title: Increase of blood CSF3R+ myeloid-derived suppressor cell predicts breast cancer recurrence [Myeloid]

city: Taipei

first: Chung-Hsing

last: Chen

address: No.1 Ai-Guo West Road

department: Department of Mathematics

institute: University of Taipei

summary: Early detection of recurrence by using specific biomarkers is still a clinically unmet need although methodologies for monitoring tumor markers, cell-free DNA and circulating tumor cells have been established for decades. Because recurrence is developed from metastatic or dormant cancer cells that are under immune surveillance, alteration in the population and function of immune cells may promote recurrence. In this study, we utilized an animal model to imitate breast tumor recurrence after surgical resection and investigated the abundance and gene expression profile of immune cells by using two NanoString Panels. Our results showed that myeloid-derived-suppressor cells (MDSC) were significantly increased during recurrence. Comparison of our NanoString data with a single-cell RNA sequencing dataset of MDSC in another spontaneous breast cancer model identified colony-stimulating factor 3 receptor (Csf3r)-positive MDSC as a potential marker to predict tumor recurrence. In vitro experiments demonstrated that Csf3R+ MDSC exhibited enhanced ROS levels and stronger T cell suppression ability. Furthermore, these findings were validated in two published PBMC databases.

overall_design: An orthotopic model by inoculating luciferase-tagged mouse 4T1 (4T1-luci) breast cancer cells into the 4th mammary fat pad of BALB/c mice was established to study the alteration of immune cell populations in blood during tumor recurrence. At 3 weeks after inoculation, paired normal and tumor-bearing mice were euthanized for blood collection and mononuclear cell isolation. Tumors of another 3 tumor-bearing mice were removed by surgical resection and tumor recurrence was monitored by detecting the presence of bioluminescence using an IVIS imaging system. When a bioluminescent signal appeared, the mouse was euthanized for blood collection. Tumor recurrence in the mice was variable and was detected around 2-4 weeks after tumor dissection (thus weeks 5 to 7 after cancer cell inoculation). PBMC were spun down by centrifugation at 1500 rpm for 10 min at 4℃ and washed twice with phosphate-buffered saline (PBS) and RNA was isolated by using Direct-Zol RNA Miniprep Kits (ZYMO RESEARCH). Isolated mononuclear cells were subjected to NanoString analysis using nCounter Mouse Myeloid Innate Immunity V2 panel (754 genes) and Mouse PanCancer Immune Profiling Panel (770 genes).

first: Y

first: C

last: Lai

first: M

last: Pan

first: W

middle: C

last: Hung


title: Increase of blood CSF3R+ myeloid-derived suppressor cell predicts breast cancer recurrence

status: Public on Aug 18 2024

country: Taiwan

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Increase of blood CSF3R+ myeloid-derived suppressor cell predicts breast cancer recurrence [Immune]

first: L

middle: Y

last: Li

middle: H

middle: S

middle: R


title: Utility analyses of AVITI sequencing platforms

status: Public on Aug 19 2024

city: Pittsburgh

first: Shuchang

last: Liu

state: PA

address: 203 Lothrop Street

country: USA

institute: University of Pittsburgh

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct


title: Chronic Stress Reinforces the BLA-mPFC-LHb Neural Circuit Leading to Depression

status: Public on Aug 17 2024

city: Beijing

first: Zhiyuan

address: YIKE Road

country: China

institute: Chinese Institute for Brain Research, Beijing(CIBR)

summary: To explore the specific subset of mPFC neurons involved in the pathophysiological process of CRS-induced depression, we performed RNAseq between noCRS and CRS treatment mice to identify the enriched genes and possible pathway. GO:BP analysis identified significantly enriched genes that are involved in synaptic signaling and regulation of membrane potential pathways.

overall_design: Differential expression analysis and GO Enrichment Analysis of RNA seq data. We performed differential expression analysis of RNA seq data obtained from mPFC-LHB projection neurons of noCRS and CRS mice.

first: Ruihuan

last: Qin

first: Xiao

last: Wen

first: Wenzhi

last: Sun


title: Transcriptome data of bone marrow long-term hematopoietic stem cells (LT-HSCs) from mice with or without 3-month serine/glycine-free diet (SGFD) treatment.

city: CHONGQING

first: Chaonan

address: Gaotanyan Street

institute: the Army Medical University

summary: The vulnerability of bone marrow hematopoiesis to perturbations of serine metabolism as well as the underlying cellular and molecular mechanisms remain poorly understood. Here we reveal a distinct serine metabolic signature of hematopoietic stem cells (HSCs) within the hematopoietic compartment.To identify the phenotype switching and function variation in BM LT-HSCs with SGFD treatment, we performed RNA-seq of LT-HSCs from the bone marrow of mice with or without3-month SGFD treatment.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of BM LT-HSCs (Lin-c-Kit+Sca1+CD34-CD135-) from mice with or without 3-month SGFD treatment.

first: Kuan

last: Yu

first: Xinliang

first: Changhong

last: Du

first: Junping

last: Wang


title: Inhibition of circulating glycocholic acid-regulated signaling potentiates immune checkpoint therapy in colorectal cancer

city: Shanghai

first: Senlin

last: Zhao

address: 270 Dong An Road

department: Colorectal Surgery

institute: Cancer Hospital, Fudan University

summary: Serum bile acids (BAs) are an important risk factor for the initiation and progression of cancer, but their roles in colorectal cancer (CRC) remain largely unknown. The present study showed that glycocholic acid (GCA), a primary BA, was highly accumulated in the serum of patients with CRC. In a mouse model of CRC, GCA diet promoted programmed death-ligand 1 (PD-L1) expression in tumors, which attenuated CD8+ T cell-mediated antitumor responses in the tumor microenvironment (TME), and promoted the occurrence and development of CRC. Increased PD-L1 expression was caused by the reduction in activity of the BA receptor farnesoid X receptor (FXR). Mechanistically, FXR acted as transcriptional repressor for the transcription factor SRY-box transcription factor 14 (SOX14), and suppressed the palmitoylation and stabilization of PD-L1 by inhibiting the SOX14-mediated expression of zinc finger DHHC-type palmitoyl transferase 9 (DHHC9). Notably, genetically silencing SOX14 and DHHC9 in cancer cells or administering an FXR agonist synergized with anti-PD-1 therapy, leading to reduced tumor growth in GCA-fed mice. Together, the present findings reveal a previously unrecognized mechanism of BA in remodeling the TME to mediate CRC resistance to immunotherapy, which may have clinical implications for developing immunotherapy strategies for patients with CRC.

overall_design: To explore the function of GCA , we cocultred MC38 cells with or without GCA for 24h. We then performed gene expression profiling analysis using data obtained from RNA-seq of these treatments. Comparative gene expression profiling analysis of RNA-seq data for MC38 cells treated with or without GCA(CON and GCA).

first: Jing

last: Zhang

first: Yushuai

last: Mi

first: Zijuan

last: Hu

first: Xinyang

last: Zhong

first: Ye

last: Xu

first: Sanjun

last: Cai

first: Xinxiang

first: Ping

last: Wei

first: WanJun

first: Dawei


title: ALKBH5 cooperated with LINC00659 promote gastric cancer progression by JAK1 mRNA m6A-YTHDF2-dependent modification

city: Nanjing

first: Yuan

last: Fang

address: guangzhou road

institute: The First Affiliated Hospital of Nanjing Medical University

summary: N6-methyladenosine (m6A) modification is the most prevalent RNA epigenetic regulation in eukaryotic cells. Recent studies focused on the association between m6A and non-coding RNAs. The demethylase ALKBH5 acts as critical oncogenes or tumor suppressors through multiple mechanisms in various cancers. Here, we find that ALKBH5 is highly expressed in GC tissues and is associated with poor prognosis. ALKBH5 promoted the proliferation and metastasis both in vitro and in vivo. ALKBH5 was recruited by LINC00659, which removed m6A modifications of JAK1, leading to the upregulated expression of JAK1.Since ALKBH5 and LINC00659 have oncogenic role in gastric cancer (GC) progression with poor prognosis, ALKBH5-LINC00659/m6A/JAK1 axis can be new biological mechanisms behind GC development and future therapeutic opportunities.

overall_design: MeRIP-seq in both ALKBH5-knockdown and controlled BGC-823 cells were performed to identify mRNA m6A modification

first: Yongqian

last: Shu


title: ALKBH5 cooperated with LINC00659 promote gastric cancer progression by JAK1 mRNA m6A-YTHDF2-dependent modification [polyA]

overall_design: Total RNAs conducted RNA sequencing (RNA-seq) using LINC00659-knockdown and controlled BGC-823 cells


title: ALKBH5 cooperated with LINC00659 promote gastric cancer progression by JAK1 mRNA m6A-YTHDF2-dependent modification [2-m6A]

overall_design: MeRIP-seq of BGC-823 cells


title: Increased IL-6 expression in microglia prior to detection of virus in the brain of rhesus macaques with acute SIVmac239 infection

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

summary: Knowledge on immune activation in the brain during acute HIV infection is crucial for the prevention and treatment of HIV associated neurological disorders (HAND), which is prevalent in people living with HIV (PLWH), even in those treated with antiretroviral therapy. In this study, we determined regional brain (basal ganglia, thalamus, and frontal cortex) immune and virological profiles 7 and 14 days after infection (dpi) with SIVmac239 in rhesus macaques. Basal ganglia and thalamus were infected earlier (7dpi) than frontal cortex (14 dpi) and contained higher quantities of viruses than the latter. Increased immune activation of astrocytes and significant infiltration of monocytes/macrophages in thalamus at 14 dpi coincided with elevated plasma viral load, while SIV was only localized within monocytes/macrophages. RNA signatures of pro-inflammatory responses including IL-6 were detected at 7 dpi in microglia and interestingly preceded reliable detection of virus in tissues and was maintained long term in the brain of chronically infected macaques. Countering the pro-inflammatory response, the anti-inflammatory response was detectable, but delayed till 14 dpi, as TGF-β expression in significantly higher numbers of perivascular monocytes/macrophages; though this anti-inflammatory response was not detected in chronic infection. Our data provide evidence that the interplay of acute pro-inflammatory and anti-inflammatory responses in the brain likely contribute to the overt neuro-inflammation, but that inflammatory markers such as IL-6 may serve as hyperacute biomarkers of low-level brain infection.

overall_design: 11 adule male rhesus macaques were used. 8 were infected with SIVmac239. 3 were sacrificed on day 7, 5 were sacrificed on day 14. 3 were uninfected controls. Brain tissue from the frontal cortex and blood was sampled at necropsy. Basal ganglia and thalamus tissue were also collected from one animal.

first: Raja

middle: M

last: Gopalakrishnan

first: Malika

last: Aid

first: Noe

last: Mercado

first: Caitlin

last: Davis

first: Shaily

last: Malik

first: Emma

last: Geiger

first: Valerie

last: Varner

first: Rhianna

last: Jones

first: Steven

middle: E

last: Bosinger

first: Cesar

last: Piedra-Mora

first: Amanda

middle: J

last: Martinot

first: Dan

last: Barouch

first: R

last: Reeves

first: C

last: Tan


title: Genotype-phenotype-epiphenotype analysis to decipher severity, penetrance, pleiotropy and mechanisms in CHD8-related neurodevelopmental disorder

status: Public on Aug 16 2024

city: Manchester

first: Siddharth

last: Banka

address: Oxford Road

country: United Kingdom

institute: University of Manchester

type: Methylation profiling by high throughput sequencing

summary: Peripheral blood DNA methylation (DNAm)-based episignature analysis has emerged as an important diagnostic tool. We analysed the relationship between variant type/severity, clinical phenotypes, and epiphenotypes in a cohort of individuals with rare CHD8 variants. Furthermore, we performed DNAm studies in Chd8+/- mouse neocortex to comparatively assess the effect of CHD8 loss-of-function on DNA methylome in a cross-species, cross-tissue manner.

overall_design: To investigate DNA methylome changes in CHD8-IDDAM mouse neocortical models.

first: Albert

last: Basson

first: Conor

last: Mohan


title: Detection of ToLCNDV resistance in cucumber through agroinoculation under controlled condition

city: Coimbatore

first: Rajasree

last: venkatachalam

state: Tamil Nadu

address: TNAU - RI Block, Tamil Nadu Agricultural University, Lawley Rd, P N Pudur,

country: India

institute: Tamil Nadu Agricultural University, Coimbatore, India

summary: In this study, Agrobacterium tumefaciens containing recombinant plasmids were used to agroinoculate cucumber seedlings with tandem repeats of DNA-A genome of Tomato leaf curl New Delhi virus (ToLCNDV). The inoculated seedlings, representing both resistant and susceptible accessions, were monitored for symptoms over a period of four weeks. Symptom development was observed in susceptible genotypes, while the resistant genotype remained symptomless. Leaf samples were collected from both agroinoculated and control plants for further analysis. This research sheds light on the pathogenicity of ToLCNDV in cucumber and highlights the potential resistance mechanisms in certain accessions.

overall_design:
Uppermost leaves of each cucumber seedlings were agroinoculated with 20 µl of Agrobacterium culture mixture followed by pricking with needle. Plants uninoclated with ToLCNDV was assumed as control plants.
P1C - Resistant Control
P1V - Resistant Virus inoculated
P2C - Susceptible Control
P2V -Susceptible Virus inoculated

first: V

last: Rajasree

first: E

last: Naveena


title: Strigolactones negatively regulate Tobacco mosaic virus resistance in Nicotiana benthamiana

city: 长沙

first: 别帅骏

last: 别

state: 长沙

address: 芙蓉区远大二路892号

department: 实验大楼

institute: 湖南省农业科学院

summary: Strigolactones (SLs) are plant hormones that regulate diverse developmental processes and environmental responses in plants. It has been discovered that SLs play an important role in regulating plant immune resistance to pathogens, but there are currently no reports on their role in the interaction between Nicotiana benthamiana and Tobacco mosaic virus (TMV). In this study, the exogenous application of SLs weakened the resistance of N. benthamiana to TMV, promoting TMV infection, whereas the exogenous application of Tis108, an SL inhibitor, resulted in the opposite effect. Virus-induced gene silencing (VIGS) inhibition of two key SL synthesis enzyme genes, NtCCD7 and NtCCD8, enhanced the resistance of N. benthamiana to TMV. Additionally, we conducted a screening of N. benthamiana related to TMV infection. TMV-infected plants treated with SLs were compared to the control by using RNA-seq. KEGG enrichment analysis and weighted gene co-expression network analysis (WGCNA) of differentially expressed genes (DEGs) suggested that plant hormone signaling transduction may play a significant role in the SL-TMV-N. benthamiana interactions. This study reveals new functions of SLs in regulating plant immunity and provides a reference for controlling TMV diseases in production.

overall_design: After TMV inoculation, SL spraying, TMV + SL co-treatment, CK, we observed the virus infection, analyzed the transcriptome, and explored the cause.

first: Renyan

last: Huang

first: Shuaijun

last: Bie


title: Curcumin- loaded Pickering Emulsions with Immunomodulatory Ability for Treatment of Periodontitis

city: Chengdu

first: linke

last: Li

address: No.111, North Section 1, Erhuan Road, Jinniu District

institute: Southwest Jiaotong University

summary: Periodontitis (PD) as a chronic inflammatory disease instigated by periodontal pathogenic bacteria and mediated by the host immune response, resulting in the destruction of supporting periodontal tissue and tooth loss in adults. Constructing an injectable delivery system that allows for sustained drug release within periodontal pockets to continuously eliminate pathogenic bacteria, reduce periodontal inflammation, and promote periodontal tissue regeneration is an effective strategy for periodontitis treatment. Here, we explore the therapeutic potential and underlying mechanisms of curcumin-loaded Pickering emulsion (PE-CUR) in periodontitis treatment. The Pickering emulsion formulation offers an effective delivery system, enhancing curcumin's bioavailability and therapeutic efficacy. In vitro studies, we demonstrate that the PE-CUR exhibit excellent biocompatibility and anti-inflammatory property by elimination of reactive oxygen species (ROS). In addition, PE-CUR significantly eliminate key periodontal pathogens, including Porphyromonas gingivalis (P. gingivalis) and Staphylococcus aureus (S. aureus). In a rat model of periodontitis, PE-CUR significantly attenuates periodontal tissue inflammation and alveolar bone loss, indicating a protective effect against periodontal tissue destruction. Mechanistically, PE-CUR promotes the expression of anti-inflammatory factors and inhibits the release of pro-inflammatory factors by regulating macrophage polarization from M1 to M2 and modulating the MAPK and PI3K-AKT signaling pathway. Furthermore, PE-CUR decreases the formation of osteoclasts as well as stimulates the activation and differentiation of osteoblasts successively, thereby ameliorating the periodontal inflammation and promoting the alveolar bone regeneration. Overall, our findings elucidate the therapeutic mechanisms of PE-CUR in periodontitis, suggesting its potential as a promising treatment strategy warranting further clinical investigation.

overall_design: To investigate the anti-inflammatory and osteoclast-inhibitory effects of PE-CUR on RAW264.7 cells, we plated RAW264.7 cells in 24-well plates and treated them with 100 ng/mL lipopolysaccharide (LPS) and 2 mg/mL PE-CUR for 24 hours.

first: Linke

first: Xiao

first: Hui

last: Zhang

first: Rui

last: Chen


title: Feed-forward Cysteine Regulation Maintains Melanoma Differentiation State and Limits Metastatic Spread

city: Boston

first: Deyang

last: Yu

state: MA

address: 360 Longwood Ave.

institute: Dana-Farber Cancer Institute

summary: The inherent ability of melanoma cells to alter the differentiation-associated transcriptional repertoire to evade treatment and facilitate metastatic spread is well accepted and has been termed phenotypic switching. However, how these facets of cellular behavior are controlled remains largely elusive. Here we show that cysteine availability, whether from lysosomes (CTNS-dependent) or exogenously derived (SLC7A11-dependent or as N-acetylcysteine), controls melanoma differentiation-associated pathways by acting on the melanocyte master regulator MITF. Functional data indicate that low cysteine availability reduces MITF levels and impairs lysosome functions, which affects tumor ferroptosis sensitivity but improves metastatic spread in vivo. Mechanistically, cysteine-restrictive conditions reduce acetyl-CoA levels to decrease p300-mediated H3K27 acetylation at the melanocyte-restricted MITF promoter, thus forming a cysteine feed-forward regulation that controls MITF levels and downstream lysosome functions. These findings collectively suggest that cysteine homeostasis governs melanoma differentiation by maintaining MITF levels and lysosome functions, which protect against ferroptosis and limit metastatic spread.

overall_design: To compare the gene expression profiling between lysohigh and lysolow cells, G361 lysohigh and lysolow cells grown in DMEM growth media reaching around 80 % confluence were used for RNA extraction and RNA was isolated using TRIzol reagent. Following RNA quality assessment, library preparation,RNA sequencing, raw sequencing reads were mapped to GRCh38.90 using HiSat2.168 and quantitated based on genes as counts per million reads (CPM) using SeqMonk v48.2. Differential gene expression across each of the two states Lysohigh and Lysolow were calculated as average Log2fold (L2F) changes with significance (p) based on unpaired two-sided students’ t-test

first: Jiaxin

last: Liang

first: Hans

last: Widlund

first: Pere

last: Puigserver


title: Transcriptome analysis of cancer stem cells in triple-negative cancer

city: Charleston

first: Gary

last: Hardiman

state: SC

address: 135 Cannon Street

department: Medicine

institute: Medical University of South Carolina

summary:
Cancer stem cells (CSCs) are thought to be the source of drug resistance, metastasis and tumor recurrence in cancer treatment.  The goal of this study was to identify the differentially expressed genes between CSCs and non-stem cancer cells (NSCs).
RNA sequencing and bioinformatic analyses revealed that 963 genes are differentially expressed (FDR < 0.4) in TNBC CSCs as compared to NSCs.

overall_design: Flow cytometry cell sorting was employed to isolate CSCs and NSCs from SUM149 triple-negative breast cancer (TNBC) cells. RNA samples were prepared using an RNeasy mini kit (Qiagen).  RNA sequencing was performed to identify transcriptome profilings

first: Gavin

last: Wang

last: Hazard

first: Willian

middle: A

last: da Silveira


title: Trajectory modeling of first trimester placenta highlight differences between cytotrophoblast progenitors and trophoblast stem cells [scRNA-seq]

city: La Jolla

first: Robert

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

institute: UCSD

summary: Cytotrophoblast (CTB) are bipotent progenitor epithelial cells of the human placenta, which can differentiate into invasive extravillous trophoblast (EVT) and multinucleated syncytiotrophoblast (STB). Trophoblast stem cells (TSC) have also been shown to be bipotential. In this study, we set out to probe the transcriptional diversity of first trimester CTB and compare TSC to various subgroups of CTB.  We performed single-cell RNA sequencing on six normal placentae, four 6-week placentae, two of which were separated into basal and chorionic fractions prior to sequencing, and two 13-week placentae. We also sequenced three TSC lines, derived from 6-8 week placentae, to evaluate similarities and differences between primary CTB and TSC.  CTB clusters displayed notable distinctions based on gestational age, with 6-week placentae showing enrichment for specific CTB subtypes, further influenced by origin from the basal or chorionic plate. Differential expression analysis of CTB from basal versus chorionic plate highlighted pathways associated with proliferation, unfolded protein response, and oxidative phosphorylation. We identified trophoblast states representing initial progenitor CTB, precursor STB, precursor and mature EVT, and multiple CTB subtypes. CTB progenitors were enriched at 6-weeks, with basal plate cells biased toward EVT, and chorionic plate cells toward STB, precursors. Clustering and trajectory inference analysis indicated that TSC were most like EVT precursor cells, with only a small percentage of TSC on the pre-STB differentiation trajectory. This was confirmed by flow cytometric analysis of 6 different TSC lines, which showed uniform expression of proximal column markers ITGA2 and ITGA5. Additionally, we found that only ITGA5+ CTB could be plated in 2D, and these cells formed only EVT upon spontaneous differentiation.  Our findings suggest that distinct CTB states exist in different regions of the placenta as early as six weeks gestation and that current TSC lines most closely resemble ITGA5+ CTB, biased toward the EVT lineage.

overall_design: For whole placental samples, chorionic villi were minced and subjected to three sequential enzymatic digestions. After filtration, cells were counted and loaded on the 10x Genomics chip. For basal and chorion samples, under a microscope we collected the tips (basal fraction) and the base (chorionic fraction) of the villi while the middle section was discarded. The two fractions were subjected to the same sequential enzymatic digestion and after filtration cells were separated on a Percoll (Sigma-Aldrich) gradient.

first: Francesca

last: Soncin

first: Mana

last: Parast


title: Trajectory modeling of first trimester placenta highlight differences between cytotrophoblast progenitors and trophoblast stem cells [Spatial Transcriptomics]


title: Polyethylene terephthalate microplastics generated from disposable water bottles induce interferon signalling pathway in mouse lung epithelial cells

city: Ottawa

first: Sabina

last: Halappanavar

state: Ontario

address: 251 Sir Frederick Banting Driveway

department: Healthy Environments and Consumer Safety Branch

country: Canada

institute: Health Canada

overall_design: FE1 cells were treated with two types of commercial microplastics (100 nm polystyrene (PS) and polymethyl methacrylate (PMMA) ) and two types of in-lab generated microplastics (polyethylene terephthalate (PETE) and  polypropylene (PP-TW)) at 0, 12.5, 25 and 50 mg/mL concentrations. Cells were harvested and pelleted after 48 h exposure to microplastics.   Total RNA was extracted from pelleted cells for microarray experiments.

first: Luna

last: Rahman

first: Andrew

last: William


title: ASGR1 Is a Promising Target for Lipid Reduction in Pigs with PON2 As Its Inhibitor

first: Yunjun

last: Yin

address: 2 Yuanmingyuan West Road

institute: China Agricultural University

summary: Although the role of asialoglycoprotein receptor 1 (ASGR1) in lowering lipid levels is well established, recent studies indicate that ASGR1 inhibition can cause unexpected liver damage in pigs, raising a serious issue about whether ASGR1 can be a good target for treating ASCVD. Here, we utilized the CRISPR/Cas9 system to regenerate ASGR1-knockout pigs, who displayed decreased lipid profiles without observable liver damage, which were confirmed by the lower levels of serum ALT and AST, reduced expression of inflammation markers, and normal histological morphology. Also, we implemented immunoprecipitation combined with mass spectrometry (IP-MS) and discovered that Paraoxonase-2 (PON2) can interact with and significantly degrade ASGR1 in a dose-dependent manner. This degradation led to reduced lipid levels in mice, accompanied by little inflammation. Our study highlights the effectiveness and safety of degrading ASGR1 to reduce lipid levels in pigs and provides a potential inhibitor of ASGR1.

overall_design: To gain a better understanding of ASGR1 gene expression patterns, we conducted RNA-Seq analysis on liver tissues of WT (WT1/WT2/WT3) and ASGR1+/- (S03/S04/S05) pigs.


title: RNA-seq in Cal33 cells after overexpression of CES2 expression

city: guangzhou

first: xianyue

last: Ren

state: guangdong

address: 55 Lingyuan West Road, Guangzhou

institute: Guanghua School of Stomatology, Hospital of Stomatology, Sun Yat-sen University

summary: To explore the molecular mechanisms of CES2  in oral squamous cell carcinoma, RNA-seq analysis was performed to compare the gene expression profiles of CES2 overexpression and vector (control) groups.

overall_design: RNA-seq analysis was performed to compare the gene expression profiles of CES2 overexpression and vector (control) groups. Each group contains three repetitions.

first: X

middle: B

first: Q

last: Liu

first: C

first: L

last: Pan

first: S

last: Zhang

first: Y

middle: L

last: Huang

first: P

last: Feng

first: B

last: Cheng


title: Role of CB2 in adipose tissue ILC2s

city: Los Angeles

first: Benjamin

last: Hurrell

address: 1450 Biggy Street

institute: USC

summary: Development of type 2 diabetes mellitus (T2DM) is associated low-grade chronic type 2 inflammation and disturbance of glucose homeostasis. Group 2 innate lymphoid cells (ILC2s) play a critical role in maintaining adipose homeostasis via production of type 2 cytokines. Here, we demonstrate that CB2, a G-protein coupled receptor (GPCR) and member of endocannabinoid system, is expressed on both visceral adipose tissue (VAT)-derived murine and human ILC2s. Moreover, we utilize a combination of ex vivo and in vivo approaches to explore the functional and therapeutic impacts of CB2 engagement on VAT ILC2s in T2DM model. Our results show CB2 stimulation of ILC2s protects against insulin-resistance onset, ameliorates glucose tolerance, and reverses established insulin-resistance. Our mechanistic studies reveal that the therapeutic effects of CB2 are mediated through activation of AKT, ERK1/2 and CREB pathways on ILC2s. The results reveal that CB2 agonist can serve as candidate for prevention and treatment of T2DM.

overall_design: Activated lung ILC2s were FACS sorted and cultured 18h

first: Pedram

last: Shafiei-Jahani


title: Transcriptome profiling identified dysregulated signaling related to adipogenesis, metabolism, and inflammation in polycystic ovary syndrome patients

city: Taipei

first: Chia-Lang

last: Hsu

address: No. 7, Zhongshan S. Rd.

department: Department of Medical Research

institute: National Taiwan University Hospital

summary: Polycystic ovary syndrome (PCOS) is a female endocrine disorder characterized by hyperandrogenism, chronic anovulation, and polycystic ovaries. PCOS is often accompanied by symptoms such as insulin resistance, abdominal obesity, and chronic inflammation. Adipose tissue is a crucial endocrine organ involved in metabolic disorders. Metabolic issues and chronic inflammation in PCOS are linked to dysfunctional adipose tissue. Mesenchymal progenitor cells (MPCs) are the precursor cells of adipocytes and can regulate the immune system. In this study, we used induced pluripotent stem cells (iPSCs) from patients with PCOS to derive MPCs and compare the transcriptome profiles between PCOS and HC iPSC-derived MPCs. We also challenged iPSC-derived MPCs with testosterone to assess the impact of androgen on MPCs. We found that 1026 genes differed between PCOS and HC iPSC-derived MPCs. Gene set enrichment analysis showed adipogenesis and metabolic function were reduced, but the inflammatory response was raised in PCOS iPSC-derived MPCs. The critical signals for early adipogenesis, including TGFβ, BMP, WNT, and CEBPA, differed between PCOS and HC iPSC-derived MPCs. After adipogenic induction, mature adipocytes were lower in PCOS iPSC-derived MPCs than HC. Lipolysis, the process involved in fat metabolism, was lower in adipocytes derived from PCOS MPCs than in HC. The testosterone treatment results indicated that genes related to oxidative phosphorylation and fatty acid metabolism were upregulated in HC iPSC-derived MPCs but downregulated in PCOS iPSC-derived MPCs. Short-term androgen stimulation may benefit body functions in HC. The impact of testosterone varied among individuals with HC and PCOS, possibly because of a genetic tendency towards PCOS. This study explains important factors that help us understand PCOS.

overall_design: To investigate the functional difference between iPSC-derived MPCs from PCOS and healthy control (HC), RNA-seq analysis was conducted on eight iPSC-derived MPCs, comprising four from individuals with PCOS and four from HC.

first: M


title: Macropahge-specific Irf3 prevents viral inflammation

city: Lexington

first: Saurabh

last: Chattopadhyay

state: KY

address: 760, Press Avenue

institute: University of Kentucky

summary: Viral inflammation contributes to pathogenesis and mortality during respiratory virus infections. We recently uncovered Irf3, a critical component of innate antiviral immune responses, interacts with pro-inflammatory transcription factor NF-kB, and inhibits its activity. Irf3, using this mechanism, suppresses inflammatory gene expression in virus-infected cells and mice. In this study, we evaluated the cells responsible for Irf3-mediated suppression of viral inflammation using newly engineered conditional Irf3Δ/Δ mice. Irf3Δ/Δ mice, upon respiratory virus infection, showed increased susceptibility and mortality. Irf3 deficiency caused enhanced inflammatory gene expression, lung inflammation, immunopathology, and damage, which were accompanied by increased infiltration of pro-inflammatory macrophages. Deletion of Irf3 in macrophages (Irf3-MKO) displayed, similar to Irf3Δ/Δ mice, increased inflammatory responses, macrophage infiltration, lung damage, and lethality, indicating Irf3 in these cells suppressed lung inflammation. RNA-seq analyses revealed enhanced NF-kB-dependent gene expression along with activation of inflammatory signaling pathways in infected Irf3MKO lungs. Targeted analyses revealed activated MAPK signaling in Irf3MKO lungs. Therefore, Irf3 inhibited inflammatory signaling pathways in myeloid cellsmacrophages to prevent viral inflammation and pathogenesis.

overall_design: To understand the role of Irf3 in macrophages in suppressing viral inflammation, we generated C57/BL6 mice with Irf3 knock out in macrophages. This was done by crossing Irf3 fl/Δ mice with LysM-Cre mice. The two groups -Irf3 fl/Δ and Irf3 fl/Δ Cre+ were then subjected to intransal inoculation of either PBS or Sendai virus (52 strain). The lung from these animals (n=3 per group) was harvested 5 days post infection, RNA was isolated and sent for gene expression analysis studies.


title: Gene expression of ERAP2 proficient and deficient patient-derived organoids post IFNg-stimulation

city: Trondheim

first: Atle

middle: van  Beelen

last: Granlund

address: Postboks 8905 MTFS

country: Norway

institute: Norwegian University of Science and Technology

summary: RNA-seq analysis of total RNA isolated from patient-derived organoids established from eight individuals. The organoids are genotyped with regards to rs2910686. The analysis aimed at characterizing the epithelial gene expression changes in ERAP2 proficient vs. ERAP2 deficient patient-derived organoids. ***Please note that raw data is not provided as Norwegian law does not allow public access to human sequences raw data

overall_design:
Organoids were estabished from patient biopsies from four ERAP2 proficient (rs2920686 CC/CT) and four ERAP2 deficient (rs2920686 TT) individuals. After organoid growth and differentiation,  they were stimulated with IFNg (24hours) in order to induce in inflammatory response and ERAP2 expressions. Each organoid culture was seeded in triplicates. For each experimental run two donors were used, and one ERAP2 proficient and deficient were grown in parallelle.

***************************************************************
Raw data could not be deposited due to Norwegian law. We will not deposit raw data in any other db.
***************************************************************

first: Siri

last: Sæterstad

first: Marianne

last: Doré Hansen

first: Ann

last: Østvik

first: Torunn

last: Bruland

last: vB Granlund


title: The origins of IgA-secreting cells in the acinar structures of the nasal turbinates [RNA-seq]

city: Rehovot

first: Jingjing

address: Herzl 234

country: Israel

institute: Weizmann Institute of Science

summary: Nasal vaccination elicits a humoral immune response that provides protection from airborne pathogens, yet the origins and specific immune niches of antigen-specific IgA-secreting cells in the upper airways remain unknown. Here, we define glandular acinus structures of the nasal turbinates as an immunological niche that recruits IgA-secreting plasma cells from the nasal-associated lymphoid tissues (NALT) in response to intranasal vaccination. Using intact organ imaging, we investigated the cellular events that support antibody-mediated immune responses in the mouse upper airways. Through visualization of antigen-specific T and B cells in the upperairways, we demonstrate that nasal vaccination induced extensive B cell expansion in the subepithelial dome (SED) of the NALT, followed by invasion into commensal bacteria-driven chronic germinal centers (GCs) in a T cell-dependent manner. Antigen-specific B cell response in the NALT required pre-expansion of cognate T cells, which initiate the immune response in the inter-follicular regions of the NALT, and occurred effectively in the presence of Monophosphoryl-Lipid A (MPLA), a synthetic, non-toxic TLR-4 agonist. NALT ablation and blockade of PSGL-1 demonstrated that intranasal vaccination generates IgA+ plasma cells that home to the nasal turbinates through the blood circulation where they are positioned primarily around glandular acinus structures. Thus, the glandular part of the nasal turbinate is an immunological niche that hosts NALT-derived IgA-secreting cells. These cellular events can be manipulated to design vaccines against inhaled pathogens or in the treatment of upper airway allergic responses.

overall_design: Mars-mRNA sequence of nasal turbinates. Turbinates were collected at 7 days post boost. Each group included five to ten NT biological replicates.  Treatments: naïve, prime, or PandB (prime and boost).

first: Liat

last: Stoler-Barak

first: Ziv

last: Shulman


title: Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells [RNA-seq]

city: Philadelphia

first: Robert

middle: Babak

last: Faryabi

state: Pennsylvania

address: Room 553 BRB II/III, 421 Curie Boulevard

institute: University of Pennsylvania

summary: Recent sequencing-based experiments mapping ensemble interaction frequency among regulatory elements in cancer cells support the existence of complex topological assemblies of enhancers and promoters known as promoter-enhancer hubs or cliques. Yet, the prevalence of promoter-enhancer hubs in individual cells, factors regulating their dynamics and assembly, as well as their role in transcriptional dysregulation in cancer remain unclear. Here, we systematically integrated functional genomics, transcription factor screening, and optical mapping of promoter-enhancer interactions to identify key promoter-enhancer hubs, examine heterogeneity of their assembly, determine their regulators, and elucidate their role in gene expression control in individual triple negative breast cancer (TNBC) cells. Optical mapping of individual SOX9 and MYC alleles revealed the existence of frequent multiway interactions among gene promoters and enhancers within promoter-enhancer hubs. Our single-allele studies further demonstrated that lineage-determining SOX9 and signaling-dependent NOTCH1 transcription factors compact MYC and SOX9 promoter-enhancer hubs, respectively. Together, our findings suggest that promoter-enhancer hubs are dynamic and heterogeneous topological assemblies controlled by oncogenic transcription factors potentially in a cancer subtype-restricted manner to facilitate aberrant gene expression.

overall_design: RNA-sequencing (RNA-seq) to elucidate SOX9 target genes in TNBC; MB157 stably expressing SOX9 were transfected with control sgRNA or sgRNA targeting SOX9 for four days and were subjected to FACS for top 50% sgRNA expressing cells

first: Yeqiao

last: Zhou


title: Intrauterine hyperglycemia during late gestation caused mitochondrial dysfunction in skeletal muscle of male offspring through CREB/PGC1A signaling

city: Hangzhou

first: Yishang

last: Yan

state: zhejiang

address: The Key Laboratory of Reproductive Genetics

institute: Zhejiang University

summary: Short-term intrauterine hyperglycaemia inhibited the growth and reduced the lean mass of male offspring, leading to decreased endurance exercise capacity. The myofiber composition of the tibialis anterior muscle of GDM male offspring became more glycolytic and less oxidative. The morphology and function of mitochondria in the skeletal muscle of GDM male offspring were destroyed. A total of 993 upregulated and 653 downregulated genes were identified via RNA-seq. The transcription of specific genes related to metabolic processes and mitochondria according to RNA-seq was mostly inhibited.

overall_design: We firstly observed the adverse mitochondrial structure and function in GDM adult male mice. To explore the effect of intrauterine hyperglycemia on foetal skeletal muscle, we ran RNA-sequence on limb muscle of foetal mice at embryonic day 18.5. Then, we performed the gene expression profiling analysis using data obtained from RNA-seq of skeletal muscle of CTR or GDM feotal mice.


title: Transcriptomic dissection of an appendicularian larva at single cell resolution

city: Bergen

first: Simon

last: Henriet

address: Thormøhlensgate 55

institute: University of Bergen

summary: Oikopleura dioica is a larvacean urochordate that has arisen as an emerging model due to its specific characteristics. Through single cell analysis, we have mapped the different cell populations that are present during its development, and instruct the formation of lineage-specific structures.

overall_design: O. dioica individuals (embryos and larvae) were dissociated at 10 time-points. Cells were isolated and analyzed using scRNA-seq recommendations from 10xGenomics

first: Anthony

last: Leon

first: David

last: Lagman

first: Daniel

last: Chourrout


title: Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells [ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin immynoprecipitation DNA-sequencing (ChIP-seq) to evaluate FLAG (Flag-dCas9-KRAB) colocalization and H3K27ac and H3K9me3 levels after inactivation of TNBC-restricted SOX9 enhancers; MB157 stably expressing Flag-tagged dCas9-KRAB were transfected with control sgRNA or sgRNA targeting SOX9.EC1, SOX9.EC2, and SOX9.EC3 for five days


title: Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells [CUT&RUN]

overall_design: Cut & Run to evaluate changes in enhancer activity H3K27ac after SOX9 knock-out (KO);   MB157 stably expressing Cas9 were transfected with control sgRNA or sgRNA targeting SOX9 for four days and were subjected to FACS for top 50% sgRNA expressing cells


title: Transcriptional profiling sheds light on the cellular and fibrotic aspects of idiopathic subglottic tracheal stenosis

city: Vienna

first: Martin

last: Direder

state: Vienna

address: Lazarettgasse 14

department: Orthopedic and Trauma Surgery

country: Austria

institute: Medical University Vienna

summary: Transcriptional analysis of idiopathic subglottic tracheal stenosis

overall_design: Single cell RNA-sequencing gene expression comparison of subglottic tracheal stenosis with healthy trachea. Single-cell suspension from all samples were prepared using MACS Milteny  Multi Tissue Dissociation Kit 1 (Miltenyi). Libraries were generated using Chromium Next GEM Single Cell 5´GEM, Library & Gel Bead Kit v5.2, Chromium Next GEM Chip K Single Cell Kit and Single Index Kit TT Set A (all 10x Genomics, Pleasanton, CA, USA).

first: Maria

last: Laggner

first: Dragan

last: Copic

first: Katharina

last: Klas

last: Bormann

first: Kontrad

last: Hoetzenecker

first: Hendrik

last: Jan Ankersmit

first: Michael

last: Mildner


title: Human platelet lysate enhances in vivo activity of CAR-Vδ2 T cells by reducing cellular senescence and apoptosis

city: Houston

first: Norihiro

last: Watanabe

state: Texas

address: 1102 Bates Ave

institute: Baylor College of Medicine

summary: Vγ9Vδ2 T cells are an attractive cell platform for the off-the-shelf cancer immunotherapy due to their lack of alloreactivity and inherent multi-pronged cytotoxicity, which could be further amplified with chimeric antigen receptors (CARs). In this study, we sought to enhance the in vivo longevity of CAR-Vδ2 T cells by modulating ex vivo manufacturing conditions and selecting an optimal CAR costimulatory domain. Specifically, we compared the anti-tumor activity of Vδ2 T cells expressing anti-CD19 CARs with costimulatory endodomains derived from CD28, 4-1BB or CD27 and generated in either standard fetal bovine serum (FBS)- or human platelet lysate (HPL)-supplemented medium. We found that HPL supported greater expansion of CAR-Vδ2 T cells with comparable in vitro cytotoxicity and cytokine secretion to FBS-expanded CAR-Vδ2 T cells. HPL-expanded CAR-Vδ2 T cells showed enhanced in vivo anti-tumor activity with longer T cell persistence compared to FBS counterparts, with 4-1BB costimulated CAR showing the greatest activity. Mechanistically, HPL-expanded CAR Vδ2 T cells exhibited reduced apoptosis and senescence transcriptional pathways compared to FBS-expanded CAR-Vδ2 T cells and increased telomerase activity. This study supports enhancement of therapeutic potency of CAR-Vδ2 T cells through a manufacturing improvement.

overall_design: To investigate the transcriptomic differences of CAR-Vδ2 T cells manufactured in FBS and HPL, we generated CD19.CAR(41BBz)-Vδ2 T cells in either FBS- or HPL-supplemented media from four donors.

first: Rong

last: Zheng

first: Chonghui

last: Cheng

first: Feiyan

last: Mo


title: Impact of immune repertoire in Muscle – Invasive Bladder Cancer (MIBC) on predicting response and survival after neoadjuvant cisplatin-based chemotherapy (NAC)

first: Daria

last: Kessler

state: California

address: 9139 Hargis St.

institute: Saint John's Health Center

summary: Purpose: Neoadjuvant cisplatin-based Chemotherapy (NAC) followed by cystectomy is the standard of care for patients with muscle-invasive bladder cancer (MIBC). Unfortunately, only a third of patients achieve pathologic complete response (pCR). The aim of this study is to deeply investigate the role played by peripheral immunogenicity and the Tumor and Immune Microenvironment (TIME) in patients undergoing NAC to identify predictive and pharmacodynamic biomarkers associated with treatment response or treatment resistance. Experimental design: N= 19 patients with MIBC received NAC and were classified as pCR (n=10) or non-pCR (n=9). Bulk RNA-seq was performed on 13 formalin-fixed paraffin-embedded (FFPE) tumor biopsies collected before treatment with NAC and immune protein evaluations using GeoMx Digital Spatial Profiling (DSP) technology were performed on matched FFPE tumor biopsies collected before and after treatment with NAC. Matching Peripheral blood collected prior treatment initiation and during cystectomy was assessed for lymphocytes and neutrophils counts. Kaplan–Meier analyses and Cox PH regression models were used for survival analyses (OS).    Results: Genes associated with immune signaling and DNA repair signaling correlated with treatment outcome of patients with MIBC undergoing NAC.  At baseline, gene expression analysis and digital special profile highlighted an abundance of B cells and a reduced neuroendocrine phenotype in the TME of pCR vs. no-pCR. Increased protein expression of immune checkpoints molecules (e.g. LAG3, ICOS, PD-L1) was also observed in the TME of patients with no-pCR.  In peripheral blood, a significant increase of lymphocytes and decrease of neutrophils counts, respectively, was observed in pCR vs no-pCR following NAC.  Conclusions: When confirmed on a larger cohort, our results might lead  to novel therapeutic strategies and to novel biomarkers predicting patients likely to respond to NAC.

overall_design: To identify preditive biomarkers associated with treatment response in MIBC patients undergoing NAC, we analyzed a set of 13 FFPE tumor biopsies collected before treatment with NAC from 8 pCR and 5 non-pCR MIBC patients, respectively, using whole gene expression profile. RNA was isolated from the tumor regions of  the FFPE specimens and subjected to whole gene expression profiling by RNA-seq.

first: Alberto

last: Mendoza-Valderrey

first: Jane

last: Choe

first: Douglas

last: Hanes

first: Xinmin

last: Li

first: Warren

last: Allen

first: Gianna

last: Jimenez

first: Jennifer

last: Linehan

first: Przemyslaw

last: Twardowski

last: Ascierto


title: Oncogenic transcription factors instruct promoter-enhancer hubs in individual triple negative breast cancer cells

first: Robert

last: Faryabi

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

overall_design: Refer to individual Series

first: Yeqiao

last: Zhou


title: Adult sex change leads to extensive forebrain reorganization in clownfish

city: Atlanta

first: Larry

last: Young

address: 954 Gatewood Rd NE

department: Department of Psychiatry

institute: Emory University

summary: Sex differences in the brain have been demonstrated in all major vertebrate lineages but are not well understood at a molecular and cellular level. Sex-changing fishes provide a unique opportunity to uncover mechanisms underlying sexual differentiation of the brain and regulation of sexual phenotypes. Sex change requires the complete transformation of the gonads and behaviors, which in turn require transformation of sexually-differentiated control mechanisms in the brain. However, detailed molecular and cellular profiling of sex differences in the brains of sex-changing fish is lacking. In this study we applied single nucleus RNA-sequencing (snRNA-seq) to generate the first atlas of sex differences in preoptic area (POA) and telencephalon of the model anemonefish Amphiprion ocellaris. We uncovered remarkably widespread sex differences in cell-type abundance and cell-type transcriptome.  The most prominent difference was observed in the dorsal medial telencephalon where females displayed more than twice as many glutamatergic neurons as males and more than 400 differentially expressed genes consistent with immature neuronal development in males relative to females.  These results provide an unparalleled level of depth to our understanding of sexual differentiation in the brain of a sex-changing fish, and richly characterizes numerous specific sexual dimorphisms that must develop during sex change.

overall_design: Single nuclei RNA sequencing was performed on nuclei isolated by Fluorescence-activated cell sorting (FACS) from the combined telencephalon and POA of Amphiprion ocellaris (common clownfish) males and females for comparison between the sexes (two replicates per sex, three individuals pooled per replicate).

first: Coltan

middle: G

last: Parker

first: Zachary

middle: V

last: Johnson

first: George

middle: W

last: Gruenhagen

first: Brianna

last: Hegarty

first: Abigail

last: Histed

first: Jeffrey

middle: T

last: Streelman

first: Justin

last: Rhodes


title: RNA 5-methylcytosine marks mitochondrial double-stranded RNAs for degradation and cytosolic release

city: Daejeon

first: Sujin

last: Kim

address: 291, Daehak-ro

department: Chemical and Biomolecular Engineering

country: South Korea

institute: KAIST

summary: Mitochondria are essential regulators of innate immunity. They generate long double-stranded RNAs (mt-dsRNAs) and release them to the cytosol to trigger immune response under pathological stress conditions. Yet, the regulation of these self-immunogenic RNAs remains largely unknown. Here, we employ CRISPR screening on RNA-binding proteins residing in mitochondria and identify NOP2/Sun RNA methyltransferase 4 (NSUN4) as a key regulator of mt-dsRNA expression. We find that NSUN4 induces 5-methylcytosine (m5C) modification on mitochondrial RNAs, especially on the termini of light-strand long noncoding RNAs. These m5C-modified RNAs are recognized by complement C1q binding protein (C1QBP), which recruits polyribonucleotide nucleotidyltransferase to facilitate RNA turnover. Suppression of NSUN4 or C1QBP results in increased mt-dsRNA expression while C1QBP deficiency also leads to increased cytosolic mt-dsRNAs and subsequent immune activation. Collectively, our study unveils the mechanism underlying the selective degradation of light-strand mitochondrial RNAs and establishes a molecular mark for mitochondrial RNA decay and cytosolic release.

overall_design: RNA Bisulfite-seq following NSUN4, C1QBP or PNPT1 downregulation in HEK-293T cells.

first: Stephanie

last: Tan

first: Yoosik


title: Circular RNA vectors encapsulated in lipid nanoparticles for sustained protein replacement therapy in the retina

city: Guangzhou

first: Cheng

last: Wu

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

institute: Sun Yat-sen University

summary: Circular RNAs (circRNAs) have recently emerged as promising vectors for sustained therapeutic protein production due to their enhanced stability from exonuclease degradation. Here, we engineered circRNAs expressing reporters and neurotrophic factors, and systematically compared their expression kinetics to conventional linear mRNAs. CircRNAs achieved 10-20 fold higher and more persistent protein expression in vitro over several weeks. We further demonstrated that circRNA-expressed nerve growth factor (NGF) provided lasting neuroprotection in a neuronal injury model compared to short-lived effects from NGF protein delivery. A major challenge for clinical translation of circRNAs is efficient intracellular delivery. We address this issue through lipid nanoparticle (LNP) encapsulation technology.  LNPs successfully delivered circRNAs to retina after intravitreal or subretinal injection in mice, achieving localized and prolonged expression. As proof-of-concept, LNP-formulated circRNA expressing NGF promoted retinal ganglion cell survival in a mouse optic nerve crush injury model, demonstrating advantages over NGF protein injections. Collectively, this work establishes circRNA vectors as promising candidates for safe, sustained therapeutic protein production, and elucidates a delivery platform to overcome translational barriers. Realization of this technology may enable transformative treatments for chronic neurodegenerative protein deficiency diseases.

overall_design: Single cells from six independent mouse retina samples were captured in ？batches (CTR1，CTR2, ONC1, ONC2, ONC_NGF1, ONC_NGF2) using the 10X Chromium system.

first: Zhi

last: Xie

first: Wenbing

last: Jiang

first: Jiaqi

last: Yang


title: Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [ChIP-seq]

city: Chikusa-ku

first: Hitoshi

last: Ohtani

state: Nagoya

address: Furo-cho

department: Graduate School of Bioagricultural Sciences

country: Japan

institute: Nagoya University

summary: Long terminal repeats (LTRs), which comprise promoter and enhancer region of intact endogenous retroviruses (ERVs), are known to be co-opted for fine-tuning host-coding gene expression as cis-regulatory elements. Since LTRs are mainly silenced by the deposition of repressive epigenetic marks, a substantial activation of LTRs have been found in human cells after treatment with epigenetic inhibitors. Although LTR12C family had highest relative abundance of transcripts among the de-repressed ERV families, functional consequences of the activated LTR12C for host-coding genes remain uncover due to genome-wide alteration of epigenetic landscape resulting in broad transcriptional changes after the epigenetic inhibitor treatments. Here, we transactivated more than 600 LTR12C elements by using single guide RNA-based dCas9-Suntag-VP64, which is a kind of the site-specific targeting technology CRISPR activation system, with minimal off-target events. Interestingly, most of transactivated LTR12C elements acquired H3K27ac-marked enhancer feature, while 20% of them along with enrichment of H3K4me3-marked promoter feature. The enrichment of H3K4me3 signal was likely brought about by downstream regions of LTR12C, such as internal regions of intact ERV9 or other type of retrotransposons.

overall_design: To investigate hitone modification changes in HEK293T after CRISPRa, we performed ChIP-seq.

first: Gangning

last: Liang

first: Peter

last: Jones


title: Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [RNA-seq]

overall_design: To investigate LTR expression level in HEK293T, A2780, MCF7, and HCT116 after CRISPRa or 5-Aza-CdR treatment, we performed total RNA-seq.


title: Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer


title: Single-cell Transcriptome Landscape and Cell Fate Decoding in Human Brain Organoids after Transplantation

city: Nanjing

first: Yan

last: Liu

state: Jiangsu

address: 101Longmian Avenue, Jiangning District

department: School of Pharmacy

institute: Nanjing Medical University

summary: Human stem cells and derivatives have been widely used to treat neurological diseases, and the fate of transplantation cells has not been well clarified. In order to explore the changes in fate of the human brain organs (HBOs) before and after transplantation, we transplanted HBOs into the prefrontal cortex (PFC) and hippocampus (HIP), respectively. Then we performed single-cell transcriptome sequencing. We obtained a total of 5 samples: before transplantation (group D0) and four groups of samples after transplantation (group HIP-2MPT, PFC-2MPT,HIP-4MPT,and PFC-4MPT). Our studies have shown that after transplantation, HBO has accepted the regulation of host's factors, which leads to the similarity of HBOS cell fate to the brain area of transplantation. It may help better understand cell transplantation and regeneration medicine.

overall_design: For scRNA-seq, 1 sample D0 , 2 samples 2MPT(PFC and HIP) and 2 samples 4MPT (PFC and HIP);

first: Shibo

last: Xu


title: Black Soldier Fly larvae (Hermetia illucens) meal is a viable protein source for Atlantic salmon (Salmo salar) during a large-scale controlled field trial  under commercial-like conditions

city: Ås

first: Linn

middle: Haug

last: Eide

address: Oluf Thesens vei 6

institute: Norwegian University of Life Sciences

summary: Black soldier fly larvae meal (BSFL) from Hermetia illucens is a promising alternative protein source in diets for farmed fish. The larvae can efficiently convert low-value organic material into high quality protein in a production cycle with low arable land and freshwater inputs. A few recent studies have shown that BSFL is a suitable protein source for Atlantic salmon (Salmo salar) in smaller controlled experiments. However, industry-relevant field trials conducted under large scale near-commercial conditions over a longer period are lacking. In this study, a feeding trial was performed to evaluate the impact of BSFL on growth performance and health of Atlantic salmon during the grow out phase in seawater, in a commercial site in Vestland county, Norway. A total of 320,000 post-smolt Atlantic salmon were distributed into six duplicate sea cages and fed one of three diets (commercial-like control diet and two test diets partially replacing the protein content of the control diet with 4 % and 8 % defatted BSFL meal) for 21 weeks, until a relevant commercial slaughter size of 4.5-5.0 kg was reached.  Health parameters were assessed including histology of the distal intestine (DI), in addition to DI microbiota identification (by 16s rRNA-seq) and salmon RNA-seq of DI and head kidney (HK). The results showed that the inclusion of BSFL meal supported growth performance and had no adverse effect on gut health. The beta diversity of the distal intestine microbiota and the relative abundance of families Lactobacillaceae and the chitinolytic Bacillaceae increased in the fish fed the BSFL diets. Additionally, no histopathological changes were attributable to BSFL meal intake. Results from RNA-seq in DI revealed that BSFL inclusion modulates metabolic processes associated with lipids, the response to estrogens, the activity of immune receptors (to chemokines), phagocytosis and extracellular vesicles. Based on these results, black soldier fly larvae meal is a suitable alternative protein ingredient in inclusions of up to at least 8 % for Atlantic salmon under industrial fish farming conditions.

overall_design: To investigate if increasing inclusion of black soldier fly larvae meal (0 %, 4 % and 8 %) in the diets for farmed Atlantic salmon has an impact on gene expression in the distal intestine and head kidney. We performed gene expression profiling analysis using data obtained from 10 fish per dietary group.

last: Haug Eide

first: Byron

last: Morales-Lange


title: Single-cell RNA-sequencing reveals the role of p300/CBP in calcium handing ability of prepubertal RV cardiomyocytes.

city: Shanghai

first: Yingying

last: Xiao

address: No.355, Luding Road

institute: Shanghai Children’s Hospital, School of Medicine, Shanghai Jiaotong University

summary: The expression of genes is determined by the openness and accessibility of chromatin, which is the most basic phenomenon in the field of life sciences.The histone acetylase p300/CBP (CBP and P300 have similar structures and functions) can catalyze the acetylation of the lysine at the 27th position of histone H3(H3K27ac), which changes the the openness and accessibility of chromatin. Thus, p300/CBP are considered to be two of the most important transcription co-factors. To further understanding the role of p300/CBP in regulating calcium handing of prepubertal RV CMs, we first detected its expression in the prepubertal RV.The expressions of p300/CBP in the prepubertal dysfunctional RV were significantly downregulated, consistent with the data of p300-ChIP-seq, which showing the loss of p300 chromatin occupancy in calcium handing genes. Then we knocked out p300/CBP in neonatal mouse. p300/CBP knockout cardiomyocytes showed a impaired calcium handing ability, similar to that in prepubertal dysfunctional RV cardiomyocytes. These results confirmed the role of p300 in regulating the calcium handing ability of prepubertal RV CMs.

overall_design: We used C57/BL6J mice in this study and knocked out p300/CBP in neonatal mouse. The right ventricular tissue of mouse pups on postnatal day 21 were collected for ScRNA-seq analysis.

first: Haifa

last: Hong

first: Lincai

last: Ye


title: The transcriptome of golden hamster

city: Zhengzhou

first: Ying

last: Peng

address: No.1 Jianshe East Road, Erqi District, Zhengzhou City, Henan Province

institute: ；The First Affiliated Hospital of Zhengzhou University

summary: Cumulative research demonstrated that heart muscles in the dilated cardiomyopathy (DCM) patients are marked by down-regulated expression of α-myosin heavy chain (α-MHC) coding by MYH6 while it remains unknown whether this reduction contributes to DCM. In our work, we proved that the expression level of α-MHC was decreased in the heart of DCM patients compared to that of non-failure donors. We established two Myh6 down-expressed Syrian Hamster models: one with α-MHC deficiency across all systems, the other with α-MHC knockdown specifically in the heart by using adeno-associatedvirus (AAV).  Besides the animal models, we also programmed MYH6 knockout human-induced pluripotent stem cells (hiPSCs) which differentiated later into cardiomyocytes (hiPS-CMs) in vitro. We found α-MHC deficiency in vivo or in vitro both resulted in DCM phenotypes, meanwhile we demonstrated α-MHC deficiency is a causative factor of DCM. We also proved that the DCM-associated α-MHC deficiency was mediated by the autophagy flux. At the same time, the DCM phenotypes were attenuated by rapamycin, an autophagy activator, and exacerbated by inhibiting autophagic activities. Transcriptomic and proteomics results revealed that cardiomyocytes with α-MHC deficiency apparently exhibited actin cytoskeleton dysfunction. Our data demonstrated that α-MHC deficiency influenced the actin cytoskeleton network to regulate the autophagy activity suggesting that overexpress α-MHC or regulating autophagy would be a promising therapeutic candidate for DCM.

overall_design: WT and Myh6 loss of heterozygosity (LOH) femal hamsters were sacrificed at 25w before the DCM onset, and the hearts were performed for RNAseq analysis.

first: Yafei

last: Zhai

first: Jinxin

last: Miao

first: Yaohe

last: Wang

first: Jianzeng

last: Dong


title: Dilated Cardiomyopathy

sample_organism:
Homo sapiens
Mesocricetus auratus
Mus musculus


title: Circular RNA circASH1L protects miRNA-129-5p from target-directed microRNA degradation in human skin wound healing [miR129 overexpression]

city: Chengdu

first: Qizhang

address: No. 14, Section 3rd, Renmin Nan Road. Chengdu, Sichuan 610041, China

institute: Department of Oral and Maxillofacial Surgery, West China Hospital of Stomatology,

summary:
In an RNAseq analysis, we have identified the microRNA hsa-miR-129-5p with high levels in acute wounds (day1 to day7) compared to normal skin.
The biological function of this miRNA in human epidermal keratinocytes during wound repair has not been studied.
To study the genes regulated by miR-129-5p , we transfected miR-mimics targeting miR-129-5p into human primary epidermal keratinocytes to over-express miR-129-5p expression.
We performed a global transcriptome analysis of keratinocytes upon miRNA overexpression using Affymetrix arrays.

overall_design: Gene expression profiling of keratinocytes transfected with either mimics control (n = 3) or miR-129-5p mimics (n =3) for 24 hours was carried out by using human Clariom™ S assay (ThermoFisher Scientific) at the Bioinformatics and Expression Analysis (BEA) core facility at Karolinska Institutet.

first: Ning

middle: X

last: Landén

first: Zhuang


title: Genome-wide tongue epithelia transcriptomic profiles from K14-rtTA;TRE-FLBmi-1 (KrTB) and KrTB+Doxycycline (KrTB+DOX).

city: New York City

first: Jorge

last: Baquero

state: NY

address: 1300 York Avenue

department: Pharmacology

institute: Weill Cornell Medical College

summary: We developed a transgenic mouse model (truncated K14-rtTA; TRE/Bmi1, KrTB) containing a doxycycline- (dox) controlled, Tet-responsive element system to selectively overexpress Bmi1 only in the basal epithelial SCs of the tongue. Here, we used this model to assess Bmi1 actions in tongue epithelia. Genome-wide transcriptomics revealed increased levels of transcripts involved in the cellular response to hypoxia in Bmi1-overexpressing (KrTB+DOX) mice.

overall_design: Examination of genome-wide transcript levels in mouse tongue epithelia samples. 8 samples were analyzed, 4 biological replicates per condition (KrTB vs. KrTB+DOX

first: Xiao-Han

last: Tang

first: Annalisa

last: Ferrota

first: Tuo

last: Zhang

first: Krysta

last: DiKun

first: Lorraine

last: Gudas


title: Investigating the role of ERBB2 during colorectal cancer in the ApcMin/+ mouse model

city: College. Station

first: David

last: Threadgill

address: 400 Bizzell St

department: Cell Biology and Genetics

institute: Texas A&M University

summary: The ERBB family consists of four receptors (EGFR, ERBB2, ERBB3, and ERBB4) that are critical in normal development and physiology of mammalian gastrointestinal epithelial tissues. Amplifications or mutations in ERBB2 are commonly found in CRC, suggesting a possible therapeutic target. Patients with ERBB2-amplification in breast and gastroesophageal cancer are routinely treated with the ERBB2-directed antibody trastuzumab. However, ERBB2 is not commonly targeted in clinical practice of treating CRC. Notably, ERBB2 status could guide therapy as a negative marker for EGFR-targeted therapy (cetuximab) and identify likely responders for ERBB2-directed therapy. Although the most common marker for negative efficacy of anti-EGFR therapy is KRAS mutations, many patients with KRAS wild-type tumors do not respond to EGFR inhibition. As the primary EGFR-directed antibodies for CRC do not inhibit ERBB2, alterations increasing ERBB2 may serve as a superior negative predictor of EGFR therapy since previous studies demonstrate that ERBB2 amplification confers resistance to cetuximab in preclinical models. Despite the compelling evidence, the utility of ERBB2 as a target for molecular therapy of primary CRC tumors in preclinical models is largely unexplored. As such, our goal is to further characterize the influece of ERBB2 in the initiation and progression of CRC.

overall_design: To investigate the role of ERBB2 in colorectal cancer progression in the ApcMin/+ mouse model, we utilized a transgene expressing cre recombinase under the control of the intestinal epithelial-cell specific promoter, Villin [Tg(Vil1-cre)], to recombine the conditional Erbb2tm1Mll (Erbb2f) allele. Colorectal tumors and adjacent normal tissue were harvested from 100 day-old conditional Erbb2-deficient C57BL/6J [ApcMin/+, Erbb2f/f, Tg(Vil1-cre)] and littermate control (ApcMin/+, Erbb2f/f) mice. Five replicates from each group were analyzed.

first: Michael

middle: P

last: McGill


title: The transcriptome of humans

overall_design: WT and Myh6 knock out (KO) hiPS-CMs at D30 were performed for RNAseq analysis.

first: Jianchao

first: Xiaowei

last: Li

first: Xiaoyan

last: Zhao


title: Endogenous retrovirus LTR12C hold potential locus-dependent activities as promoter and/or enhancer [BiSulfite-seq]

first: Hitoshi

last: Ohtani

overall_design: To investigate DNA methylation changes in HEK293T after CRISPRa, we performed WGBS.

first: Gangning

last: Liang

first: Peter

last: Jones


title: The transcriptome of mouse

first: Ying

last: Peng

overall_design: WT male mice at 12W were sacrificed,and the hearts were performed for RNAseq analysis.

first: Yafei

last: Zhai

first: Jianzeng


title: The combination of agrin, BRP44, and insulin (ABI) promote human CM proliferation

first: Yingying

last: Xiao

summary: Human cardiomyocytes (CMs) differ from those of rodents in many aspects, and methods that effectively improve cardiac performance in rodents have been unsuccessful in humans, indicating a translational gap between humans and rodents in cardiac regeneration. The CM proliferation transition between the neonatal and adult stages is well-established in humans and rodents. The aim of the study is to analyze human atrial CM proliferation-transition for narrowing down the translational gap between humans and rodents in cardiac regeneration.At first we extracted decellularized samples (DS) from human atrial specimens collected during routine congenital cardiac surgery from children diagnosed with ventricular septal defect (VSD). The DS was next used for cell culture and proteomic analyses. The proteins (such as Agrin, BRP44, and insulin) identified in the proteomic analysis were further verified by testing their ability to promote CM proliferation. The results showed that the combination of agrin, BRP44, and insulin (ABI) enhanced the effect of agrin.To further confirmed the role of ABI on human CM proliferation, we performed RNA-seq on the ABI-treated HiPSC-CMs. The results showed that ABI induced abundant enrichment of cell-cycle associated genes, which highlighting the synergy of hormones and anti-oxidation/metabolism in human CM proliferation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for human induced pluripotent stem cell–derived cardiomyocytes (HiPSC-CMs) cultured for 7 days with ddH2O 1: 1000 diluted in medium or ABI (Agrin (100 ng/mL), BRP44 (1 ng/mL), and insulin (10μg/mL)) diluted in medium

first: Lincai

last: Ye

first: Haifa

last: Hong


title: Assessment of ‘molecular organ age’ in pre-transplant kidney biopsies

city: Cambridge

first: Roy

address: Cambridge Biomedical Campus, Francis Crick Ave

institute: MRC Laboratory of Molecular Biology

summary: Clinical kidney biopsies variably contain cortex and medulla depending on biopsy depth and angle. Therefore, biopsy composition may alter the transcriptional profile and confound conclusions drawn from differential gene expression analysis. To account for this in retrieval biopsies, we assessed differences in gene expression between paired cortex and medulla samples in n=5 human kidneys.

overall_design: Comparative gene expression profiling analysis of RNA-seq data kidney biopsies taken from cortex and medulla

first: Patrick

last: Trotter

first: James

last: McCaffrey

first: Benjamin

last: Stewart

first: John

middle: R

last: Ferdinand

first: Kevin

last: Loudon

first: Alexandra

last: Riding

first: Jonathan

last: West

first: Ashley

last: Ferro

first: Robert

last: Kirkpatrick

first: Menna

last: Clatworthy


title: Lithocarpus edulis transcriptome project

city: Fukuoka

first: Akiko

last: Satake

address: Motooka 744

institute: Kyushu University

summary: In the family Fagaceae, fertilization is delayed by several weeks to more than one year after pollination, leading to one- or two-year fruiting species depending on whether fruiting occurs in the same or the next year of flowering. Although delayed fertilization was recorded over a century ago, underlying mechanisms remain to be explored. To uncover the key genes associated with delayed fertilization, we obtain and analyze the comparative molecular phenology data over two years in one-year (Quercus glauca) and two-year fruiting species (Lithocarpus edulis).

overall_design: Lead and bud samples were collected from May 2017 to February 2019 from Lithocarpus edulis (Le). Samples were collected from three individuals. Sample title indicates "year_month and day_individual ID".

first: Kayoko

last: Ohta

first: Noriko

last: Takeda-Kamiya

first: Kiminori

last: Toyooka

first: Junko

last: Kusumi


title: Deubiquitinase OTUB1 regulates doxorubicin-induced cardiotoxicity

first: Fei

last: Xu

state: Shanghai

address: 1609 Xietu Road

institute: Zhongshan Hospital, Fudan University

summary: Wild-type (WT) and Otub1-heterozygously knock-out mice were applied in the study. Doxorubicin (DOX)-induced subacute cardiotoxicity mouse model was established by 6 intraperitoneal injections during a 2-week period. The differentially expressed genes were analyzed by RNA-sequencing and clustering analyses.

overall_design: Three wild-type (WT) and 3 Otub1-heterozygously knock-out (Het) mice were injected with DOX for 6 times in 2 weeks.

first: Tongtong

last: Zang

first: Li

last: Shen


title: Quercus glauca transcriptome project

overall_design: Lead and bud samples were collected from May 2017 to February 2019 from Quercus glauca (Qg). Samples were collected from three individuals. Sample title indicates "year_month and day_individual ID".


title: Fagaceae transcriptome project

sample_organism:
Quercus glauca
Lithocarpus edulis

platform_organism:
Quercus glauca
Lithocarpus edulis

overall_design: Refer to individual Series


title: Pre transplantation Kidney Biopsies

middle: Robert

address: Department of Medicine

institute: University of Cambridge

summary: RNA seq of kidney biopsies taken at time of retrivial.

overall_design: Biopsies taken at time of Human Kidney organ retrevial from mutiple individules. The Kidenys were then transplanted. Biopsies were then librarypreped and sequence for combined analysis.

first: Roy


title: METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (nascent tRNA)

first: Xiaoyang

last: Dou

address: 320 Yue Yang Road

institute: CAS Center for Excellence in Molecular Cell Science, CAS

summary: METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m6A methyltransferase complex (MTC, also known as m6A writer) that installs m6A. Surprisingly, depletion of METTL3 or METTL14 displayed distinct effects on mouse embryonic stem cell (mESC) self-renewal. While comparable global hypo-methylation in RNA m6A was observed in Mettl3 or Mettl14 knockout mESCs, respectively. Mettl14 knockout led to a globally decreased nascent RNA synthesis, whereas Mettl3 depletion resulted in transcription upregulation, suggesting that METTL14 might possess an m6A-indenepent role in gene regulation. We found that METTL14 colocalizes with the repressive H3K27me3 modification and PRC2 complex. Mechanically, METTL14, but not METTL3, recognizes H3K27me3 and recruits KDM6B to induce H3K27me3 demethylation independent of METTL3. Depletion of METTL14 thus led to a global increase in H3K27me3 level along with a global gene suppression  . The regulation of H3K27me3 by METTL14 is essential to the transition of mESCs from self-renewal to differentiation. This work reveals a regulation mechanism on heterochromatin by METTL14 in a manner distinct from METTL3 and independently of m6A, and critically impacts transcriptional regulation, stemness maintenance and differentiation of mESCs.

overall_design: Examination of transcription rate changes upon Mettl14 knockout in mESCs

first: Chuan

last: He

first: Jun

last: Liu


title: METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (mRNA)

overall_design: Examination of H3K27me3 methytransferase inhibitor effects on gene expression changes regulated by Mettl14 knockout

first: Lulu

last: Huang


title: METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (nuclear RNA)

overall_design: Examination of nuclear RNA expression changes upon Mettl3 and Mettl14 knockout in mESCs.


title: METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (m6A MeRIP-Seq)

summary: METTL3 and METTL14 are two components that form the core heterodimer of the main RNA m6A methyltransferase complex (MTC, also known as m6A writer) that installs m6A. Surprisingly, depletion of METTL3 or METTL14 displayed distinct effects on mouse embryonic stem cell (mESC) self-renewal. While comparable global hypo-methylation in RNA m6A was observed in Mettl3 or Mettl14 knockout mESCs, respectively. Mettl14 knockout led to a globally decreased nascent RNA synthesis, whereas Mettl3 depletion resulted in transcription upregulation, suggesting that METTL14 might possess an m6A-indenepent role in gene regulation. We found that METTL14 colocalizes with the repressive H3K27me3 modification and PRC2 complex. Mechanically, METTL14, but not METTL3, recognizes H3K27me3 and recruits KDM6B to induce H3K27me3 demethylation independent of METTL3. Depletion of METTL14 thus led to a global increase in H3K27me3 level along with a global gene suppression  . The regulation of H3K27me3 by METTL14 is essential to the transition of mESCs from self-renewal to differentiation. This work reveals a regulation mechanism on heterochromatin by METTL14 in a manner distinct from METTL3 and independently of m6A, and critically impacts transcriptional regulation, stemness maintenance and differentiation of mESCs.

overall_design: Examination of m6A level changes in Mettl3 and Mettl14 knockout and their respective control mESCs


title: Circular RNA circASH1L protects miRNA-129-5p from target-directed microRNA degradation in human skin wound healing [circASH1L knockdown]

first: Qizhang

last: Wang

summary:
In an RNAseq analysis, we have identified the circular RNA cASH1L with high levels in acute wounds (day1 to day7) compared to normal skin.
The biological function of cASH1L in human epidermal keratinocytes during wound repair has not been studied.
To study the genes regulated by cASH1L, we transfected siRNA targeting the diagnostic junctions of cASH1L into human primary epidermal keratinocytes to knockdown cASH1L expression.
We performed a global transcriptome analysis of keratinocytes upon circRNA knockdown using Affymetrix arrays.

overall_design: Gene expression profiling of keratinocytes transfected with either siRNA control (n = 3) or si-cASH1L (n =3) for 24 hours was carried out by using human Clariom™ S assay (ThermoFisher Scientific) at the Bioinformatics and Expression Analysis (BEA) core facility at Karolinska Institutet.

first: Ning

last: Landén

first: Zhuang


title: METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (ChIP-Seq)

overall_design: Examination of different histone modifications changes upon Mettl14 and Mettl3 knockout in mESCs


title: Gene expression profiling of corneal and limbal epithelial cells in young and aged mice

status: Public on Aug 15 2024

city: Kensington

first: Alexander

last: Richardson

state: NSW

address: Crn Botany and High St

country: Australia

institute: UNSW Sydney

summary: Using the K14CreERT2-Confetti transgenic mouse, we analyzed differential gene expression between Confetti+ and Confetti- cells  in an attempt to uncover novel limbal epithelial stem cell markers

overall_design:
Confetti+ and Confetti- cells were isolated from the corneal epithelium of 6, 18 and 60-week-old mice, then sorted into 96-well plates and analyzed using scRNA sequencing.
Please note that the raw data R2 mate file for the 'Corneolimbal, 60 week old, Confetti- 9' sample is corrupted and thus only R1 file is included as raw data.

first: Susan

last: Corley

first: Naomi

last: Delic

first: Hui

last: Li

first: Andrew

last: Lloyd

first: Nick

last: Di Girolamo


title: METTL14 is a chromatin regulator independent of RNA N6-methyladenosine (CUT & RUN)

overall_design: Examination of METTL3 and METTL14 genomic bindings in mESCs


title: Gene expression profile at single cell level of PBMC from HFD/STZ-induced type 2 diabetic mice

city: Huzhou

first: Yunliang

last: Yao

state: Zhejiang

address: 759 East Second Ring Road

department: Medical School

institute: Huzhou University

summary: T2DM patients are believed to have long-term chronic inflammation. We used single cell RNA sequencing (scRNA-seq) to analyze the diversity  of immune cell in peripheral blood mononuclear cells （PBMC）from  HFD/STZ-induced type 2 diabetic mice

overall_design: PBMCs of  from  T2D modeld or healthy control mice were separated by Ficoll gradient centrifugation and analyzed using scRNAseq.

first: Yang

first: Lixia

last: Huo


title: ZMAT1 promotes osteoclast formation and bone loss through TRIM46 mediated YAP1 degradation. [CUT&Tag]

first: Yijin

last: Hou

address: No. 168, Changhai Road

institute: Department of Traumatic Orthopedics, Changhai Hospital, Naval Medical University

summary: Osteoclasts and osteoblasts play a critical role in bone remodeling, and their dysregulation leads to pathological bone loss. However, precise regulation of their differentiation remains not fully elucidated. This study investigates the role of transcriptional regulator Zinc Finger Matrin-Type 1 (Zmat1) in both osteoclastogenesis and osteoblastogenesis. Zmat1 deficiency resulted in decreased osteoclast activity, and reduced bone resorption. Mechanististically, ZMAT1 was significantly upregulated during osteoclast differentiation and acted as a transcriptional repressor of the E3 ubiquitin ligase TRIM46, which then regulates YAP1 degradation via K48-linked ubiquitination. Furthermore, Zmat1 deficiency also enhanced osteoblast activity and bone formation. These findings highlight a novel ZMAT1/TRIM46/YAP1 axis, providing new insights into the transcriptional regulation of both osteoclast and osteoblast differentiation, and present potential therapeutic targets for osteoporosis.

overall_design: There are no relevant reports on the role of Zmat1 as a transcription factor in osteoclast differentiation. To clarify the role of Zmat1 as a transcription factor in osteoclastogenesis, we constructed a Zmat1-overexpressing RAW264.7 cell line and set up a control group. Under RANKL stimulation, cells were collected, incubated with antibodies, and DNA was extracted. The DNA was then sequenced using Second Generation high-throughput sequencing technology. The results indicated that Zmat1 plays a regulatory role in gene transcription one sample were set up for each group.

first: Xinyu

last: Chang


title: Beta,Beta-Dimethylacryloyl shikonin, mechanism of preventing and treating zebrafish soybean meal enteritis

city: Qinzhou City

first: Xin

last: Lu

address: 12 Binhai Avenue, Qinnan District, Qinzhou City, Guangxi, China

institute: Beibu Gulf University

summary: The aim of this study is to explore through transcriptomics, β, β Dimethylacryloyl shikonin, mechanism for preventing and treating in zebrafish.

overall_design: We set up the FM group, the SBM group, andthe  D3 group, with 3 replicates in each group. A total of 9 groups were obtained from RNA seq data for gene expression profiling analysis.

first: Xiao

last: Cai

first: Yingrui

last: Wu

first: Yinhui

last: Peng

first: Qingfang

last: Gong


title: Transcriptome profiling of cell lines from Ixodes scapularis

city: Boston

first: Yanhui

last: Hu

state: MA

address: 77 Avenue Louis Pasteur

department: Genetics

institute: Harvard Medical School

summary: The goal of this study was to identify and compare baseline mRNA expression levels for a set of Ixodes scapularis cell lines originally reported in Munderloh et al. 1994 Journal of Parasitology 80(4):533-43. Three unmodified I. scapularis cell lines were included in the study:  ISE6, IDE2, and ISE18. In addition, one cell population modified by insertion of a transgenic cassette using Sleeping Beauty transposition was also included:  ISE18SB. The ISE18SB cells are a non-clonal cell population fully enriched for expression of a DsRed fluorescent marker gene included within the transposon insertion cassette. For all replicate samples, cells were collected after reaching approximately 60% confluency under standard culture conditions, then processed for RNA-seq analysis.

overall_design: Cells were cultured in airtight-capped flasks at 34 degrees C in a normoxic cell culture incubator in standard I. scapularis cell line media (Munderloh and Kurtii 1989 Experimental & Applied Acarology, 7:219-229) made in-house in our laboratory. For all replicate samples, cells were collected after reaching approximately 60% confluency (i.e., at Day 4 after seeding to fresh media). Approximately 5.5 x 10^6 cells per replicate sample were collected and processed for bulk RNA-seq analysis. All replicates were collected and processed together. RNA was extracted using Trizol and Zymo Research Direct-zol RNA Miniprep Kits. RNA was analyzed at the Biopolymers Facility at Harvard Medical School using an Agilent TapeStation as a quality control step. RIN analysis was not possible given the species; however, for all samples, the results of electrophoretic analysis profiles and quantitative PCR (qPCR) were consistent with high-quality RNA. KAPA mRNA HyperPrep Kits were used to build poly-A selected mRNA libraries. NGS was performed using an Illumina NovaSeq 6000 sequencing system with an SP flow cell. Reads were mapped to I. scapularis reference genome GCF_016920785.2 using STAR version 2.7.9a. Gene count extraction was done using FeatureCounts version 2.0.1. Normalization and conversion to FPKM values were performed using DEseq2 version 1.40.2.

first: Matthew

last: Butnaru

first: Weihang

last: Chen

first: Srishti

last: Goswami

first: Norbert

last: Perrimon

first: Stephanie

last: Mohr


title: ZMAT1 promotes osteoclast formation and bone loss through TRIM46 mediated YAP1 degradation.

overall_design: Extract bone marrow-derived mononuclear macrophages from wild-type C57BL/6 mice and stimulate with M-CSF for 3 days. Set up control groups: Control_1, Control_2, Control_3. The experimental groups are set up as follows: stimulate with LPS for 3 days: LPS_3d_1, LPS_3d_2, LPS_3d_3; stimulate with LPS for 4 hours: LPS_4h_1, LPS_4h_2, LPS_4h_3; stimulate with RANKL for 3 days: RANKL_3d_1, RANKL_3d_2, RANKL_3d_3; stimulate with RANKL for 4 hours: RANKL_4h_1, RANKL_4h_2, RANKL_4h_3.


title: LncRNA LOC730101 promotes darolutamide resistance in prostate cancer by suppressing miR-1-3p [RNA-Seq]

city: Houston

first: Tianyi

last: Zhou

state: TX

address: 3517 Cullen Blvd

department: Biology and Biochemistry

institute: University of Houston

summary: This study investigates the role of noncoding RNAs in resistance to the anti-androgen drug daro-lutamide in prostate cancer. RNA sequencing identified LOC730101 as a significantly elevated lncRNA in darolutamide-resistant cells. Silencing LOC730101 reduced cell proliferation, indicating its role in drug resistance.

overall_design: To investigate the lncRNA function in DaroR resistant cells

first: Steven

last: Nguyen

first: Jacky

first: Bin

last: He

first: Qin

last: Feng


title: Profiling IgG and IgA antibody responses during vaccination and infection in a population at high risk of gonorrhoea

city: Manchester

first: Fidel

last: Ramirez Bencomo

state: England

address: Michael Smith Building

department: FBMH/SBS/EIGen

institute: The University of Manchester

summary: Development of a vaccine against gonorrhoea is a global priority, driven by the rise in antibiotic resistance and the need to protect against infection and reproductive health consequences. Although Neisseria gonorrhoeae (Ng) infection does not induce substantial protective immunity, there is evidence that highly exposed individuals may develop immunity against re-infection with the same strain. In contrast, retrospective epidemiological studies have shown that immunisation with vaccines containing Neisseria meningitidis (Nm) outer membrane vesicles (OMVs) provides a degree of cross-protection against Ng infection. To examine this phenomenon, we conducted a clinical trial of 4CMenB (Bexsero®, GSK), a licensed vaccine against Nm that contains OMVs and recombinant antigens, with 50 adults in coastal Kenya who have high exposure to Ng. The study comprised a single arm open label study of two doses of Bexsero; humoral and cellular immune responses were measured at three time points over six months. Using a dedicated microarray of Ng antigens, we show that serum IgG and IgA reactivities against the gonococcal homologs of the recombinant antigens in the vaccine peaked at 10 weeks but had declined by 24 weeks. The reverse was the case for most antigens originating from the OMV component. A cohort of similar individuals with laboratory-confirmed gonococcal infection were compared before, during, and after infection: their reactivities were weaker and differed from the vaccinated cohort. We conclude that the cross-protection of the 4CMenB vaccine against gonorrhoea could be explained by cross-reaction against a diverse selection of antigens derived from the OMV component.

overall_design: A panel of recombinant gonococcal proteins were printed in 5 replicates on a non-commercial protein microarray. Selected proteins from the proteome of the gonococcal strain FA1090 included transmembrane beta-barrel outer membrane proteins and proteins of non-cytoplasmic origin containing a signal peptide at their N-termini. FA1090 gonococcal strain lacks the expression of outer membrane lactoferrin-binding proteins A and B, so these antigens were included in the final selection based on the amino acid sequence of gonococcal strains NG104 and NG102, respectively. Additionally, major outer membrane porin proteins (PorB) from seven different alleles were also included in the final antigen selection. All proteins were expressed in E. coli as His-tagged proteins. Proteins with transmembrane sections were purified from inclusion bodies and the rest were purified from cytoplasmic fraction as soluble forms. Human IgG (at 11 different concentration points) was distributed in each array copy as control. Sera were profiled for anti-human IgG and anti-human IgA-specific analysis of reactivity to the spotted proteins.

first: Jeremy

last: Derrick

first: Lenka

last: Stejkal

first: Angela

last: Thistlethwaite

last: RamirezBencomo


title: LncRNA LOC730101 promotes darolutamide resistance in prostate cancer by suppressing miR-1-3p [Hi-C]

last: Wu


title: Oocyte-specific deletion of Eif5 causes apoptosis of mouse oocytes within the early growing follicles by mitochondrial fission defect and DNA damage

city: guangzhou

first: Weiyong Wang

last: Wang

address: 382 Outer Ring East Road, Guangzhou Higher Education Mega Center

institute: south china university of technology

summary: Mutations in several translation initiation factors are closely associated with premature ovarian insufficiency (POI). Here, we demonstrate that the conditional knockout of eukaryotic translation initiation factor 5 (Eif5) in both mouse primordial and growing oocytes resulted in the apoptosis of oocytes within the early growing follicles. The further studies revealed that Eif5 deletion in oocytes downregulated the levels of mitochondrial fission-related proteins (FIS1, MFF, MTFR2 and p-DRP1) and upregulated the levels of the integrated stress response (ISR)-related proteins (SLC7A1, SHMT2 and AARS1) and genes (Atf4, Ddit3 and Fgf21). Consistent with this, Eif5 deletion in oocytes resulted in mitochondrial dysfunction characterized by elongated form, aggregated distribution beneath the oocyte membrane, decreased ATP content and mtDNA copy number, and excessive accumulation of reactive oxygen species (ROS) and mitochondrial superoxide. Meanwhile, Eif5 deletion in oocytes led to a significant increase in the levels of DNAdamageresponse proteins (γH2AX, p-CHK2, and p53) and proapoptotic proteins (PUMA and BAX), as well as a significant decrease in the levels of anti-apoptotic protein BCL-xL. Collectively, these findings indicate that Eif5 deletion in mouse oocytes results in the apoptosis of oocytes within the early growing follicles via mitochondrial fission defect and excessive ROS-induced DNA damage. This study provides new insights into pathogenesis and genetic diagnosis for POI.

overall_design: To investigate the function of Eif5 ni female fertility, we specifically deleted in oocytes at primordial follicles and primary follicles.


title: Effect of Matrigel, Laminin and Poly-L-Ornithine coating substrates on primary enteric glial cells and comparison to in vivo enteric glia

city: Bonn

first: Sven

last: Wehner

address: Venusberg-Campus 1

department: Department of Surgery

country: Germany

institute: University Clinics Bonn

summary: Enteric glial cells are important players in the control of motility, intestinal barrier integrity and inflammation. During inflammation, they switch into a reactive phenotype enabling them to release inflammatory mediators, thereby shaping the inflammatory environment. While a plethora of well-established in vivo models exist, cell culture models necessary to decipher the mechanistic pathways of enteric glial reactivity are less well standardized. In particular, the composition of extracellular matrices (ECM) can massively affect the experimental outcome. Considering the growing number of studies involving primary enteric glial cells, a better understanding of their homeostatic and inflammatory in vitro culture conditions is needed. We examined the impact of different ECMs on enteric glial culture homeostasis and immune responsiveness. We used 3’ bulk mRNA sequencing to compare cultured cells with in vivo enteric glial transcriptomes isolated from Sox10iCreERT2Rpl22HA/+ mice. Transcriptional analysis revealed strong similarities between enteric glia on Matrigel and laminin with enrichment of gene sets supporting neuronal differentiation, while cells on poly-L-ornithine showed enrichment related to cell proliferation. Comparing cultured and in vivo enteric glial transcriptomes revealed a 50% overlap. IL-1β treatment showed distinct coating-dependent gene expression signatures, with an enrichment of genes related to myeloid and epithelial cell differentiation on Matrigel and laminin coatings, while poly-L-ornithine induced more gene sets related to lymphocyte differentiation. Together, changes in differentiation and immune activation of primary enteric glial cells proved a strong effect of the ECM. We identified Matrigel and laminin as pre-eminent substrates for murine enteric glial cultures. These new insights will help to standardize and improve enteric glial culture quality and reproducibility between studies in the future, allowing a better comparison of their functional role in enteric neuroinflammation.

overall_design: comparative gene expression analysis of enteric glial cells grown on different extracellular matrix substrates with or without immune activation via IL-1b and comparison to in vivo glia (n=5 biological replicates)

first: Linda

last: Schneider

first: Reiner

first: Ebrahim

last: Hamza


city: Suzhou

first: zigang

last: qiao

address: Chongwen Road

department: Suzhou Institute of Systems Medicine

institute: Chinese Academy of MedicalSciences & Peking Union Medical College

summary: This study aimed to analyze and compare the test transcripts of peripheral blood mononuclear cells (PBMCs) isolated from 4 healthy donors and 4 septic patients' whole blood.

overall_design: Gene expression profiling analysis of RNA-seq data for PBMCs from healthy volunteers or septic patients

first: Zigang

last: Qiao


title: Immune signature and monocytic leukemia cells are resistant to MDM2 inhibition

city: Portland

first: Peter

last: Ryabinin

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

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

overall_design: Refer to individual Series