title: miRNA signatures underly chemoresistance in the gemcitabine-resistant pancreatic ductal adenocarcinoma cell line MIA PaCa-2 GR

city: Loma Linda

first: Nathan

middle: R

last: Wall

state: California

address: 11234 Anderson St, Loma Linda LLUMC B Level Room B125, CA 92354,

institute: Loma Linda University

summary: Chemotherapy resistance is a major clinical issue for pancreatic adenocarcinoma (PDAC).  MicroRNAs (miRNAs) play an important role in cancer progression and chemoresistance. In this study, we addressed the association between miRNA expression profiles and gemcitabine (Gem) resistance. A Gem sensitive (GS) PDAC cancer cell line, MIA PaCa-2, and its Gem resistant (GR) progeny MIA PaCa-2 GR, was used to determine miRNA expression changes by resistance to Gemcitabine. miRNA-seq was used to determine the miRNA expression profiles in these cell lines. Ingenuity Pathway Analysis (IPA) was performed to determine the biological functions of differentially expressed miRNAs. In total, 1867 miRNAs were detected in the two cell lines. We found that the miRNA expression profiles were different between the GR and its sensitive isogenic parental GS cell line, and certain differentially expressed miRNAs were only detected in one or the other of these PDAC cell lines. A total of 97 (5.2%) miRNAs were significantly differentially expressed between GR and the GS cell lines, of which 65 (3.5%) miRNAs were upregulated and 32 (1.7%) miRNAs were downregulated. The miRNAs with the most significant differential expression in the GR cell line as compared with GS were primarily involved in the following biological processes: cell proliferation, cell migration & invasion, chemo-sensitization, alternative splicing, apoptosis, and angiogenesis. These miRNAs from cell lines were further refined to a subset and were analyzed in patient samples where expression was used to identify patients with recurrent tumors. Taken together, the results suggest that these miRNAs may play important roles in Gem resistance in PDAC.  This study’s findings provides a basis for further research in the diagnosis and treatment selection for PDACs with gemcitabine resistance.

overall_design: To investigate miRNA changes between sensitive parental cells (Mp2) and adapted resistant cells (Mp2GR), Mp2 cells were treated with IC50 concentration of Gem until growth continued. We incrementally increased the concentration of Gem until 500nm concentration was achieved. Cells were maintained in 500nm Gem until RNA harvest.

first: Ryan

middle: N

last: Fuller

first: Paul

last: Vallejos

first: Janviere

last: Kabagwira

first: Tiantian

first: Charles


title: SWI/SNF chromatin-remodeling factor BAF60b restrains inflammatory diseases by affecting regulatory T cells migration [ATAC-Seq]

status: Public on Jul 01 2024

city: Hangzhou

first: Xiaoqian

last: Liu

address: 866 Yuhangtang Road, Xihu District

country: China

institute: Zhejiang University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Regulatory T (Treg) cells play a critical regulatory role in the immune system by suppressing excessive immune responses and maintaining immune balance. The effective migration of Treg cells is crucial for controlling the development and progression of inflammatory diseases. However, the epigenetic mechanisms responsible for directing Treg cells into the inflammatory tissue remain incompletely elucidated. In this study, we identified BAF60b, a subunit of SWI/SNF chromatin remodeling complexes, as a positive regulator of Treg cells migration that inhibits the progression of inflammation in experimental autoimmune encephalomyelitis (EAE) and colitis animal models. Mechanistically, transcriptome and genome-wide chromatin landscaped analyses demonstrated that BAF60b interacts with the transcription factor RUNX1 to promote the expression of CCR9 on Treg cells, which in turn affects their ability to migrate to inflammatory tissues. Our work provides insights into the essential role of BAF60b in regulating Treg cells migration and its impact on inflammatory diseases.

overall_design: To investigate the role of BAF60b in Treg cells, we established conventional BAF60b knockout mice. We isolated GFP+Treg cells from spleen of wild-type and BAF60b-deficient mice for ATAC-Seq

first: Kuai

first: Lie

last: Wang


title: Elevated MG-H1 in glo1-/-aldh3a1-/- zebrafish caused microvasculature alterations and glucose metabolism impairment via decreased proteasome activity

city: Mannheim

first: Shu

last: Li

address: Neckarpromenade

country: Germany

institute: ECAS

type: Expression profiling by high throughput sequencing

summary: Dicarbonyl stress is characterized by the abnormal accumulation of dicarbonyl reactive metabolites, leading to increased modification of proteins, DNA and lipids, thereby contributing to cellular and tissue dysfunction in diabetes, diabetic complications and other diseases. glo1 knockout zebrafish exhibited moderately increased MG levels, yet this was inadequate to induce trunk vessels alterations due to elevated ALDH activity and mRNA expression levels, which partially act as compensatory mechanism. Excess 4-HNE induced pancreas dysfunction in aldh3a1 knockout zebrafish larvae, inhibiting insulin expression and thereby facilitating hyperglycemia and hyaloid vasculature alterations. To evaluate the combined function of Glo1 and Aldh3a1 in glucose homeostasis and diabetic microvasculature, glo1-/-aldh3a1-/-  zebrafish were generated using CRISPR/Cas9 technology.  Multiple experiments are performed regarding vasculature alterations, glucose homeostasis, transcriptome, and metabolomics in Tg(fli1:EGFP) zebrafish. glo1-/-aldh3a1-/- zebrafish larvae displayed angiogenic hyaloid vasculature caused by the elevated MG-H1 and decreased proteasomal chymotrypsin-like activity, which could be rescued by the MG-H1 scavenger L-carnosine and proteasome activator Betulinic acid treatments. In adult glo1-/-aldh3a1-/- zebrafish, impaired glucose metabolism, angiogenic retina vasculature and thickened GBM were observed. Thus, our data suggested that an important upstream factor contributing to these phenomena in the context of lacking glo1 and aldh3a1 is MG-H1, possibly through reduced proteasome activity.

overall_design: glo1-/-aldh3a1-/-zebrafish were generated using CRISPR/Cas9 technology.  Multiple experiments are performed regarding vasculature alterations, glucose homeostasis, transcriptome, and metabolomics in Tg(fli1:EGFP) zebrafish.

first: Hao

first: Jens

last: Kroll


title: Metabolomic and Transcriptomic Analysis of Monoterpene Biosynthesis in Muscat and Neutral Grape Hybrids

city: Zhengzhou

first: Yongzhou

address: No. 28, Gangwan Road, Guancheng District

institute: Chinese Academy of Agricultural Sciences Zhengzhou Fruit Research Institute

summary: Monoterpenes are typical aroma components of muscat grape cultivars. However, the molecular mechanism of monoterpene biosynthesis between muscat and non-muscat grape remains unclear. In this study, two F1 hybrids with different aroma profiles from the cross between 'Midknight Beauty' and 'Red Globe' grapes were chosen for comprehensive transcriptome and metabolome analysis to study the unique monoterpenoid accumulation pattern and related candidate genes. The results showed that in the hybrid progeny, the concentrations of most terpenoids differed at different times, and the concentration of most terpenoids increased from the pre-veraison to veraison, followed by a decreasing trend from veraison to maturity. In the F1 generation, the concentration of monoterpenes accumulated in Muscat grapes was significantly higher than that in Neutral grapes. Furthermore, linalool，α-terpineol, and L-α-terpineol may be important odorants that affect the floral characteristics of Muscat grapes because of their high odor activity values (OAVs). Transcriptional analysis identified 3 VvDXS (LOC100249323, LOC100268079, LOC100247834), 1 VvHDS (LOC100257071), 1 VvMVK (LOC100251148), 1 VvHMGR (LOC100265082), and 1 VvGGPPS (LOC100257234) in the MEP and MVA pathways. Meanwhile, 11 TPS genes that may be involved in the regulation of monoterpenes were identified. Among them, VvTPS (LOC100853562) showed consistency with the accumulation of monoterpenes and had a high expression level， MYB (LOC100255488), GATA (LOC100262474), and ERF (LOC100255943, LOC100260401) were selected as candidate transcription factors (TFs). The findings provide new insights for the subsequent functional validation and further investigation of genes related to monoterpene synthesis in Muscat aroma grapes.

overall_design: Skin mRNA profiles of E-L 34, E-L 37, and E-L 38 stages Muscat type and Neutral type / 'Midknight Beauty' grape and 'Red Globe' grape cross-group

first: Caili

last: Yang

first: Liangliang

last: He

first: Yinhua

last: Song

first: Peng

last: Zhang

first: Sanjun


title: Epidermal Growth Factor Rejuvenates Aged Hematopoietic Stem Cells [EGFR Dominant Negative]

city: West Hollywood

first: AGCT

last: Core

state: CA

address: 8687 Melrose Ave, PDC B230

department: BMS

country: USA

institute: Cedars Sinai Medical Center

summary: Hematopoietic aging is associated with decreased hematopoietic stem cell (HSC) self-renewal capacity and increased risk for myelodysplasia and leukemia. Deficient DNA repair contributes to the decline in HSC self-renewal capacity during aging and it remains unclear whether extrinsic signals can rejuvenate aged HSCs. Here, we demonstrate that augmentation of non-homologous end-joining (NHEJ) DNA repair in aged HSCs via treatment with epidermal growth factor (EGF) rejuvenates HSC function. Seven day culture of BM CD34-ckit+sca-1+lin- (34-KSL) HSCs from aged C57BL/6 mice with EGF suppressed myeloid skewing and increased production of multipotent CFU-granulocyte, erythroid, monocyte and megakaryocyte (CFU-GEMM) colonies. Aged, EGF-treated HSCs displayed increased donor multilineage engraftment in primary competitively transplanted mice and in secondary mice compared to mice transplanted with aged, control HSCs. Donor cell engraftment within the bone marrow (BM) KSL and SLAM+KSL HSC population was > 2-fold increased in mice transplanted with aged, EGF-treated HSCs. Systemic administration of EGF to aged mice for 6 weeks also increased long term – HSC self-renewal capacity as measured by increased donor bone marrow (BM) competitive repopulation in primary and secondary transplanted mice. Conversely, deletion of EGFR in Scl/Tal1+ hematopoietic cells was associated with increased myeloid skewing and depletion of LT-HSCs in middle aged mice. Mechanistically, EGF treatment decreased DNA damage in aged HSCs through activation of DNA PK-cs, Artemis and NHEJ repair. Inhibition of DNA PK-cs blocked EGF-mediated restoration of multipotent differentiation and suppression of myeloid skewing in aged HSCs, suggesting that the restoration of hematopoietic potential in aged HSCs is dependent on EGF-mediated activation of DNA PK-cs. EGF treatment also converted the transcriptome of aged HSCs from enrichment for genes involved in cell death and survival to genes involved in HSC generation and identity. These data suggest that extrinsic activation of EGFR signaling can restore key functional capacities in aged HSCs.

overall_design: For mRNA sequencing, BM CD34-KSL cells were sorted from mice with Tal1-tTA+/TRE-EGFR-tr+ genotype that were maintained in drinking water with 0.2 g/L doxycycline (expressing wild-type EGFR only, EGFR-WT) or without doxycycline (except EGFR-WT, also expressing a cytoplasmic tyrosine kinase domain-deleted form of EGFR, EGFR-DN). Total RNA was prepared using Qiagen RNeasy Micro Kit (Qiagen). Then bulk RNA sequencing was performed

first: John

middle: P

last: Chute

first: Peibin

last: Yue

first: Vivian

middle: Y

last: Chang


title: Reprogramming of 3D genome structure underlying HSPC development in zebrafish

city: Guangzhou

first: Feifei

state: Guangdong

address: Guangzhou Higher Education Mega Center, Panyu District

institute: South China University of Technology

summary: Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals; however, the mechanism underlying HSPC development is not fully understood. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision, its dynamic and role in HSPC development is poorly investigated. Here, we performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish. Chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure and characteristics. We revealed the multi-scale reorganization of 3D genome and its influence on transcriptional regulation and transition of cell function during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably, PU.1 was identified as a potential factor mediating formation of promoter-involved loops and regulating gene expression as well as HSPC function. Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factor involved in HSPC chromatin interactions, which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision.

overall_design: To characterize the probably Hi-C loops,we identified distal enhancers genome-widely taking advantage of H3K4me3 chip-seq data,and loops were assigned to non-functional elements.

first: Min

first: Xiaoli

first: Wenqing

first: Bingxiang

last: Xu

first: Yibo

last: Lu

first: Jingyi

last: Lai

first: Yiming

last: Ling

first: Huakai

first: Ziyang

last: An


title: Reprogramming of 3D genome structure underlying HSPC development in zebrafish [ChIP-seq]

overall_design: To characterize the function of Hi-C loops,we identified distal enhancers genome-widely taking advantage of H3K27ac chip-seq data,and loops were assigned to functional elements.

last: Liu


title: Differential gene expression between gastric cancer cells treated with recombinant human growth-arrest specific 6 (GAS6) protein or cultured with Cancer-associated fibroblasts (CAFs).

city: Suwon

first: Tae Hoon

last: Kim

address: 206, World cup-ro, Yeongtong-gu

department: surgery

country: South Korea

institute: Ajou university

summary: We aimed to determine the differences in gene expression levels between SNU668 cells and SNU668 cells co-cultured with CAFs or treated with recombinant human GAS6 protein using microarray analysis. We selected genes that showed a fold change increase of more than 2-fold compared to WT in SNU668 cells. Then, we identified genes involved in chemoresistance.

overall_design: To investigate the chemotherapeutic response in the GAS6/AXL signaling pathway, we performed the SNU668 cell line treated with recombinant human GAS6 protein or co-cultured with CAFs.

first: Hoon

last: Hur

first: Tae

middle: H


title: Melanotransferrin (MELTF, MFI2, CD228) expression attenuates malignant melanoma progression in the A375-luc2 murine metastasis model and human patients

city: Tucson

first: Georg

middle: Thomas

last: Wondrak

state: Arizona

address: UA Cancer Center, 1515 N Campbell Ave, Room 3971

department: Pharm/Tox

institute: University of Arizona

summary: The cell-surface glycoprotein melanotransferrin (MELTF) is a member of the iron-binding transferrin superfamily expressed in human melanocytes and other cell types. Dysregulated MELTF-expression in malignant melanoma and other malignancies has been reported before but its specific role in melanomagenesis remains elusive. We performed CRISPR/Cas9-based MELTF deletion in human A375-luc2 malignant melanoma cells followed by transcriptomic analysis in order to explore the mechanistic role of MELTF in malignant melanoma.

overall_design:
Differential expression between isogenic human malignant melanoma A375-BRAFV600E/NRASQ61 wildtype (n=3), A375-BRAFV600E/NRASQ61 MELTF knockout (n=3, clone A7), and  A375-BRAFV600E/NRASQ61 MELTF knockout (n=3, clone A18) cell lines was assessed using the nCounter PanCancer Progression Panel code set.
Total RNA analyzed for gene expression of 770 transcripts by nCounter PanCancer Progression panel

first: Jana

last: Jandova

middle: T


title: Model integration of circadian and sleep-wake driven contributions to rhythmic gene expression reveals novel regulatory principles

city: Lausanne

first: Maxime

last: Jan

state: Suisse

address: University of Lausanne

department: CIG

country: Switzerland

institute: University of Lausanne

summary: We monitored gene expression in the liver of 10-12 week-old male C57BL/6J mice for 24 hours before and until 48 hours after the end of a single total sleep deprivation (SD) episode. The aim was to characterise the response to SD and recovery thereafter.

overall_design: Mice were sleep deprived for 6 hours starting at light onset (ZT0-ZT6; Time T24-T30) of the light-dark cycle. Control mice (NSD, Non Sleep Deprived) were sacrificed at ZT0, ZT3, ZT6, ZT12, ZT18 of the first day of experimentation (named samples T0-T24 and corresponding to the 24 hours before SD), serving as a baseline day (Day 0). On Day 1, SD mice were sacrificed at the same time of day as on Day 0 (samples T27-42, with T27 and T30 samples being taken after 3h and 6h SD, respectively), on Day 2 at ZT0, ZT6, ZT12, ZT18 (samples T48-66), as well as ZT0 and ZT6 on Day 3 (samples T72-78). Two groups of mice were allowed to recover for 7 days after SD, before being sacrificed at ZT0 and ZT6 (Day 8, samples T192-198). We collected 3-4 replicates per time point and condition, and 8 replicates of ZT0 controls from two different animal batches.

first: Sonia

last: Jimenez

first: Charlotte

last: Hor

first: Paul

last: Franken


title: Characterization of the genes that were regulated by feeding nisin

city: Kyoto

first: Eriko

last: Kage-Nakadai

state: Kyoto

address: 53 Kawahara-cho, Shogoin, Sakyo-ku

country: Japan

institute: Koyto Univ.

summary: In the present study, we investigated the effects of feeding nisin using Caenorhabditis elegans as a model animal. The lifespan of the adult C. elegans fed nisin was significantly longer than that of uninfected animals (control). Transcriptional profiling comparing fed- and unfed animals suggested that genes related to "defence responses" were upregulated by nisin.

overall_design: Transcriptional profiling of four-day-old worms that were fed or unfed nisin for one day, by deep sequencing, using Illumina HiSeq.


title: Reprogramming of 3D genome structure underlying HSPC development in zebrafish [RNA-seq]

first: Feifei

last: Li

overall_design: To comprehensively dissect 3D genome rearrangement and its relation to transcriptional changes of zebrafish HSPC,we get RNA-seq results from adult sample. Then, conjoint analysis of RNA-seq with other datas can reveal the function of transcriptional factors, such as PU.1 .

first: Min

last: He

first: Xiaoli

first: Wenqing

last: Zhang


title: Characterization of the genes that were regulated by feeding Lactococcus Lactis.

summary: In the present study, we investigated the effects of feeding Lactococcus lactis using Caenorhabditis elegans as a model animal. The survial of the adult C. elegans fed L. lactis was significantly better than that of unfed animals (control) upon infection with pathogens.

overall_design: Transcriptional profiling of three-day-old worms that were fed L. lactis L1, L2 or E. coli OP50 (control) for one day, by deep sequencing, using Illumina HiSeq.


title: Acute atopic dermatitis and urticaria imprints peripheral monocytes with proinflammatory-prone signature

city: xiamen

first: Qingxiang

last: Gao

address: Xiang'an south way

institute: Xiamen University

summary: Monocytes from patients with type 2 immune disorders exhibited an augmented inflammatory response upon LPS stimulation. RNA-seq analysis demonstrated significant upregulation of inflammatory cytokines, including IL-6, IL-12, and IL-1b. Moreover, there was a conspicuous enrichment of signaling pathways associated with inflammation. ATAC sequencing revealed heightened chromatin accessibility in patient monocytes, particularly in the promoter regions of inflammatory genes.

overall_design: Monocytes in  peripheral blood mononuclear cells (PBMCs) from patients diagnosed with atopic dermatitis and urticaria were collected for RNA-seq


title: Gene expresison of effector and exhausted CD8+ T cells from viremic people living with HIV

city: Kuala Lumpur

first: Won Fen

last: Wong

address: Lembah Pantai

department: Medical Microbiology

country: Malaysia

institute: Universiti Malaya

summary: The differential expression of metabolic genes between effector and exhausted CD8+ Tcells has been characterized in the people living with HIV (PLWH) using 768 genes from the NanoString Human Metabolic Pathways Panel.

overall_design: Seven T cell subsets were used for the comparison of metabolic landscape. Naïve CD8+ T cells were isolated from healthy controls, while different stages of effector memory, effector, and exhausted CD8+ T cells were purified from viremic PLWH. RNA were harvested from the purified cells, quantified and prepared for the gene expression analysis using Nanostring Human Metabolic Pathways Panel.

first: Yee

last: Chan

first: Won

middle: F


title: Endothelial autophagy promotes atheroprotective communication between endothelial and smooth muscle cells via exosome-mediated delivery of miR-204-5p

city: Harbin

first: Zhen

last: Tian

address: Baojian Road

institute: Harbin medical university

type: Non-coding RNA profiling by high throughput sequencing

summary: Background: Cellular communication among different types of vascular cells is indispensable for maintenance of vascular homeostasis and prevention of atherosclerosis (AS). However, the biological mechanism involved in cellular communication among these cells and whether this biological mechanism can be used to treat AS remain unknown. This study hypothesizes that endothelial autophagy mediates the cellular communication of vascular tissue through exosome-mediated delivery of AS-related genes.Methods: ApoE-/- mice fed with high-fat diet (HFD) were received rapamycin to activate autophagy, or were intravenously injected with adeno-associated virus (AAV) vectors carrying shRNA against Atg7 mRNA under the Tie (tyrosine kinase) promoter to specifically inhibit endothelial autophagy. miRNA microarray, in vivo and in vitro experiments and human vascular tissues/blood vessels were used to explore the molecular mechanisms of atheroprotective effect of endothelial autophagy. Exosomes were isolated and characterized. Immunofluorescence and exosomes coculture experiments were conducted to examine the role of endothelial autophagy in regulating communication between endothelial cells (ECs) and smooth muscle cells (SMCs) via exosome.Results: Endothelial autophagy was inhibited in ECs of thoracic aortas in HFD fed ApoE-/- mice. Furthermore, rapamycin alleviated HFD-triggered atherosclerotic burden and endothelial dysfunction, while endothelial-specific depletion of Atg7 aggravated atherosclerotic burden. miRNA microarray, in vivo and in vitro experiments and human vascular tissues analysis revealed that endothelial autophagy alleviated endothelial dysfunction by downregulating miR-204-5p expression by directly targeting BCL2 to regulate apoptosis in ECs. Moreover, endothelial autophagy decreased miR-204-5p expression by loading this molecule into multivesicular bodies and secreting them out of cells via exosomes, and ECs-derived exosomal miR-204-5p could be transferred to SMCs, antagonized SMCs calcification.Conclusions: Our study first revealed that endothelial autophagy was a critical regulator of atherogenesis by transferring miR-204-5p from ECs to SMCs by exosomes, and endothelial autophagy activation by rapamycin, could alleviate AS in a “one stone hit two birds” manner.

overall_design: The small RNA sequencing in the exosomes of the human umbilical vein endothelial cells treated palmitic acid with/without pretreated with atg7 siRNA or rapamycin were performed on an Illumina SE50 platform

first: Hua

last: Ning

first: Xinyue

last: Wang

first: Yu

first: Tianshu

last: Han

first: Changhao

last: Sun


title: Supramolecular Mimic of Glial Cell Line-Derived Neurotrophic Factor and its Bioactivity on Human Dopaminergic Neurons

city: Chicago

first: Oscar

last: Carballo-Molina

state: Illinois

address: 303 East Superior Street, Lurie 11-231

department: Simpson Querrey Institute for Bionanotechnology

institute: Northwestern University

summary: The cardinal motor symptoms of Parkinson´s disease (PD) are caused by the degeneration of dopaminergic neurons, making it in principle amenable to treatment by cell replacement therapy. Although this strategy has shown promise in animal models, it has not been as successful in clinical trials. One likely reason for this lack of success is the poor survival of grafted neurons. In animal models, glial cell line-derived neurotrophic factor (GDNF) increases the survival of transplanted dopaminergic neurons, but the ability of GDNF to promote survival is undoubtedly limited by its diffusion away from the graft site and its degradation. We report here on supramolecular nanofibers that display a GDNF-mimetic peptide on their surfaces. This nanostructure mimicked the biological effects of GDNF on human dopaminergic neurons by improving cell survival and promoting morphological, synaptic and electrophysiological maturation, as well as a neuroprotective effect that correlates with the upregulation of genes related to these biological processes. The GDNF nanostructures also enhanced the morphological maturation of human midbrain-like organoids. Thus, the GDNF supramolecular mimic provides a self-assembling matrix that could be delivered in the future with transplanted dopaminergic neurons to enhance their survival and maturation in vivo.

overall_design: To evaluate the genes up and downregulated by the GDNF mimic nanostructure, we seeded human-induced pluripotent stem cells-derived dopaminergic neurons on coverslips coated with GDNF mimic nanostructure and compared their relative gene expression changes to scramble GDNF mimic nanostrucutre 4 days after treatment. Gene expression profiling was performed using single-end RNA-Seq data obtained from 3 biological replicates per condition.

first: Zois

last: Syrgiannis

first: Samuel

last: I Stupp

first: Matias

middle: A

last: Alvarez-Saavedra


title: RNA-seq of three groups mice in livers.

city: Xian yang

first: Hongbo

state: Shannxi

address: Xi nong road

department: College of Food Science and Engineering

institute: Northwest A&F University

summary: We sought to examine whether  urolithin A  could  alleviate the alcohol-related liver disease. RNA-sequencing (RNA-seq) on mice livers were performed in order to identify the key biological processes and pathways regulated by urolithin A.

overall_design: 5 Ctrl mice, 5 Alc mice, 5 Alc UA mice


title: Maternal and donor human milk support robust intestinal epithelial growth and differentiation in a fetal intestinal organoid model

city: New Haven

first: Eduardo

middle: Gabriel

last: Gonzalez Santiago

state: Connnecticut

address: 375 Congress Ave Rm 407

department: Pediatrics

institute: Yale University

summary: Necrotizing enterocolitis (NEC) is a severe gastrointestinal complication of prematurity. Using small intestinal organoids derived from fetal tissue of a gestational age similar to an extremely preterm infant, this study aims to assess the effect of diet on intestinal epithelial growth and differentiation to elucidate the role nutrition type plays in intestinal development and modifies the risk for NEC. Organoids were cultured for 5 days in growth media and 5 days in differentiation media supplemented 1:40 with four different diets: maternal milk (MM), donor human milk (DHM), standard formula, or extensively hydrolyzed formula. Images were captured daily and organoids were quantified. Organoids were preserved for RNA sequencing and immunofluorescence staining with Ki67, cleaved caspase 3, and chromogranin-A. Media was saved for cytokine/chemokine and growth factor analysis.Human milk supplementation improved growth and differentiation of intestinal organoids generating larger organoids during the growth phase and organoids with longer and wider buds during differentiation compared to formula. Ki67 staining confirmed the proliferative nature of milk-supplemented organoids and chromogranin A staining proved that MM-supplemented organoids induced highest enteroendocrine differentiation. Human milk supplementation also upregulated genes involved in proliferation and promoted a homeostatic immune landscape while those supplemented with formula had a downregulation of cell-cycle-promoting genes and a more inflammatory immune signature. Our results show that MM, and to a lesser extent DHM, support robust intestinal epithelial proliferation and differentiation, suggesting a critical role for factors enriched in human milk in intestinal epithelial health.

overall_design: The investigate the impact that different diets have fetal intestinal organoid growth and development to elucidate the role diet plays in neonatal intestinal health.


title: Chromatin profiling of A549 cells

city: Vancouver

first: Bettina

middle: Maria

last: Fuglerud

state: BC

address: 675 W 10th Ave

country: Canada

institute: BC Cancer

summary: We analyzed SOX9 chromatin binding upon TGFB1 treatment as well as the global effect of SOX9 knockdown and TGFB1 treatment by ChIP-sequencing and ATAC-sequencing of A549 cells transfected with siSOX9 or control siRNA and treated with TGFB1.

overall_design: A549 Cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) in humidified atmosphere with 5% CO2 at 37C. Cells were harvested for ATAC-seq and ChIP-seq and libraries were generated for high-throughput sequencing.

first: Pamela

last: Hoodless


title: Effect of canonical aryl hydrocarbon receptor pathway inhibitor on human umbilical vein endothelial cells

city: New York

first: Yang

last: Lin

state: NY

address: 455 Main Street 06W

institute: Weill Cornell Medicine

summary: To study the effect of blockade of canonical aryl hydrocarbon receptor (AHR) pathway in human endothelial cells, we treated human umbilical vein endothelial cells (HUVECs) with a canonical AHR inhibitor, Stemreginin 1 (SR1) and performed bulk RNAseq analysis.

overall_design: Samples were derived from 3 individual patients. Cells from each patient were treated with either 1: 10, 000 DMSO (vehicle), or 0.5uM SR1 in 1: 10, 000 DMSO. After 48 hours, RNA samples were collected for comparisons.

first: Fuqiang

last: Geng

first: Shahin

last: Rafii


title: Circadian control of duodenal regulatory T cells by enteric neurons and eosinophils

first: Tomasz

last: Ahrends

address: 1230 York Ave

institute: The Rockefeller University

summary: Multiple intestinal functions including nutrient absorption and peristalsis display regional specialization as well as time-of-day effect under the control of circadian rhythm. We investigated the role of these adaptations on intestinal immune system and response to dietary antigens. We found that oral challenge during the night resulted in more protective tolerance, which correlated with nocturnal expansion of regulatory T (Treg) cells in proximal small intestine lamina propria. Expansion of Treg cells was supported by eosinophils and clock gene-dependent rhythmic production of follistatin by enteric neurons. Circadian entrainment of these changes depended on light exposure and locomotor activity but not the time of food intake. These data suggest that circadian and regional adaptations in the intestine limit the severity of allergic reactions during the active phase.

overall_design: CD11c-high and CD11c-low duodenum lamina propria eosinophils were sorted for RNAseq at ZT3 (AM) and ZT15 (PM)


title: EF-P dependent genes in Salmonella Typhimurium

city: Chuncheon-si

first: Yong-Joon

last: Cho

state: Gangwon-do

address: 1, Kangwondaehak-gil

department: Department of Molecular Bioscience

institute: Kangwon National University

summary: Elongation factor P (EF-P) is required to enhance peptidyl transferase on pausing ribosomes, which can be induced by certain codons on mRNA. It regulates expression of genes in specific conditions. Therefore, to search EF-P mediated ribosome stalling motif, ribosome profiling has been used on organisms such as yeast and E. coli. However, it has not been addressed on the intracellular pathogen Salmonella Typhimurium. Through the ribosome profiling, 135 sites in 128 genes were identified as EF-P dependent sequences and many of these sites had consecutive proline codons specifically at P site of the ribosome. As a motif level, PPG was the most abundant amino acid sequence at EPA site of the ribosome and followed by APP and DPP sequence. Also, our findings revealed that salmonella-specific gene, ugtL, is regulated by frameshifting caused during translation as ribosome stalled in the DPP motif. In addition, we showed that both proline motif and EF-P are engaged in this regulation, and it affects the resistance to antimicrobial peptides. In conclusion, this study emphasized the importance of poly proline motif on EF-P and suggested a possible mechanism how EF-P affects the physiology of Salmonella.

sample_organism: Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S

overall_design: To investigate EF-P mediated ribosome stalling motif and its relevance on the virulence of S. Typhimurium, we conducted ribosome profiling in wild-type and efp strain and found genes that are regulated by EF-P.

first: Seungwoo

last: Baek

first: Eunna

last: Choi

first: Allen

last: Buskirk

first: Eun-Jin

last: Lee


title: RNA sequencing facilitates quantitative analysis of U251-NC and U251-COL8A1 transcriptomes

first: Mingkai

last: Liu

address: Guangzhou Higher Education Mega Centre, Panyu District

summary: To investigate the function of COL8A1 in GSCs progression, we established U251-COL8A1 cell lines with COL8A1 overexpressed. Then we performed gene expression profiling analysis using data obtained from RNA-seq of 2 cells (U251NC and U251-COL8A1)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for U251-NC and U251-COL8A1.

first: Weiye

last: Liang

first: Jian

last: Wang


title: Effects of depletion of Rho-associated, coiled-coil-containing protein kinase 2 in the kidney medullary tussue of murine model.

city: Minato City

first: Kensuke

last: Sekiguchi

state: Please Select

address: 3-19-18 Nishishinbashi

institute: Jikei University

summary: Rho and its effector Rho-associated, coiled-coil–containing protein kinase 2 (ROCK2) play crucial roles in a variety of cellular functions, such as cell adhesion and cytoskeletal rearrangement . We here investigated the role of ROCK2 in the kidney medullary tissue using tubular specific ROCK2 knockout mice.

overall_design: To investigate the role of ROCK2 in kidney tubular cells, we established the tubular specific ROCK2 knockout mice. RNA-seq on the kidney medullary tissue.

first: K

last: Matoba


title: Streptomyces clavuligerus Transcriptome using adpA deleted and overexpressed mutants

city: Samsun

first: ASLIHAN

middle: KURT

last: KIZILDOĞAN

address: ONDOKUZ MAYIS ÜNİVERSİTESİ, -

department: Agricultural Biotechnology

country: Turkey

institute: Ondokuz Mayıs University

summary: RNA seq analysis was performed using adpA-deleted and adpA-overexpressed Streptomyces clavuligerus strains to determine its regulatory effect on tunicamycin and other secondary metabolites production

overall_design: adpA gene in S. clavuligerus was deleted by I-Sce meganuclease strategy and S. clavuligerus delta adpA null mutant was obtained. In addition, adpA gene was inserted into replicative pSPG containing Pglyp, glycerol inducible promoter, and transferred into S. clavuligerus cells by conjugation. A vector control that includes pSPG in S. clavuligerus was also constructed.

first: Aslihan

last: KURT-KIZILDOGAN

first: Cigdem

last: OTUR


title: EZH2 Inhibition Enhances PD-L1 Protein Stability through USP22-Mediated Deubiquitination in Colorectal Cancer

city: BEIJING

first: Qianqian

last: Yin

address: 49 North Garden Road, Haidian District

department: Center of Basic Medical Research

institute: Peking University Third Hospital

summary: Background: Previous studies have shown that EZH2 regulates tumor PD-L1 expression at the transcriptional level and has an impact on tumor immune environment and prognosis. However, whether EZH2 can regulate PD-L1 expression at the post-translational level remains unclear. Therefore, this study aims to investigate the effects of EZH2 inhibition on PD-L1 expression and protein stability in colorectal cancer cells, uncover its underlying mechanisms, and provide new therapeutic strategies for anti-tumor immune therapy. Methods: Multiple colorectal cancer cell models were used to examine the effects of EZH2 inhibition on PD-L1 expression and protein stability at both the protein and transcriptional levels. Transcriptome analysis was performed to identify differentially expressed genes associated with EZH2 inhibition and potential effectors involved in EZH2-mediated regulation of PD-L1 protein stability. Validation of candidate genes was conducted through public database analysis and knockdown or overexpression models. Finally, the combined effects of EZH2 inhibitors and anti-PD-1 immune therapy were evaluated using a mouse xenograft model. Results: We observed that inhibition of EZH2 function upregulated PD-L1 expression and enhanced its protein stability in colorectal cancer cells. Transcriptome analysis revealed that ubiquitin-specific protease 22 (USP22) played a crucial role in mediating EZH2-regulated PD-L1 protein stability. EZH2 affected USP22 expression through its classical epigenetic regulatory function, thereby modulating PD-L1 expression stability and influencing the tumor immune microenvironment. Combination treatment with EZH2 inhibitors and anti-PD-1 immune therapy improved the tumor microenvironment, promoted immune cell infiltration, and exerted synergistic anti-cancer effects. Conclusion: This study elucidated the mechanisms by EZH2 regulate PD-L1 expression and stability, providing new insights into therapeutic strategies for colorectal cancer. The combination of EZH2 inhibitors and anti-PD-1 immune therapy can synergistically enhance anti-tumor effects. These findings offer a potential therapeutic approach to improve the effectiveness of EZH2 inhibitors in cancer treatment and contribute to a better understanding of the role of EZH2 in tumor immune regulation.

overall_design: To investigate the effects of EZH2 inhibition on PD-L1 expression and protein stability in colorectal cancer cells, we performed  RNA sequencing profiles of EPZ-6438-treated and DMSO-treated HCT116 cells.

first: Jiaqi

last: Huang

first: Jianling

last: Yang

first: Lixiang

last: Xue


title: BIN2 Inhibition Suppress Cancer Progression and Protect Ovarian function through Downregulating HDAC1 and RPS6 Phosphorylation Respectively [CUT&Tag]

city: Hefei

first: 丛蓉

last: 李

address: 安徽医科大学东校区弘毅楼1202室

institute: Nanjing Medical university

summary: Malignant tumors, or cancers, are increasingly menacing people's life and health. For your female cancer patient, the ideal therapy should achieve dual purpose: suppress tumor progression meanwhile protect ovarian function. We previously showed that activated (phosphorylated) BIN2 in mouse ovaries regulates primordial follicle activation and oocyte quality through p-RPS6, and in this study, we found that BIN2 knockout or inhibition of BIN2 phosphorylation by BPP could suppress the genesis and progression of ovarian cancer. However, in human female ovarian cancer tissues, we didn’t see the increment of p-RPS6 although we observed a significant raise of p-BIN2. From this discrepancy between normal ovaries and ovarian cancer tissue, we guessed that p-BIN2 has other targets that are more important in ovarian cancer progression. Through mass spec identification, we found that only the constitutively active form of BIN2 (T423D & S424D) baits HDAC1, indicating that HDAC1 is a more important target of BIN2 in ovarian cancer. Next, we did saw Bin2 knockout or inhibition significantly decreased p-HDAC1 (S421) meanwhile increased H3K27ac. Moreover, chip seq showed that BIN2 inhibition significantly increased the binding of H3K27ac to multiple oncogenes. Besides, BIN2 knockout or inhibition could meanwhile protect ovarian function in mice with chemical carcinogen-induced in-situ ovarian cancers or with ovarian cancer cell transplantation. This study suggested that BIN2 inhibition could both suppress ovarian tumorigenesis and protect ovarian fertility, but through distinct mechanisms.

overall_design: To investigate the function Bin2 inhibition in the suppression of ovarian cancer progression, we treated A2780 cell with BPP peptide which competed the phosphorylation site of BIN2 .  We then performed gene expression profiling analysis using data Obtained from RNA seq of A2780 treated with BPP and TAT peptide.

first: Cong-Rong

last: Li

first: Shi-Ya

last: Xie

first: Shu-Ping

last: Zhang

first: Yan-Jie


title: BIN2 Inhibition Suppress Cancer Progression and Protect Ovarian function through Downregulating HDAC1 and RPS6 Phosphorylation Respectively [RNA-Seq]

address: 安徽医科大学东校区弘毅楼1202室


title: BIN2 Inhibition Suppress Cancer Progression and Protect Ovarian function through Downregulating HDAC1 and RPS6 Phosphorylation Respectively

address: 安徽医科大学东校区弘毅楼1202室

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

overall_design: Refer to individual Series


title: METTL7B is an essential epigenetic regulator of lineage specification in glioblastoma [scRNAseq]

city: London

first: James

last: Nicholson

address: 4 Newark St

department: Blizard Institute

country: United Kingdom

institute: Queen Mary University of London

summary: Glioblastomas are the most common malignant brain tumours in adults; they are highly aggressive, heterogeneous and plastic. We have identified METTL7B as an essential regulator of lineage specification in glioblastoma, with impact on both tumour size and invasiveness in in vivo models. Single cell transcriptomic analysis of these tumours and of cerebral organoids derived from expanded potential stem cells overexpressing METTL7B identified a regulatory role for the gene in the neural stem cells to astrocyte differentiation trajectory. Mechanistically, METTL7B downregulates the expression of key neuronal differentiation players, including SALL2, via DNA methylation and post-translational modifications of histone marks.

overall_design: 1) scRNAseq of GIC xenografts, with scrambled or anti-METTL7B shRNA   2) scRNAseq of control (PK/PK-Cas9) COs vs METTL7B-OE COs

first: Silvia

last: Marino

first: Myrianni

last: Constantinou

first: Eleni

last: Maniati

first: Sara

last: Badodi


title: METTL7B is an essential epigenetic regulator of lineage specification in glioblastoma [DNAme]

type: Methylation profiling by genome tiling array

overall_design: DNA methylation analysis of GIC19 and iNSC19 upon silencing or overexpression of METTL7B respectively (n = 4 replicates per group).


title: METTL7B is an essential epigenetic regulator of lineage specification in glioblastoma [RNAseq]

overall_design:
RNAseq of GIC19 and NSC19 upon silencing or overexpression of METTL7B respectively.
Identification of Differentially expressed genes (DE) between GIC19 shM7B vs scr, and NSC19 M7B vs PK


title: METTL7B is an essential epigenetic regulator of lineage specification in glioblastoma [ChIPseq]

overall_design: ChIP-seq to analyze tri-methylation of K27 on histone H3 (H3K27me3) in GIC and iNSC cells upon modulation of METTL7B expression


title: Single cell  gene expression in mouse Hematopoietic cell and Blood after Plasmodium stimulated

first: Qingxiang

last: Gao

summary: Plasmodium infection induced change in the Bone marrow and Blood cells. Here we addressed whether a prior Plasmodium infection would imapct the cell type and gene expression of Bone marrow and Blood cells by single cell RNA-seq.

overall_design: Mice were infected with Plasmodium yoelii for 4 weeks and subjected to CLP-induced sepsis for twenty-four hours. Bone marrow were harvest and sort by FACS for single cell RNA-seq. PBMC were harvest for single cell RNA-seq .

first: Yanhui

last: Zhu

first: Shih-Chin

last: Cheng


title: On the effects of 30 GHz sinusoidal wave exposure on glioblastoma organoids

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary:
In this study, we evaluated the effects of milli-meter waves on structured Glioblastoma organoids to assess the possibility of therapeutic applications. The exposure setup was completely developed, and the dosimetry carried on based on both numerical and experimental activities. Our results showed that continuous milli-meter waves at 30.5 GHz affect cell proliferation and apoptosis, thus not affecting the differentiation status of the organoids composing of GBM cells. By applying the power level of 0.1 W (RMS), we obtain a synergistic effect with the chemotherapeutic Temozolomide in terms of GBM cell death. All these data open the way to an interventional window in which to treat GBM cells (i.e. with TMZ) exploiting 30.5 GHz CW exposure for potential therapeutic purposes thus improving GBM future management, which remain extremely difficult so far.
Our investigation sheds light on the characterization of possible bio-effects of MMW (30.5 GHz CW) on GBM organoids highlighting cell and molecular responses in a relevant 3D tumor model.

overall_design: Gene expression was measured using Affymetrix platform in 3D primary GBM cultures exposed or not to 30 GHz sinusoidal waves.

last: Bresolin

first: Luca

last: Persano


title: Casein kinase II promotes piRNA production through direct phosphorylation of USTC component TOFU-4

city: Shrewsbury

first: Chunwei

last: Zheng

state: MA

address: 70 Shrewsbury Green Dr, Unit L, Unit L

institute: UMass medical school

summary: Piwi-interacting RNAs (piRNAs) are genomically encoded small RNAs that engage Piwi Argonaute proteins to direct mRNA surveillance and transposon silencing. Despite advances in understanding piRNA pathways and functions, how the production of piRNA is regulated remains elusive. Here, using a genetic screen, we identify casein kinase II (CK2) as a factor required for piRNA pathway function. We show that CK2 is required for the localization of PRG-1 and for the proper localization of several factors that comprise the ‘upstream sequence transcription complex’ (USTC), which is required for piRNA transcription. Loss of CK2 impairs piRNA levels suggesting that CK2 promotes USTC function. We identify the USTC component twenty-one-U fouled-up 4 (TOFU-4) as a direct substrate for CK2. Our findings suggest that phosphorylation of TOFU-4 by CK2 promotes the assembly of USTC and piRNA transcription. Notably, during the aging process, CK2 activity declines, resulting in the disassembly of USTC, decreased piRNA production, and defects in piRNA-mediated gene silencing, including transposons silencing. These findings highlight the significance of posttranslational modification in regulating piRNA biogenesis and its implications for the aging process. Overall, our study provides compelling evidence for the involvement of a posttranslational modification mechanism in the regulation of piRNA biogenesis.

overall_design: The small RNA cloning was conducted. Samples were pretreated with homemade PIR-1.

first: Gangming

first: Craig

last: Mello


title: p53 deficient breast cancer cells reprogram pre-adipocytes towards tumor protective immunomodulatory cells (WEA)

city: Rehovot

first: Anat

last: Gershoni

address: 234 Herzl street

department: Molecular Cell Biology

country: Israel

institute: Weizmann Institute

summary: The TP53 gene is mutated in approximately 30% of all breast cancer cases. Adipocytes and preadipocytes, which constitute a substantial fraction of the stroma of normal mammary tissue and of breast tumors, undergo transcriptional, metabolic and phenotypic reprogramming during breast cancer development and play an important role in tumor progression. We report here that p53 loss in breast cancer cells facilitates the reprogramming of preadipocytes, inducing them to acquire a unique transcriptional and metabolic program that combines impaired adipocytic differentiation with augmented cytokine expression. This, in turn, promotes the establishment of an immunosuppressive tumor microenvironment, including increased abundance of myeloid-derived suppressor cells and elevated expression of the checkpoint ligand PD-L1. We also describe a potential gain-of-function effect of several common p53 missense mutations on the inflammatory reprogramming of preadipocytes. Altogether, our study implicates p53 loss in breast cancer cells as a driver of tumor-supportive adipose tissue reprogramming, expanding the network of non-cell autonomous mechanisms whereby p53 may act as a tumor suppressor. Further elucidation of the interplay between p53 mutations and adipocytes within the tumor microenvironment may suggest novel therapeutic targets for the treatment of breast cancer patients.

overall_design:
To investigate the effect of p53-deficient breast cancer cells on adipocyte differentiation, conditioned media from p53 wild-type and knockout WEA cancer cells was applied to differentiating 3T3-L1 adipocytes.
We performed RNA-seq on 3T3-L1 cells before differentiation, after regular differentiation (as a control), and after differentiation with cancer cell conditioned media. Three replicates of each condition were taken.
Pathway enrichment analysis was performed on the sequencing data from the 3T3-L1 cells.

first: Ori

last: Hassin


title: p53 deficient breast cancer cells reprogram pre-adipocytes towards tumor protective immunomodulatory cells


title: p53 deficient breast cancer cells reprogram pre-adipocytes towards tumor protective immunomodulatory cells (WEP)

overall_design:
To investigate the effect of p53-deficient breast cancer cells on adipocyte differentiation, conditioned media from p53 wild-type and knockout WEP cancer cells was applied to differentiating 3T3-L1 adipocytes.
We performed RNA-seq on 3T3-L1 cells before differentiation, after regular differentiation (as a control), and after differentiation with cancer cell conditioned media. Three replicates of each condition were taken.
Pathway enrichment analysis was performed on the sequencing data from the 3T3-L1 cells.


title: Characterizing the gene expression profiles of 4T1 and 4T1.2 cells at different stages of bone metastsis using SMART-Seq2 technology

city: Beijing

first: Hanqiu

address: Haidian District

institute: Tsinghua university

summary: Bone metastasis, a frequent and devastating occurrence in breast cancer, affects over 70% of patients over time. Intriguingly, cancer cells residing within the bone microenvironment can serve as "cancer seeds," disseminating to distant organs and driving extensive metastasis. Even post-successful primary tumor removal, quiescent cells can persist, contributing to bone recurrence. This phenomenon underscores the remarkably low efficiency of bone metastasis establishment and underscores the significance of comprehending the molecular underpinnings of this early bone-seeding phase. Deciphering the mechanisms orchestrating tumor cell dormancy and reawakening holds pivotal implications for designing effective anti-cancer therapies. Dormant tumor cells within the bone might be likened to being ensnared in an "extended seeding phase" prior to eventual expansion. Conceivably, shared signaling molecules could govern both proficient bone metastatic colonization and the re-emergence of indolent metastatic cells. Consequently, the molecular facilitators enabling bone colonization could also be integral to the reactivation of dormant tumor cells within the bone milieu. In this study, we conducted single-cell RNA sequencing (scRNA-seq) analysis on tumor cells procured from the initial stages of bone colonization within experimental bone metastasis models. Our investigation unearthed potential factors that foster tumor cell survival during this critical seeding phase.

overall_design: Female BALB/c mice were subjected to intracardiac (IC) injections of 4T1 and 4T1.2 cells labeled with Firefly-luciferase and mCherry. At various time points, including Day 4 (early seeding phase, D4), Day 10 (progression phase, D10), and Day 16 (late-stage bone metastasis phase, D16), a subset of mice were sacrificed to recover metastatic tumor cells from the hindlimbs. The mCherry+ tumor cells were subsequently isolated using fluorescence-activated cell sorting (FACS). Utilizing single-cell cDNA amplification and next-generation sequencing (NGS) library construction, we conducted comprehensive analysis. Furthermore, we isolated in vitro cultured cells and primary tumor cells injected into the mammary fat pad to generate supplementary scRNA-seq data, serving as additional controls for our study.

first: Xuxiang

last: Wang

first: Tengjiang

first: Guoyuan

last: Xu


title: METTL7B is an essential epigenetic regulator of lineage specification in glioblastoma

first: James

last: Nicholson


title: Human iPSC-derived neural stem cells display a radial glia-like signature in vitro and favorable long-term safety in transplanted mice

city: Milan

first: Stefano

last: Beretta

address: Via Olgettina, 60

institute: San Raffaele Telethon Institute for Gene Therapy

summary: Human induced pluripotent stem cell-derived neural stem/progenitor cells (hiPSC-NSCs) are a promising source of cell therapy approaches to treat neurodegenerative and demyelinating disorders. Despite ongoing efforts to characterize hiPSC-derived cells in vitro and in vivo, we lack comprehensive genome- and transcriptome-wide studies addressing hiPSC-NSC identity and safety, which are critical for establishing accepted criteria for prospective clinical applications. Here, we evaluated the transcriptional and epigenetic signatures of hiPSCs and differentiated hiPSC-NSC progeny, finding that the hiPSC-to-NSC transition results in a complete loss of pluripotency and the acquisition of a radial glia-associated transcriptional and gene regulatory signatures. Importantly, hiPSC-NSCs share with somatic human fetal NSCs (hfNSCs) the main transcriptional and epigenetic patterns associated with NSC-specific biology. In vivo, long-term observation (up to 10 months) of mice intracerebrally transplanted as neonates with hiPSC-NSCs showed robust engraftment and widespread distribution of hiPSC-NSCs in the host brain parenchyma. Engrafted hiPSC-NSCs displayed multilineage potential and preferentially generated glial cells. No hyperproliferation, tumor formation, or expression of pluripotency markers was observed. Finally, we identified a novel candidate transcription factor involved in the astroglial commitment of hiPSC-NSCs. Overall, these comprehensive in vitro and in vivo analyses clarify the cell identity and safety profile of hiPSC-NSCs, supporting their continuing development as an alternative to somatic hfNSCs in treating neurodegenerative and demyelinating disorders.

overall_design: Single-cell RNA-seq (scRNA-seq) on 3 sample clones of human iPSC-derived neural stem/progenitor cells (hiPSC-NSCs) and one sample from the human fetal NSC (hfNSCs) line.

first: Marco

last: Luciani

first: Ivan

last: Merelli

first: Vasco

last: Meneghini

first: Angela

last: Gritti


title: Genome editing by dual nucleases records deep lineage hierarchy with high fidelity.

city: Guangzhou

first: Cheng

last: Chen

address: Kaiyuan Ave 190

institute: Guangzhou Institute of Biomedicine and Health, Chinese Academy of Science

summary: Single-cell lineage tracing based on CRISPR/Cas9 gene editing tracks both cell states and genetic lineages at a single-cell resolution. We developed DuTracer, a single-cell lineage tracing method, to avoid rapid target exhaustion and barcode information dropout. Firstly, we introduced this system into HEK293T cells and initiated DuTracer for tracing. We collected single-cell transcriptome and barcode amplicon, demonstrating that this system could record more hierarchical information with minimal inter-site deletions. Subsequently, we applied DuTracer to a mouse embryoid body differentiation model to track lineage transitions of different cell types. We revealed cell potency hierarchy during the stochastic differentiation process of mES cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: For HEK293T cells, we sequentially induced the gene editing of Cas12a and Cas9 and harvested the cells at D22. For embryoid body (EB) differentiation, we designed six induction strategies. We sampled cells at different time points between D8 and D14 to capture potential differentiation cascades. Single cell RNA-seq was performed using BGI DNBelab C4 kits. For all seven libraries, the obtained cDNAs were split into two halves. One half was used to generate the RNA-seq libraries and the other half was used to make amplicon libraries.

first: Yuanxin

last: Liao


title: SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes

city: Seattle

first: Christopher

last: Seward

state: WA

address: Stubbs Lab, Rm 404, 720 Broadway

institute: Pacific Northwest Research Institute


title: Gene expression profile of an osteoblast precursor cell line treated with rhLTα1β2

summary: To investigate the function of lymphotoxin alpha in the regulation osteoblasts, murine pre-osteoblast cell line MC3T3-E1 clone #4 was treated with recombinant human lymphotoxin alpha1/beta2 for different times. Subsequently, we extracted total RNA from the treated cells, performed reverse transcription and cDNA library for RNA-Seq analysis.

overall_design: 3T3 were treated recombinant LTAlpha1Beta2 for different times. After treatment, cells were lysed for RNA extraction, cDNA library construction, RNA-seq and downstream analysis.


title: SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes [ChIP-seq]

summary:
A common way to investigate gene regulatory mechanisms is to identify differentially expressed genes using transcriptomics, find their candidate enhancers using epigenomics, and search for over-represented transcription factor (TF) motifs in these enhancers using bioinformatics tools. A related follow-up task is to model gene expression as a function of enhancer sequences and rank TF motifs by their contribution to such models, thus prioritizing among regulators.
We present a new computational tool called SEAMoD that performs the above tasks of motif finding and sequence-to-expression modeling simultaneously. It trains a convolutional neural network model to relate enhancer sequences to differential expression in one or more biological conditions. The model uses TF motifs to interpret the sequences, learning these motifs and their relative importance to each biological condition from data. It also utilizes epigenomic information in the form of activity scores of putative enhancers and automatically searches for the most promising enhancer for each gene. Compared to existing neural network models of non-coding sequences, SEAMoD uses far fewer parameters, requires far less training data, and emphasizes biological interpretability.
We used SEAMoD to understand regulatory mechanisms underlying the differentiation of neural stem cell (NSC) derived from mouse forebrain. We profiled gene expression and histone modifications in NSC and three differentiated cell types and used SEAMoD to model differential expression of nearly 12,000 genes with an accuracy of 81%, in the process identifying the Olig2, E2f family TFs, Foxo3, and Tcf4 as key transcriptional regulators of the differentiation process.

overall_design: Mouse embryonic neural stem cells were isolated from dissected frontal cortex tissue of E14.5 embryos, cultured, and differentiated into several brain cell types. Chromatin was collected from these samples 0 or 4 days after differentiation. ChIP-seq for H3k27ac histone modifications was performed. Each H3k27ac ChIP-seq sample has 2 biological replicates and an associated “input” control.

first: Shounak

last: Bhogale

first: Lisa

middle: J

last: Stubbs

first: Saurabh

last: Sinha


title: Expression profiling of METTL14 depleted human embryoid bodies

city: Boston

first: Hui

last: Pan

address: 1 Joslin Place

department: Bioinformatics and Biostatistics Core

institute: Joslin Diabetes Center

summary: N6-methyladenosine (m6A) is the most abundant chemical modification in mRNA, and plays important roles in human embryonic stem cell pluripotency, maintenance, and differentiation. However, the role of m6A and the precise mechanisms involved during the development of β-cells are unexplored. Here, we explored the requirement of METTL14-mediated m6A RNA methylome in human embryonic stem cell (hESC) differentiation by simultaneously inducing METTL14 knockdown in H1 and MEL1 hESCs with doxycycline (Dox) treatment and differentiating hESCs towards the three embryonic germ layers using embryoid body (EB) formation assays.

overall_design: Inducible METTL14 KD H1 and MEL1 hESCs were generated by transducing the cells with SMARTvector human lentiviral vectors containing shRNAs targeting METTL14 from Dharmacon (iKD1; V3SH7669-224822773, iKD2; V3SH7669-225341368, iKD3; V3SH7669-229883026, iSCR; VSC10712). Puromycin (2 μg/ml) was added to the culture media starting from post transduction day 4 to select stable inducible knockdown hESCs. Inducible METTL14 KD H1 and MEL1 hESCs were dissociated into single cells and 500 cells per microwell were seeded in AggreWell™400 24 well plates according to the manufacturer instructions. AggreWell™ EB Formation Medium - supplemented with doxycycline (2μg/ml) to induce shRNA expression - was refreshed every other day for ten days. EBs were then harvested, washed with DPBS, and lysed in TRIzol for RNA isolation using RNeasy Kit (Qiagen) according to the manufacturer instructions. RNA libraries were prepared using TruSeq Stranded Total Library Prep (Illumina) and sequencing was performed on NovaSeq 6000 according to the manufacturer instructions. Approximately 50 million paired-end 100-bp reads were generated for each sample.

first: Sevim

last: Kahraman

first: Dario

last: DeJesus

first: Rohit

last: Kulkarni


title: Identification and characterization of long non-coding RNAs in intestinal immune regulation of largemouth bass, Micropterus salmoides, under acute heat stress

city: Guiyang

first: Lei

last: Gan

address: Guizhou University, Guiyang, Guizhou, People’s Republic of China

department: college of animal science

institute: Guizhou university

summary: Long noncoding RNAs (lncRNAs) are non-protein coding RNAs with a length of more than 200 bp, which play a vital regulatory role in intestinal immunity. Exposure to high temperature leads to death in many fish species, which is implicated in fish enteritis. Our study showed that fish enteritis was induced by acute heat stress. To date, which lncRNAs are participated in this process is still unclear. In the present study, based on the intestinal sequencing data of largemouth bass Micropterus salmoides, a total of 347,351,492 clean reads were generated from six cDNA libraries. Among them, 3399 novel lncRNA transcripts from 2488 lncRNA genes were identified. As expected, these lncRNAs exhibited shorter transcript lengths than protein-coding genes similar to those lncRNAs reported from other fish species. In total, 216 novel lncRNAs were differentially expressed (DE) in largemouth bass intestine (absolute log2 fold change > 2 and p-value < 0.05) and that 210 neighboring genes were cis-regulated by these DE-lncRNAs. An analysis of GO/KEGG enrichment showed that most of these cis-genes seemed to be significantly enriched in immune regulation (p < 0.05) and lncRNA MSTRG.8573 had an important role in regulating jak-stat signaling pathway during this process. Through this study, we showed a catalog of novel DE-lncRNAs involved in the occurrence of enteritis in largemouth bass under acute heat stress, which could provide some useful references by regulating lncRNAs to solve the heat stress-induced fish enteritis for further studies.

overall_design: 120 healthy fish were randomly divided into two groups, and respectively maintained at two temperatures, 26℃ and 34℃, with three parallels in each group. After 9h (determined by our pre-experiment), 9 fish samples were taken from the 26℃ group (control group) and 34°C group (9h_HS group) with 3 fish per parallel, respectively. As soon as the intestine samples were collected, they were quickly frozen in liquid nitrogen, and then preserved at -80℃ for RNA extraction.

first: Dadong

last: Yan


title: SEAMoD: A fully interpretable neural network for cis-regulatory analysis of differentially expressed genes [RNA-seq]

overall_design: Mouse embryonic neural stem cells were isolated from dissected frontal cortex tissue of E14.5 embryos, cultured, and differentiated into several brain cell types. RNA was collected from these samples 0 or 4 days after differentiation. RNA-seq was performed. Each RNA-seq sample has 2-3 biological replicates.


title: Aberrant proximal tubule DNA methylation underlies phenotypic changes related to kidney dysfunction in patients with diabetes

city: Narita-shi

first: Takeshi

last: Marumo

state: Chiba

address: Kouzunomori 4-3

department: School of Medicine

institute: International University of Health and Welfare

summary: Epigenetic mechanisms are considered to contribute to diabetic nephropathy by maintaining memory of poor glycemic control during the early stages of diabetes.  However, DNA methylation changes in the human kidney are poorly characterized, because of the lack of cell type-specific analysis. We examined DNA methylation in proximal tubules purified from diabetic nephropathy patients and identified differentially methylated CpG sites, given the critical role of proximal tubules in the kidney injury. Hypermethylation was observed at CpG sites annotated to genes responsible for proximal tubule functions, including gluconeogenesis, nicotinamide adenine dinucleotide synthesis, transporters of glucose, water, phosphate, and drugs, in diabetic kidneys, while genes involved in oxidative stress and the cytoskeleton exhibited demethylation. Methylation levels of CpG sites annotated to ACTN1, BCAR1, MYH9, UBE4B, AFMID, TRAF2, TXNIP, FOXO3, and HNF4A were correlated with the estimated glomerular filtration rate, while methylation of the CpG site in RUNX1 was associated with interstitial fibrosis and tubular atrophy. Hypermethylation of G6PC and HNF4A was accompanied by decreased expression in diabetic kidneys. Proximal tubule-specific hypomethylation of metabolic genes related to HNF4A observed in control kidneys was compromised in diabetic kidneys, suggesting a role for aberrant DNA methylation in the dedifferentiation process. Multiple genes with aberrant DNA methylation in diabetes overlapped genes with altered expressions in maladaptive proximal tubule cells, including transcription factors PPARA and RREB1. In conclusion, DNA methylation derangement in the proximal tubules of patients with diabetes may drive phenotypic changes, characterized by inflammatory and fibrotic features, along with impaired function in metabolism and transport.

overall_design: DNA was extracted from 15 samples of normal micro-dissected proximal tubules and 18 samples of micro-dissected proximal tubules obtained from patients with diabetic nephropathy by NucleoSpin Tissue XS (MACHEREY-NAGEL GmbH & Co. KG, Düren, Germany). DNA was then subjected to bisulfite conversion using the EZ DNA Methylation Gold Kit (Zymo Research, Irvine, CA). Genome-wide DNA methylation analysis was performed using the Illumina Infinium MethylationEPIC Kit (Illumina, San Diego, CA) using the iScan reader (Illumina). The data were assembled using the GenomeStudio methylation software (Illumina).


title: Bone morphogenetic protein 4 (BMP4) mediates inflammation and endothelial-mesenchymal transition (EndoMT) in the vascular remodeling of angiotensin (Ang) II -induced abdominal aortic aneurysm

city: Hangzhou

first: Xihao

last: Wang

address: Gudun road,num.1229

institute: Zhejiang Hospital

summary: Abdominal aortic aneurysm (AAA) is one of the most common fatal macrovascular diseases worldwide which generates huge economic burdens on humanity. Regretfully, the pathogenesis of AAA is still not well clarified. In our study, 10×single-cell sequencing revealed that endothelial cells (ECs) dysfunction and endothelial-mesenchymal transition (EndoMT) appeared in progress of angiotensin (Ang)-II induced AAA. Three different types of ECs, including Mature ECs, EndoMT ECs and Injury & inflammation ECs successively appeared during the progression of AAA. Compared with Mature ECs, EndoMT ECs and Injury & inflammation ECs had stronger extracellular matrix synthesis function and lower metabolic level. Transcription factor analysis revealed that interferon regulatory factor 6 (Irf6) and homeobox A9 (Hoxa9) may be the critical regulons in Injury & inflammation ECs. According pseudotime trajectory and KEGG enrichment analysis, we speculated bone morphogenetic protein 4 (BMP4) regulated EndoMT, thus participating in Ang II-induced AAA. Our study represented BMP4 promotes phenotypic transition, cell migration and invasion of ECs by PI3K/AKT/mTOR pathways in vitro. Protein-protein interaction (PPI) analysis and co-immunoprecipitation (Co-IP) revealed that biglycan (BGN), a kind of small leucine-rich proteoglycan, directly combined with BMP4, which enhanced conversion degree of EndoMT. BMP4 reprogrammed ECs from anti-inflammatory to proinflammatory phenotype, which eventually led to AAA.

overall_design: The Abdominal aorta of mouse from the Control, AAA groups were harvested and analyzed using scRNA-seq.

first: Yingzheng

last: Weng

first: Jiangjie

last: Lou

first: Lijiang

last: Tang


title: Impaired repopulating ability of Uhrf2-/- hematopoietic progenitor cells in mice. [CUT & Tag]

city: Fukushima

first: Kazuhiko

last: Ikeda

state: Fukushima

address: 1 Hikariga-oka

department: Blood Transfusion and Transplantation Immunology

institute: Fukushima Medical University

summary: We generated Uhrf2-/- mice to clarify the role of deletion of UHRF2 in hematopoiesis.  In competitive repopulation assay, the proportions of Uhrf2-/- cells were decreased relative to Uhrf2+/+ cells in all lineages.

overall_design: We then performed CUT&Tag analysis Uhrf2-KO and WT LSK cells for H3K9me3.

first: Koki

last: Ueda

first: Keiji

last: Minakawa


title: Impaired repopulating ability of Uhrf2-/- hematopoietic progenitor cells in mice.

overall_design: Refer to individual Series


title: Metastable Intermediates Identified in Epithelial to Mesenchymal Transition are Regulated by G-quadruplex DNA Structures

city: Crawley

first: Jessica

last: King

address: 35 Stirling Hwy

department: School of Molecular Sciences

country: Australia

institute: University of Western Australia

summary: Cancer is a heterogenous disease, with multiple cellular subpopulations present within a single tumour mass that differ genetically and morphologically, and thus respond differently to chemotherapeutics. Epithelial-to-Mesenchymal transition (EMT) has been shown to play a role in tumour heterogeneity. Single-cell sequencing is critical to identify cell-type-specific transcriptomic differences with multiplexing methods increasing experimental scope with reduced cost. Cell hashing with barcoded antibodies is commonly used to multiplex samples but is limited to samples expressing target antigens. Antigen-independent methods of barcoding cells, such as barcoded lipid-anchors, have gained traction but present substantial populations that cannot be unambiguously demultiplexed. Herein we report a multiplexed single-cell transfection-enabled cell hashing sequencing (scTECH-seq) platform, which uses antigen-independent endocytic uptake to barcode cells, resulting in efficient, uniform barcoding with high cell recovery. We apply this methodology to identify distinct metastable cell states in human mammary cells undergoing EMT and show that stabilisation of G-quadruplex DNA has the potential to inhibit EMT.

overall_design:
We performed single-cell RNA-seq of human mammary epithelial cells to identify metastable intermediate cell states in TGF-β induced epithelial-to-mesenchymal transition (EMT). We also treated cells with pyridostatin to investigate the role G-quadruplex structures play in EMT. We combined this with our new method scTECH-seq to multiplex samples and quantify transcripts in the presence and absence of pyridostatin in TGF-β induced EMT.
Please note that processed data generated from both [GEX] and [CBO] samples, is linked to the corresonding [GEX] sample records.

first: Cameron

middle: W

last: Evans

first: Ulrich

middle: D

last: Kadolsky

first: Marck

last: Norret

first: Munir

last: Iqbal

first: Clémentine

last: Mercé

first: Sugandha

last: Bhatia

first: Philip

last: Gregory

first: Erik

last: Thompson

first: Alka

last: Saxena

first: K

middle: S

last: Iyer

first: Nicole

middle: M

last: Smith


title: The Local Density of H3K9me3 Dictates The Stability of HP1a Condensates-mediated Genomic Interactions

city: Shanghai

first: YING

last: FENG

address: 393 Middle Huaxia Road

institute: Shanghaitech University

summary:
The human genome can be demarcated into different domains based on distinct epigenetic states. The trimethylation of histone H3 lysine 9 (H3K9me3) is essential for the formation of constitutive heterochromatin nanodomains. It is unclear what degrees or densities of H3K9me3 in genomic regions are required for their stable interactions.
We demonstrate that the levels of H3K9me3 at the loci are positively correlated with their association with HP1a condensates. Epigenetic perturbation-induced Genome organization (EpiGo)-KRAB introduces ~20 kilobases of H3K9me3 at the TCF3 locus, which is sufficient to establish a stable association between TCF3 and HP1a condensates. In addition, EpiGo-mediated H3K9me3 also led to stable genomic interaction between IDR3 and TCF3. In sum, these data suggest that the density of H3K9me3 could dictate the stability of interactions between genomic loci and HP1a condensates.

overall_design: Here we utilize CRISPR-based DNA imaging to investigate the role of endogenous or ectopic H3K9me3 in chromatin dynamics and genomic interactions. Three loci (IDR3, TCF3 and PR1) with distinct levels of H3K9me3 were chosen to examine the genomic interactions and their association with endogenous HP1a condensates, a heterochromatin marker.

first: Hanhui

last: Ma

first: Ying

last: Feng

first: Li

last: Guo

first: Hui

last: Zheng


title: RNA-seq reveals distinct renal responses to murine trypanosomosis in susceptible and tolerant mice

city: Glasgow

first: John

last: Ogunsola

state: State

address: 243 Henry Wellcome Building

institute: University of Glasgow

summary:
To understand broad mechanisms that underlie differential susceptibilities to murine trypanosomiasis, we infected BALB/c and C57BL/6 mice with Trypanosoma brucei
We obtained kidneys from infected mice at early (day 7) and late (day 21) infection time points and performed bulk RNA seq on the kidney lysates using poly-A enrichment

overall_design:
Comparative transcriptomic analysis of RNA-seq data for the kidney of Trypanosoma brucei infected mice with differential susceptibilities at early and late infection time points
BALB/c: susceptible
C57BL/6: resistant

first: Anneli

last: Cooper

first: Juan

last: Quintana

first: Annette

last: MacLeod


title: Epigenetic study on CBP inhibiting differentiation of porcine muscle satellite cells (RNA-Seq)

city: Wuhan

first: Xuan

middle: Wen

last: Wang

state: Hubei Province

address: No. 1 Shizishan Street

institute: Huazhong Agriculture University

summary: These data are transcriptome sequencing data of porcine muscle satellite cells at the stage of proliferation and differentiation.

overall_design: These data are transcriptome sequencing data of porcine muscle satellite cells at the stage of proliferation and differentiation, which are repeated in three groups of control group and test group

first: Peng

last: Zhou


title: Epigenetic study on CBP inhibiting differentiation of porcine muscle satellite cells (ATAC-Seq)

summary: These data are ATAC-Seq data of porcine muscle satellite cells at the stage of proliferation and differentiation.

overall_design: These data are ATAC-Seq data of porcine muscle satellite cells at the stage of proliferation and differentiation, which are repeated in three groups of control group and test group


title: Epigenetic study on CBP inhibiting differentiation of porcine muscle satellite cells (CUT&Tag)

summary: The data are the cut&tag data sequencing data of H3K4me3, H3K27Ac and H3K27me3 of pig muscle satellite cells at the stage of proliferation and differentiation.

overall_design: Yhe data are the cut&tag sequencing data of H3K4me3, H3K27Ac and H3K27me3 of porcine muscle satellite cells at the stage of proliferation and differentiation. The control group and the experimental group each have two replicates.


title: Mitochondrial SHMT2 is a crucial therapeutic target in dedifferentiated thyroid cancer (2nd study)

city: daejeon

first: Seung-Jin

last: Park

address: gwahakro

institute: KRIBB

summary:
The roles of the serine/glycine metabolic pathway (SGP) have recently been evident in certain types of tumor physiology; however, the pathological  relevance of SGP in undifferentiated thyroid cancer remains unexplored. Herein, we employed a comparative transcriptome analysis of bulk RNA sequencing coupled with single-cell RNA sequencing, showing that the high expression of SHMT2 and MTHFD2 is tightly associated with a low thyroid differentiation score (TDS) and poor clinical features in thyroid cancer. In addition, unique metabolic reprogramming of SGP-relevant pathways in dedifferentiated cancer cells, and a distinct trajectory of a subpopulation of tumor cells with a high mitochondrial one-carbon pathway was observed. More importantly, such dramatic changes are functionally relevant, as inhibition of SHMT2 significantly compromises mitochondrial respiration and decreases tumor  size by upregulating TDS markers. Taken together, our results highlight the importance of the mitochondrial one-carbon pathway, including SGP, in undifferentiated thyroid cancer and suggest that SHMT2 is a novel therapeutic target.
RNA-seq data of 65 fresh frozen normal tissues were generated. Total RNA was isolated by RNeasy Mini Kit (Qiagen, CA, USA), according to the manufacturer's protocol. The quality and integrity of the RNA were confirmed by agarose gel electrophoresis and ethidium bromide staining, followed by visual examination under ultraviolet light. Sequencing library was prepared using TruSeq RNA Sample Preparation kit v2 (Illumina, CA, USA) according to the manufacturer’s protocols. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads, fragmented, and converted into cDNAs. Then, adapters were ligated and the fragments were amplified on a PCR. Sequencing was performed in paired end reads (2x75 bp) using NextSeq 500 platform (Illumina).

overall_design: Seong E Lee

first: Seongyeol

first: Shinae

last: Yi

first: Seon-Kyu

last: Kim

first: Bon

last: Koo

first: Yea

middle: E

last: Kang


title: Epigenetic study on CBP inhibiting differentiation of porcine muscle satellite cells

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


title: Phosphorylation of SIK1 by Akt1 activates STAT3 signal pathway in breast cancer cell.

first: sun

last: zicheng

state: GuangDong

address: zhongshan 2 Road

institute: sun yat-sen university

summary: As a member of AMPK-related kinases, salt-inducible kinase 1 (SIK1) regulates energy response-related physiopathological processes, such as gluconeogenesis and lipid metabolism. More recently, instead of AMPK, SIK1 has been strikingly defined as a major player for tumor suppressor liver kinase 1 (LKB1) deficient NSCLC. However, the exact roles and upstream regulators of SIK1 in breast cancer are not well defined.We found that Akt1 can directly phosphorylate SIK1 and inhibit the kinase activity of SIK1, promoting the progress of breast cancer. To investigate the mechanism of Akt1 phosphorylated SIK1 promoting the progression of breast cancer, we constructed a stable expression of SIK1 WT and S435D in BT549, and  then performed gene expression profiling analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BT549 Overexpressing SIK1 WT and S435D.

first: Zicheng

last: Sun

first: Qiwei

last: Jiang

first: Bing

last: Gao


title: SETD2 loss sensitizes kidney cancer cells to DNA hypomethylating agents [methylation]

city: Charleston

first: Aguirre

last: de Cubas

state: SC

address: 86 Jonathan Lucas St

department: Microbiology and Immunology

institute: Medical University of South Carolina

summary: Genome-wide DNA methylation profiling of SETD2-null 786-0 RCC cells treated with decitabine (100nM and 300nM) or DMSO vehicle. The Illumina Infinium HumanMethylation EPIC BeadChip was used to obtain DNA methylation profiles across approximately 850K CpGs.

overall_design: Bisulfite converted DNA from 6 samples were hybridized to the Illumina Infinium HumanMethylation EPIC BeadChip

first: W

middle: K

last: Rathmell


title: Taxonomy of introns, their evolution, and the role of minor introns in stress response

city: Storrs

first: Rahul

middle: N

last: Kanadia

state: CT

address: 75 N. Eagleville Road

department: Physiology and Neurobiology

institute: University of Connecticut

summary: Despite the high conservation of minor introns across eukaryotic supergroups, specific lineages have completely lost minor intron splicing, which has raised questions about their evolution and purpose. Addressing these questions requires identification of the introns that are affected by minor spliceosome inhibition. To this end, we applied principles of Linnaean taxonomy combined with position-weight matrices to produce five intron classes: minor, minor-like, hybrid, major-like and major. We classified introns across the genomes of 263 species of six eukaryotic supergroups, which can be viewed at the Minor Intron Database (MIDB). Transcriptomic analysis revealed that ~40% of the minor introns are responsive to minor spliceosome inhibition, while an additional 5% of the minor-like and hybrid introns are also affected. We propose that minor-like introns represent an intermediate in the conversion of minor to major introns and uncover the importance of a guanine at the -1 position of the 5’ splice site in facilitating this shift in spliceosome dependence. Finally, we find that minor introns are aberrantly spliced in fish and plants upon cold stress, thereby providing a potential explanation for their high degree of conservation in these lineages.

sample_organism:
Danio rerio
Mus musculus

platform_organism:
Danio rerio
Mus musculus

overall_design:
Splicing analysis of RNA-seq data for two rnpc3 mutant and WT zebrafish lines

RNA-seq on 2 control and 2 U11 mutant E14 dorsal telencephalon in mouse.

first: Joan

last: Heath

first: Anouk

last: Olthof


title: Long-term Urolithin A treatment ameliorates disease pathology in Alzheimer's Disease mouse models [MET_DC]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary:
Alzheimer's disease (AD) is a progressive neurodegenerative disorder associated with learning, memory, and cognitive deficits. Neuroinflammation and lysosomal dysfunction are thought to play key roles in the progression of AD pathology. Diverse measures have been applied to treat AD, but currently, there is no effective treatment. Urolithin A (UA) is a gut microbial metabolite of ellagic acid shown to stimulate mitophagy and acts as a potent anti-inflammatory and anti-oxidant agent. However, long-term safety and the potential role of UA in altering pathology of AD is still largely unclear. In this study, we investigated the underlying mechanisms for the beneficial effects of UA in multiple mouse models of AD. We report that long-term UA treatment significantly improves learning and memory, olfactory function, and synaptic function of neurons in AD transgenic mice. We demonstrate that UA decreases soluble and insoluble Ab1-42, total Tau, and Tau phosphorylation. Furthermore, alterations in lysosomal cathepsins, particularly upregulation of cathepsin Z, was observed in the AD mice brains and normalized by UA treatment. Notably, UA treatment also ameliorates neuroinflammation, DNA damage, mitochondrial dysfunction, and restores lysosomal functions in AD mice brains. Collectively, these results provide new insights into the role of UA in regulating lysosomal dysfunction, cathepsins, and suggests that UA may have a potential therapeutic application for AD.
To understand what metabolism-related gene expression changes are induced by Urolithin A, WT (C57BL6/J), 3xTgAD and 3xTgAD/PolB+/- mice were treated with water or Urolithin A (200mg/kg/day) by oral gavage for 5 months starting when the mice were 12m of age, thereafter hippocampi tissues was collected from each mouse and subjected to RNA isolation.

overall_design: We analyzed a total of 23 samples of mouse hippocampus either treated with Urolithin A or not as follows: controls_vehicle (n=4), 3xAD_vehicle (n=5), 3xAD/PolB+/-_vehicle (n=4), 3xAD_UA (n=5), and 3xAD/PolB+/-_UA (n=5). Analysis employed nCounter Advanced Analysis suite of tools.

first: Vilhelm

last: Bohr


title: SETD2 loss sensitizes kidney cancer cells to DNA hypomethylating agents

summary: Large-scale sequencing efforts in Clear cell renal cell carcinoma (ccRCC) have found a high prevalence of mutations in chromatin-related genes.  Prominent within this group is SETD2, which is mutated in 15% of ccRCC and is associated with aggressive disease. SETD2 is a methyltransferase responsible for trimethylating lysine 36 on histone H3 (H3K36me3). Although it is not completely understood how SETD2 loss contributes to ccRCC tumorigenesis, it is thought that it reprograms the epigenetic landscape of the cell. Here we explore the impact that SETD2/H3K36me3 loss has on the DNA methylome in ccRCC cells. DNA methylation was measured using the EPIC DNA methylation assay in 786-O ccRCC cells and non-cancerous transformed proximal tubule kidney cells (HKC) with and without SETD2. Sensitivity to DNA hypomethylating agents was assessed by dose-response assay using 5-aza-2'-deoxycytidine. Apoptosis was measured via Annexin-V/PI staining by flow cytometry. Mitochondrial fitness was evaluated by electron microscopy and flow cytometry. Moreover, activity of 5-aza-2'-deoxycytidine, a DNA hypomethylating agent, in was assessed in SETD2 WT/KO xenografts in NOD-Scid mice. SETD2 loss resulted in DNA hypermethylation in HKC cells and to a greater extent in 786-O. Dose-response assays showed that SETD2-null ccRCC cells are sensitive to 5-aza-2'-deoxycytidine. Furthermore, Annexin-V/PI staining revealed more apoptotic and necrotic cells in SETD2-null cells following 5-aza-2'-deoxycytidine treatment, which was rescued using a Caspase inhibitor. In addition, 5-aza-2'-deoxycytidine induced profound changes in mitochondria in SETD2-null cells, including loss of membrane potential and size reduction. Indeed, in vivo experiments verified increased SETD2-null xenografts’ sensitivity to 5-aza-2'-deoxycytidine. We show that SETD2 loss in ccRCC cells causes DNA hypermethylation, creating a synthetic lethal dependency with DNA hypomethylating agents.

overall_design: RNAseq profiles in HKC and 786-0 kidney cells treated with DMSO or Decitabine (100nM or 300nM)\


title: Long-term Urolithin A treatment ameliorates disease pathology in Alzheimer's Disease mouse models [I]

summary: Alzheimer's disease (AD) is a progressive neurodegenerative disorder associated with learning, memory, and cognitive deficits. Neuroinflammation and lysosomal dysfunction are thought to play key roles in the progression of AD pathology. Diverse measures have been applied to treat AD, but currently, there is no effective treatment. Urolithin A (UA) is a gut microbial metabolite of ellagic acid shown to stimulate mitophagy and acts as a potent anti-inflammatory and anti-oxidant agent. However, long-term safety and the potential role of UA in altering pathology of AD is still largely unclear. In this study, we investigated the underlying mechanisms for the beneficial effects of UA in multiple mouse models of AD. We report that long-term UA treatment significantly improves learning and memory, olfactory function, and synaptic function of neurons in AD transgenic mice. We demonstrate that UA decreases soluble and insoluble Ab1-42, total Tau, and Tau phosphorylation. Furthermore, alterations in lysosomal cathepsins, particularly upregulation of cathepsin Z, was observed in the AD mice brains and normalized by UA treatment. Notably, UA treatment also ameliorates neuroinflammation, DNA damage, mitochondrial dysfunction, and restores lysosomal functions in AD mice brains. Collectively, these results provide new insights into the role of UA in regulating lysosomal dysfunction, cathepsins, and suggests that UA may have a potential therapeutic application for AD.

overall_design: APP/PS1 mice were treated with daily gavage of Urolithin A (20mg/kg/day) or not (water) by gavage from 2m of age til 7m of age, then hippocampi were collected. Thereafter, some mice (washout groups) ceased gavage and were allowed to age one more month before hippocampi were collected. Samples were: controls (n=4), APPPS1_control (n=3), APPPS1_UA (n=4), washout controls (n=5), washout APPPS1 controls (n=3), and washout APPPS1_UA (n=5).


title: Nucleoporin Elys attaches peripheral chromatin to the nuclear pores in interphase nuclei

city: Stockholm

first: Artem

last: Ilin

address: Svante Arrhenius väg 20C

department: MBW

country: Sweden

institute: Stockholm University

summary: Transport of macromolecules through the nuclear envelope (NE) is mediated by nuclear pore complexes (NPCs) consisting of nucleoporins (Nups). Elys/Mel-28 is the Nup that binds and connects the decondensing chromatin with the reassembled NPCs at the end of mitosis. Whether Elys links chromatin with the NE during interphase is unknown. Using DamID-seq, we identified Elys binding sites in Drosophila late embryos and divided them into those associated with nucleoplasmic or NPC-linked Elys. These Elys binding sites are located within active or inactive chromatin, respectively. Strikingly, Elys knockdown in S2 cells results in peripheral chromatin displacement from the NE, in decondensation of NE-attached chromatin, and in derepression of genes within. It also leads to slightly more compact active chromatin regions. Our findings indicate that NPC-linked Elys, together with the nuclear lamina, anchors peripheral chromatin to the NE, whereas nucleoplasmic Elys decompacts active chromatin.

overall_design: DamID-seq and RNA-seq

last: Ilyin


title: Long-term Urolithin A treatment ameliorates disease pathology in Alzheimer's Disease mouse models [AD_DC]

summary:
Alzheimer's disease (AD) is a progressive neurodegenerative disorder associated with learning, memory, and cognitive deficits. Neuroinflammation and lysosomal dysfunction are thought to play key roles in the progression of AD pathology. Diverse measures have been applied to treat AD, but currently, there is no effective treatment. Urolithin A (UA) is a gut microbial metabolite of ellagic acid shown to stimulate mitophagy and acts as a potent anti-inflammatory and anti-oxidant agent. However, long-term safety and the potential role of UA in altering pathology of AD is still largely unclear. In this study, we investigated the underlying mechanisms for the beneficial effects of UA in multiple mouse models of AD. We report that long-term UA treatment significantly improves learning and memory, olfactory function, and synaptic function of neurons in AD transgenic mice. We demonstrate that UA decreases soluble and insoluble Ab1-42, total Tau, and Tau phosphorylation. Furthermore, alterations in lysosomal cathepsins, particularly upregulation of cathepsin Z, was observed in the AD mice brains and normalized by UA treatment. Notably, UA treatment also ameliorates neuroinflammation, DNA damage, mitochondrial dysfunction, and restores lysosomal functions in AD mice brains. Collectively, these results provide new insights into the role of UA in regulating lysosomal dysfunction, cathepsins, and suggests that UA may have a potential therapeutic application for AD.
To understand what gene expression changes are induced by Urolithin A, WT (C57BL6/J), 3xTgAD and 3xTgAD/PolB+/- mice were treated with water or Urolithin A (200mg/kg/day) by oral gavage for 5 months starting when the mice were 12m of age. Thereafter, hippocampi tissue was collected from each mouse and subjected to RNA isolation.

overall_design: We analyzed a total of 35 samples of mouse hippocampi. Mice were either treated with Urolithin A or not as follows: controls (n=7), 3xAD_veh (n=8), 3xAD_UA (n=7), 3xAD/PolB+/-_veh (n=7) and 3xAD/PolB+/-_UA (n=6). Analysis employed Rosalind (https://rosalind/onramp.bio/) with Hyperscale architecture developed by Rosalind, Inc. (San Diego, CA).


title: Biomechanical Stress–Mediated Mesenchymal Fibulin-1–WNT Signaling Regulates Initiation of Successional Dental Lamina [single-cell RNA-seq]

city: Beijing

first: Songlin

last: Wang

address: No. 4 Tiantanxili, Dongcheng District

institute: Beijing Laboratory of Oral Health, Capital Medical University

summary: Mesenchymal environments are considered to maintain the quiescent state of SDL within the stem-cell niche. We used single cell RNA sequencing (scRNA-seq) to analyze the subtypes and functions of the mesenchyme surrounding SDL.

overall_design: Total 12 samples of SDL and surrounding mesenchyme from mandibular permanent canine of miniature pig embryos at E60 were microdissected and pooled, and then used for scRNAseq.


title: Biomechanical Stress–Mediated Mesenchymal Fibulin-1–WNT Signaling Regulates Initiation of Successional Dental Lamina [single-cell spatial transcriptomics]

summary: Mesenchymal environments are considered to maintain the quiescent state of SDL within the stem-cell niche. To reveal expressional heterogeneity and cell-cell interaction in the mesenchyme and the dental epithelium, we performed spatial transcriptome  to analyze the subtypes and functions of the mesenchyme surrounding SDL.

overall_design: We dissected the mandibular bone containing one DC and one PC from E60 miniature pigs. These mandible slice samples were embedded in Tissue-Tek OCT (Sakura Finetek, Torrance, CA, USA) on dry ice and cut at 10-μm thickness using a Leica Cryostat CM1850 (Wetzlar, Germany), after which the frozen sections were transferred to a Visium slide (10x Genomics, Shanghai, China).


title: Biomechanical Stress–Mediated Mesenchymal Fibulin-1–WNT Signaling Regulates Initiation of Successional Dental Lamina

overall_design: Refer to individual Series


title: Effect of JAK-JAK Geometry on Gene Expression Levels in Cells Treated with Type I and III Interferons

city: Chicago

first: Juan

middle: L

last: Mendoza

state: IL

address: 920 E 58th Street

institute: The University of Chicago

summary:
To evaluate the role of receptor geometry in interferon signaling, we engineered cell lines that express wild-type and mutant IFNλ cognate receptors (IFNλR1) with rotated intracellular registers with respect to the associated JAK1.
We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cell lines treated with 3 indicated interferons at 24hr.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for wild-type vs geometry-optimized HEK293 cells post-interferon treatment

first: Theint

last: Aung


title: Effect of mstr-1 knockout on global mRNA expression in C. elegans

city: Toronto

first: Matthew

last: Eroglu

state: ON

address: 686 Bay St

department: DSCB

institute: Hospital for Sick Children

summary:
We isolate and sequence total RNA from wild type (N2) and mstr-1(on33) worms and compare global mRNA expression to understand the mstr-1 null phenotype
Significantly DE genes are then compared to transcripts bound by MSTR-1 from CLIP-seq data co-uploaded with this dataset

overall_design: Worms were grown to L4 stage and RNA from whole worms was extracted and sequenced by TCAG at SickKids Hospital. 3 biological replicates are included

first: Brent

last: Derry