp deletion, 17bp deletion and CRISPRi around rs73156934-tagged cis-regulate element(CRE)), six CUT&TAG histone modification datasets and 1 Micro-C dataset from wild-type HAP1 cells, and three 4C-seq datasets for validating CRE-gene regulatory relationships in HAP1 cells.

first: Yao

last: Zhou

first: Mulin

last: JunLi


title: Endogenous fine-mapping of functional regulatory elements in complex genetic loci in HAP1 [ATAC-seq]


title: Vitamin A deficiency results in an uncontrolled immune response and aggravates liver damage during obstructive cholestasis

summary:
Background: Vitamin A is an essential nutrient that mammals obtain from dietary carotenoids and retinyl esters. Bile salts aid in the intestinal absorption of vitamin A, after which it is stored in the stellate cells of the liver. Vitamin A-metabolites, such as
retinoic acids, are important for cell differentiation, proliferation and immunological processes, and act mostly by activating the nuclear receptors Retinoic Acid Receptor (RAR) and Retinoid Xreceptor (RXR). These receptors also perform key functions in the liver by regulating bile salt, lipid and glucose homeostasisas well is the intrahepatic immune response.
Chronic liver diseases are characterized by hepatic vitamin A loss often leading to vitamin A deficiency (VAD). We found that VAD strongly aggravates liver damage in bile duct ligated (BDL) rats and in biliary atresia patients. Here, we performed a transcriptome analysis to characterize the cell biological processes in the rat liver that are disturbed in obstructive cholestasis under VADconditions.
Methods: Rats were made VAD by omitting vitamin A  from the diet for 16 weeks, followed by ligation of the common bile duct (BDL). 7 days later, the animals were sacrificed. During the 7 days of BDL, half of the animals received daily IP injections with retinyl-palmitate (vitamin A therapy). Bile salt concentrations and liver damage markers (AST/ALT) were determined in serum. Whole genome gene expression in liver tissue was analyzed with the Illumina platform RatRef-12 beadchip. False discovery rate (FDR) was set at a stringent 1%. Data were confirmed by quantitative real time PCR, Western blotting and/or histochemistry.
Results: BDL induced dramatic liver damage in VAD rats with serum liver damage markers (AST/ALT)approximately 10-fold increased compared to BDL rats receiving a vitamin A-sufficient (VAS) diet. Only 20 genes were differentially expressed between sham-treated VAS and VAD rats and clustered in the vitamin A metabolism, immune response, carbohydrate and lipid homeostasis. In contrast, 1583 genes were differentially expressed between the BDL-treated VAS and VAD rats. The strongest effects were observed in genes from the vitamin A metabolism, immune response, collagen production and oxidative stress response. Importantly, all the liver damage markers were efficiently reversed by retinyl-palmitate therapy, which was mirrored by an almost complete normalisation of the transcript profile in VAS-BDL rats.
Conclusions: We conclude that vitamin A deficiency dramatically aggravates liver damage caused by obstructive cholestasis. The transcriptome analysis suggests that a disturbed immune response may be the predominant  causative factor.

overall_design: 8 groups consisting of 4-5 biological replicates per group

first: M

last: Hoekstra

middle: O

last: Hoeke

last: Heegsma

first: H

last: Moshage

first: K

last: Faber


title: A Polycomb Group Protein EED Epigenetically Regulates Responses in Lipopolysaccharide Tolerized Macrophages via Metabolic Flux and TGF-/Runx3 Axis

city: Bangkok

first: Tanapat

last: Palaga

address: Payathai Road, Pathumwan

department: Microbiology

country: Thailand

institute: Chulalongkorn University

summary: To avoid exaggerated inflammation and injury, innate immune cells adapt to become hypo-responsive or “tolerance” in response to successive exposure to stimuli, which is a part of innate immune memory. Polycomb repressive complex 2 (PRC2) mediates the transcriptional repression by catalyzing histone H3 lysine 27 trimethylation (H3K27me3) but little is known about its roles in tolerant macrophages. We examined the impact of deletion of the PRC2 component, EED on lipopolysaccharide (LPS)-induced tolerant macrophages. In Eed KO macrophages, significant reduction in global H3K27me3 and increased global active histone mark, H3K27ac was observed. Eed KO macrophages exhibited dampened pro-inflammatory cytokine productions (TNF-α and IL-6) while increased non-tolerizeable genes upon LPS tolerance. In addition, LPS tolerized Eed KO macrophages exhibited lower glycolytic activity than its wild-type control. RNA-Seq analyses revealed that the hallmarks of hypoxia, TGF-β, and Wnt/β-catenin signaling were enriched in LPS tolerized Eed KO macrophages. Among the upregulated genes, EED was found to be associated with the Runx3 promoter. Silencing Runx3 in Eed KO macrophages partially rescued the dampened pro-inflammatory response during LPS tolerance.  Enrichment of H3K27me3 was decreased in genes that are upregulated in Eed KO LPS tolerance macrophages. Taken together, our results provided mechanistic insight into how the PRC2 via EED regulates LPS tolerance in macrophages via TGF-/Runx3 axis by epigenetically silencing genes that play a central role during LPS tolerance.

overall_design: CUT&Tag DNA-Sequencing for H3K27me3 on LPS-tolerant wild-type and Eed knock-out macrophages

first: Atsadang

last: Boonmee

first: Salisa

last: Benjaskulluecha

first: Patipark

last: Kueanjinda

first: Benjawan

last: Wongprom

first: Thitiporn

last: Pattarakankul

first: Kittitach

last: Sri-Ngern-Ngam

first: Supawadee

last: Umthong

first: Junichiro

last: Takano

first: Haruhiko

last: Koseki


title: Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders

city: Chapel Hill

first: Hyejung

last: Won

state: NC

address: 116 Manning Dr #6110

department: Genetics

institute: UNC Chapel Hill

summary: A meta-genome-wide association study across eight psychiatric disorders has highlighted the genetic architecture of pleiotropy in major psychiatric disorders. However, mechanisms underlying pleiotropic effects of the associated variants remain to be explored. We conducted a massively parallel reporter assay to decode the regulatory logic of variants with pleiotropic and disorder-specific effects. Pleiotropic variants differ from disorder-specific variants by exhibiting chromatin accessibility that extends across diverse cell types in the neuronal lineage and by altering motifs for transcription factors with higher connectivity in protein-protein interaction networks. We mapped pleiotropic and disorder-specific variants to putative target genes using functional genomics approaches. In vitro CRISPR perturbation of selected variants confirmed the variant-gene relationships, and in vivo CRISPR perturbation of a pleiotropic and a disorder-specific gene suggests that pleiotropy may involve regulation of genes expressed broadly across neuronal cell types and with higher network connectivity.

overall_design: To explore molecular mechanisms underlying pleiotropy, we conducted CROP-seq (CRISPR knockout followed by single-cell RNA sequencing) in the mouse neocortex on two genes: Anp32e (mapped to a pleiotropic locus), and Kmt5a (mapped to a disease-specifc locus). CRISPR guide-RNAs (gRNAs) targeting Anp32e and Kmt5a were expressed via CROPseq-tRFP lentiviral library in neonatal Cas9 transgenic mice. At two weeks of age, single cells from the neocortex were dissociated, sorted for RFP expression, then procssed with 10x Genomics 3' workflow for construction of single-cell gene expression and gRNA libraries. The high-throughput sequencing (HTS) data from the gene and gRNA libraries were used for downstream analysis (cell type annotation, differential gene expression analysis, etc).

first: Jiseok

last: Lee


title: Integrative Analysis of the Roles of lncRNAs and mRNAs in Ischaemic Preconditioning to Alleviate Liver Ischaemia–Reperfusion Injury in Mice

city: Haerbin

first: Yongliang

last: Hua

state: Heilongjiang

address: Department of Pediatric Surgery, the First Affiliated Hospital of Harbin Medical University, Key Laboratory of Hepatosplenic Surgery, Harbin, Heilongjiang, China

institute: 哈医大一院

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

summary:
schemic preconditioning (IPC) has been developed for protection of liver from ischemia reperfusion injury, which results in tolerance to subsequent insults of ischemia. But little is known about the underlying biological pathophysiology of long non-coding RNAs (lncRNAs) in the liver ischemia-reperfusion (I/R) injury. Our study aims to provide a mechanism for the function of IPC against liver I/R injury and to giving rise to new research perspectives of lncRNAs.
In this study, 18 mice (C57BL/6) were involved and randomly divided into the following groups (6 mice per group): the Sham group, the I/R group, and I/R+IPC group. Serum and liver tissue samples were collected for analysis from a mouse liver model of I/R injury and I/R+IPC. Then we randomly selected 5 mice per group and extracted their liver samples for microarray analysis and subsequent bioinformatics analysis.

overall_design: A total of 18 mice were randomly divided into the following groups (6 mice per group): the sham group, the I/R group (subjected to partial (70%) liver I/R), and I/R+ IPC group (apply IPC to I/R group). The procedures of partial liver I/R group and IPC group have been performed as described previously15. Briefly, the mice were anesthetized with intraperitoneal injection of sodium pentobarbital (60 mg/kg), and a midline laparotomy was performed. Then, using an atraumatic clip clamped the left lateral and median lobes of the liver at its base. The I/R group was subjected to 75 minutes of ischemia and 2 hours of reperfusion. The I/R+IPC group was performed with 10 minutes of ischemia followed by 10 minutes of reperfusion prior to 75 minutes of ischemia and persistent reperfusion for 2 hours. The sham group received a laparotomy and operative procedures of hepatic hila without process of clamping vessel. The serum and liver samples were collected for further analysis. During the operation, the body temperature should stay close to 37 degrees Celsius by a heating lamp.

first: Yong

last: Ma


title: Genomic 8-oxoguanine modulates gene transcription independent of its repair by DNA glycosylases OGG1 and MUTYH [RNA-seq]

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

department: Department of Neuromedicine and Movement Sciences

country: Norway

institute: Norwegian University of Science and Technology

summary: It has been suggested that the oxidtaive DNA base lesion 8-oxo-7,8-dihydroguanine (OG) and its repair has epigenetic-like properties and mediates transcription, but genome-wide evidence of this interdependence is lacking. Here, we applied an improved OG-sequencing approach reducing artificial background oxidation and RNA- sequencing to correlate genome-wide distribution of OG with gene transcription in HAP1 cells deficient for OGG1 and/or MUTYH.  Our data identified moderate enrichment of OG in the genome that is mainly driven by the genomic context and not affected by DNA glycosylase-initiated repairs. Regardless of DNA glycosylase activity, OG  in promoter regions correlated with expression of genes related to metabolic processes and damage response pathways indicating that it functions as a sensor of cellular stress to regulate transcription. Our work provides novel insights into the mechanism underlying transcriptional regulation by OG and DNA glycosylases OGG1 and MUTYH and suggests that oxidative DNA damage accumulation and its repair utilize different pathways.

overall_design: Gene expression analysis of two clones of HAP1 WT, OGG1 and MUTYH single knockout and OGG1/MUTYH double knockout cells

first: Tobias

last: Obermann

first: Teri

last: Sakshaug

first: Vishnu

last: Kanagaraj

first: Andreas

last: Abentung

first: Mirta

last: de Sousa

first: Lars

last: Hagen

first: Antonio

last: Sarno

first: Magnar

last: Bjørås


title: murine lung

city: Giessen

first: Marek

last: Bartkuhn

state: Hessen

address: Aulweg 132

department: Biomedical Informatics and Systems Medicine

institute: Justus-Liebig-University Giessen


title: The impact of reduced PLCG2 expression on microglial biology and disease pathology in a murine model of Alzheimer’s disease

first: Andy

middle: P

last: Tsai

state: California

address: 290 Jane Stanford Way E365

institute: Stanford University

summary: Differential expression analysis identified inflammation-related pathways in AD samples with reduced PLCG2 expression

overall_design: To investigate the role of PLCG2, differential expression analysis by comparing 5xFAD PLCG2+/- mice with 5xFAD mice at 7.5 months of age was performed using gene expression data from the NanoString Neuropathology and Glial panels

first: Chuanpeng

last: Dong

first: Peter

last: Lin

first: Stephanie

last: Bissel

first: Adrian

last: Oblak

first: Miguel

last: Moutinho

first: Guixiang

last: Xu

first: Yunlong

last: Liu

first: Kwangsik

last: Nho

first: Bruce

middle: T

last: Lamb

first: Gary

middle: E

last: Landreth


title: miRNAs were involved in the radioresistance of esophageal squamous cell carcinoma

city: Beijing

first: Aiping

last: Luo

address: Panjiayuannanli 17, Chaoyang District

institute: National Cancer Center, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: Cancer cells associated with radioresistance are likely to give rise to local recurrence and distant metastatic relapse. However, it remains unclear whether specific miRNAs have direct roles in radioresistance and/or prognosis. In this study, we performed a human miRNA expression array analysis to identify miRNAs upregulated or downregulated in the radioresistant cells. To confirm the results, we selected several candidate miRNAs according to the fold change and function of miRNAs, and detected their expression levels in the radioresistant cells and their parental cells using qRT-PCR. Moreover, we further investigate that specific miRNAs predicts pathological response to preoperative radiotherapy in locally advanced ESCC

overall_design: To establish a radioresistant cell model, we treated human ESCC cell lines (KYSE30, KYSE70 and KYSE180) by applying continuous 2 Gy fractionated irradiations to 60 Gy, and finally obtained a radioresistant subpopulation (designated as KYSE30R, KYSE70R and KYSE180R). These radioresistant and parental cells were selected for RNA extraction and hybridization on Affymetrix microarrays.

first: Zhihua

first: Xuantong

last: Zhou


title: Characterization of extrachromosomal circular DNA for human dilated cardiomyopathy

city: shanghai

first: Zhenhao

address: shanghaixuhui

institute: Fudan University

summary: Extrachromosomal circular DNAs (eccDNAs) are prevalent in different tumors, and have been shown to be important oncogenic drivers. While recent studies have found many eccDNAs in non-tumor cells, to date, the nature and characteristics of eccDNAs in human heart failure are rarely known. In this study, we provided a comprehensive analysis of eccDNAs in human heart failure caused by dilated cardiomyopathy (DCM). Using the Circle-Seq method, we identified the expression profile of eccDNAs in heart samples from DCM patients and healthy controls. Most eccDNAs were less than 1kb and enriched in two peaks. Analysis of the genomic distribution of eccDNAs revealed that eccDNAs were derived from all chromosomes and half of these eccDNAs carried at least one gene or gene fragment. Most eccDNAs originated from 5’UTR, 3’UTR, CpG island, long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs). In addition, eccDNAs were more enriched on gene-rich chromosomes 17 and 19. In conclusion, our work delineated the eccDNAs profiling of human healthy heart and DCM and explored potential functions of eccDNAs in the development of DCM.

overall_design: EccDNA expression profiles of of dilated cardiomyopathy patients and healthy controls were generated by high-throughput sequencing


title: Transcriptomic insight into differential gene expression patterns of the camel pathogenic nematode, Parabronema skrjabini, at specific developmental stages

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: Parabronema skrjabini is an widespread but neglected blood-feeding nematode. The P.skrjabini can ,as a pathogen ,causes the large ruminants clinical and pathological effects, with even severe infections being fatal, which is of a major veterinary importance in many developing countries. However, there is little information that controls the developmental changes of the parasite survived and developed in insect and ruminant hosts. Here we have collected P.sktjabini of four specific developmental stages and allows for complete understanding the key characteristics of development. We analyzed the transcriptomic changes accompanying the four specific developmental stages using RNA-seq and pinpointed the development-dependent function genes and biological processes.

overall_design: P.skrjabini were collected at four different developmental stages (egg, larva, adult female,adult male ) for RNA-seq.

first: Wenlong

last: Wang

first: Chenchen

last: Feng

first: Chunxia


title: Tumor regression of recurrent chemo-resistant placental site trophoblastic tumor after anti-PD-1 immune checkpoint inhibitor therapy

city: Kanazawa

first: Shin-ichi

last: Horike

state: Ishikawa

address: 13-1 Takaramachi

department: Research Center for Experimental Modeling of Human Disease

institute: Kanazawa University

summary: A placental site trophoblastic tumor (PSTT), characterized by mononuclear and multinuclear extravillous trophoblasts that penetrate the uterus and its vessels, is a rare gestational trophoblastic neoplasia. Due to its rarity, the prognostic factors and ideal treatment are unclear. Recurrent PSTT is thought to be resistant to chemotherapy, but monoclonal antibodies, such as the anti-programmed cell death protein 1 (PD-1) agent pembrolizumab, have recently been reported to be clinically effective for several cancers. We present a recurrent and chemo-resistant PSTT case exhibiting complete response after administration of pembrolizumab. This case suggests a new approach for the management of drug-resistant PSTT.

overall_design: Comaprison between placental site trophoblastic tumor and 6-week gestational whole villus tissues. There is no biological replicate for each conditions.

first: Kyosuke

last: Kagami

first: Masanori

last: Ono

first: Ayumi

last: Matsuoka

first: Kayo

last: Kayahashi

first: Atsushi

last: Tajima

first: Hirokazu

last: Usui

first: Yasunari

last: Mizumoto

first: Mitsuhiro

last: Nakamura

first: Hiroshi

last: Fujiwara


title: Single cell RNA-seq data of colonic and small intestinal epithelium from  Ecsit fl/fl and Ecsit cKO mice

city: Nanjing

first: Yuying

last: Jiang

address: 101 Longmian Avenue

institute: Nanjing Medical University

summary: To investigate the specific role of Ecsit in intestinal homeostasis, we generated Ecsit floxed/Vil1-Cre-ERT2 mouse model, and injected tamoxifen (3mg) intraperitoneally for 5 consecutive days to achieve conditional deletion of Ecsit in the intestinal epithelium at a specific time. These Ecsit fl/fl Vil1-Cre-ERT2 mice (Ecsit cKO) and Control mice (Ecsit fl/fl) mice were euthanized 12 days after the last injection for single cell RNA-seq on small intestinal and colonic epithelium.

overall_design: Data of small intestinal epithelium is from two independent experiments, in which experiment, cells were mixed from 3 mice. Data of colonic epithelium is from one experiment in which cells were mixed from 3 mice.

first: Shuo

last: Yang


title: Transcriptome profile of C2C12 wild-type and Fam134b knockout myoblasts and differentiated myotubes

status: Public on Dec 28 2024

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

summary: To evaluate the effect of Fam134b absence we performed transcriptomic analysis on undifferentiated and differentiated myotubes

overall_design: Total RNA was extracted from n=4 for each experimantal group

first: R

first: P

last: Grumati


title: Abnormal H3K27me3 underlies degenerative spermatogonial stem cells in cryptorchid testis [RNA-Seq]

status: Public on Dec 25 2024

city: Yokohama

last: Tomizawa

address: 3-9 Fukuura, Kanazawa-ku

department: School of Medicine

institute: Yokohama City University

summary: Cryptorchidism is the most frequent congenital defect in newborn males characterized by the absence of the testis from the scrotum. Approximately 90% of patients with untreated bilateral cryptorchidism exhibit azoospermia due to defective spermatogenesis in the affected testis. While abnormal spermatogonial stem cell maintenance or differentiation is suggested to cause germ cell degeneration in the cryptorchid testis, underlying molecular mechanisms remain unclear. Here we profiled spermatogonial epigenetic landscapes using surgically induced cryptorchid testis in the mouse. We show that cryptorchidism leads to alterations in local, but not global H3K27me3 and H3K9me3 in undifferentiated spermatogonia. Of these, the loss of H3K27me3 leads to activation of developmental and apoptotic pathway genes that are repressed by the polycomb machineries in germ cells. Cryptorchid spermatogonia exhibit the increase of H3K27me3 demethylases KDM6A and KMD6B. Furthermore, we reveal that an increased temperature leads to Kdm6a/b upregulation in germline stem cells cultured in vitro. Thus, our study suggests that a temperature-dependent histone demethylation induces mRNA dysregulation due to the partial loss of H3K27me3 in spermatogonia.

overall_design: We performed RNA-seq and ChIP-seq (H3K27me3 and H3K9me3) using sorted GFRa1+/Kit- spermatogonia from control and cryptorchid mice (day 10 post-surgery) to analyze epigenetic abnormalities that can affect gene expression.

first: Kazushige

last: Kuroha

first: Ivana

last: Dočkal

first: Uroš

last: Radović

first: Kuniko

last: Nakajima

first: Ikue

last: Hoshi

first: Shion

last: Matsuda

first: Noriko

last: Kojitani

first: Kazuyuki

last: Ohbo


title: Abnormal H3K27me3 underlies degenerative spermatogonial stem cells in cryptorchid testis [ChIP-Seq]

first: Shin-ichi


title: Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary [ChIP-Seq]

status: Public on Dec 23 2024

city: Cambridge

first: Azad

last: Alizada

state: Cambridgeshire

address: University of Cambridge Li Ka Shing Centre, Robinson Way

department: Cancer Research UK Cambridge Institute

country: United Kingdom

institute: University of Cambridge

summary: The gene-regulatory mechanisms behind the female germline piRNA pathway in ovaries of metazoan species remain largely unexplored. Here, using the Drosophila model and combinations of ChIP-seq, RNA-seq, ATAC-seq, and single-cell approaches, we reveal the transcription factors that regulate the female germline piRNA pathway in animal ovaries.

overall_design: Ectopic Ovo ChIP-seq after enforced ovo expression in ovarian somatic cells (OSCs). Characterization of the ectopic Ovo binding sites following enforced ovo expression in OSCs

first: Gregory

last: Hannon

first: Benjamin

middle: C

last: Nicholson


title: Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary

summary: The gene-regulatory mechanisms controlling the expression of the germline PIWI-interacting RNA (piRNA) pathway components within the gonads of metazoan species remain largely unexplored. In contrast to the male germline piRNA pathway, which in mice is known to be activated by the testis-specific transcription factor A-MYB, the nature of the ovary-specific gene-regulatory network driving the female germline piRNA pathway remains a mystery. Here, using Drosophila as a model, we combined multiple genomics approaches to reveal the transcription factor Ovo as regulator of the germline piRNA pathway in ovarian germ cells. Ectopic expression of Ovo in ovarian somatic cells activates germline piRNA pathway components, including the ping-pong factors Aubergine, Argonaute-3, and Vasa, leading to assembly of perinuclear cellular structures resembling nuage bodies of germ cells. We found that in ovarian somatic cells, transcription of ovo is repressed by l(3)mbt, thus preventing expression of germline piRNA pathway genes in the soma. Cross-species ChIP-seq and motif analyses demonstrate that Ovo is binding to genomic CCGTTA motifs within the promoters of germline piRNA pathway genes, suggesting a regulation by Ovo in ovaries analogous to that of A-MYB in testes. Our results also show consistent engagement of the Ovo transcription factor family at ovarian piRNA clusters across metazoan species, reflecting a deep evolutionary conservation of this regulatory paradigm from insects to humans.


title: GATA2 upregulation restores androgen receptor chromatin association and advances darolutamide resistance in prostate cancer (ChIP-Seq)

city: Houston

first: Tianyi

last: Zhou

state: TX

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: Darolutamide is the latest FDA-approved antiandrogen for the treatment of metastatic prostate cancer. Despite its efficacy in prolonging disease-free survival, drug resistance invariably develops. This study aims to understand the molecular mechanisms underlying darolutamide resistance and identify potential therapeutic targets for overcoming the resistance.

overall_design: To investigate AR chromatin binding in DaroR resistant cells and its correlation with the gene expression

first: Chengtai

last: Yu

first: Yali

last: Han

first: Bin

last: He

first: Qin

last: Feng


title: The spatially informed mFISHseq assay resolves biomarker discordance and predicts treatment response in breast cancer

city: Bratislava

first: Evan

last: Paul

address: Ilkovičova 8

country: Slovakia

institute: MultiplexDX

summary:
Background: Breast cancer (BCa) is a heterogeneous disease requiring precise diagnostics to guide effective treatment. Current assays fail to adequately address the complex biology of BCa subtypes/risk groups and accurately predict responses to treatments like antibody-drug conjugates (ADCs). To address these limitations, we developed and validated a novel diagnostic, prognostic, and predictive tool, mFISHseq.
Methods: Our approach, mFISHseq, integrates multiplexed RNA fluorescent in situ hybridization with RNA-sequencing, guided by laser capture microdissection. This technique ensures tumor purity, allows unbiased profiling of whole transcriptome data, and explicitly quantifies intratumoral heterogeneity.
Results: In a retrospective cohort study involving 1,082 FFPE breast tumors, mFISHseq demonstrated high analytical validity with 93% accuracy compared to immunohistochemistry across training and test sets. Our consensus subtyping approach provided near-perfect concordance with other molecular classifiers (κ > 0.85) and reclassified 30% of samples into subtypes with distinct prognostic implications. Consensus risk groups mitigated misclassification of single samples and provided prognostic information about both early and late relapse. High risk patients had enriched innate and adaptive immune signatures, which predicted response to neoadjuvant immunotherapy. Furthermore, we identified patients responsive to ADCs, as evidenced by a 19-feature classifier for T-DM1 sensitivity, validated on the multicenter, phase II, prospective I-SPY2 trial. To demonstrate the clinical potential, we deployed mFISHseq as a research use only test on 48 patients, revealing insights into the efficacy of novel targeted therapies, such as CDK4/6 inhibitors, immune checkpoint inhibitors, and ADCs.
Conclusion: The mFISHseq method solves a long-standing challenge in the precise diagnosis and classification of BCa subtypes/prognostic risk groups, and allows accurate response prediction for patients, including those treated with immunotherapies and ADCs.

overall_design: Out of a starting cohort of 1,082 breast samples, we excluded one sample for revoked informed consent, four samples for damaged FFPE blocks or sections rendering them unable to be processed, 63 samples because pathology review revealed benign/healthy tissue or DCIS/LCIS, and one sample had missing clinical data. This left a cohort of 1,013 breast tumors available for later analyses. The published 1,254 breast cancer samples are comprised of 1,014 patients with invasive breast cancer (1 sample has no clinical data), 99 subtype samples from patients who had an extra region of interest (ROI) collected by laser capture microdissection (LCM), 25 patients with in situ carcinoma (24 DCIS/1 LCIS), 24 no tumor tissues (i.e., tissues dissected from tumor specimens that contained only healthy, atypical ductal hyperplasia, or other benign cells upon pathological review), 12 true healthy samples, 41 scroll samples used for the LCM vs. no LCM experiment, and 39 positive control samples. The Macherey Nagel NucleoSpin total RNA FFPE XS kit was used for RNA isolation. After RNA isolation, RNA quantity was measured using the Qubit RNA HS (High Sensitivity) Assay Kit with a Qubit 4 Fluorometer and RNA quality using the Agilent High Sensitivity RNA ScreenTape with an Agilent 4150 TapeStation. The DV200 value of the sample (i.e., the percentage of fragments more than 200 bases in length) was calculated as recommended by Illumina. Samples with DV200 values over 15% were considered viable samples for library preparation. We used the Takara SMARTer Stranded Total RNA-Seq Kit v3 - Pico Input Mammalian kit to prepare total RNA-SEQ libraries following the manufacturer's instructions. We included a single natural positive control sample in each library preparation batch and a synthetic spike-in control in each sample to control for batch library preparation effects. Following library preparation, the quantity and fragment size range of the library was assessed using both the Qubit dsDNA HS kit (Qubit 4 Fluorometer) and the Agilent High Sensitivity DNA ScreenTape kit (Agilent 4150 TapeStation). Successfully prepared libraries contained sufficient library to pool on an Illumina NovaSeq 6000 sequencing instrument and fragment range spanning 200 - 1,000 bp, with a local maximum of 250 - 350 bp. Depending on pool size, individual sequencing libraries were pooled and sequenced on an Illumina NovaSeq 6000 using SP, S1, S2, or S4 flow cells. Pooled libraries were spiked with 10% PhiX as recommended by both Illumina and Takara for low-complexity libraries sequenced on patterned flow cells. Paired-end sequencing (2 x 100 bp) was conducted to obtain approximately 100 million reads per sample.

first: Barbora

last: Huraiová

first: Natália

last: Valková

last: Matyašovská

first: Daniela

last: Gábrišová

first: Soňa

last: Gubová

first: Helena

last: Ignačáková

first: Tomáš

last: Ondris

first: Michal

last: Gala

first: Silvia

last: Bendíková

first: Jarmila

last: Bíla

first: Katarína

last: Buranovská

first: Diana

last: Drobná

first: Zuzana

last: Krchňáková

first: Maryna

last: Kryvokhyzha

first: Daniel

last: Lovíšek

first: Viktoriia

last: Mamoilyk

first: Veronika

last: Mančíková

first: Nina

last: Vojtaššáková

first: Michaela

last: Ristová

first: Iñaki

last: Comino-Méndez

first: Igor

last: Andrašina

first: Pavel

last: Morozov

first: Thomas

last: Tuschl

first: Fresia

last: Pareja

first: Jakob

middle: N

last: Kather

first: Pavol

last: Čekan


title: Sialic acid blockade inhibits the metastatic spread of prostate cancer to bone

city: Newcastle upon Tyne

first: Jennifer

last: Munkley

state: Tyne & Wear

address: International Centre for Life

institute: Newcastle University

summary:
To identify signalling pathways altered by ST6GAL1 in prostate cancer cells, we established DU145 and PC3 stable cell lines in which ST6GAL1 was overexpressed.
We then performed differential gene expression, Gene Ontology and GSEA analyses using data obtained from RNA-seq of the control and OE cell lines.

overall_design:
Comparative gene expression profiling analysis of RNA-seq data for Lenti-ORF negative control PC3 and DU145 prostate cancer cells vs PC3 and DU145 cells with ST6GAL1 overexpression.

Please note that the PC3 samples and updated processed data files have been added to the records on Jan 16, 2025.

first: Kirsty

last: Hodgson

first: Margarita

last: Orozco-Moreno

first: Emily

last: Archer Goode

first: Matthew

last: Fisher

first: Rebecca

last: Garnham

first: Richard

last: Beatson

first: Helen

last: Turner

first: Karen

last: Livermore

first: Yuhan

last: Zhou

first: Laura

last: Wilson

first: Eline

last: Visser

first: Johan

last: Pijnenborg

first: Nienke

last: Eerden

first: Sam

last: Moons

first: Emiel

last: Rossing

first: Gerald

last: Hysenaj

first: Rashi

last: Krishna

first: Ziqian

last: Peng

first: Kyla

last: Putri Nangkana

first: Edward

last: N Schmidt

first: Adam

last: Duxfield

first: Ella

last: Dennis

first: Rakesh

last: Heer

first: Michelle

last: Lawson

last: Macauley

first: David

last: Elliott

first: Christian

last: Büll

first: Emma

last: Scott

last: Boltje

last: Drake

first: Ning

last: Wang


title: An inflammatory state defines a high-risk T-lineage acute lymphoblastic leukemia subgroup

city: Toronto

first: Soheil

last: Jahangiri

state: Ontario

address: 610 University Ave

department: Princess Margaret Cancer Centre

institute: University Health Network

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

overall_design: Refer to individual Series


title: An inflammatory state defines a high-risk T-lineage acute lymphoblastic leukemia subgroup [bulkRNA-Seq]

summary: T-cell acute lymphoblastic leukemia (T-ALL), a malignant neoplasm of immature T cells, is a particularly aggressive leukemia with diverse subtypes and limited therapeutic options. Recent studies showed that the responsiveness of drugs in preclinical models of T-ALL is linked to the specific biological characteristics exhibited by the T-ALL subtype. In order to comprehensively explore the underlying heterogeneity of T-ALL, we performed an integrative analysis of bone marrow biopsies from newly diagnosed T-ALL patients. Leveraging a combination of cellular indexing of transcriptomes and epitopes by sequencing (CITE-seq) along with T-cell receptor sequencing (TCR-seq), we obtained a comprehensive molecular characterization of T-ALL. Our analysis uncovered a distinct subset of inflammatory T-ALLs (iT-ALLs) resembling early T-cell precursor (ETP) leukemias, characterized by enriched expression of hematopoietic stem and progenitor signatures, inflammatory gene programs, and poor survival outcomes. Furthermore, our investigation revealed a significant association between the transcription factor interferon regulatory factor 5 (IRF5) activity and the iT-ALL subgroup. Utilizing an IRF5 scoring system, we demonstrated its potential as a robust biomarker for classifying T-ALL patients and predicting disease prognosis. Our work provides a framework for identifying high-risk T-ALL patients based on the IRF5 activity and a rational for considering the inflammatory state in tailoring therapeutic interventions.

overall_design:
Cryopreserved primary human BM and PBMC of TALL patients were sequenced
NOTE FROM SUBMITTER: Since these are patient data we are not submitting the raw fastq files.

first: Mark

last: Gower

first: Ximing

last: Li

first: Brian

last: Lin

first: Alicia

middle: G

last: Aguilar-Navarro

first: Minerva

last: Fernandez

first: Gibran

last: Edun

first: Mursal

last: Nader

first: Andy

last: Zeng

first: Andrea

last: Aruda

first: Anne

last: Tierens

first: John

last: Dick

last: Minden

first: Johann

last: Hitzler

first: Courtney

last: Jones

first: Gregory

last: Schwartz

first: Igor

last: Dolgalev

first: Anastasia

last: Tikhonova


title: Single-cell RNA-seq of alveolar myofibroblasts and other clusters

first: Marek

last: Bartkuhn

summary: Alveolar myofibroblasts emerge during postnatal lung development and are substantially cleared following the completion of the alveolar stage of lung development. In this study, we hypothesized that alveolar myofibroblast descendants that escape apoptotic clearance are reactivated in resposne to injury during adult life.

overall_design: Acta2-Cre-ERT2; tdTomatoflox and Gli1Cre-ERT2; tdTomatoflox pups received a single s.c. injection of tamoxifen at postnatal day 4 (P4), and lineage-labeled cells were FACS-sorted at various time points and subjected to scRNA-seq. In another set of mice, adult Acta2-Cre-ERT2; tdTomatoflox or Gli1Cre-ERT2; tdTomatoflox mice were treated with tamoxifen before or after being infected with PR8.

first: Elie

last: El-Agha

first: Ali

last: Khadim


title: An inflammatory state defines a high-risk T-lineage acute lymphoblastic leukemia subgroup [CITE-seq]

first: Soheil

last: Jahangiri

first: Mark

last: Gower

first: Ximing

last: Li

first: Brian

last: Lin

last: Aguilar-Navarro


title: CPSF1 inhibition promotes widespread use of intergenic polyadenylation sites and impairs glycolysis in prostate cancer cells [PAC-seq]

status: Public on Dec 20 2024

city: Minneapolis

first: Scott

last: Dehm

address: Mayo Mail Code 806, 420 Delaware St SE

institute: Masonic Cancer Center, University of Minnesota

summary: The goal of this study was to compare globlal poly(A) site usage changes upon CPSF1 knockdown in LNCaP, LNCaP95, and 22Rv1 prostate cancer cells.

overall_design: Comparative poly(A) cluster (PAC) profiling in LNCaP, LNCaP95, and 22Rv1 cells between three groups total. LNCaP, LNCaP95, 22Rv1 cells with CPSF1 knocked down via shRNA (shCPSF1-1, shCPSF1-2 and control shCtrl)

first: Kiel

last: Tietz

first: Braedan

last: McCluskey


title: CPSF1 inhibition promotes widespread use of intergenic polyadenylation sites and impairs glycolysis in prostate cancer cells [RNA-seq]

summary: The goal of this study was to compare globlal expression changes upon CPSF1 knockdown in LNCaP, LNCaP95, and 22Rv1 prostate cancer cells.

overall_design: Comparative gene expression profiling in LNCaP, LNCaP95, and 22Rv1 cells between three groups total. LNCaP, LNCaP95, 22Rv1 cells with CPSF1 knocked down via shRNA (shCPSF1-1, shCPSF1-2 and control shCtrl)


title: An epigenetic pathway regulates MHC-II expression and function in B cell lymphoma models

city: Chicago

first: Lu

last: Wang

state: Illinois

address: 303 E. Superior Street Simpson Querrey 7-414

department: Biochemistry and Molecular Genetics

institute: Northwestern University

summary: There is a growing recognition of the prognostic significance associated with the expression of major histocompatibility complex (MHC) class II in tumor cells within the context of anti-cancer immunity. Mutations or homozygous deletions of MHC-II genes are frequently encountered in B-cell lymphomas that develop in immune-privileged sites, and therefore have been linked to the survival of patients with B-cell lymphoma. However, the understanding of the regulation of MHC class II expression by epigenetic and genetic factors remains incomplete. In this study, we have identified a crucial signaling pathway comprised of the histone H2AK119 deubiquitinase BAP1, the interferon regulatory factor IRF1, and the MHC-II transactivator CIITA, which directly activates the expression of MHC-II cluster genes. Disruption of the BAP1/IRF1/CIITA axis leads to a functional attenuation of MHC-II expression without affecting expression of the genes involved in cell cycle or proliferation. Notably, loss of BAP1 has no effect on B cell lymphoma cell growth in vitro while significantly accelerates tumor growth in immunocompetent mice in vivo. Indeed, by utilizing single-cell RNA-seq, a significant reduction in immune cell infiltration was observed in BAP1-depleted tumors, indicating a potential tumor suppressive function of BAP1 by regulating the tumor microenvironment and immune response. Finally, we demonstrated that pharmacological inhibition of PRC1, which deposits histone H2K119Ub and functions as an antagonist of BAP1, could rescue the MHC-II genes in BAP1 deficient B-cell lymphoma cells. These findings establish the rationale for therapeutic strategies aimed at restoring tumor-specific MHC class II expression and enhancing immunotherapy outcomes at epigenetic levels in B-cell lymphoma treatment.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: To determine the function of BAP1 in transcriptional regulation in mouse B cell lymphoma cells, we depleted BAP1 by CRISPR in mouse B cell lymphoma cell line A20 and conducted ChIP-seq, RNA-seq, and ATAC-seq analysis.

first: Zibo

last: Zhao


title: Impact of c-JUN deficiency on thalamus  development in mice and human neural  models [ATACseq, RNAseq, CUT&Tag]

city: Macau

first: Jiantao

last: Shi

address: niversity of Macau Avenida da Universidade Taipa, Macau, China

department: ICMS

institute: University of Macau

summary: c-Jun is a gene expression regulator. By forming homo- or heterodimer, c-Jun binds to DNA and regulates gene transcription. c-Jun is deeply involved in embryonic development but its effect on nervous system development especially in higher mammal is unclear. In this study, we combined H1ESC derived neural progenitor cells (NPCs), cerebral organoids (COs),Thalamus Organoids(ThOs) and mouse model to study the role of c-Jun in early nervous system development. c-Jun KO promoted NPCs induction and differentiation while weakened NPCs’ adhesion ability. c-Jun KO COs got more robust neural ectoderm and expanded Pax6+/Nestin+ cortex-like layer while less tight junctional core. c-Jun KO mouse embryos on E14.5 showed malformation of thalamus in diencephalon with tight junction loose and cell lose. Taken together, the consistent trend in three models implied that c-Jun deletion promoted neural differentiation while weakened the tight junctions. The thalamus/diencephalon was vulnerable to dysplasia when lose c-Jun in early mouse embryonic development.

overall_design: To investigate the function of c-Jun, we established 2 H1ESCs cell lines which the target gene (c-Jun) has been knocked  out by CRISPR/Cas9. H1 ESC cell line used as wild type control. We then induced the 3 cell lines into cerebral organoids, thalamus organoids and performed gene expression profiling anlysis using data obtained from RNA-seq, ATAC-seq. At last, we performed Differential Expression Gene Analysis and Gene Expression Heat Map online using the seq data and did comparation between the wild type and knockout cell lines.


title: scRNA-seq of total mouse aortic cells after CD8+ T cell depletion with CITE-seq and cell Hashing

city: Würzburg

first: Antoine-Emmanuel

last: Saliba

address: Josef-Schneider-Straße 2 / D15

institute: Helmholtz Institute for RNA-based Infection Research

summary: scRNA-seq of aortic cells in atherosclerotic mice with CD8+ T cell depletion after establishment of atherosclerotic lesions

overall_design: We performed single-cell RNA-seq analysis with CITE-seq and cell hashing of total viable aortic cells from Ldlr-/- mice fed a high fat diet for 13 weeks and treated with a CD8 depleting antibody for the last 4 weeks of high fat diet

first: Clement

last: Cochain

first: Panagiota

last: Arampatzi

first: Alma

last: Zernecke

first: Sarah

last: Schäfer


title: Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary [RNA-seq]

first: Azad

last: Alizada

summary: The gene-regulatory mechanisms behind the female germline piRNA pathway in ovaries of metazoan species remain largely unexplored. Here, using the Drosophila model and combinations of RNA-seq, ATAC-seq, and single-cell approaches, we reveal the transcription factors that regulate the female germline piRNA pathway in animal ovaries.

overall_design: Differential RNA-seq analysis between the wild-type ovarian somatic cells (OSC) and the l(3)mbt knockout OSCs. Differential RNA-seq analysis between the OSCs and the fGS/OSS (mix of female germ-line stem cells/ovarian somatic sheet). Differential RNA-seq analysis between the germline and somatic cells FACS sorted from the transgenic vas-GFP fly ovaries. Differential RNA-seq analysis between the OSCs overexpressing the ectopic Ovo vector and the control OSCs nucleofected with the empty vector

first: Gregory

middle: J

last: Hannon

first: Benjamin

last: Nicholson


title: Neonatal inflammation impairs developmentally-associated subsets of microglia and promotes highly reactive microglia subset

city: Paris

first: Adrien

last: Dufour

address: 48, boulevard serurier

country: France

institute: INSERM

summary: Single-cells inDrops RNAseq analyses of neonatal neuroinflammation mice models comprising 20 samples with technical and biological replicates


title: Impact of c-JUN deficiency on thalamus  development in mice and human neural  models

summary: c-Jun is a gene expression regulator. By forming homo- or heterodimer, c-Jun binds to DNA and regulates gene transcription. c-Jun is deeply involved in embryonic development but its effect on nervous system development especially in higher mammal is unclear. In this study, we combined H1ESC derived neural progenitor cells (NPCs), cerebral organoids (COs) and mouse model to study the role of c-Jun in early nervous system development. c-Jun KO promoted NPCs induction and differentiation while weakened NPCs’ adhesion ability. c-Jun KO COs got more robust neural ectoderm and expanded Pax6+/Nestin+ cortex-like layer while less tight junctional core. c-Jun KO mouse embryos on E14.5 showed malformation of thalamus in diencephalon with tight junction loose and cell lose. Taken together, the consistent trend in three models implied that c-Jun deletion promoted neural differentiation while weakened the tight junctions. The thalamus/diencephalon was vulnerable to dysplasia when lose c-Jun in early mouse embryonic development.

overall_design: To investigate the function of c-Jun,we established 2 H1ESCs cell lines which the target gene(c-Jun) has been knocked  out by CRISPR/Cas9.1H1ESC cell line used as wild type control.We then induced the 3 cell lines into cerebral organoids and performed gene expression profiling anlysis using data obtained from RNA-seq of those 3 different cells at two time points. At last,we perfpormed Differential Expression Gene Analysis and Gene Expression Heat Map online using the seq data and did comparation between the wild type and knockout cell lines.


title: RNA-Seq of lung fibroblasts of Atm defecient and wildtype mice.

status: Public on Dec 22 2024

city: Tel-Aviv

first: Amit

last: Levon

address: Ramat Aviv

country: Israel

institute: Tel-Aviv University

summary: We applied RNA-Seq on lung fibroblasts derived from Atm defecient as well as wildtype mice to further understand and reveal a novel pathawy involved in the premture senescence caused by the loss of Atm.

overall_design: 15 samples were analyezd. 3 strains of lung fibroblasts were established from  Atm-/- and Atm+/+ C57BL/6 mice (3 for each genotype) and samples were taken for RNA seq at passage 2 and passage 8. As a control , 3 Atm+/+ strains were irradiated with 10 Gy IR to induce stress induced premature senescence (SIPS).

first: Majd

last: Haj

first: Yann

last: Frey

first: Ran

last: Elkon

first: Judith

last: Campisi

first: Yael

last: Ziv

first: Yosef

last: Shiloh


title: ATAC-seq of IMR90 cells during OIS under TPR depletion

status: Public on Dec 19 2024

city: Edinburgh

first: Yatendra

last: Kumar

email: yaten2020@gmail.com, ykumar@ed.ac.uk

address: Crewe Road south

department: MRC HGU

institute: MRC Human Genetics Unit, The University Of Edinburgh

summary: During oncogene-induced senescence there are striking changes in the structure of the nucleus and the organisation of heterochromatin. This is accompanied by activation of a pro-inflammatory gene expression programme – the senescence associated secretory phenotype (SASP) – driven by transcription factors such as NF-κB. Here we show that TPR, a protein of the nuclear pore complex basket, is required for the very early activation of NF- κB signalling during the stress-response phase of oncogene-induced senescence. This is prior to activation of the SASP and occurs without affecting NF-κB nuclear import. We show that TPR is required for the activation of TBK1 signalling at these early stages of senescence and we link this to the formation of heterochromatin-enriched cytoplasmic chromatin fragments thought to bleb off from the nuclear periphery. These cytoplasmic chromatin fragments appear to lack nuclear pore components. Our data suggest that TPR at the nuclear pore is involved in the loss of structural integrity of the nuclear periphery during senescence. We propose that this acts as a trigger for activation of cytoplasmic nucleic acid sensing, NF-κB signalling, and activation of the SASP, during senescence.

overall_design: ATAC-seq profiling of IMR90 Cells at day 3 and day 8 of RAS mediated senescence.

first: Bethany

last: Bartlett


title: Affinity maturation of antibody responses is mediated by differential plasma cell proliferation

city: New York

first: Gabriela

middle: S

last: Silva Santos

state: NY

address: 1230 York Avenue

institute: The Rockefeller University

summary: Increased antibody affinity over time after vaccination is a prototypical feature of immune responses. Recent studies have shown that a diverse collection of B cells, producing antibodies with a wide spectrum of different affinities, are selected into the plasma cell (PC) pathway. How affinity-permissive selection enables PC affinity maturation remains unknown. Here we report that PC precursors (prePC) expressing high affinity antibodies received higher levels of T follicular helper (Tfh) and divided at higher rates than their lower affinity counterparts once they left the GC. Thus, differential cell division by selected prePCs accounted for how diverse precursors developed into a PC compartment that mediated serological affinity maturation.

overall_design: S1PR2-CreERT2 R26 ZsG mice were immunized with the hapten-carrier NP-OVA followed by tamoxifen administration 5 days after immunization. ZsG labeled Fas+ GL7+ CD38- GC B cells and their progeny B220- CD138+ TACI+ were sorted 14 days after immunzation.  Multiplexed mouse samples: M1-M6.

first: Andrew

last: MacLean

first: Lachlan

last: Deimel

first: Pengcheng

last: Zhou

first: Mohamed

middle: A

last: ElTanbouly

first: Julia

last: Merkenschlager

first: Victor

last: Ramos

last: Santos

first: Thomas

last: Hägglöf

first: Christian

last: Mayer

first: Brianna

last: Hernandez

first: Anna

last: Gazumyan

first: Michel

last: Nussenzweig


title: Lung cancer-intrinsic SOX2 expression mediates resistance to checkpoint blockade therapy by inducing Treg cell-dependent CD8+ T cell exclusion

first: Charles

middle: Arthur

last: Whittaker

state: MA

institute: Koch Institute

summary: Tumor-intrinsic signaling pathways can drastically affect the tumor immune microenvironment (TME), promoting tumor progression and resistance to immunotherapy by excluding immune cell populations from the tumor. Several tumor-cell intrinsic pathways have been reported to modulate myeloid cell infiltration and subsequent T cell recruitment. Clinical evidence suggests that excluding cytotoxic T cells from the tumor core mediates resistance to immunotherapy. Here, we find that tumor cell-intrinsic SOX2 expression in non-small cell lung cancer induces the exclusion of cytotoxic T cells from the tumor core and promotes resistance to checkpoint blockade therapy. CD8+ T cell exclusion was dependent on regulatory T cell-mediated suppression of tumor vasculature. Depleting tumor-infiltrating regulatory T cells via Glucocorticoid-Induced TNFR-Related protein (GITR) restored CD8+ T cell infiltration and, combined with checkpoint blockade therapy, reduced tumor growth.

overall_design: Comparison of gene expression in three replicates each of the KPS2.SIY (expressing SIY-GFP and Sox2) and KPCt.SIY (expressing SIY-GFP) cells derived from the mouse lung adenocarcinoma KP parental cell line driven by KrasG12D and Trp53-/- deletion.

first: Elen

last: Torres-Mejia

first: Sally

last: Weng

first: Kim

last: Nguyen

first: Ellen

last: Duong

first: Leon

last: Yim

first: Stefani

last: Spranger


title: Transcriptional regulation of the germline piRNA pathway in the Drosophila ovary [ATAC-seq]

first: Azad

last: Alizada

overall_design: Differential chromatin accessibility (ATAC-seq) analysis between the wild-type ovarian somatic cells (OSC) and the l(3)mbt-knockout OSCs. Characterization of the chromatin accessibility landscape of the Drosophila melanogaster ovary using ATAC-seq

first: Gregory

last: Hannon

first: Benjamin

last: Nicholson


title: Navigating Illumina Methylation Data: Biology vs. Technical Artefacts

city: Ulm

first: Selina

last: Glaser

address: Albert-Einstein-Allee 11

institute: Ulm University and Ulm University Medical Center

summary:
Illumina-based BeadChip arrays have revolutionized genome-wide DNA methylation profiling, pushing it into diagnostics. However, comprehensive quality assessment remains a challenge within a wide range of available tissue materials and sample preparation methods. This study tackles two critical issues: differentiating between biological effects and technical artefacts in suboptimal quality samples and the impact of the first sample on the Illumina-like normalization algorithm.
We introduce three quality control scores based on global DNA methylation distribution (DB-Score), bin distance from copy number variation analysis (BIN-Score), and consistently methylated CpGs (CM-Score), that rely on biological features rather than internal array controls. These scores were explored and benchmarked across independent study cohorts. Additionally, we reveal deviations in beta values caused by different sample rankings with the Illumina-like normalization algorithm, verified these with whole-genome methylation sequencing data and showed effects on differential DNA methylation analysis.
Our findings underscore the necessity of consistently utilizing a pre-defined normalization sample within the ranking process to boost the reproducibility of the Illumina-like normalization algorithm. In conclusion, our study delivers valuable insights, practical recommendations, and R functions designed to enhance the reproducibility and quality assurance of DNA methylation analysis, particularly for challenging sample types.

overall_design: Six paired samples from patients with Burkitt lymphoma, once formalin-fixed paraffin-embedded (FFPE) tissue and once cryo preserved material, as well as 5 non-neoplastic samples were collected from the ICGC MMML-Seq consortium. In addition, 1 sample from the peripheral blood of healthy donors were used as normalization sample.

first: Ole

last: Ammerpohl


title: An essential role for the ultra-conserved poison exon of Tra2b in fertility in mice (iCLIP-seq)

first: Graham

last: Smith

address: Framlington Place

department: Bioinformatics Support Unit

summary: Alternative splicing-induced inclusion of poison exons containing in-frame stop codons is a mechanism that can be used to attenuate gene expression. Poison exon have been implicated in cancer, but how they operate within the context of normal development and physiology is poorly understood. Several splicing regulator genes, including Tra2b, contain ultra-conserved poison exons that function within regulatory loops to fine-tune their activity. To investigate the physiological role of poison exons in vivo, we created mice lacking either Tra2b or its poison exon, specifically during spermatogenesis to reveal both are essential for male fertility. The mouse Tra2b gene is essential for mitotic proliferation of germ cells, whereas, in contrast, the Tra2b poison exon is critically required during meiosis and not needed by mitotically proliferating cell populations within the germline. Poison exon deletion causes infertility, with a block in male meiotic prophase where Tra2β protein expression levels normally increase. Deletion of the Tra2b poison exon changes expression patterns of genes important for meiosis and splicing patterns of Tra2β target exons, suggesting Tra2b poison exon splicing prevents meiotic cells accumulating toxic levels of Tra2b expression. Our data provide a new physiological explanation for Tra2b poison exon ultra-conservation and indicate the importance of evaluating poison exon function within a physiological context.

overall_design: Individual-nucleotide resolution UV crosslinking and immunoprecipitation (iCLIP-seq) ofTra2beta  protein done in triplicate in adult mouse testis

first: Caroline

last: Dalgliesh

first: Saad

last: Aldalaqan

last: Atallah

first: Andrew

last: Best

first: Emma

last: Scott

first: Ingrid

last: Ehrmann

first: Joel

last: Mannion

first: Barbora

last: Badurova

first: Raveen

last: Sandher

first: Yve

last: Mende

first: Brunhilde

last: Wirth

first: Sara

last: Wells

first: Gemma

last: Codner

first: Lydia

last: Teboul

first: Ann

last: Hedley

first: Colin

last: Miles

first: Dirk

last: de Rooij

first: Louise

last: Reynard

first: Mary

last: Herbert

first: David

last: Elliott


title: Genomic 8-oxoguanine modulates gene transcription independent of its repair by DNA glycosylases OGG1 and MUTYH

status: Public on Dec 21 2024

city: Trondheim

first: Katja

last: Scheffler

address: Edvard Griegs Gate 8

institute: Norwegian University of Science and Technology

summary: It has been suggested that the oxidtaive DNA base lesion 8-oxo-7,8-dihydroguanine (OG) and its repair has epigenetic-like properties and mediates transcription, but genome-wide evidence of this interdependence is lacking. Here, we applied an improved OG-sequencing approach reducing artificial background oxidation and RNA- sequencing to correlate genome-wide distribution of OG with gene transcription in HAP1 cells deficient for OGG1 and/or MUTYH.  Our data identified moderate enrichment of OG in the genome that is mainly driven by the genomic context and not affected by DNA glycosylase-initiated repairs. Regardless of DNA glycosylase activity, OG  in promoter regions correlated with expression of genes related to metabolic processes and damage response pathways indicating that it functions as a sensor of cellular stress to regulate transcription. Our work provides novel insights into the mechanism underlying transcriptional regulation by OG and DNA glycosylases OGG1 and MUTYH and suggests that oxidative DNA damage accumulation and its repair utilize different pathways.

overall_design: Examination of 8-oxo-7,8-dihydroguanine (OG) acrosss the genome in two clones of HAP1 WT, OGG1 and MUTYH single knockout and OGG1/MUTYH double knockout cells from three independent experiments

first: Tobias

last: Obermann

first: Teri

last: Sakshaug

first: Vishnu

last: Kanagaraj

first: Andreas

last: Abentung

first: Mirta Mittelstedt

last: de Sousa

first: Lars

last: Hagen

first: Antonio

last: Sarno

first: Magnar

last: Bjørås


title: Inhibition of ATM in Mouse-derived lung fibroblasts

first: Amit

last: Levon

summary: The main goal is to examine the transcriptome of primary lung fibroblasts that undergo premature senescence after prolonged inhibition of ATM.

overall_design: 27 samples were analyzed. 3 replicates for each condition, cells irradiated with 10 Gy IR were used as a positive control of senescent cells.

first: Majd

last: Haj

first: Yann

last: Frey

first: Ran

last: Elkon

first: Yael

last: Ziv

first: Judith

last: Campisi

first: Yosef

last: Shiloh


title: Genome-wide CRISPR knockout screening with viral replicons for identification of host factors involved in viral replication

city: San Francisco

first: Amy

middle: L

last: Kistler

state: CA

address: 499 Illinois St, 4th floor

institute: Chan Zuckerberg Biohub

summary: Pooled CRISPR knockout (KO) screens using live viruses are a proven and valuable approach for identifying essential host factors acting across viral life cycles. Here we describe the development of a pooled genome-wide CRISPR KO screening approach using stable viral replicon cell lines to specifically identify host factors essential for viral replication. Virus replicons are non-infectious, therefore enabling the study of highly virulent viruses under standard biosafety level 2 containment. We developed a stable fluorescent dengue virus type 2 (DENV-2) replicon cell line to perform a pooled genome-wide FACS-based CRISPR KO screen. This benchmark DENV-2 replicon screen successfully identified host genes previously known to be required for viral DENV-2 replication (e.g., endoplasmic reticulum membrane complex and oligosaccharyltransferase complex components) and confirmed two additional genes (DOHH and ZFP36L2) involved in replication that have not been recovered in prior live virus screens. We applied this replicon screening approach to two highly divergent viruses: chikungunya virus (CHIKV), a positive-sense RNA virus that replicates at the plasma membrane, and Ebola virus (EBOV), a negative-sense RNA virus that replicates in cytoplasmic inclusion bodies. The CHIKV replicon screen identified two genes known to be required for replication (G3BP1 and G3BP2) and several additional, novel genes (CLEC4G, CSDE1, GOLGA7, HNF1A, and PCBD1). We verified two of them (CSDE1 and GOLGA7) in live CHIKV replication assays. A distinct set of genes (EHMT1, EHMT2, and USP7) were recovered in the EBOV replicon screen and were further confirmed using independent transient transfection assays. Thus, viral replicon-based screens provide a useful approach that can be extended to viruses of diverse taxa to identify host pathways essential for viral replication and to uncover potential novel targets for host-directed medical countermeasures.

overall_design: Comparative sequence analysis of sgRNAs integrated in genomic DNA collected from 2 populations of Huh7.5.1-Cas9 cells harboring different stable fluorescent viral replicons (DENV2, CHIKV, and ZEBOV). Each replicon cell line was transduced with a pool of lentiviruses harboring the Brunello sgRNA library. An unsorted cell populuation was harvested at day 0 post-transduction, and FACS-sorted populations with different types of fluorescent replicon signal (GFP-low and/or GFP-high) were harvested 19 days post-transduction. For each viral replicon cell line, gDNA was extracted from the sorted cells and unsorted cells, sequenced, and compared to compute enrichment scores of targeted genes recovered in the sorted vs unsorted cell populations.

first: Karen

last: Cheng

first: Madhura

last: Bhave

first: Andrew

last: Markhard

first: Duo

last: Peng

first: Karan

middle: D

last: Bhatt

first: Katherine

last: Travisano

first: Josette

last: Medicielo

first: Leila

last: Njoya

first: Sanae

last: Lembirik

first: Manu

last: Anantpadma

last: Puschnik

first: Jens

middle: H

last: Kuhn