title: THUMPD2 catalyzes N2-methylation on the spliceosome catalytic center of U6 snRNA and regulates pre-mRNA splicing and retina degeneration

city: Memphis

first: Beisi

last: Xu

state: Tennessee

address: 262 Danny Thomas Pl

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hosipital

summary: How the relatively evolutionarily conserved spliceosome is able to manage the enormously expanded number of splicing events that occur in humans (~200,000 vs. ~400 reported for yeast) is not well understood. Here, we show deposition of one RNA modification-N2-methylguanosine (m2G)-on the G72 nucleoside of U6 snRNA (known to function as the catalytic center of the spliceosome) results in profoundly increased pre-mRNA splicing activity in human cells. This U6 m2G72 modification is conserved among vertebrates. Further, we demonstrate that THUMPD2 is the methyltransferase responsible for U6 m2G72 and show that it interacts with an auxiliary protein (TRMT112) to specifically recognize both sequence and structural elements of U6. THUMPD2 KO blocks U6 m2G72 and down-regulates the pre-mRNA splicing activity of major spliceosome, yielding thousands of changed alternative splicing events of endogenous pre-mRNAs. Notably, the aberrantly spliced pre-mRNA population of the THUMPD2 KO cells elicits the nonsense-mediated mRNA decay (NMD) pathway and restricts cell proliferation. We also show that THUMPD2-mediated control of the U6 m2G72 modification is associated with age-related macular degeneration and retinal function. Our study thus demonstrates how an RNA epigenetic modification of the major spliceosome differentially regulates global mRNA splicing and impacts physiology and disease.

overall_design: RNA-seq were performed to study the DEG and Alternative Splicing by THUMPD2 KO. Two individual THUMPD2 knockout (KO#1, KO#2) HEK293T cells were performed to assure the reproducibility. Each have two replicates and > 240M reads.

first: Wen-Qing

last: Yang

first: Jian-Yang

last: Ge

first: Xiao-Feng

last: Zhang

first: Lin

last: Lin

first: Wen-Yu

last: Zhu

first: Yi-Gong

last: Shi

first: Bei-Si

first: Ru-Juan

last: Liu


title: IL-36 receptor deletion aggravates lung injury and mortality in experimental murine sepsis through epithelial

status: Public on Jan 02 2024

city: tianjin

first: huachen

last: wang

address: pingjiang road 23

country: China

institute: the second hospital of tianjin medical university

type: Expression profiling by high throughput sequencing

summary: Inflammation resolution is critical for sepsis induced acute lung injury (ALI) recovery. Interleukin-36 receptor (IL-36R) is a potent anti-inflammatory factor. However, its role in ALI resolution remains unclear. We investigated the effects of IL-36R during the ALI resolution process in a murine cecal ligation and puncture (CLP)-induced ALI model. Knockout IL-36R signaling aggravates CLP-induced lung injury, as manifested by elevated bacterial load and increased neutrophils recruitment to the lung. Thereafter, we used IL-36R knockout mice to discern the source cell of IL-36R during ALI. We found that IL-36R is predominantly generated by epithelial cells during the ALI process. Furthermore, we sorted lung epithelial cells on the ALI process. IL-36R-specific loss in epithelial cells leads to apoptosis through NF-κB pathway. Together, our findings identify molecules that are likely involved in sepsis induced lung injury that may inform biomarker and therapeutic development.

overall_design: On the third day of CLP, total RNA was extracted from the lung epithelial cells of 6 mice which were sepsis induced acute lung injury. Three of the mice knockout IL-36R while the other three were wild type mice. Subsequently, RNA-seq analysis was performed to examine gene expression in the lung epithelial cells.


title: The pathological alterations in hearts from polycystic ovary syndrome mice [male_PAMH]

city: shanghai

first: Ling

last: Gao

address: 419 Fangxie Rd

institute: Fudan University

summary: Polycystic ovary syndrome (PCOS), the most common endocrine disease in reproductive-aged women, is associated with an increased prevalence and extent of coronary artery disease. However, the underlying mechanism remains unclear. Here, we observed that hearts from PCOS mice were characterized by increased total macrophage accumulation. Monocyte-derived macrophages were significantly increased in the hearts of PCOS mice owing to enhanced circulating monocyte supply. Compared with control mice, PCOS mice showed a significant increase in splenic monocyte output, associated with elevated hematopoietic progenitors in the spleen and sympathetic tone. Compared with non-PCOS animals, PCOS-induced mice showed significantly exacerbated atherosclerotic plaque development and post-MI cardiac remodeling. Conditional Vcam1 silencing in PCOS mice significantly suppressed cardiac inflammation and improved post-MI cardiac injury. Our data documented new mechanisms through which PCOS may affect cardiovascular health in women.

overall_design: Pregnant mice were treated with prenatal Anti-mullerian hormone (PAMH) treatment or PBS, and male offspring from each group were used for experiment. Then, we performed comparative gene expression profiling analysis of RNA-seq data for heart tissues from PAMH-treated male mice and control male mice.


title: Transcriptome profiling of regulatory T cells from children with Transient Hypogammaglobulinemia of Infancy

city: Krakow

first: Magdalena

last: Rutkowska-Zapala

address: Wielicka 265

country: Poland

institute: Jagiellonian University Medical College

summary:
In this study, we aimed to determine the role of Treg cells in the pathomechanism of THI, based on the gene expression profile analysis performed on isolated Treg cells.
Study was performed in THI patients at two time points, during, and in resolution phase of hypogammaglobulinemia, we showed changes in the expression profile of genes important for Treg lymphocyte biology and function. In parallel, we analyzed expression profiles of long intergenic non-coding RNA as well as microRNA precursors. This study improved our understanding of the role of Treg-related genes in the etiopathogenesis of THI.

overall_design: Microarray expression analysis was performed for Treg cell population isolated from THI patients in two time-points: during (THI-1) and in resolution phase of hypogammaglobulinemia (THI-2).

last: Rutkowska-Zapała

first: Agnieszka

last: Grabowska

first: Marzena

last: Lenart

first: Anna

last: Kluczewska

last: Szaflarska

first: Krzysztof

last: Kobylarz

last: Pituch-Noworolska

first: Maciej

last: Siedlar


title: Modeling Braf-induced thyroid cancer development and cell redifferentiation using pluripotent stem cell-derived organoids

city: Brussels

first: Mirian

last: Romitti

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: To generate a papillary thyroid carcinoma organoid model by inducing the BrafV637E mutation in mouse embryonic stem cells derived functional thyroid follicles to better comprehend the oncogenic events driven by Braf-oncogene and develop a drug screening tool. We performed gene expression profiling analysis using data obtained from bulk RNA-seq of organoid model with and without induction of BrafV637E expression induction, after MEK and PI3K inhibitors addition).

overall_design: Comparative gene expression profiling analysis of bulk RNA-seq data of organoids developped from G4 RosaLuc TRE-Nkx2-1-Pax8_bTg-NES-BrafV637E-ERT2 mouse embryonic stem cells with addition of Br-cAMP, Br-cAMP+4-Hydroxytamoxifen and Br-cAMP+4-Hydroxytamoxifen+PD0325901+LY204002.

first: Hélène

last: Lasolle

first: Pierre

last: Gillotay

first: Andrea

last: Schiavo

first: Barbara

last: de Faria da Fonseca

first: Olivier

last: Monestier

first: Benilda

last: Aganahi

first: Laura

last: Chomette

first: Marina

last: Kisys Polisel

first: Ana

last: Silva Maia

first: Sabine

last: Costagliola


title: Effects of the G-quadruplex-binding drugs Quarfloxin and CX-5461 on the malaria parasite Plasmodium falciparum

city: Cambridge

first: Holly

last: Craven

address: 208 Molteno Building, Tennis Court Road

department: Pathology

country: United Kingdom

institute: University of Cambrdige

summary: P. falciparum is the deadliest causative agent of human malaria. This parasite has historically developed resistance to many drugs, including the current frontline treatments, so new therapeutic targets are needed Our previous work on guanine quadruplexes (G4s) in the parasite’s DNA and RNA has highlighted their influence on parasite biology, and also revealed G4 stabilising compounds as promising candidates for drug repositioning. In particular, quarfloxin, a former anticancer agent, kills blood-stage parasites at all developmental stages, with fast rates of kill and nanomolar potency. Here we explored the molecular mechanism of quarfloxin and its related derivative CX-5461. In vitro, both compounds bound to P. falciparum-encoded G4 sequences. In cellulo, quarfloxin was more potent than CX-5461, and could prevent establishment of blood-stage malaria in vivo in a murine model. CX-5461 showed clear DNA damaging activity, as reported in human cells, while quarfloxin caused weaker signatures of DNA damage. Both compounds caused transcriptional dysregulation in the parasite, but the affected genes were largely different, again suggesting different modes of action.  Therefore, CX-5461 may act primarily as a DNA damaging agent in both Plasmodium parasites and mammalian cells, whereas the complete anti-malarial mode of action of quarfloxin may be parasite-specific, and remains elusive.

overall_design: Differential gene expression analysis from RNA-sequencing for Plasmodium falciparum 3d7 WT parasites. 30-32h.p.i trophozoites were cocultered with 2X EC50 of either Quarfloxin, Cx5461 or a no drug control for 4 hours. Three semi-biological repeats were collected.

middle: M

first: Guilherme

last: Nettesheim

first: Pietro

last: Cicuta

first: Andrew

last: Blagborough

first: Catherine

middle: J

last: Merrick


title: Genome-wide maps of chromatin architecture in human adipose derived stem cells isolated from abdominal (ABD) and gluteofemoral (GLU) subcutaneous adipose tissue

city: St Petersburg

first: Edina

last: Erdős

address: 501 6th Ave S

country: USA

institute: Johns Hopkins University

summary: Over the past two decades, studies have identified distinct transcriptional signatures between ABD and GF-adipose tissues and between both body shapes. Remarkably, a significant fraction of these depot specific gene expression patterns and more recently the differential chromatin structure profiles have been shown to be conserved during the culture and in vitro differentiation of the precursor cells into mature adipocytes. Our team and others have also shown distinct DNA methylation levels between ABD and GF-AT, that are preserved in isolated ADSCs cultured in vitro. Altogether, these data suggest that depot specific epigenomic profiles contribute significantly to the unique transcriptional profiles of ABD vs GF adipose tissues depots. To extend these earlier studies and to determine how the differential gene expression patterns in different adipose depots may be significantly influenced by chromatin landscape we performed H3K4me3, H3K4me2, H3K27me3, H3K9me3 and CTCF ChIP-seq and ATAC-seq on chromatin isolated from ABD and GF-ADSCs. We paired this with highly differentially expressed genes between ABD and GF-ADSCs. Then, to evaluate the potential role for long range chromatin interactions we utilized an H3K27Ac Hi-ChIP approach to capture putative regulatory loops with at least one anchor being marked by this enhancer associated histone mark. This in-depth analysis of the chromatin structure and organization of ABD and GF-ADSCs provides a better understanding of the intrinsic genomic regulatory features that help define the functionally distinct phenotypes of different subcutaneous adipose tissue depots and how they influence fat distribution in women.

overall_design: Human adipose derived stem cells (hASC) isolated from abdominal (ABD) and gluteofemoral (GLU) adipose tissue obtained from premenopausal women were used to perform assess chromatin structure by H3K27ac hiChIP-seq.

first: T

middle: F

last: Osborne

first: S

middle: R

last: Smith


title: The pathological alterations in hearts from polycystic ovary syndrome mice [female_PAMH]

first: Ling

last: Gao

overall_design: Polycystic ovary syndrome (PCOS) in female mice was induced by prenatal Anti-mullerian hormone (PAMH) treatment; control mice were prenatally treated with PBS. Then, we performed comparative gene expression profiling analysis of RNA-seq data for heart tissues from PCOS mice and control mice.


title: Plasma small extracellular vesicles microRNAs profile in advanced ovarian cancer

city: Changsha

first: Jie

last: Tang

address: No. 932, Lushan South Road, Yuelu District, Changsha City, Hunan Province

institute: Hunan Cancer Hospital

type: Non-coding RNA profiling by high throughput sequencing

summary: No residual disease after debulking Surgery (R0 resection) is the most critical independent prognostic factor for advanced ovarian cancer (AOC). Therefore, it is of paramount importance to preoperatively estimate the likelihood of R0 resection for choosing the best therapeutic strategy. Our study aimed to develop a non-invasive and reliable detection method for AOC patients with a high risk of residual disease. An integrated plasma small extracellular vesicles (sEVs) microRNA profiling was generated by RNA sequencing in AOC patients with no residual disease patients (R0) and residual disease (non-R0). We identified and validated a logistic model based on plasma sEVs miRNAs to predict residual disease in AOC patients.

overall_design: Plasma small extracellular vesicles microRNAs profile of advanced ovarian cancer patients with residual disease (non-R0=20) or no residual disease (R0=17)

first: Mu

last: Liu

first: Xiaofang

last: Zhou


title: Unveiling FOS as a Potential Diagnostic Biomarker and Emetine as a Prospective Therapeutic Agent for Diabetic Nephropathy

city: Guangzhou

first: Jiaqiong

last: Lin

address: Guangzhou dadaobei 1838

institute: South medical university

summary: To gain a comprehensive understanding of emetine's impact on high glucose-induced M1 macrophage polarization in the pathogenesis of diabetic nephropathy (DN), we employed transcriptome sequencing. Our study included two experimental groups: the high glucose-induced damage group and the high glucose-induced damage with emetine pretreatment group. Differential gene expression analysis, accompanied by functional enrichment analysis, was conducted to identify crucial pathways and biological processes involved. This investigation provides significant insights into the role of emetine in DN, enhancing our knowledge regarding its underlying mechanisms. Furthermore, this research contributes to a deeper comprehension of the pathogenesis of diabetic nephropathy and offers valuable prospects for the development of potential therapeutic targets and strategies for diabetic nephropathy.

overall_design: The experimental design of this study involved two groups: a high glucose-induced damage group and a high glucose-induced damage with emetine pretreatment group.


title: SMARCAL1 modulates cellular triglyceride storage and expenditure in response to cell growth states via interaction with ANGPTL3 (RNA-Seq 2)

city: Boston

first: Yu-Xin

last: Xu

state: United States

address: 185 Cambridge Street Simches Research Building, CPZN 5.500

department: Center for Genomic Medicine

institute: Massachusetts General Hospital

summary: SMARCAL1 is a chromatin regulator. Biallelic mutations of SMARCAL1 cause Schimke Immunoosseous Dysplasia (SIOD), a disease with severe growth defects and premature death. Atherosclerosis and hyperlipidemia are common phenotypes among SIOD patients. However, little is known about their genesis and development. Here we show that SMARCAL1 is vital in regulating cellular lipid metabolism. Using a proteomic approach, we found that SmarcAL1 interacts with angiopoietin-like 3 (Angptl3), a key lipoprotein regulator. SmarcAL1 deficiency in cell models resulted in substantial accumulation of triglycerides (TGs) and fatty acids (FAs). SmarcAL1 KO in mice drastically increased plasma TG level. The nuclear SmarcAL1 translocates into cytoplasm, surprisingly, enriched at peroxisomes, where it interacts with Angptl3. This shuttling provides a regulatory control over cellular lipid metabolism via SmarcAL1-regulated gene expression, in response to cell growth states. Inactivation of SmarcAL1 gene reduced the expression of the genes responsible for FA metabolism, suggesting that SmarcAL1 plays a key role in regulating lipid metabolism. Indeed, the Angptl3-mediated TG partition is largely dependent on SmarcAL1 activity. This activity was further supported by two opposite SMARCAL1 single-tissue expression profiles linked to two quantitative trait loci that are differentially associated with body mass index. Thus, SMARCAL1 is crucial for cellular lipid metabolism, and ANGPTL3-regulated SMARCAL1 activities enable cells to response to cell growth states for TG storage or expenditure.

overall_design: Rat hepatoma McA cell lines with heterologous SmarcAL1 KO or WT SmarcAL1 were generated using CRISPR genome editing system. Total RNA from those cell lines were used for RNA-seq assays to detect the gene expression difference between the cells with SmarcAL1 KO and the control cells with WT SmarcAL1.


title: Morphogen Stimulated Endocytic Recycling Drives Cytoneme Loading for Mammalian Tissue Patterning

first: Yong-Dong

last: Wang

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: During development, morphogens build tissues by instructing cell fate across long distances. Directly visualizing morphogen transport in situ has been unfeasible, so the molecular mechanisms ensuring successful morphogen delivery remain unclear. To tackle this longstanding problem, we developed a mouse model for compromised Sonic Hedgehog (SHH) morphogen delivery and discovered that endocytic recycling promotes SHH loading into signaling filopodia called cytonemes. We optimized methods to preserve in vivo cytonemes for advanced microscopy and show endogenously-expressed SHH localized to cytonemes in developing mouse neural tubes. Depletion of SHH from neural tube cytonemes alters neuronal cell fates and compromises neurodevelopment. Mutation of the filopodial motor Myosin 10 (MYO10) reduces cytoneme length and density, which corrupts neuronal signaling activity of both SHH and WNT. Combined, these results demonstrate that cytoneme-based signal transport provides essential contributions to morphogen dispersion during mammalian tissue development and suggest MYO10 is a key regulator of cytoneme function.

overall_design: RNA-sequencing data of litters of E9.5 control (wild type) and Disp1CS/INDEL embryos generated from Disp1CS/+ females and Disp1INDEL/+ males, and litters of E8.5 control (Myo10+/+) and Myo10m1J/m1J embryos generated from Myo10m1J/+ females and Myo10m1J/+ males.

first: Eric

middle: T

last: Hall

first: Miriam

middle: E

last: Dillard

first: Shariq

middle: S

last: Ansar

first: Stacey

middle: K

last: Ogden


title: In vitro and in vivo preclinical characterization of a preconceptionally administered maternal vaccine against severe neonatal Escherichia coli K1 infections

city: PARIS

last: FRAPY

address: 156 rue de vaugirard

department: Immunologie, Infectiologie et Hématologie (I2H)

country: France

institute: INSERM U1151 INEM

summary:
Preterm birth is currently the leading cause of neonatal morbidity and mortality. Genetic, immunological and infectious causes are suspected. Preterm infants have a higher risk of severe bacterial neonatal infections, most of which are caused by Escherichia coli an in particular E. coli K1strains. Women with history of preterm delivery have a high risk of recurrence and therefore constitute a target population for the development of vaccine against E. coli neonatal infections.
Here, we characterized the immunological, microbiological and protective properties of a live attenuated vaccine candidate in adult female mice and their pups against after a challenge by K1 and non-K1 strains of E. coli. Our results show that the E. coli K1 E11 aroA vaccine induces strong immunity, driven by polyclonal bactericidal antibodies. In our model of meningitis, pups born to mothers immunized before mating were well protected against various K1 and non-K1 strains of E. coli.
Given the very high mortality rate and the neurological sequalae associated with neonatal E. coli K1 meningitis, our results constitute preclinical proof of concept for the development of a live attenuated vaccine against severe E. coli infections in women at risk of preterm delivery.

overall_design: Investigation and comparison of vurilence genes present in E. coli K1 E11 WT vs delta aorA strains by RNAseq analysis. Two culture conditions (1) bacterial culture in LB medium until exponential phase - OD=0.600; (2) bacterial culture in DMEM medium until exponential phase - OD=0.600.

first: Youssouf

last: SEREME

first: David

last: SKURNIK


title: Gene expression changes in response to low R:FR in wild-type and hfr1pil1 mutants for  96 hours.

city: Shanghai

first: Chuanwei

last: Yang

address: 2005 Songhu Road, Yangpu District

department: school of life sciences

institute: Fudan university

summary: RNA-sequencing was performed using Col-0 and hfr1-4pil1-2 seedlings upon 96 hours (96hr) low R:FR treatment. We analysed global gene expression changes in Arabidopsis thaliana in response to 96hr low R:FR, in order to identify the different effects of negative regulator in long-term treatments.

overall_design: Three-day-old seedlings grown under white light were treated with or without low R:FR for 96 hr, shoot tissue were collected.

first: Lin

last: Li


title: RNA-seq analysis of SCC1 cells after JQ1, I-BET and/or INF-r treatment

city: Richmond

first: Jiong

state: Virginia

address: 800 E Leigh Street, suite 212

institute: VCU

summary: In order to examine how BET inhibition affects the  gene transcriptome in HNSCC cells, we performed RNA-sequencing  in SCC1 cells treated with JQ1, I-BET, and/or INF-r.

overall_design: Examination of RNA-seq of SCC1 cells with JQ1, I-BET, and/or INF-r.


title: Wildtype C-Raf gene dosage and dimerization drive prostate cancer metastasis

city: Los Angeles

first: Owen

last: Witte

state: California

address: 675 Charles E Young Dr S, 5720 MRL Bldg; MC 729022

department: Microbiology, Immunology, and Molecular Genetics

institute: University of California, Los Angeles

summary: To investigate the function of C-Raf overexpression in driving metastasis, we established C-Raf overexpression lines and C-Raf metastasis derived lines from mice in RWPE-1 and BPH-1 cells.

overall_design:
We then performed gene expression analysis using data obtained from RNA-seq of these cell lines
Comparative gene expression analysis of RNA seq data from BPH-1 and RWPE-1 cells and their derivatives.

first: Ta

last: Lisa


title: Immune evasion of dormant disseminated tumor cells is due to their scarcity and can be overcome by T cell immunotherapies

city: Seattle

first: Cyrus

last: Ghajar

state: WA

address: 1100 Fairview Ave. N. P.O. Box 19024

institute: Fred Hutch

summary: The period between “successful” treatment of localized breast cancer and the onset of distant metastasis can last many years, representing an unexploited window to eradicate disseminated disease and prevent metastases. We find that the source of recurrence – disseminated tumor cells (DTCs) – evade endogenous immunity directed against tumor neoantigens. Although DTCs downregulate major histocompatibility complex I, this does not preclude recognition by conventional T cells. Instead, the scarcity of interactions between two relatively rare populations – DTCs and endogenous antigen-specific T cells – underlies DTC persistence. This scarcity is overcome by any one of three immunotherapies that increase the number of tumor-specific T cells: T cell-based vaccination, or adoptive transfer of T cell receptor- or chimeric antigen receptor- T cells. Each approach achieves robust DTC elimination, motivating discovery of MHC-restricted and -unrestricted DTC antigens that can be targeted with T cell-based immunotherapies to eliminate the reservoir of metastasis-initiating cells in patients.

overall_design: To investigate the immuno-evasive properties of dormant DTCs in the lung, we inoculated WT Balb/c mice and T cell deficient athymic nude mice with either the metastatic D2A1 cell line or the dormant D2.0R cell line via tail vein injection. Four weeks after tumor cell injection, tumor cells were FACS purified from the lungs or harvested from in vitro culture to identify differentially expressed genes in metastatic compared to dormant cells, and immune competent compared to immunocomprimised hosts.

first: Erica

middle: G

last: Goddard

first: Miles

middle: H

last: Linde

first: Santino

last: Iannone

first: Stanley

last: Riddell


title: The pathological alterations in hearts from polycystic ovary syndrome mice

first: Ling

last: Gao

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

overall_design: Refer to individual Series


title: AP-1 inhibition on the treatment of down syndrome derived aminocytes(DSACs)

city: Zhengzhou

first: zhenglong

last: guo

state: Henan

address: NO.7, Weiwu road

institute: Henan Provincial People's Hospital

summary: MX1 mediated AP-1 involved transcriptional regulation play an important role in the pathogenesis of DS through integration analysis of ATAC-seq and RNA-seq， therefore，AP-1 inhibition may be a potential therapeutic target for the treatment of DS-associated phenotye.

overall_design: To explore the role of inhibiting AP-1 activity on DS, DSACs were treated with 40 μM T-5224 (M9373, Abmole, Houston, USA) for 48 hours, and dimethyl sulfoxide (DMSO) treated DSACs were used as NC group.

first: Zhenglong

last: Guo

first: Bingtao

last: Hao

first: Shixiu

last: Liao


title: RNA-seq analysis of trans-differentiated ARPE-19 cells transduced by AAV9-AIPL1 vectors

status: Public on Jan 01 2024

city: Sochi

first: Alima

last: Galieva

state: Krasnodar region

address: Olympic Ave, 1

department: Gene therapy department

country: Russia

institute: Sirius University of Science and Technology

summary: Inherited retinal disorders (IRD) have become a primary focus of gene therapy research since the success of AAV-based therapeutics (voretigene neparvovec-rzyl) for Leber congenital amaurosis type 2 (LCA2). Dozens of monogenic IRDs could be potentially treated with a similar approach using adeno-associated virus (AAV) to transfer a functional gene into the retina. Here, we present the results of design, production and in vitro testing of the AAV serotype 9 (AAV9) vector carrying the codon-optimized (co) copy of aryl hydrocarbon receptor interacting protein like-1 (AIPL1) as a possible treatment for LCA4. The pAAV-AIPL1co was able to successfully transduce retinal pigment epithelium cells (ARPE-19) and initiate expression of human AIPL1. Intriguingly, cells transduced with AAV9-AIPL1co showed much less antiviral response than AAV9-AIPL1wt (wild type AIPL1 ) transduced. RNA-sequencing (RNA-seq) analysis of trans-differentiated ARPE-19 cells transduced with AAV9-AIPL1co demonstrated the significant differences in expression of genes involved in innate immune response. In contrast, AAV9-AIPL1wt induced prominent activation of multiple interferon-stimulated genes. The key part of possible regulatory molecular mechanism is activation of dsRNA-responsive antiviral oligoadenylate synthetases, and significant increase in level of histone coding genes’ transcripts overrepresented in RNA-seq data (i.e. H1, H2A, H2B, H3 and H4). The RNA-seq data suggests that AAV9-AIPL1co exhibiting less immunogenicity than AAV9-AIPL1wt can be used for potency testing using relevant animal models to develop future therapeutics for LCA4.

overall_design: ARPE-19 cells were transduced with AAV9-AIPL1wt, AAV9-AIPL1co or AAV9-GFP (control) vectors. RNA-sequencing of these samples and of non-transduced cells was performed, 3 replicates for each condition

first: Alexander

last: Egorov

last: Malogolovkin

first: Andrew

last: Brovin

last: Karabelsky


title: Negative feedback of IFN-I signaling through IFN-competent RIG-I-like receptor-induced HSPA6

city: Tianjin

first: Fengqi

last: Li

state: Tianjin

address: No. 92, Weijin Road, Xuefu Street, Nankai District

department: School of Pharmaceutical Science and Technology

institute: Tianjin university

summary: The RIG-I-like receptors (RLRs) form filaments to activate type-I interferon (IFN-I) and NF-KB signaling through their adaptor protein MAVS and downstream cascades. These filaments are recognized and regulated by cell-encoded machinery for correct activation. Here, we identified the stress-sensitive heat shock protein, HSPA6, was induced to express upon RLR-MAVS activation to act as a negative regulator of IFN-I signaling. Interestingly, by using MAVS-KO cells, we showed that HSPA6 was upregulated dependent on the presence of IFN-competent RLRs but not MAVS.  Gene knockout (KO) tests indicated that the E3 ligases, stress granules (SGs), and transcription factors IRF1 and AP1 were all shared to induce HSPA6 and the canonical IFNb. Kinetic analysis showed that HSPA6 upregulated slower than IFNb, implicating these two genes competed machinery for transcription activation. Further tests suggested the induced HSPA6 bound to IFN-competent MDA5 to dissolve the filaments and downregulated IFN induction. Thus, our study uncovered a new gene activation mechanism by the IFN-competent RLRs to serve as negative feedback, arguing for a gene regulatory role of functional filaments of innate immunity.

overall_design: We performed an RNA-seq to compare gene expression in WT and GOF MDA5 (G495R) expressing cells. And exclude the gene expression after IFN treatment stimulation.

first: Yi

last: Lei

first: Zhenxiang

last: Zhao

first: Xiaoxin

last: Ji

first: Dongpeng

last: Zheng

first: Yixin

last: Huang

first: Jingjing

last: An

first: Chuhan

first: ZhaoKun

last: Wang

first: Yajun

last: Si

first: Xinyao

last: Chen

first: Yifu

last: Liu

first: Zichuan

first: Zixiang

last: Zhu

first: Xin

last: Mu


title: The pathological alterations in hearts from polycystic ovary syndrome mice [NWZ_HFD]

first: Ling

last: Gao

address: 419 Fangxie Rd

institute: Fudan University

summary: Polycystic ovary syndrome (PCOS), the most common endocrine disease in reproductive-aged women, is associated with an increased prevalence and extent of coronary artery disease. However, the underlying mechanism remains unclear. Here, we observed that hearts from PCOS mice were characterized by increased total macrophage accumulation. Monocyte-derived macrophages were significantly increased in the hearts of PCOS mice owing to enhanced circulating monocyte supply. Compared with control mice, PCOS mice showed a significant increase in splenic monocyte output, associated with elevated hematopoietic progenitors in the spleen and sympathetic tone. Compared with non-PCOS animals, PCOS-induced mice showed significantly exacerbated atherosclerotic plaque development and post-MI cardiac remodeling. Conditional Vcam1 silencing in PCOS mice significantly suppressed cardiac inflammation and improved post-MI cardiac injury. Our data documented new mechanisms through which PCOS may affect cardiovascular health in women.

overall_design: Mice were fed with high fat diet (HFD) or normal chow from 4-week age to 12-week age. Then, we performed comparative gene expression profiling analysis of RNA-seq data for heart tissues from HFD-fed female mice and normal chow (NC) -fed female mice


title: Fluorinated rhodacyanines induce apoptosis via mitochondrial damage and cell cycle arrest

city: Worcester

first: Patipark

last: Kueanjinda

state: MA

address: 368 Plantation St

institute: University of Massachusetts Medical School

summary: Rhodacyanine, a series of cyanines derived from rhodanine, exerts anticancer effects. This study intended to uncover the biological mechanism underlying the anticancer effects of a a fluorinated rhodacyanine in HeLa cervical cancer cells. Initially, the cytotoxic activities of 15 compounds were screened, Rho-7 exhibited the most effective compound against Hela cell growth with IC50 values at 0.03 µM. Interestingly, Rho-7-targeted mitochondrial damage leads to cancer cell death by increasing reactive oxygen species (ROS) levels. Additionally, Rho-7 can trigger Hela cells to undergo apoptosis and cell cycle arrest at the G2/M phase. Rho-7 could downregulate the expression of anti-apoptotic Mcl-1 genes or upregulate the level of pro-apoptotic Bad and Bik genes. Our findings suggest that the anticancer activity of Rho-7 involve ROS generation, cell cycle arrest and apoptotic induction, as well as alteration of pro-and anti-apoptotic genes, displaying a therapeutic potential of Rho-7 in cervical cancer treatment.

overall_design: In this study, transcriptomics  were used to identify the gene expression profiling of the Hela cells.Technical and biological normalization of the raw counts of each gene was performed using transcriptomics. Technical normalization, a positive control factor was calculated for each sample.

first: Sukanya

last: Unson

first: Sutthida

last: Wongsuwan

first: Nattanit

last: Suddee

first: Thitiya

last: Lasing

first: Pornchai

last: Kaewsapsak

first: Sunchai

last: Payungporn

first: Tirayut

last: Vilaivan

first: Tanatorn

last: Khotavivattana

first: Jaruwan

last: Chatwichien

first: Chanat

last: Aonbangkhen


title: Extracellular matrix remodelling in human dental pulp upon carious 2 lesion through the prism of single-cell RNA sequencing analysis

city: Zurich

first: Genome

last: Informatics

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich (FGCZ)

country: Switzerland

institute: ETH ZURICH / University of Zurich

summary: Carious lesion is a bacteria caused destruction of tooth mineralized matrices, that can lead to pulp necrosis, if left untreated. Prior to reaching pulp, the advancing bacterial invasion evokes molecular and cellular changes in the underlying pulp tissue, that include reparative dentinogenesis and immune reaction. The balance between these two processes determines the outcome of carious lesion, yet the detailed molecular map of pulp reaction to progressing carious is missing. In this study we used single cell RNA sequencing (scRNAseq) and generated a high-resolution molecular map of carious lesion.

overall_design: Third molars were extracted from 5 patients  of 18-35 years of age and dental pulp enzimatically dispersed to single cell suspension. 10’000 cells per sample were loaded into the 10X Chromium controller and library preparation (single cell 3’ v2 or v3 protocol). The resulting libraries were sequenced in an Illumina NovaSeq sequencer according to 10X Genomics recommendations (paired end reads, R1=26, i7=8, R2=98) to a depth of 50.000 reads per cell.

first: Thimios

middle: A

last: Mitsiadis

first: Anamaria

last: Balic


title: mRNA transcriptome sequencing of CD45- lung tumor cells from tumor-burdened lungs of  KrasLSL-G12D/+Tp53fl/fl and KrasLSL-G12D/+Tp53fl/flUsp25-/- mice 10 weeks after they were intranasally injected with Ad-Cre

city: Wuhan, China

first: Ci

last: Yang

address: 115 East Lake Road

institute: Wuhan University

summary: Comparative gene expression profiling analysis of RNA-seq data in  CD45- lung tumor cells from tumor-burdened lungs of  KrasLSL-G12D/+Tp53fl/fl and KrasLSL-G12D/+Tp53fl/flUsp25-/- mice  10 weeks after they were intranasally injected with Ad-Cre.

overall_design: To investigate the mechanisms by which USP25 promotes lung tumorigenesis, we performed the transcriptomic analysis of the CD45- lung tumor cells from KrasLSL-G12D/+Tp53fl/fl (n=2) and  KrasLSL-G12D/+Tp53fl/flUsp25-/-  mice (n=2).

first: Hong-Xu

last: Li

first: Bo

last: Zhong

first: Dandan

last: Lin


title: COMBINATION OF MESENCHYMAL STEM CELLS-DERIVED EXOSOMES AND SILVER NANOPARTICLES: PERSPECTIVES ON WOUND HEALING

city: Hanoi

first: Quang

middle: Minh

last: Dang

address: 458 Minh Khai Street

country: Viet Nam

institute: Vinmec-VinUni Institute of Immunology

summary: Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing. Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing. Extracellular vesicles (EVs) are on the edge of innovation aimed at regenerative and therapeutic applications, including wound healing, by containing therapeutic agents originating from secreting cells. Moreover, silver nanoparticles (AgNPs) play a role in wound healing because they have antiseptic activities. Therefore, in this study, we used sequencing technology to investigate the mRNA profile in UCMSC-derived exosomes (EXs). We also attempted to determine the role of the transcriptome, particularly in cutaneous wound healing, using bioinformatics analysis. Additionally, we investigated the efficacy of utilising a combination of UCMSC-derived EXs and AgNPs on burned animal models. Results showed that a large number of protein-coding genes (4578 genes) have been detected in UCMSC-derived EXs, among which 2004 genes are upregulated in exosomes while 2574 genes are downregulated compared to secreting cells. Interestingly, many genes enriched in exosomes were associated with the biology of the wound healing process. Gene ontology (GO) term and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analysis indicated the upregulated exosomal genes belonging to GO terms and KEGG pathways related to signaling pathways such as DNA replication, ribosome, cell cycle, and pyrimidine metabolism. Further investigations that aimed to test exosomes and AgNPs in wound healing stimulation confirmed the faster healing capacity belongs to all exosomes, AgNPs, and a combination of EXs and AgNPs in the early healing process. The exosomes also expressed their capacity to enhance the dermal fibroblast proliferation. Our findings indicated the selective sorting of mRNAs into EXs, the potential of EXs, and the combination of EXs with AgNPs in cutaneous wound healing.

overall_design:
To investigate the role of umbilical cord mesenchymal stem cells (UC-MSC) and their secretome in the regulation of wound healing, we isolated and cultured mesenchymal stem cells from the umbilical cord, and isolated exosomes secreted by these cells.
We then performed gene expression profiling analysis using RNA-seq of a triplicate of UCMSC-derived exosomes and their corresponding mother cells
Comparative gene expression profiling analysis of RNA-seq data for UC-MSCs and their exosomes.

first: Uyen

last: Than

first: Hoai

last: Nguyen

first: Huyen

first: Nhung

last: Hoang

first: Thanh

first: Duc

last: Vu

first: Huong

last: Phi

first: Quynh

last: Luu

first: Hai

middle: X

last: Do

first: Huy

last: Dao

first: Xuan

first: Nam


title: A biphenotypic lymphocyte subset displays both T- and B-cell functionalities

city: shanghai

first: yifan

last: zhang

address: no

institute: fudan university

summary: T cell/B cell mixed phenotypic lymphocytes have been observed in different disease contexts, yet their presence and function in physiological conditions remain elusive. Here, we provide evidence for the existence of a lymphocyte subset endogenously expressing both T- and B-cell lineage markers in mice by single cell RNA sequencing.

overall_design: Bone marrow, lymph node and peripheral blood cells isolated from C57BL/6J female mice were stained with Live/Dead dye and lymphocytes were isolated using a BDFACSAria™ IIISorter. Cells were manually counted by Trypan blue and AO-PI after each centrifugation and resuspension. Single cells were processed using Chromium Controller (10x Genomics) according to the manufacturer's protocol. By using Chromium Next GEM Single Cell 5' Kit v2 and Chromium Next GEM Chip K Single Cell Kit , we performed single cell TCR/BCR-seq and 5’ gene expression profiling.

first: Yifan

last: Zhang

first: Cuiyuan

last: Guo


title: Transcriptome analysis of long non-coding RNAs in Mycobacterium avium complex-infected macrophages

city: Yokohama

first: Shiori

last: Maeda

state: Kanagawa

address: 1-7-22 Suehiro-cho Tsurumi-ku

department: Center for Integrative Medical Sciences

country: Japan

institute: RIKEN

summary: Mycobacterium avium complex (MAC) is a non-tuberculosis mycobacteria widely distributed throughout environment. Even though the MAC infection is currently increasing in old women and patients with affected immune system, comprehensive analysis of MAC-infected host cell transcriptome, in particular that of long non-coding RNAs (lncRNAs), has scarcely been reported. Using in vitro cultured primary mouse bone marrow-derived macrophages (BMDMs) and CAGE technology, we analyzed the transcriptional and kinetic landscape of macrophage genes, with focusing on lncRNAs, during MAC infection. MAC-infected macrophages induced immune/inflammatory response genes and other genes as similar as M1 activation, consistent with previous reports, although Nos2 and Arg1 revealed distinct expression profiles from M1 activation. We identified 31 up-regulated and 30 down-regulated lncRNA promoters corresponding to 18 and 27 lncRNAs, respectively. The up-regulated lncRNAs were clustered into two groups, early and late up-regulated groups, which were predicted to associate with the immune activation and the immune response to infection, respectively. Further, the Ingenuity IPA analysis predicted canonical pathways and upstream transcription regulators associated with differentially expressed lncRNAs. Several differentially expressed lncRNAs that have been reported elsewhere revealed various expressional change by M1 or M2 pre-activation and the following MAC infection. Finally, we showed that expressional change of lncRNAs in MAC-infected BMDMs is predominantly mediated by Tlr2, but there may be other weakly sensing mechanism for MAC infection. Taken together, we identified differentially expressed lncRNAs in MAC-infected BMDMs, which revealed diverse features implying their distinct role in MAC infection and macrophage polarization.

overall_design: Bone marrow cells, generated from 8-12 week old BALB/c male mice, were harvested from the femurs. Cells were cultured for 10 days at 37 oC under 5% CO2 in RPMI-1640 containing 10% FBS, 40 ng/ml GM-CSF, 20 ng/ml M-CSF, and 50 μ/ml ampicillin in 90 mm x 15 mm petri dishes with vent. After 10 days, bone marrow-derived macrophages (BMDMs) were harvested and were plated in 6-well plates at 2 x 106 cells per well overnight. BMDMs were infected with log phase Mycobacterium avium subsp. hominissuis (MAH) strain TH-135 (MOI = 200) for 4 hours. Cells were washed to remove extracellular mycobacteria, replenished with fresh medium, and incubated for 0, 4, 12, and 24 hours post infection. For M1 or M2 pre-activation experiments, BMDMs were plated in 6-well plates at 2 x 106 cells per well overnight, followed by stimulation with IFNγ (100 unit/ml) or IL-4/IL-13 (100 units/ml each) for 24 hours. Cells were infected with MAH for 4 hours, washed to remove extracellular mycobacteria, and incubated for 24 hours post-infection. Quadruplicate samples were produced at each condition.

first: Mitsunori

last: Yoshida

first: Yoshihiko

last: Hoshino

first: Harukazu

last: Suzuki


title: OLFM4 promotes the progression of intestinal metaplasia through MYH9/GSK3β/β-catenin pathway

first: hongfa

last: wei

state: Guangdong Province

address: No. 74 Zhongshan Second Road, Yuexiu District, Guangzhou

institute: Sun Yat-sen University

summary: Intestinal metaplasia (IM), precancerous lesions of gastric carcinoma (PLGC) induced by factors like nitrite, Helicobacter pylori, or bile acid, carries a high risk of progressing to gastric cancer. IM is categorized into complete intestinal metaplasia (CIM) and incomplete intestinal metaplasia (IIM). Patients with IIM are at a higher risk of developing gastric cancer, emphasizing its importance for early screening. Besides the diagnostic challenges, the mechanisms underlying its progression remain a mystery. OLFM4, a gene associated with stemness characteristics, has been linked to promoting gastric and colorectal cancers. Our investigation used pathological sections from two clinical centers, biopsies of IM tissues, PLGC cell models, animal models, and organoids to explore OLFM4's role in IIM. OLFM4 expression was observed highly in IIM, with superior diagnostic accuracy of IIM compared to CDX2 and MUC2 for the first time. OLFM4, along with MYH9, was highly expressed in IM organoids and PLGC animal models. OLFM4, in combination with MYH9, accelerated the ubiquitination of GSK3β and resulted in increased β-catenin levels through the Wnt signaling pathway, finally promoting the proliferation and invasion abilities of PLGC cells.  In conclusion, OLFM4 serves as a novel biomarker for IIM and is utilized as an important auxiliary means to delimit the key population for early gastric cancer screening. This study provides new insights into the mechanisms of progression and a new target of therapy in intestinal metaplasia.

overall_design: comparative gene expression profiling analysis of RNA-seq data for PLGC cells

first: HF

last: Wei

first: WC

last: Li

first: K

first: H

last: Yu


title: Transcriptional regulator DhyR positively modulates biosynthesis of daptomycin in Streptomyces rosesporus

city: Chengdu

first: Fuqiang

last: He

state: Sichuan

address: No.17, 3rd Section of People's South Road.

institute: Sichuan University

summary: The production of daptomycin (DAP)  is precisely regulated by a complex regulatory network in Streptomyces roseosporus (S. roseosporus). Although the most biosynthetic pathway of DAP has been elucidated, the regulatory mechanism of its biosynthesis at transcriptional level is not fully understood. In the present study, a transcriptional regulator DhyR has been identified based on our previous quantification proteomics identification in S. roseosporus, and further the dhyR gene deletion mutant has been carried out to reveal DhyR function through transcriptome sequencing and loss-of function validation, which demonstrates DhyR positively regulates DAP biosynthesis in S. rosesporus. In-frame gene deletion of dhyR results in the significant downregulation of the transcription levels of all structural genes in DAP biosynthetic gene cluster and significantly decreases production of DAP. In contrast, overexpression of dhyR enhances transcription levels of DAP biosynthetic gene cluster and leads to a 23% increase of DAP yield. Moreover, the deletion of dhyR resultes in the significant down-regulation of transcription levels of another three regulatory genes, including atrA, depR1 and ssig-05090, which have been demonstrated to be closely associated with the DAP biosynthesis. Transcriptome analyses also support that DhyR modulates carbohydrate metabolism, amino acid metabolism and synthesis and transport pathways of siderophore in S. roseosporus. In summary, our findings indicate that DhyR functions as a pleiotropic regulator of primary and secondary metabolism to involve in DAP biosynthetic regulation of S. roseosporus.

overall_design: To investigate the function of transcriptional regulator  DhyR  in Streptomyces rosesporus MT19, we established the deletion of dhyR gene strain by CRISPR-Cas9 system. Comparative gene expression profiling anaysis of RNA-seq data for wide-type Streptomyces rosesporus and its deletion of dhyR gene strain.

first: Shufang

last: Liang

first: Min

last: Tang

first: Xinpeng

last: Liu

first: Haiyi

last: Wang

first: Yun

last: Wu

first: Dan


title: TAG Synthesis and Oxidation Activated by YAP/TEAD Confers ROS Resistance in Cancer Stem Cells

city: Taipei

first: Jiun-Han

last: Lin

address: No. 155, Sec. 2, Linong St. Beitou Dist., Taipei City

country: Taiwan

institute: National Yang Ming Chiao Tung University

summary: RNA-seq analysis revealed CSCs upregulated in TAG synthesis enzymes, such as ACSL1/4, LPIN2, DGAT1/2, and PNPLA3, and the anti-ferroptosis arsenal, GPX4, all of which were relevant to CSC radioresistance, sphere formation, and tumor initiation.

overall_design: Compare the TAG synthesis pathway in adherent culture and spheroid culture (CSCs). The related protein expression were inhibited bu ues inhibitor or shRNA.

first: Jiun

first: Shih

middle: C

last: Hung

first: Han

last: Hsu

first: Tien

middle: W


title: PURPL Represses Radiation-induced Apoptosis to Promote Radioresistance in Cutaneous Melanoma by Direct Interfering with BID Cleavage

city: GuangZhou

first: shuo

last: Han

address: Shatai South Road

institute: Southern medical university

summary: During the treatment of cutaneous melanoma, the presence of radioresistance compromised the therapeutic effects of radiotherapy. Yet, the mechanism of radioresistance in melanoma still remains unclear. Bioinformatic analysis of the transcriptomic sequencing showed PURPL was top up-regulated genes in response to ionizing radiation (IR) treatment in melanoma cells. Loss of PURPL notably repressed melanoma cell viability, colony formation, migration and invasiveness which potentiated PURPL’s role in radioresistance of melanoma. Further, loss-of- and gain-of-function analysis indicated that PURPL repressed IR-induced DNA damage and apoptosis. Mechanistically, RNA pulldown was performed and BID was identified as the interacting protein partner of PURPL. As the core gene of the mitochondrial apoptosis pathway, BID could be cleaved by Caspase-8 to generate tBID, which promotes the permeability of the mitochondrial membrane and the release of cytochrome c. IR treatment promotes the interaction between BID and Caspase-8 which was further strengthened by the loss of PURPL. The in vivo assays further verified the in vitro findings. Collectively, our study supports the pro-radioresistance role of PURPL in melanoma by inhibiting the interaction between BID and Caspase-8, which may provide a novel target for clinical radiotherapy.

overall_design: In order to investigate the mechanism of melanoma developing resistance to ionizing radiation, we conducted transcriptome sequencing on melanoma cells A375 after irradiation, and analyzed the differentially expressed genes.


title: Schwann cell regulation by NR2F2 using Cut&Run

city: Madison

first: John

last: Svaren

state: WI

address: 1500 Highland Ave.

department: Comparative Biosciences

institute: University of Wisconsin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We  focused on NR2F1 and NR2F2 (CoupTF1/CoupTF2) since they are expressed from neural crest through Schwann cell maturity, and found that knockdown of nuclear receptors Nr2f1 and Nr2f2 in primary Schwann cells downregulated genes such as Myelin Basic Protein (Mbp), Desert Hedgehog (Dhh), and N-Myc Downstream Regulated 1 (Ndrg1). In this study, we have elucidated a NR2F-regulated target gene network in Schwann cells, which revealed enrichment for non-myelinating Schwann cell genes. We used Cut&Run in S16 Schwann cells to show novel, genome-wide binding sites of NR2F1/2 and downstream transcription factors, YY1, SREBP1, Retinoid X Receptor (RXRG) and TEA-Domain factor (TEAD1). Our study elucidates the transcriptional cooperation that forms unique enhancer landscapes and the regulatory network that targets non-myelinating Schwann cells.

overall_design: Since nuclear receptor motifs are enriched in SOX10-bound enhancers in Schwann cells compared to oligodendrocytes (Lopez-Anido et al., 2015), we tested if NR2F1/2 proteins localize to SOX10-bound enhancers in S16 Schwann cells. We performed Cut&Run assays for NR2F2 (Skene and Henikoff, 2017). We also analyzed binding of NR2F1, but found that it is expressed at lower levels than NR2F2 and that the pattern of binding was less distinct compared to NR2F2. Finally, we performed ChIP-seq analysis for the enhancer mark, H3K27 acetylation (Rada-Iglesias et al., 2011), to identify those enhancers that are active in the S16 Schwann cell line.

first: Raghu

last: Ramesh

first: Harrison

last: Pantera


title: Correction of the Exon 2, Exon 2-8 and Exons 8-9 duplications in DMD patient myogenic cells by a Single CRISPR/Cas9 system

city: EVRY

first: Corre

last: Guillaume

address: 1 rue de l'internationale

institute: GENETHON

summary: Duchenne Muscular dystrophy (DMD), a yet-incurable X-linked recessive disorder that results in muscle wasting and loss of ambulation is due to mutations in the dystrophin gene. Exonic duplications of dystrophin gene are a common type of mutations found in DMD patients. In this study, we utilized a single guideRNA CRISPR strategy targeting intronic regions to delete the extra duplicated regions in patient myogenic cells carrying duplication of exon 2, exons 2 to 9, and exons 8 to 9 in the DMD gene. Immunostaining on CRISPR corrected derived myotubes demonstrated the rescue of dystrophin protein. RNA sequencing of the corrected differentiated myogenic derivatives indicated rescue of dystrophin related molecular pathways. Examination of predicted close-match off-targets evidenced no aberrant gene editing at these loci. Here, we demonstrated a single guide CRISPR strategy that can be utilized to delete multi-exons duplication in patient DMD genes without significant off target effect, leading to restoration of transcriptome in the corrected patient derived cells. This study further expands the application of single guide CRISPR strategy as a potential therapeutic approach for patients with larger DNA region duplication in DMD patients.

overall_design:
To remove the exonic DMD duplication , we perfomed a transfection of single guide RNA system with CRISPR in 3 different cell lines (myoblasts containing 3 different types of DMDduplications)
We then performe comparative gene expression profilling between the correted myotubes and the duplicated ones after differenciation of myoblasts into myotubes for 8 days.

first: Isabelle

last: Richard

first: Matteo

last: Bovolenta

first: Juliette

last: Lemoine

first: Alan

last: Dorval

first: Auriane

last: Dubois

first: Tao


title: Aberrant expression of the DCT gene is implicated in the hyperpigmentation of the visceral peritoneum of the chicken

city: guangzhou

first: xu

last: dong

state: Guangdong

address: wushan

institute: South China Agricultural University

summary: Hyperpigmentation of the visceral peritoneum (HVP) has recently garnered significant attention within the poultry industry due to its potential implications for the health of afflicted animals and its adverse effects on the appearance of commercial chicken carcasses.  Unfortunately, the heritable characteristics of HVP are not yet fully understood. Motivated by poultry industry demand, we deployed multi-omics comparing the clinical HVP and normal samples profiling the potential regulating molecular landscape in cell and genome resolution, specifically, aiming to decipher the precise molecular genomic marker. Specifically, we identified the signature genes for the HVP phenotype and found that the signature gene of melanogenesis strongly enriched in the HVP group. At the melanocyte level, overexpression of the DCT gene can promote the proliferation of melanocytes, with exogenous Tyr addition. On the contrary, significantly lower melanin content in the supernatant of cells was detected after siRNA interference relative to untreated cells. Through single-cell sequencing, the hyperexpression of melanogenesis-associated genes in melanocytes was echoed. In summary, molecular features of the HVP phenotype were systematically revealed, which may partially explain the strong heterogeneities of the peritoneum phenotype. The hyperpigmentation of the peritoneum is attributed to an excess deposition of melanin, where the DCT hyperexpression can be regarded as a molecular marker related to the deposition of peritoneal melanin. Future directions should deploy gene editing technology to alert the gene expression of DCT to change the phenotype of pigmentation in the visceral peritoneum.

overall_design: In this experiment, ten 40-day-old Huiyang Bearded Chickens, each with normal and black peritoneum color, were selected. Following humane slaughter in compliance with animal welfare requirements, peritoneum tissues were swiftly separated using scissors. The tissues were immediately rinsed 2-3 times in 4-degree pre-chilled 1×PBS on ice and then transferred to a 1.5mL centrifuge tube for scRNA-seq.

first: Zhenhui

last: Li

first: Xu

last: Dong


title: Pycallingcards: an integrated environment for visualizing, analyzing, and interpreting Calling Cards data

city: Saint Louis

first: Juanru

last: Guo

state: MO

address: 4515 McKinley Ave

department: Department of Genetics

institute: Washington University in St. Louis  School of Medicine

summary: Unraveling the transcriptional programs that control how cells divide, differentiate, and respond to their environments requires a precise understanding of transcription factors'(TFs) DNA-binding activities. Calling cards (CC) technology uses transposons to capture transient TF binding event at one instant in time and then read them out at a later time. This methodology can also be used to simultaneously measure transcription factor binding and mRNA expression from single cells CC and to record and integrate TF binding events across time in any cell type of interest without the need for purification. Despite these unique advantages, there has been a lack of dedicated bioinformatics tools for the detailed analysis of CC data. Here, we introduce Pycallingcards, a comprehensive Python module specifically designed for the analysis of single-cell and bulk CC data across multiple species. The package introduces two innovative peak callers, CCcaller and MACCs, enhancing the accuracy and speed of pinpointing TF binding sites from CC data. Pycallingcards offers a fully integrated environment for data visualization, motif finding, and comparative analysis with RNA-seq and ChIP-seq datasets. To illustrate its practical application, we have reanalyzed previously published mouse cortex and glioblastoma datasets. This analysis revealed novel cell-type specific binding sites and potential sex-linked TF regulators, furthering our understanding of TF binding and gene expression relationships. Thus, Pycallingcards, with its user-friendly design and seamless interface with the Python data science ecosystem, stands as a critical tool for advancing the analysis of TF function via CC data.

overall_design: Calling Cards were transfected into k562 cells in multiple replicates. Transfected cells were selected with puromycin and bulk Calling Cards libraries were prepared.

first: Xuhua

last: Chen

first: Allen

last: Yen

first: Joseph

middle: D

last: Dougherty

first: Robi

last: Mitra


title: A single-cell analysis of the NK cell landscape reveals that dietary restriction boosts NK cell antitumor immunity via Eomesdermin

city: Beijing

first: Chen

last: Donglin

state: 北京Beijing

address: Tsinghua

institute: Tsinghua

summary: Natural killer (NK) cells are primarily responsible for tumor surveillance, and their activation entirely depends on optimal metabolic signals. The adaptation of NK cell anti-tumor responses to nutritional stress is still poorly understood. Here, based on single-cell RNA sequencing, we discovered that dietary restriction (DR) enriches the rejuvenated subset of CD27+CD11b+ NK cells and improves their activation via Eomesodermin (Eomes), a transcription factor upregulated during DR treatment. Eomes reverses the differentiation of rejuvenated to senescent NK cells by antagonizing the T-bet-Zeb2 axis while improving chemotaxis and adhesion. Furthermore, DR increases the chromatin accessibility of Eomes to genes that regulate chemotaxis and adhesion in NK cells. To summarize, tumor control under dietary restriction requires Eomes-regulated NK cell anti-tumor immunity.

overall_design: NK cells were isolated from the spleen of normal and dietary restriction mice by flow cytometry, and analyzed using scRNAseq

first: Junming

last: He

first: Donglin


title: Neuregulin 4 mediates the metabolic benefits of mild cold exposure by promoting beige fat thermogenesis

city: Ann Arbor

first: Jiandie

last: Lin

state: MI

address: 210 Washtenaw Ave

department: Life Sciences Institute

institute: University of Michigan

summary: Interorgan crosstalk via secreted hormones and metabolites is a fundamental aspect of mammalian metabolic physiology. Beyond the highly specialized endocrine cells, peripheral tissues are emerging as an important source of metabolic hormones that influence energy and nutrient metabolism and contribute to disease pathogenesis. Neuregulin 4 (Nrg4) is a fat-derived hormone that protects mice from nonalcoholic steatohepatitis (NASH) and NASH-associated liver cancer by shaping hepatic lipid metabolism and the liver immune microenvironment. Despite its enriched expression in brown fat, whether NRG4 plays a role in thermogenic response and mediates the metabolic benefits of cold exposure remain unexplored. Here we show that Nrg4 expression in inguinal white adipose tissue (iWAT) is highly responsive to chronic cold exposure. Nrg4 deficiency impairs beige fat induction and renders mice more susceptible to diet-induced metabolic disorders under mild cold conditions. Using mice with adipocyte and hepatocyte-specific Nrg4 deletion, we reveal that adipose tissue-derived NRG4, but not hepatic NRG4, is essential for beige fat induction following cold acclimation. Furthermore, treatment with recombinant NRG4-Fc fusion protein promotes beige fat induction in iWAT and improves metabolic health in diet-induced obese mice. These findings highlight a critical role of NRG4 in mediating beige fat induction and preserving metabolic health under mild cold conditions.

overall_design: To investigate the impact of Nrg4 deficiency on beige fat during cold acclimation, we subjected wild-type and NRG4 AKO (Nrg4 knockout) mice to an environment maintained at 8 degrees Celsius for a period of ten days in a temperature-controlled chamber. Following this acclimation, inguinal white adipose tissue (iWAT) samples were harvested for gene profile analysis.Each sample subjected to RNA sequencing consisted of pooled RNA from two mice with the same genotype.

first: Zhimin

first: Peng

last: Zhang

first: Tongyu

last: Liu

first: Xiaoxue

last: Qiu

first: Siming


title: Methylation profiling of CNS white matter samples across different age groups.

city: Münster

first: Christian

last: Thomas

address: Pottkamp 2

country: Germany

institute: Institute of Neuropathology Münster, Germany

summary: This study comprises DNA methylation profiles of 15 white matter samples obtained from CNS autopsies across different age groups to study age-associated epigenetic changes. The samples comprise 5 young, 5 adult and 5 old indivudials.

overall_design: Bisulphite converted DNA from the 15 white matter samples were hybridised to the MethylationEPIC BeadChip array.


title: Methylation profiling of directly converted human fibroblasts from young, adult and old donors into oligodendrocytes (dc-hiOL) to study age-associated changes.

summary: This study comprises DNA methylation profiles of 9 directly converted human fibroblasts from young, adult and old donors into oligodendrocytes (dc-hiOL).

overall_design: Bisulphite converted DNA from the 9 dc-hiOL samples were hybridised to the MethylationEPIC BeadChip array.


title: Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef-building corals [Methyl-seq]

city: University Park

first: KELLY

middle: Johanna

last: GOMEZ-CAMPO

state: Pennsylvania

address: 212 Mueller Laboratory

department: Biology

institute: PSU

type: Methylation profiling by high throughput sequencing

summary: Acclimatization through phenotypic plasticity represents a more rapid response to environmental change than adaptation and is vital to optimize organisms’ performance in different conditions. Generally, animals are less phenotypically plastic than plants, but reef-building corals exhibit plant-like properties. They are light-dependent with a sessile and moddular construction that facilitates rapid morphological changes within their lifetime. We induced phenotypic changes by altering light exposure in a reciprocal transplant experiment and found that coral plasticity is a colony trait emerging from comprehensive morphological and physiological changes within the colony. Plasticity in skeletal features optimized coral light harvesting and utilization and paralleled with significant methylome and transcriptome modifications. Network-associated responses resulted in the identification of hub genes and clusters associated to the change in phenotype: inter-partner recognition and phagocytosis, soft tissue growth and biomineralization. Furthermore, we identified hub genes putatively involved in animal photoreception-phototransduction. These findings fundamentally advance our understanding of how reef-building corals repattern the methylome and adjust a phenotype, revealing an important role of light sensing by the coral animal to optimize photosynthetic performance of the symbionts.

overall_design:
To examine the phenotype to methylome association, we conducted a reciprocal transplant experiment to induce light-mediated phenotypic responses in the reef-building Elkhorn coral Acropora palmata and investigated DNA methylation and transcriptional responses potentially responsible for plasticity. Extensive biometrics revealed not only changes in coral tissue pigmentation and metabolic rates but also in skeletal morphology after five weeks. This skeletal remodeling was accompanied by intragenic methylome repatterning, discovered by signal detection with machine learning-based analysis. We further integrated differentially methylated (DMG) and expressed (DEG) gene datasets to elucidate how light responses integrate into gene regulatory networks controlling functional traits. By exploring the resulting hub genes and gene clusters, we were able to predict functional associations with observed phenotype changes and identify markers of plasticity in reef-building corals. Moreover, our results contribute to emerging evidence that epigenetics contribute to the machinery that can alter DNA structure during skeletal remodeling in metazoans.
To induce phenotypic plasticity, we performed a reciprocal transplant experiment. We sampled 3 colonies (representing 3 distinct multilocus genotypes, or genets, as detected with Standard Tools for Acroporid Genotyping STAGdb) from a depth of 2-3 m, each at least 300 m apart. We collected ~7 cm2 fragments from HL (n= 42 Upperside) and LL (n = 42 Underside) surfaces of branch surfaces keeping track of genet identification. We settled them in a reef-deployed PVC structure designed to simulate the light condition and colony position of source colonies. We placed all coral fragments in their original light condition and orientation (i.e. HL Uppersides facing up) and allowed them to heal and acclimate. Subsequently, we randomly divided HL fragments into control (Upperside Control) and treatment groups (Upperside Treatment), equal grouping was done for LL fragments (Underside Control and Underside Treatment). To induce phenotypic plasticity, coral fragments in treatment groups were flipped to the opposite light condition and position (i.e. high light fragments were flipped to a low light condition, while LL fragments were flipped to a HL position). This second acclimatory period was carried out for 5+ weeks. Four group conditions were analyzed after 13+ weeks of experiment: HL controls (n= 21 Upperside Control), HL⇾LL treatments (High Light to Low Light, n = 21, Upperside Treatment), LL controls (n= 21 Underside Control), LL⇾HL treatments (Low Light to High Light, n = 21, Underside Treatment)).

first: Kelly

last: Gomez-Campo

first: Robersy

last: Sanchez

first: Isabel

last: Martinez-Rugerio

first: Xiaodong

last: Yang

first: Tom

last: Maher

first: C

last: Osborne

first: Susana

last: Enriquez

first: Iliana

middle: B

last: Baums

first: Sally

last: Mackenzie

first: Roberto

last: Igelsias-Prieto


title: Phenotypic plasticity for improved light harvesting, in tandem with methylome repatterning in reef-building corals [RNA-seq]


title: mRNA transcriptome sequencing of CD45- lung tumor cells from tumor-burdened lungs of  KrasLSL-G12D/+Lkb1fl/fl and KrasLSL-G12D/+Lkb1fl/flUsp25-/- mice 10 weeks after they were intranasally injected with Ad-Cre

first: Ci

summary: Comparative gene expression profiling analysis of RNA-seq data in  CD45- lung tumor cells from tumor-burdened lungs of  KrasLSL-G12D/+Lkb1fl/fl and KrasLSL-G12D/+Lkb1fl/flUsp25-/- mice  10 weeks after they were intranasally injected with Ad-Cre.

overall_design: To investigate the mechanisms by which USP25 promotes lung tumorigenesis, we performed the transcriptomic analysis of the CD45- lung tumor cells from KrasLSL-G12D/+Lkb1fl/fl (n=2) and  KrasLSL-G12D/+Lkb1fl/flUsp25-/-  mice (n=2).

first: Hong-Xu

last: Li

first: Bo

last: Zhong

first: Dandan


title: Transcriptomic Analysis of Outer Medullary Collecting Duct (OMCD) from mice under control or high-Salt diet.

city: PARIS

first: Caroline

last: Prot-Bertoye

address: 15 rue Ecole de Médecine

institute: CNRS EMR8228, INSERM UMRS 1138

summary: We applied RNAseq analysis on microdissected outer medullary collecting duct renal segments from mice fed a normal (0.3% Na+) or high Na+ (3%) diet for 3 days. Among 11688 genes sequenced, 293 have an expression significantly modified (p<0.05), 78 with a -1<log2FC>1. In addition to expected results like the decreased expression of genes participating at the Na+ reabsorption (Scnn1a, SGK1), we observed the stimulation of ATP12a gene that participate at a recently described Na+ secretion pathway.

overall_design: Comparison of gene abundance by RNA-sequencing between outer medullary collecting duct (OMCD) of WT C57BL/6J mice under normal or 3 days-high salt diet.

first: Gilles

last: Crambert

first: Chloé

last: Rafael

first: Lydie

last: Cheval

first: Beata

last: Gyorgy


title: Evaluation and mechanism study of cardiotoxicity caused by antipsychotics using human-induced pluripotent stem cell-derived cardiomyocytes

city: Hangzhou

first: Yuhong

last: Cao

address: pingle road 325

institute: ZheJiang Institute For Drug Control

summary: In this study, a comprehensive evaluation model for studying the cardiac toxicity of antipsychotic drugs was established by using iPSC-CMs. Six antipsychotic drugs, including aripiprazole, risperidone, quetiapine, haloperidol, clozapine, and olanzapine, all induced concentration-dependent QT prolongation in iPSC-CMs upon acute administration, and high concentrations of these drugs caused disorganized sarcomere arrangement in iPSC-CMs.

overall_design: The experiments were divided into two groups, the control group and the Aripiprazole treatment group , n=3

first: Xiaochen

last: Wang

first: Ping

last: Liang

first: Rong

last: Kuang


title: Multiomic Profiling Reveals Metabolic Alterations Mediating Aberrant Platelet Activity and Inflammation in Myeloproliferative Neoplasms [human RNA-Seq]

first: Fan

last: He

address: Room 8834, 320 S. Euclid Ave, CSRB building

institute: Washington University School of Medicine in St. Louis

summary: To investigate the effects of α-KG on monocyte gene expression, magnetic beads-sorted CD14+ human monocytes from MPN patients (PT, n = 3) and healthy individuals (HI, n = 2) were incubated with α-KG (250μM) or DMSO control for 6 hours. Cell pellets were collected for RNA-seq analysis.

overall_design: gene expression profiling analysis of human primary monocytes

first: Stephen

last: Oh

first: Jorge

last: Di Paola


title: Multiomic Profiling Reveals Metabolic Alterations Mediating Aberrant Platelet Activity and Inflammation in Myeloproliferative Neoplasms [scRNA-Seq]

summary: Platelets from patients with myeloproliferative neoplasms (MPNs) exhibit a hyperreactive phenotype. Here, we performed a single cell RNA-seq analysis of primary PBMC samples from essential Thrombocythemia (ET) and healthy individuals (HI) and found significant enrichment of transcripts related to platelet activation, mTOR and oxidative phosphorylation (OXPHOS) in ET platelets.

overall_design: PBMC scRNA-seq


title: Multiomic Profiling Reveals Metabolic Alterations Mediating Aberrant Platelet Activity and Inflammation in Myeloproliferative Neoplasms [mouse RNA-Seq]

summary: To study therapeutic impacts of α-KG on MPN, cKIT+ cells from JAK2 V617F CD45.2 C57BL/6J mice were isolated and transplanted into irradiated CD45.1 C57BL/6J mice. Two weeks after transplant, mice were randomly grouped and supplemented with regular water or 1% α-KG in drinking water daily for 6 weeks. Bone marrow samples were collected for bulk RNA-seq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow samples from mice supplemented with regular water or 1% α-KG in drinking water.


title: Oseltamivir enhances 5-FU sensitivity in esophageal squamous carcinoma with high SPNS1

city: taiyuan

first: xin

last: yang

state: shanxi

address: 56 Xinjian South Road, Yingze District, Taiyuan City, Shanxi Province

institute: shanxi medical university

summary: Abstract Background: Sphingolipid transporter 1 (SPNS1) is a significant differentially expressed gene (DEGs) in esophageal squamous cell carcinoma (ESCC), but its role in cancer is unclear. This study aimed to investigate the role and potential mechanism of SPNS1 in ESCC. Methods: Transcriptomic data from 155 pairs of ESCC samples and GSE53624, and proteomic data from PXD021701 including 124 ESCC samples, were analyzed to determine the clinic relevance of SPNS1 in ESCC. The effects of SPNS1 on various phenotypes of ESCC cells, including proliferation, invasion, migration, apoptosis, and chemotherapy resistance, were assessed using MTT, Transwell, wound healing assay, and flow cytometry. Transcriptome sequencing was performed in ESCC cell lines with SPNS1 knockdown and DEGs correlated with SPNS1 were screened out and performed bioinformatics analysis. The correlation between NEU1, one of the identified DEG, and SPNS1 and the potential mechanism was validated. Results: SPNS1 was significantly higher in ESCC tissues compared to adjacent normal tissues. Patients with high SPNS1 had a significantly poorer clinical prognosis than those with low SPNS1. Knockdown of SPNS1 significantly inhibited proliferation, migration, and invasion of ESCC cells, while promoting apoptosis. And overexpression of SPNS1 exhibited opposite functions. Furthermore, ESCC cells became more sensitive to the chemotherapy drug 5-fluorouracil (5-Fu) after SPNS1 knockdown. Transcriptome sequencing revealed that NEU1 was one significant DEG affected by SPNS1 and positively correlated with SPNS1 expression. Oseltamivir phosphate (OP), one NEU1 inhibitor, markedly reversed 5-Fu resistance, migration, and proliferation induced by high expression of SPNS1 both in vitro and in vivo. Conclusion: Our findings indicated that SPNS1 may promote the progression of ESCC by upregulating NEU1 expression and influencing chemotherapy sensitivity. These results provide new insights into potential therapeutic targets for ESCC treatment.

overall_design: the different expression about NC and SPNS1si in ESCC cell lines (KYSE150 and TE5)


title: Effects of KD USF2 on gene expressions in C2C12

city: Shenzhen Shi

first: zishuai

last: wang

state: Guangdong Sheng

address: Peng Fei Lu

institute: caas

summary: USF2 has emerged as a key player in various cellular processes, including cell cycle regulation， apoptosi, metabolism, and response to cellular stress. In the context of muscle biology, the role of USF2 is not clear. To elucidate the functional significance of USF2, we conducted knockdown (KD) experiments targeting USF2 in C2C12 myoblast cells. The KD of USF2 resulted in the differential expression of a set of genes, and  functional enrichment analysis of genes affected by KD of USF2 were performed.

overall_design: To investiage the function of USF2 in C2C12 cells, expression profiling of genes affetcted by knocking donwn USF2 were evaluated by high throughput sequencing

first: Zishuai

first: Yilong

last: Yao

first: Zhonglin

last: Tang


title: Serotonergic-dependent effects of exercise and elevated stress hormone on small non-coding RNA transcriptomics and proteomics in a mouse model of affective disorders

city: Melbourne

first: Maria

last: Kuznetsova

state: Victoria

address: 30 Royal parade

department: Florey Institute

country: Australia

institute: University of Melbourne

summary: Environmental changes may alter gene expression in depression and anxiety disorders through epigenetic regulation, including small non-coding RNAs (sncRNAs) and their major subclass, microRNAs (miRNAs). However, underlying mechanisms mediating miRNA regulation in response to changing environmental stimuli are unclear. Using the serotonin transporter (5-HTT) knockout (KO) mouse model of depression/anxiety, this study aimed to compare the effects of voluntary exercise versus chronic treatment with the stress hormone, corticosterone, on miRNA transcriptome and proteome. Using high-throughput sequencing of miRNAs and mass spectrometry (MS)-based approaches for protein expression, we described 337 differentially expressed (DE) miRNAs and 67 proteins in 5-HTT KO mice compared to wild-type (WT) control mice in standard-housing conditions. After exercise, there were 200 DE miRNAs and 3 DE proteins in WT mice, and 20 DE miRNAs and 95 DE proteins in 5-HTT KO mice, while corticosterone treatment led to 168 DE miRNAs and 1 DE protein in WT, and 21 DE miRNAs and 21 DE proteins in 5-HTT KO mice. Serotonergic dysfunction (due to the 5-HTT KO gene mutation) induced altered expression of miRNAs and proteins involved in regulation of neurodevelopment, neurogenesis and neuroinflammatory responses. Elevation of the stress hormone corticosterone activated similar (to 5-HTT KO) molecules in WT mice, while exercise caused antidepressant-like effects. We suggest that these findings indicate that functional 5-HTT might be required for the beneficial effects of exercise on miRNA expression. Our study is the first to explore how gene-environment interactions affect miRNA/proteomics composition in a mouse model of depression/anxiety and extends our understanding of gene-environmental interactions underlying these affective disorders.

overall_design: We examined hippocampal tissue of the WT and 5-HTT KO mice in standard-housing conditions and after 4 weeks of exercise and corticosterone treatment


title: K-562 cell lines

city: Tsukuba

first: Fumio

last: Kasai

address: Koyadai 3-1-1

institute: RIKEN

summary:
Divergence of K-562 genomes through in vitro clonal evolution revealed by comparing three sublines.
Comparison of three K-562 sublines

overall_design: Establishment of reference data for human cell lines


title: Core fucosylation of IL-15 receptor delineates homeostatic proliferation and apoptosis signalling required for natural killer cell development

city: Monash University

first: Harrison

last: Sudholz

state: VIC

address: 15 Innovation walk

department: Biochemistry and Molecular Biology

institute: Monash University

summary: Natural Killer (NK) cell development and effector function requires context-dependent signalling via numerous receptors including the IL-15 receptor. The modulation of receptor signalling can be regulated by the post-translational modifications affecting receptor turnover and trafficking. Core fucosylation is one such modification known to impact receptor expression and is uniquely mediated by fucosyltransferase 8 (FUT8). To investigate core fucosylation in NK cell biology, we generated mice lacking FUT8 in NK cells (Fut8fl/flNcr1cre/+). Loss of core fucose resulted in pronounced NK lymphopenia in Fut8fl/flNcr1cre/+ mice associated with a reduction in IL-15 receptor expression and loss of in vivo proliferation. Inhibition of intrinsic apoptosis pathways could not overcome compromised IL-15 receptor signalling to rescue FUT8-null NK cell development delineating the contribution of proliferation to NK cell homeostasis. Surprisingly, loss of core fucose enhanced NK cell expansion following viral infection and this was associated with upregulation of IL-2Rα following pro-inflammatory cytokine exposure and enhanced IL-2-mediated proliferation. Lastly, loss of FUT8 activity impaired TGFBR2 expression and immunosuppressive effects of TGF-β on NK cells. Taken together, we have identified fucosyltransferase 8 as a key modulator of NK cell development and function by regulating IL-15 receptor responsiveness.

overall_design: RNA-seq of enriched splenic NK cells after culturing for 5 days in the presence of 50 ng/ml IL-15; Three replicates each for WT (Ncr1-Cre- Fut8 fl/fl) and Fut8 knockout (Fut8.Ncr1; Ncr1-Cre+ Fut8 fl/fl).

first: Sebastian

last: Scheer

first: Nicholas

last: Huntington


title: Specialized retinal endothelial cells modulates blood-retina- barrier in diabetic retinopathy

city: TianJin

first: Kaiwen

last: Bao

institute: Tianjin Medical University

summary: Endothelial cells (EC) play essential roles in retinal vascular homeostasis. This study aimed to characterize retinal EC heterogeneity and functional diversity using single-cell RNA sequencing (scRNA-seq). Systematic analysis of cellular compositions and cell-cell interaction networks identified a unique EC cluster with high inflammatory gene expression in the diabetic retina; sphingolipid metabolism in this cluster is a prominent aspect correlated with changes in retinal function. Among the sphingolipid-related genes, alkaline ceramidase 2 (ACER2) showed the most significant increase. We collected plasma and vitreous samples from patients with non-proliferative diabetic retinopathy (NPDR) and PDR for mass spectrometry analysis. Metabolomic profiling revealed that the ceramide levels were significantly elevated in NPDR and further increased in PDR compared with control patients. In vitro analyses showed that the ACER2 overexpression retarded endothelial barrier breakdown induced by ceramide, while silencing of ACER2 further disrupted the injury. Moreover, intravitreal injection of the recombinant ACER2 adeno-associated virus rescued diabetes-induced vessel leakiness, inflammatory response, and neurovascular disease in diabetic mouse models. Together, this study revealed a new diabetes-specific retinal EC population and a negative feedback regulation pathway that reduces ceramide content and endothelial dysfunction by upregulating ACER2 expression. These findings provide insights into cell-type targeted interventions for diabetic retinopathy.

overall_design: Single live CD31+ cells from the retina were enriched using CD31 microbeads. The cell suspensions were mixed with filtered trypan blue to evaluate cell viability and concentration. Using the cell count and recommended cell concentration, we performed the following steps on a 10x Genomics chromium single-cell platform, and libraries were constructed according to the manufacturer’s instructions of 10x Chromium Single Cell 3′ Regent Kit v3 protocol (10X Genomics, 1000121). Briefly, single-cell suspensions were loaded to 10x Chromium. cDNA amplification and library construction were performed according to standard protocols. Libraries were sequenced using an Illumina NovaSeq 6000 sequencing system (paired-end multiplexing run, 150bp) by LC-Bio Technology Co., Ltd. (Hangzhou, China), at a minimum depth of 20,000 reads per cell.

first: Xuyang

first: Wenhui

last: Zhang

first: Ruixin

last: Liu

first: Tianwen

last: Ni

first: Bohao

last: Cui

first: Yi

last: Lei

first: Jie

last: Du

first: Ding

last: Ai

first: Hongfeng

last: Jiang

first: Huizhen

last: Lv

first: Xiaorong

last: Li


title: Multiomic Profiling Reveals Metabolic Alterations Mediating Aberrant Platelet Activity and Inflammation in Myeloproliferative Neoplasms

first: Fan

last: He

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: Phagocytes as Trojan horse for Fusobacterium nucleatum routing to the tumor tissues and enhance tumor metastasis

city: Guangzhou

first: Fangfang

last: Chen

address: No.132 Waihuandong Road, University Town

department: School of Pharmaceutical Sciences

institute: Sun Yat-sen University

summary: The facultative intracellular bacterium Fusobacterium nucleatum (Fn), mediates tumorigenesis and progression in CRC. However, the origin of intracellular Fn and the role of Fn-infected phagocytes in tumor microenvironment remains unclear. Here, we observed Fn-infected neutrophils/macrophages (PMNs/MΦ) is accumulated in CRC tumor tissues. Fn can survive inside of PMNs by reducing intracellular ROS levels. The lysozyme inhibitor Fn-MliC induced the expression of the CX3CR1 which suppressed apoptosis of phagocytes. Fn-infected phagocytes can transfer Fn to tumor cells, and Fn-infected CRC cells recruited PMNs and MΦ/monocytes through the CXCL2/8-CXCR2 and CCL5/CCR5 axis. Intracellular Fn upregulated PD-L1 expression through activating NF-κB/STAT3 pathway in PMNs. PD-L1+ PMNs infiltration promotes CRC metastasis and weaken the efficacy of immunotherapy, and eradication intracellular Fn infection retarded the Fn promoted tumor progressing in mice. These results suggest that Fn volved efficient strategies to exploit phagocytes to home to tumor tissues, inhibited immune responses and facilitate tumor metastasis.

overall_design: To explore the mechanism of Fn-MliC-attenuated apoptosis,we performed transcriptome profiling experiments in Fn-MliC-treated mouse leukocytes

first: Songhe

last: Guo

first: Yiqiu

first: Yongfan

last: Lu

first: Jinzhu

last: Mao

first: Le

first: Shengxin


title: The methyltransferase activity of Setd2 is essential for mouse embryonic development: establishment of a mouse model harboring a patient-derived Setd2 mutation

city: Shanghai

first: Shubei

address: No.1954 Huashan Rd

institute: School of Life Sciences & Biotechnology, Shanghai Jiao Tong University

summary: The histone methyltransferase SETD2 is responsible for the transcription-coupled trimethylation of histone H3 lysine 36 (H3K36me3) on all protein-coding genes through its direct interaction with the elongating form of RNA polymerase II. In mice, Setd2 is required for embryonic development, as the Setd2-null mice are embryonic lethal due to impaired vascular remodeling. In human, SETD2 is frequently mutated in various types of cancer, thus representing one of the major chromatin-modification defects that drive tumorigenesis. Notably, recent studies suggest that, despite the central roles of their catalytic activities, many chromatin modifiers contain important non-catalytic (so-called “moonlighting”) functions, which are largely substantiated by their roles in protein-protein interactions. This notion is somewhat consistent with the observation that the cancer-associated SETD2 mutations are seemingly localized throughout the whole protein, thus raising a question whether the major function(s) of SETD2 is solely dependent on its methyltransferase activity. As an answer to this question, in this short report, we have established a site-specific Setd2 knock-in mouse model harboring a patient-derived, catalytic dead Setd2 and have provided clear evidence supporting that the requirement of Setd2 in mouse embryonic development is definitely dependent on its methyltransferase activity. However, it is also notable that, in comparison with the Setd2-null mice, the Setd2 catalytic dead mice showed slightly mild defects in embryonic development and gene expression changes, suggesting potential non-catalytic functions of Setd2, which could be studied in the future by using these different Setd2 mouse models.

overall_design: Mouse embryos and yolk sacs mRNA profiles of Setd2-null (wild type-WT, heterozygous-HE, homozygous-HO) and Setd2 catalytic dead  (wild type-WT, heterozygous-HE, homozygous-HO) at embryonic day 9.5 (E9.5).Two replicates in each group.

first: Xiaojian

last: Sun


title: High power of 0.26 Terahertz radiation induced genes involved in immune system and nervous system changes in the nematode Caenorhabditis Elegans

city: Xi'an

first: Sen

last: Shang

address: West Xianning Road

institute: Xi'an Jiaotong University

summary: The biological impacts of terahertz (THz) waves as well as their biosafety have emerged as a new area of concern with the gradual application of terahertz radiation.  In recent years, many studies have been conducted to investigate the influence of terahertz on living organisms, such as animals or cell cultures; however, the biological effects of terahertz waves have not yet been fully revealed. In this study, Caenorhabditis elegans (C. elegans), one of the most acceptable model organisms for studying various forms of ionizing and non-ionizing radiation exposure was used to evaluate the effects of terahertz waves on the entire organism. In this study, the integration of transcriptome sequencing and behavioral tests of C. elegans revealed that high-power THz irradiation damaged the epidermal ultrastructures, inhibited the expression of cuticle collagen gene to impair the movement of C. elegans. Our findings offer fresh perspectives on the biological impacts of high-power THz radiation that could cause epidermal damage and provoke a systemic response.

overall_design: To investigate the effect of THz on C. elegans, we performed gene expression profiling analysis using  data obtained from RNA-seq of 3 THz treated and 3 control primary C.elegans

first: Fei

last: Gao

first: Qi


title: Identification and characterization of pathogenic ZNF687 variant in acute myeloid leukemia

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

summary: Analysis of Beat AML sequencing data revealed a recurrent frameshift variant (R939Pfs*Ter36) in Zinc Finger 687 (ZNF687) that was observed in ~1% of patients and has not been previously described. ZNF687 encodes a transcription factor containing DNA binding C2H2 zinc finger and has been studied in select other malignancies, including Paget’s disease of bone that is associated with giant cell tumor (PDB/GCT) and hepatocellular carcinoma. It is part of a network with ZMYND8 and two additional zinc finger proteins, ZNF592 and ZNF532, that associate with H3K4 demethylation machinery and regulates gene transcription. The R939Pfs*Ter36 frameshift induced overexpression of ZNF687 compared with wild-type, and the overexpressed protein was mislocalized to the cytoplasm. We further performed RNA sequencing on HEK293 cells expressing the frameshift variant, wild-type, or a previously identified variant (P937R) that has been reported as a germline ZNF687 variant characterized to predispose to PDB/GCT. We observed the R939Pfs*Ter36 frameshift to induce activation of oxidative phosphorylation, inactivation of histone methylation machinery, and significant downregulation of lysine methyltransferase 2D (KMT2D) compared with wild-type and P937R. Overall, these findings suggest that ZNF687 R939Pfs*Ter36 plays an important role in AML pathogenesis, which could aid in diagnostic precision, and may impact therapeutic responses.

overall_design: Six-well plates were seeded with 3e5 HEK293 cells overnight. The cells were transfected with ZNF687 WT, frameshift, missense variant containing plasmids and pMIG empty using Fugene6 (Promega) according to the manufacturer’s protocol. Cells were cultured and harvested for protein lysate extraction following the observation of GFP fluorescence 72h after transfection. RNA was purified using the QIAGEN RNeasy Mini Kit. Total RNA integrity was evaluated using the Bioanalyzer (Agilent). RNA-seq libraries were prepared from total RNA using the Illumina Stranded mRNA kit (Illumina). Libraries were then profiled on a TapeStation D1000 tape (Agilent) and quantified using an NGS Library Quantification Kit (Roche/Kapa) on a StepOnePlus Real Time PCR Workstation (Thermo/ABI). Libraries were sequenced on a NovaSeq 6000 (Illumina). Fastq files were generated from the resulting base call files using bcl2fastq (Illumina). The paired-end reads were aligned to hg38 (NCBI build 39) and aligned reads were analyzed using the Rsubread Package.

first: Jeffrey

last: Tyner


title: Low expression of m6A reader YTHDC1 promotes progression of ovarian cancer via PIK3R1/STAT3/GANAB axis

city: nanjing

first: xiaogang

last: wang

address: Hankou road 22

institute: nanjing university

summary: We applied YTHDC1-RIP-seq in SKOV3 cells to identify RNAs directly bound to YTHDC1. A total of 9522 potential candidate targets of YTHDC1 were revealed, and 86.39% of them were mRNA

overall_design: SKOV3 cells were used for YTHDC1-RIP-seq experiments


title: Neonatal microbes shape islet-immune interactions that determine life-long host metabolic capacity [scRNA-seq and bulk RNA-seq].

city: Salt Lake City

first: W. Zac

last: Stephens

state: UT

address: 15 N. Medical Drive, EEJMRB 4208, EEJMRB 4208

department: Pathology

institute: University of Utah

summary: The composition of the resident microbiota changes and diversifies as its host develops. Enrichment of specific taxa early in life is important for immune system development and maturation, but the impact of early life commensals on other host developmental processes is little studied. Here, we describe a critical window of postnatal life when specific microbes are necessary to establish an adequate supply of insulin-producing tissue for lifelong metabolic homeostasis of the host.

overall_design:
The main goal is to determine the effect of microbiota presence on developing neonatal pancreatic islets.
Samples are pancreatic islets purified away from acinar tissue by several rounds of hand picking.

scRNA-seq:
Each sample is representative of pooled islets from 20 animals at 15 days old (P15), either Germ-free (GF) or specific pathogen free (SPF).

bulk RNA-seq:
Islets from Germ-free (GF) and specific pathogen free (SPF) mice 10 days old (P10) or 20 days old (P20) are included.
Additionally, a subset of samples from P20 SPF mice were treated with Clodronate to diminish macrophages in order to investigate the effect of macrophages on neonatal islets.
Pacncreatic islets from male and female mice for each group are included.

first: Hill

last: Jennifer

first: Round

middle: L

last: Lune

first: Stephens

last: W Zac