title: A Genome-Wide CRISPR-Cas9 Screen Reveals the Requirement of Host Cell Sulfation for Schmallenberg Virus Infection

summary: Schmallenberg virus (SBV) is an insect-transmitted orthobunyavirus that can cause abortions and congenital malformations in the offspring of ruminants. Even though the two viral surface glycoproteins Gn and Gc are involved in host cell entry, the specific cellular receptors of SBV are currently unknown. Using genome-wide CRISPR-Cas9 forward screening, we identified 3′-phosphoadenosine 5′-phosphosulfate (PAPS) transporter 1 (PAPST1) as an essential factor for SBV infection. PAPST1 is a sulfotransferase involved in heparan sulfate proteoglycan synthesis encoded by the solute carrier family 35 member B2 gene (SLC35B2). SBV cell surface attachment and entry were largely reduced upon the knockout of SLC35B2, whereas the reconstitution of SLC35B2 in these cells fully restored their susceptibility to SBV infection. Furthermore, treatment of cells with heparinase diminished infection with SBV, confirming that heparan sulfate plays an important role in cell attachment and entry, although to various degrees, heparan sulfate was also found to be important to initiate infection by two other bunyaviruses, La Crosse virus and Rift Valley fever virus. Thus, PAPST1-triggered synthesis of cell surface heparan sulfate is required for the efficient replication of SBV and other bunyaviruses.

overall_design: Positive selection CRISPR screen with Schmallenberg virus in 293T cells

first: Thiprampai

last: Thamamongood

first: Martin

last: Schwemmle


title: Intercellular communication via miR-143-containing microvesicles controls osteoblastic bone formation in vivo

status: Public on Feb 04 2022

city: Suita

first: Daisuke

last: Okuzaki

state: Osaka

address: Yamadaoka 3-1

department: Immunology Frontier Research Center

country: Japan

institute: Osaka univ.

type: Non-coding RNA profiling by high throughput sequencing

summary: Osteoblasts are the only somatic cell type with bone-forming ability. While the cellular and molecular mechanisms underlying their differentiation and function have been identified, their dynamic control in vivo is unclear. By intravital multiphoton microscopy of live bone tissues of osteoblast fluorescent reporter mice, we visualized intact mature osteoblasts in vivo and found that they actively secrete and capture extracellular microvesicles. Microvesicles from mature osteoblasts contain the microRNA miR-143-3p, which inhibits osteoblast differentiation. Osteoblast-specific deletion of miR-143 increased bone formation and miR-143-deficient microvesicles induced recovery from bone defect. In sum, we report a novel mode of intercellular communication in vivo via microRNA-containing extracellular vesicles, which controls bone homeostasis.

overall_design: We performed next-generation sequencing analysis of small RNAs in total mOB-derived large EVs without filtration.

first: Maki

last: Uenaka


title: MicroRNA profiling of plasma exosomes of ESCC patients

status: Public on Feb 03 2022

city: Chiba

first: Huan

last: Wang

state: Chiba

address: 1-8-1 Chuo-Ku

institute: Chiba University

summary: MiRNA arrays were performed for the plasma exosomes of ESCC patients before treatment. The tumor regression grade of the primary tumor (TRG-PT) was used to evaluate the therapeutic effect of chemoradiotherapy (CRT). Patients classified as Grade 3 were considered sensitive to CRT (n=4), while those classified as Grade 0 or 1a were considered resistant to CRT (n=4).

overall_design: miRCURY LNA microRNA arrays were performed in a cohort of eight cases to investigate the difference in the miRNA expression between CRT-sensitive and CRT-resistant patients.

first: Masayuki

last: Kano


title: CCT2 promotes the proliferation and migration of head and neck squamous cell carcinoma via activating PI3K/AKT pathway

city: guangzhou

first: Lu

last: Lin

address: 74 zhongshaner road

country: China

institute: sun yat-sen university

type: Expression profiling by high throughput sequencing

summary:
Purpose: RNA-seq was used to evaluate the effect of CCT2 knockdown in HNSCC cell lines.
Methods: CCT2 was knocked down in SAS cell lines through shRNA and then RNA was extracted from control cells and knockdown cells.
Results: Using an optimized data analysis workflow, we identified 205 differentially expressed genes (DEG), of which 141 genes were down-regulated and 64 genes up-regulated, respectively (fold change >2 and adjust p-value < 0.05). RT-qPCR was used to confirm the reliability of RNA-seq data. KEGG and GSEA analysis indicated that PI3K/AKT signaling pathway might be involved in the function of CCT2, which had been proved by western blotting.

overall_design: CCT2 was knocked down by shRNA in HNSCC cell line-SAS and the RNA was prepared from control and knockdown cell for RNA-seq.

first: Lin

last: Lu

first: Jianbo

last: Sun


title: Small and long RNAs profiling of testis, developing oocytes and early embryos wild-type and Pld6-deficient golden hamster

city: Nanjing

first: Qin

last: RuiXin

state: Jiangsu

address: No. 101 Longmian Avenue, Jiangning District, Nanjing

institute: Nanjing Medical University

summary: Small and long RNAs profiling of developing oocytes and early embryos in wild-type and Pld6-deficient golden hamster females, as well as profiling of testis of wild-types and Pld6-mutents


title: Investigating the impact of MTCH-1 knockdown on gene expression in C. elegans adults

city: London

first: John

last: Labbadia

address: Darwin Building, Gower Street

department: GEE

country: United Kingdom

institute: UCL

summary: We report gene expression changes in reproductively mature (D3 adult) C. elegans hermaphrodites subjected to control or mtch-1(RNAi) conditions

overall_design: C. elegans were age-synchronised and exposed to EV control (L4440) or mtch-1(RNAi) from hatching until day 3 of adulthood. At this point, approximately 200 adults were collected and RNA was extracted in order to compare gene expression changes between the treatment groups.


title: Human Pluripotent Stem Cell-derived Islets Ameliorate Diabetes in Nonhuman Primates [human_bulk]

city: Beijing

first: Yaqi

state: Beijing

address: No.5 Yiheyuan Road Haidian District

institute: Peking University

summary: Human pluripotent stem cell-derived islets (hPSC-islets) are a promising cell resource for diabetes treatment. Here, we demonstrate that transplantation of human pluripotent stem cell-derived islets into diabetic nonhuman primates effectively restored endogenous insulin secretion and improved glycemic control. Single-cell RNA sequencing analysis of S6D2 clusters confirmed the existence of the three major pancreatic endocrine cell populations (β cells, α-like cells and δ-like cells) and their proportions, which altogether accounted for 80%. Importantly, hierarchical clustering of S6D2 hCiPSC-islets, 10 wpt kidney grafts and primary human islets showed that the hCiPSC differentiated pancreatic endocrine cells shared similar global gene expression profiles to their native counterparts in primary human islets. Single-cell RNA sequencing analysis on PBMCs revealed the potential immune response of recipient macaque to hCiPSC-islets.

overall_design: Bulk RNA sequencing analysis on hADFs, hCiPSCs, hiPSCs and hESCs to compare the global gene expression profiles.

first: Yuanyuan

last: Du

first: Zhen

last: Liang

first: Shusen

first: Dong

first: Xiaofeng

first: Liew

middle: S

last: Yi

first: Shuaiyao


title: Magnesium facilitates the healing of atypical femoral fractures: A single-cell transcriptomic study

city: St Louis

first: Nianye

last: Zheng

state: Missouri

address: 660 S Euclid Ave

department: Orthopedic Surgery

country: USA

institute: Washington University

summary: We  reported the application of single-cell mRNA sequencing to identify a unique population of fibroblasts that exits in the fracture callus of bisphosphonate-treated rats. Such unique population of fibroblasts prevented fracture healing by secreting ECM. Further, it was found that these ECM-secreting fibroblasts were enriched for myeloid genes, suggesting a bone marrow orgin. After fractures were treated with local CGRP injection or Magnesium based biometal, such population of fibroblasts was cleared off, resulting in facilitated fracture healing of bisphosphonate-treated rats.

overall_design: Eight batches of single cell libraries for sequencing: control rats on week 4, control rats on week 12, bisphosphonate-treated rats on week 4, bisphosphoante-treated rats on week 12, CGRP treated rats on week 4, CGRP treated rats on week 12, Mg treated rats on week 4, Mg treated rats on week 12. Library was prepared by using 10,000 cell for group by Chromium controller (V3 chemistry version, 10X Genomics Inc, San Francisco, USA), barcoded and purified as described by the manufacturer, and sequenced using a 2x150 pair-end configuration on an Illumina HiSeq platform at a sequencing depth of ~400 million reads.

first: Jiankun

last: Xu

first: Ling

last: Qin

first: Regis

last: O'Keefe


title: Single-cell Transcriptomic Profiling of the Hypothalamic Median Eminence during Aging

first: Zhenhua

last: Chen

state: China

address: West Beichen Road, Olympic Village, Beijing

department: State Key Laboratory of Molecular Development Biology

institute: Institute of Genetics and Developmental Biology, Chinese Academy of Sciences

summary: Aging is a slow and progressive natural process that compromises the normal functions of cells, tissues, organs and systems. The aging of the hypothalamic median eminence (ME), a structural gate linking neural and endocrine systems, may impair hormone release, energy homeostasis and central sensing of circulating molecules, leading to systemic and reproductive aging. However, the molecular and cellular features of ME aging remain largely unknown. Here we describe the transcriptional landscape of young and middle-aged mouse ME at single-cell resolution, revealing the common and cell-type-specific transcriptional changes with age. The transcriptional changes in cell-intrinsic programs, cell-cell crosstalk and cell-extrinsic factors highlight five molecular features of ME aging and also implicate several potentially druggable targets at cellular, signaling and molecular levels. Importantly, our results suggest that vascular and leptomeningeal cells may lead the asynchronized aging process among diverse cell types and drive local inflammation and cellular senescence via a unique secretome. Together, our study uncovers how intrinsic and extrinsic features of each cell type in the hypothalamic ME are changed by the aging process, which will facilitate our understanding of brain aging and provide clues for efficient anti-aging intervention at the middle-aged stage.

overall_design: Single cell RNA-seq of  median eminence in wild type mice at 3-month old and 12-month old.

first: Qingfeng

last: Wu


title: Intermittent Administration of Tacrolimus Enhances Anti-Tumor Immunity in Melanoma-Bearing Mice

city: Fuzhou

first: Zili

state: Fujian

address: 20th Chazhong Road

department: Oncology

institute: the First Affiliated Hospital, Fujian Medical University

summary: One key reason for T cell exhaustion is continuous antigen exposure. Early exhausted T cells can reverse exhaustion and differentiate into fully functional memory T cells if removed from persisting antigen stimulation. Therefore, this study viewed T cell exhaustion as an over-activation status induced by chronic antigen stimuli. This study hypothesized that blocking TCR signal intermittently to terminate over-activation signal can defer the developmental process of T cell exhaustion. In this study, B16F10 melanoma-bearing mice were treated with tacrolimus (FK506) every five days. The tumor size and tumor-infiltrating lymphocytes (TILs) were analyzed. We found that intermittent administration of tacrolimus significantly inhibited tumor growth, and this effect was mediated by CD8+T cells. Intermittent tacrolimus treatment facilitated the infiltration of CD8+TILs. RNA-seq and quantitative RT-PCR of sorted CD8+TILs showed the expression of Nr4a1 (an exhaustion-related transcription factor) and Ctla4 (a T cell inhibitory receptor) was remarkably downregulated. These results indicated that intermittently blocking TCR signal by tacrolimus can promote anti-tumor immunity and inhibit the tumor growth in melanoma-bearing mice, inhibiting the transcription of several exhaustion-related genes, such as Nr4a1 and Ctla4.

overall_design: RNA sequencing of CD8+ tumor-infiltrating lymphocytes from tacrolimus treated (4 mice) or untreated mice (4 mice).

first: Ting

first: Qi

last: Zhang

first: Nianhai

first: Xianhe

last: Xie


title: Chromosome conformation for wild type and clb5 clb6 strains arrested in meiotic prophase I

city: Edinburgh

first: Daniel

last: Robertson

state: Midlothian

address: 2.28 Michael Swann Building, Kings Buildings, Mayfield Road

department: Discovery Research Platform for Hidden Cell Biology

institute: University of Edinburgh

summary: High-resolution Hi-C in meiotic prophase arrested cells

overall_design: Purpose: to determine the impact of cohesive cohesin in anchoring cohesin mediated DNA loops, with a focus on the pericentromere.

first: Lucia

middle: F

last: Massari

first: Adele

middle: L

last: Marston


title: No observable guide-RNA-independent off-target mutation induced by prime editor [RNA-Seq]

city: Shanghai

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Prime editor (PE) has been recently developed to induce efficient and precise on-target editing, whereas its guide RNA (gRNA)-independent off-target effects remain unknown. Here, we used whole-genome and whole-transcriptome sequencing to determine gRNA-independent off-target mutations in cells expanded from single colonies, in which PE generated precise editing at on-target sites. We found that PE triggered no observable gRNA-independent off-target mutation genome-wide or transcriptome-wide in transfected human cells, highlighting its high specificity.

first: Jia

first: Xingxu

last: Huang

last: Wei

first: Ying

last: Wang

first: Xiangyang

last: Li

first: Zhi-Can

last: Fu

first: Runze

last: Gao


title: Feeding Level Is Associated With Altered Liver Transcriptome and Follicle Selection in the Hen

city: Ithaca

first: Pat

last: Johnson

state: New York

address: 507 Tower Rd

department: Animal Science

institute: Cornell University

summary: Broiler breeder hens given ad libitum access to feed have excessive ovarian follicle development with poor reproductive outcome. One strategy to improve their reproductive capacity is by restricting their feed intake. In this study, we sequenced the liver transcriptomes of hens fed ad libitum (FF, n=3) and hens given a restricted fed diet (RF, n=3) to get insight into possible signaling pathways affected by dietary treatment. Hens were reared according to commercial guidelines until 38 weeks of age, when they were assigned to either FF or continued on RF for 6 weeks. Liver mRNA samples from three hens in each group were sequenced using the Illumina HiSeq 2000/2500 technology at a depth of 100 bp. The sequencing quality of the data was determined using FastQC. Reads were aligned to UCSC Galgal4 using Tophat (v2.0.13) and transcripts were counted using cuffdiff (v.2.2.1). A multidimensional scaling plot (MDS plot) was generated to evaluate the variance among biological replicates and identified one FF hen as a sample outlier and this animal was removed from the analysis. Differential gene expression analysis was conducted using edgeR and yielded 120 differentially expressed genes. This study identified transcriptional differences in the livers of FF and RF hens which may signal metabolic status to the ovary.

overall_design: Liver mRNA profiles of 2 FF and 3 RF hens.

first: Claire

last: Stephens

first: Alexandra

last: Hill-Ricciuti

first: Laurie

last: Francoeur

first: Patricia

middle: A


title: No observable guide-RNA-independent off-target mutation induced by prime editor [TargetSeq]

last: Chen


title: No observable guide-RNA-independent off-target mutation induced by prime editor

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

overall_design: Refer to individual Series


title: Sex-associated Early-life Innate Immune Response is Transcriptionally Regulated by Epigenetic Control of Type-I IFN-inducible Gene Expression

city: Iowa City

first: Jennifer

middle: Rachelle

last: Bermick

state: IA

address: 431 Newton Road, 505 EMRB

department: Pediatrics

institute: University of Iowa

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq analysis of human cord blood monocytes display sex-associated differences in chromatin landscape with female-derived monocytes having more accessibility in type-1 immune genes.

overall_design: Chromatin accessibilty assessed by ATAC-seq in umbilical cord blood CD14+ monocytes


title: Single-cell ATAC-seq of circulating leukocytes reveals global epigenetic alterations as a prognostic factor in critical illness

city: Pittsburgh

first: Timothy

last: Billiar

state: Pennsylvania

address: 200 Lothrop Street

department: Surgery

institute: University of Pittsburgh

summary:
Background: While bulk and single cell transcriptomic patterns in circulating leukocytes from trauma patients have been reported, how these relate to changes in open chromatin patterns remain unstudied. Here, we investigated whether single-cell ATAC-seq would provide further resolution of transcriptomic patterns that align with patient outcomes.
Methods: We performed scATAC-seq on peripheral blood mononuclear cells from four trauma patients at <4hr, 24hr, 72hr post-injury and four matched healthy controls, and extracted the features associated with the global epigenetic alterations. Three large-scale bulk transcriptomic datasets from trauma, burn and sepsis patients were used to validate the scATAC-seq derived signature, explore patient epigenetic heterogeneity (Epigenetic Groups: EG_hi vs. EG_lo), and associate patterns with clinical outcomes in critical illness.
Findings: Patient subsets with gene expression patterns in blood leukocytes representative of a high global epigenetic signature (EG_hi) had worse outcomes across three etiologies of critical illness. EG_hi designation contributed independent of the known immune leukocyte transcriptomic responses to patient prognosis (Trauma: HR=0.62 [95% CI: 0.43-0.89, event set as recovery], p=0.01, n=167; Burns: HR=4.35 [95% CI: 0.816-23.2, event set as death], p=0.085, n=121; Sepsis: HR=1.60 [95% CI: 1.10-2.33, event set as death], p=0.013, n=479; Cox proportional hazards regression).
Interpretation: The inclusion of gene expression patterns that associate with global epigenetic changes in circulating leukocytes improves the resolution of transcriptome-based patient classification in acute critical illnesses. Early detection of both the global epigenetic signature and the known immune transcriptomic patterns associates with the worse prognosis in trauma, burns and sepsis.

overall_design: We longitudinally single-cell ATAC sequenced circulating mononuclear cells in 4 trauma patients (<4hrs, 24hrs and 72hrs post injury) along with paired healthy controls, total 16 samples.

middle: R

first: Harinder

last: Singh

first: Julia

last: Conroy

first: Tianmeng

first: Rami

last: Namas

first: Yoram

last: Vodovotz

first: Wei


title: Genome organization controls transcriptional dynamics during development

city: Princeton

first: Mike

last: Levine

state: NJ

address: South Dr

department: Lewis Sigler Institute

institute: Princeton University

summary: Past studies offer contradictory claims for the role of genome organization in the regulation of gene activity. Here, we show through high-resolution chromosome conformation analysis that the Drosophila genome is organized by two independent classes of regulatory sequences, tethering elements and insulators. Quantitative live imaging and targeted genome editing demonstrate that this two-tiered organization is critical for the precise temporal dynamics of Hox gene transcription during development. Tethering elements mediate long-range enhancer-promoter interactions and foster fast activation kinetics. Conversely, the boundaries of topologically associating domains (TADs) prevent spurious interactions with enhancers and silencers located in neighboring TADs. These two levels of genome organization operate independently of one another to ensure precision of transcriptional dynamics and the reliability of complex patterning processes.

overall_design: MicroC experiments were conducted on done in biological duplicates. The control line was yw. Experimental lines were CRISPR-mediated deletions of specific architectural elements. All experiments were conducted with embryos at the nc14 stage.

first: Xinyang

last: Bing

first: Philip

last: Batut


title: The role of intestinal iron absorption machinery in regulating gut hormone secretion and systemic metabolism [Ileum]

city: Neuherberg

first: Johannes

last: Beckers

address: Ingolstaedter Landstr. 1

department: Institute of Experimental Genetics

country: Germany

institute: Helmholtz Zentrum Muenchen

summary: Bariatric surgeries remain the most effective treatments for sustained weight loss and remission of type 2 diabetes.  In addition to decreased body weight and improved glucose regulation, these procedures also dramatically increase secretion of several gut hormones including GLP-1.  Despite these benefits, there are deleterious side effects to these procedures that include an increased incidence of iron-deficiency related anemias.  The transcription factor HIF2a is heavily expressed in the duodenum and regulates the molecular machinery of iron absorption from the lumen.  Lower iron levels after both gastric bypass and sleeve gastrectomy procedures occur despite dramatic upregulation of HIF2a signaling in the duodenum and are likely the result of increased hepcidin levels. Low iron diets also stimulate increased HIF2a signaling in the duodenum and produce effects similar to bariatric surgery that include reduced body weight/fat, improved glucose regulation and increased secretion of the GLP-1.  Gut-specific deletion of VHL results in a constitutive upregulation of HIF2a signaling in the small intestine and produces a dramatic phenotype that includes reduced body weight/fat, improved glucose tolerance and increased GLP-1 secretion from the intestine.  These data demonstrate an important role of HIF2a signaling in the duodenum to regulate multiple aspects of systemic metabolism and gut hormone secretion pointing towards critical cross-talk between the systems that regulate iron and other aspects of systemic physiology important to prevalent metabolic diseases.

overall_design: We performed gene expression microarray analysis of duodenum and ileum derived from rats treated with bariatric surgery and control animals

first: Simon

last: Evers

first: Yikai

last: Shao

first: Sadeesh

last: Ramkrishnan

first: Jae

middle: H

last: Shin

first: Nadia

last: Kramer

first: Martin

last: Irmler

first: Kerstin

last: Stemmer

first: Darleen

last: Sandoval

first: Yatrik

last: Shah

first: Randy

last: Seeley


title: Identification of Pyruvate Dehydrogenase A1 (p-PDH A1 S293) and  Pyruvate Kinase M2 (PKM2)  target genes by ChIP Seq in HepG2 Cells Upon Insulin stimulation.

status: Public on Feb 02 2022

city: Chuncheon

first: Jubayer

middle: Abu

last: Hossain

state: Gangwon-do

address: Chuncheon, Gangwon-do, 24252

department: Medical science

country: South Korea

institute: Hallym University College Of Medicine

summary:
Goal and Objectives: Here we first time report that p-PDH A1 (S293 in mouse but in Human is S264), and PKM2 can regulates the many genes upon Insulin in Human Heptocellular Carcinoma HepG2 cells Line. The goal of this study is to identify the target genes, of which the promoters are associated with p-PDHA1 and PKM2, which may regulate target genes' trascription. We performed Chromatin immunoprecipitation-sequencing (ChIP-Seq) experiments by using antibodies agaist p-PDHA1 and PKM2.
Methods: HepG2 cells were cultured in DMEM media, supplemented with 10% FBS and 1% penicillin/Streptomycin antibiotics. In 100 mm (diameter) dishes, the cells were seeded (1×107 – 3×107 cells per dish) and then incubated for 24 h. The media was exchanged for DMEM without serum for 12 h and the cells were then treated with 100 nM insulin for 48 h. The cells were then washed with PBS. To crosslink proteins to DNA, we added formaldehyde drop-wise directly to PBS containing samples to a final concentration of 0.75% and incubated at room temperature for 1 h. The crosslinking was stopped by adding glycine to the samples to a final concentration of 125 mM, followed by incubation for 10 min at RT. The cells were then rinsed twice with ice cold PBS and were harvested. The cell pellets were suspended in ChIP lysis buffer  with freshly added cocktail of protease/phosphatase inhibitors and incubated for 10 min on ice. Sonication of the sample was then performed with an OMNI Sonic Ruptor-400 sonicator (OMNI International, Kennesaw, GA, USA) on ice for 20 impulses of 20 sec each. This was repeated five times with a 30 sec interval for each. The sonicated sample was centrifuged at 13,000 rpm for 15 min and 200 μg of the protein–chromatin complex was used for each round of immunoprecipitation {Cap, 2020, 32046944}, performed with anti-p-PDH A1 (S293), and PKM2  antibodies overnight at 4°C. IgG antibody used as a control. The formed antibody–protein complex was captured by incubation with pre-blocked Pierce Protein A/G Beads (Pierce). After sequential washing the beads with wash buffer I, II, III and IV several times and DNA sequencing of ChIP was performed by eBiogen (Seoul, Korea).
Results: From ChIP Seq data analysis, we found that the promoters of many genes are associated with both p-PDH and PKM2. p-PDHA1 and PKM2 alone or together may regulate transcription of many genes upon insulin. In our current manuscript, we sort out the common genes which may be regulated p-PDHA1/PKM2 complex common genes in hepatocellular carcinoma cell line in response to insulin stimulation.
Conclusions: Our study represents the first detailed analysis of p-PDHA1/PKM2 complex regarding to transcriptional regulation through ChIP-seq. The optimized data analysis workflows reported here may provide a framework for comparative transcritional investigations of p-PDHA1 and PKM2. We conclude that ChIP-Seq data of p-PDHA1 and PKM2 would expedite genetic network analyses and permit the dissection of complex biologic functions as well as cancer biology studies.

overall_design: We prepared three samples. The first sample as control was used for that imunopricipited with only IgG antibody without insulin treatment. The second sample was immunopricipited with p-PDH A1 antibody and the last sample was immunopreicipited with PKM2 antibody with insulin stimulation. All samples are prepared human hepatocellular carcinoma HepG2 Cells line.

first: Jae-Bong

last: Park

first: Abu Jubayer


title: Differentially enriched miRNAs in EVs derived from young and aged osteocytes of mice

city: Changsha

first: Zhenxing

last: Wang

address: Xiangya Road #87

institute: Xiangya hospital Central South University

summary:
Young and Aged osteocytes in bone matrix secreted plenty of extracellular vesicles (EVs) with different functions. We found that EVs released from aged bone matrix (AB-EVs) during bone resorption favor adipogenesis rather than osteogenesis of BMSCs and augment calcification of vascular smooth muscle cells (VSMCs). In this work, we aim to detect the differential regulation microRNAs.
Vascular calcification often occurs with osteoporosis, a contradictory association called “calcification paradox”. We find that extracellular vesicles (EVs) released from aged bone matrix (AB-EVs) during bone resorption favor adipogenesis rather than osteogenesis of BMSCs and augment calcification of vascular smooth muscle cells (VSMCs). Intravenous or intramedullary injection of AB-EVs promotes bone-fat imbalance and exacerbates Vitamin D3 (VD3)-induced vascular calcification in young or old mice. To explore the involvement of miRNAs in the AB-EVs-induced promotion of adipocyte formation and vascular calcification, the Agilent miRNA array was conducted to compare the miRNA expression profiles in AB-EVs and YB-EVs from mouse bone specimens. Our study uncovers the role of AB-EVs as a messenger for calcification paradox by transferring functional miRNAs.

overall_design: 3 of YB-EVs isolated from 1-month-old male mice, 3 of AB-EVs isolated from 16-month-old male mice

first: Zhen-Xing

first: Chun-Yuan

last: Chen

first: Hui

last: Xie


title: Gut HIF2α signaling is increased after VSG, and gut activation of HIF2α decreases weight, improves glucose, and increases GLP-1 secretion

first: Johannes


title: Acclimation and stress response of Prochlorococcus to low salinity

first: he

middle: xia

last: yu

address: NO.164 xingang road

department: South China Sea Institute of Oceanology

institute: University of Chinese Academy of Sciences

summary: Prochlorococcus is an obligate marine microorganism which are dominant autotroph in tropical and subtropical central oceans. However, what is the low salinity boundary and how Prochlorococcus would response to low salinity exposure is still unknown. In this study, we first tested the growing salinity range of two Prochlorococcus strains, NATL1A and MED4, and then compared the global transcriptome of their low salinity acclimated cells and cells growing in normal seawater salinity. We found that MED4 could be acclimated in the lowest salinity of 25% and NATL1A could be acclimated in the lowest salinity of 28%. Measurement of the effective quantum yield of PSII photochemistry (Fv/Fm) indicated that both strains were stressed when growing in salinity lower than 34%. The transcriptomic response of NATL1A and MED4 were approximately different, with much more genes having changed transcript abundance in NATL1A than in MED4. To cope with low salinity, NATL1A downregulated the transcript of most genes involved in translation, ribosomal structure and biogenesis, while MED4 upregulated those genes. Moreover, low salinity acclimated NATL1A cells suppressed ATP-producing genes and induced the expression of photosynthesis related genes, while low salinity acclimated MED4 upregulated ATP-producing genes and downregulated photosynthesis related genes. These results indicate that the response to low salinity stress of different Prochlorococcus strains could be distinct. The study provided the first glimpse into the growing salinity range of Prochlorococcus cells and their global gene expression changes due to low salinity stress.

sample_organism: Prochlorococcus marinus subsp. pastoris str. CCMP1986

overall_design: Prochlorococcus strains MED4 and NATL1A were acclimated to different salinities (24%, 25%, 26%, 27%, 28%, 30%, 32%, 34%) by consecutive transfers from exponential growing cultures to fresh media. Three biological replicates were set up for each salinity. Five rounds of transfer were conducted for each strain. Cell abundance was monitored at day 0, day 5 and day 10, using flow cytometry. To assess the stress to low salinity, the dark-adapted photochemical efficiency (Fv/Fm) of each strain was monitored in day 10 in each round, using a handheld fluorometer (AquaPen AP 110/C, Photon Systems Instruments). To acclimate the Prochlorococcus strains, MED4 and NATL1A were growing in the Pro99 medium of salinity 28% and 34% for five rounds of inoculation. Then the acclimated cultures were inoculated in fresh medium of salinity 28% and 34%, with salinity 34% being the control. Three biological replicates were set up. During the exponential growth phase, 100 ml cultures were filtered onto 0.22 μm polycarbonate membrane to collect cells and the membranes were immediately flash frozen in RNAlater by liquid nitrogen and stored at -80℃ until RNA extraction. Total RNA was extracted from the membrane using the MagZol Reagent (Magen). Sequencing libraries were prepared using VAHTSTM Stranded mRNA-seq Library Prep Kit for Illumina® (Vazyme biotech co., Ltd) following the manufacturer’s instructions. Libraries were multiplexed and sequencing was carried out on an Illumina HiSeq system with the 2 × 150 paired-end (PE) configuration (GENEWIZ).

first: Xiayu

last: He

first: Huan

last: Liu

first: Lijuan

last: Long

first: Feng

first: Sijun

last: Huang


title: RNA m1A methylation regulates glycolysis of cancer cells through modulating ATP5D

first: xie

last: guoyou

address: 大学城中山大学

institute: 中山大学

summary: Studies on biological functions of RNA modifications such as N6-methyladenosine (m6A) in mRNA have sprung up in recent years, while the roles of N1-methyladenosine (m1A) in cancer progression remain largely unknown. We find m1A demethylase ALKBH3 can regulate the glycolysis of cancer cells via a demethylation activity dependent manner. Specifically, sequencing and functional studies confirm that ATP5D, one of the most important subunit of ATP synthase, is involved in m1A demethylase ALKBH3-regulated glycolysis of cancer cells. The m1A modified A71 at the Exon 1 of ATP5D negatively regulates its translation elongation via increasing the binding with YTHDF1/eRF1 complex, which facilitates the release of mRNA from ribosome complex. m1A also regulates mRNA stability of E2F1, which directly binds with ATP5D promoter to initiate its transcription. Targeted specific demethylation of ATP5D m1A by dm1ACRISPR system can significantly increase the expression of ATP5D and glycolysis of cancer cells. In vivo data confirm the roles of m1A/ATP5D in tumor growth and cancer progression. Our study for the first time reveals a crosstalk of mRNA m1A modification and cell metabolism, which expands the understanding of such interplays that are essential for cancer therapeutic application.

overall_design: m1A-seq in Human HeLa WT(n=2) and HeLa ALKBH3-KO(n=2)

first: Hongsheng

first: Guoyou


title: The role of intestinal iron absorption machinery in regulating gut hormone secretion and systemic metabolism [Duodenum]

last: Beckers

overall_design: We performed gene expression microarray analysis of duodenum derived from rats treated with bariatric surgery and control animals

first: Simon

last: Evers

first: Yikai

last: Shao

first: Sadeesh

last: Ramkrishnan

first: Jae

last: Shin

first: Nadia

last: Kramer

first: Martin

first: Kerstin

first: Darleen

first: Yatrik

first: Randy


title: High-throughput Sequencing of exosomal circRNAs in large artery atherosclerotic stroke

city: Qingdao

first: Qi

last: Xiao

address: No. 59 Haier Road, Qingdao, Shandong Province, China.

institute: The Affiliated Hospital of Qingdao University

summary: Exosomal circRNA sequencing was used to identify differentially expressed circRNAs between LAA stroke and normal controls.  From a further validation stage, the results were validated using RT-qPCR.

overall_design: Plasma exosomal circRNAs profiles of large artery atherosclerotic stroke and healthy controls

first: Xudong

last: Pan

first: Xiaoyan

last: Zhu


title: RNA-Seq in HG-challenged H9C2 cells with or without FGFR1 knockdown

city: Wenzhou

first: guang

last: liang

state: Wenzhou

address: Wenzhou medical university of  higher education park  chashan town

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

summary: RNA-seq is a powerful tool to analyze differential expression of cellular pathways under different conditions. The goals of this study is to analyze the potential pathways involved in cellular defense against high glucose with or without FGFR1 knowdown.

overall_design: mRNA profiles of HG-challenged H9C2 cells with or without FGFR1 knockdown

first: Xiong

last: Chen

first: Jinfu

last: Qian

first: Wu

last: Luo

first: Guang

last: Liang


title: Single cell RNA sequencing of dormant and proliferative PyMT-Bo1 breast cancer cells isolated from murine bone

city: SAINT LOUIS

first: Qihao

last: Ren

state: MO

address: 425 South Euclid Avenue, BJC-IH, Rm 7303, Washington University in St Louis

department: Cell Biology and Physiology

institute: Washington University in St Louis

summary: Transcriptome profiling of dormant (DiD+) and proliferative (DiD-) PyMT-Bo1 isolated by FACS from bone 11 days after intracardiac (IC) injection.

overall_design: PyMT-Bo1 cells were first labelled with membrane DiD dye before injected into mice. Femur and tibia were isolated and pooled together from 5 IC injected mice. 32 dormant (DiD+) and 28 proliferative (DiD-) cells were isolated by FACS sorting for single cell RNA sequencing (scRNA-seq).Single‐cell cDNA was generated using the SMARTer Ultra Low RNA Kit v4 (Takara) with modifications. 1:2,500,000 dilution of ERCC spike-in controls (Ambion) were incorporated during first-strand cDNA synthesis and subsequent steps were performed according to the manufacturer's instructions at half-reaction volumes. cDNA amplification was performed at 18 cycles and its quality was assessed using the Bioanalyzer HS DNA chip (Agilent Technologies) according to the manufacturer's instructions. Sequencing libraries were generated using 1 ng of input material using the Nextera XT Kit (Illumina) according to the manufacturer's protocol at half-reaction volumes. Libraries were pooled and paired-end sequenced (150-bp reads) on Illumina NextSeq500 on a high-throughput mode. Illumina sequence adapters were trimmed and reads were aligned to a modified version of the GRCm38/mm10 mouse genome (supplemented with ERCC, mApple, eGFP, luciferase, PyMT oncogene sequences) using the STAR aligner. Summarized gene transcript counts and TPMs were generated using RSEM.

first: Weng

last: Khoo

first: Alexander

middle: P

last: Corr

first: Tri

middle: G

last: Phan

first: Peter

middle: I

last: Croucher

first: Sheila

last: Stewart


title: Intrinsic cardiac adrenergic (ICA) cells contribute to LPS-induced myocardial dysfunction

city: Farmington

first: Duomeng

last: Yang

address: 263 Farmington Avenue

institute: Uconn health

summary: The role of ICA cells in septic cardiomyopathy is unknown. Here we show that norepinephrine (NE) secretion from ICA cells is increased through activation of Toll-like receptor 4 (TLR4) to aggravate myocardial TNF-α production and dysfunction by lipopolysaccharide (LPS). In ICA cells, LPS activated TLR4-MyD88/TRIF-AP-1 signaling that promoted NE biosynthesis through expression of tyrosine hydroxylase, but did not trigger TNF-α production due to impairment of p65 translocation. Our findings suggest that ICA cells may be a potential therapeutic target for septic cardiomyopathy.

overall_design: To further clarify the role of ICA cells in LPS-induced cardiac TNF-α and compare the differentiall expressed genes between control and LPS-treated ICA cells


title: A compensatory link between cleavage/polyadenylation and mRNA turnover regulates steady-state mRNA levels in yeast

city: Boston

first: Zarmik

last: Moqtaderi

state: MA

address: 240 Longwood Avenue C2-355

department: BCMP

institute: Harvard Medical School

summary: Cells have compensatory mechanisms to coordinate the rates of major biological processes, thereby permitting growth in a wide variety of conditions.  Here, we uncover a compensatory link between cleavage/polyadenylation in the nucleus and mRNA turnover in the cytoplasm.  On a global basis, same-gene 3’ mRNA isoforms with > two-fold differences in half-lives have steady-state mRNA levels that differ by significantly less than a factor of two.  In addition, increased efficiency of cleavage/polyadenylation at a specific site is associated with reduced stability of the corresponding 3’ mRNA isoform.  This inverse relationship between cleavage/polyadenylation and mRNA isoform half-life reduces the variability in the steady-state levels of mRNA isoforms, and it occurs in all four growth conditions tested.  These observations suggest that during cleavage/polyadenylation in the nucleus, mRNA isoforms are marked in a manner that persists upon translocation to the cytoplasm and affects the activity of mRNA degradation machinery, thus influencing mRNA stability.

overall_design: We have examined mRNA isoform stability by using 3' READS to measure mRNA 3' isoform levels after Rpb1 depletion in four different growth media.

first: Joseph

middle: V

last: Geisberg

first: Kevin

last: Struhl


title: Anti-Müllerian Hormone (AMH) Treatment Enhances Oocyte Quality, Embryonic Development and Live Birth Rate

city: East Lansing

first: Aritro

last: Sen

state: Michigan

address: 766 Service Rd., ISTB

institute: Michigan State University

summary: In this study, we determine for the first time, the effects of AMH priming on oocyte quality and competence, early embryonic development, and fertility.

overall_design: Our data offer new insights into the mechanism of AMH actions that provide an overall picture of the influence of AMH on female fertility.

first: Niharika

last: Sinha


title: Transcriptome analysis of  skeletal muscle from adipocyte-specific UCP1 knock-in (KI) pigs and wild-type (WT) pigs

city: Hangzhou

first: Chen

last: Wentao

state: Zhejiang

address: No. 866 Yuhangtang Road

institute: Zhejiang University

summary: In the present study, we conducted transcriptomics on skeletal muscle from 6-month-old UCP1 KI and wild-type (WT) pigs to explore the  transcriptional programs induced by adipocyte-specific UCP1 overexpression in skeletal muscle

overall_design: We utilized transcriptomics to identify the  regulatory pathways in skeletal muscles from adipocyte-specific UCP1 knock-in (KI) pigs. UCP1 KI changed the contents of glycerophospholipids and acyl carnitines of skeletal muscles. Several metabolic regulatory pathways were more enriched in the UCP1 KI skeletal muscle. Comparison of the transcriptomes of adipose and skeletal muscle suggested that nervous system or chemokine signaling might account for the crosstalk between these two tissues in UCP1 KI pigs. Our study reveals the transcriptional programs in the skeletal muscle of UCP1 KI pigs and suggests that a network regulates metabolic homeostasis between skeletal muscle and adipose tissue.

first: Ziye

last: Xu

first: Wentao

first: Liyi

last: Wang

first: Wenjing

last: You

first: Yanfang

first: Yizhen

first: Jianguo

last: Zhao

first: Tizhong

last: Shan


title: A preclinical rat model of heart failure with preserved ejection fraction with multiple comorbidities

city: Brussels

first: Frederick

last: Libert

address: 808 route de Lennik

department: IRIBHM

country: Belgium

institute: ULB

summary: As patients with heart failure with preserved ejection fraction (HFpEF) present with multiple comorbidities, we hypothesized, that metabolic syndrome in aging animals could lead to the development of diastolic dysfunction and HFpEF. HFpEF is a common complex morbid syndrome for which there are currently little evidence-based therapies. Obesity-prone rats were exposed to high-fat diet and compared to obesity-resistant rats fed with standard chow. Phenotyping of metabolic syndrome, associated with echocardiographic and cardiac hemodynamic measurements, was performed after 4 and 12 months. Blood and myocardial tissue sampling were performed for pathobiological evaluation. High-fat diet in obesity-prone rats elicited metabolic syndrome, characterized by increased body and abdominal fat weights, glucose intolerance and hyperlipidemia, as well as increased left ventricular (LV) systolic pressure (after 12 months). This was associated with LV diastolic dysfunction (assessed by increased LV end-diastolic pressure) and pulmonary hypertension (assessed by increased right ventricular systolic pressure). Echocardiography revealed significant concentric LV hypertrophy, while LV ejection fraction was preserved. LV remodeling was associated with cardiomyocyte hypertrophy, as well as myocardial and perivascular fibrosis. Circulating levels of soluble ST2 markedly increased in rats with HFpEF, while plasma NT-proBNP levels decreased. RNA-sequencing analysis identified clusters of genes implicated in fatty acid metabolism and calcium-dependent contraction as upregulated pathways in the myocardium of rats with HFpEF. High-fat diet during 12 months in obesity-prone rats led to the development of a relevant preclinical model of HFpEF with multiple comorbidities, suitable for investigating novel therapeutic interventions.

overall_design: Myocardial tissue from diet-induced obesity-prone (OP) rats fed with high fat food (triplicates) and obesity-resistant (OR) rats fed with standard food (triplicates).

first: Géraldine

last: HUBESCH

first: Aliénor

last: HANTHAZI

first: Angela

last: ACHEAMPONG

first: Laura

last: CHOMETTE

first: Hélène

last: LASOLLE

first: Emeline

last: HUPKENS

first: Pascale

last: JESPERS

first: Grégory

last: VEGH

first: Cécile

middle: W

last: WEMBONYAMA

first: Caroline

last: VERHOEVEN

first: Céline

last: DEWACHTER

first: Jean-Luc

last: VACHIERY

first: Kathleen

last: McENTEE

first: Laurence


title: Replication of Dengue virus in differentiating K562-megakaryocytes is promoted by virus induced suppression in the accumulation of reactive oxygen species

city: Faridabad

first: Jaskaran

last: Kaur

state: Haryana

address: NCR Biotech Science cluster Gurugram-Faridabad Expressway

department: Infection and immunology

country: India

institute: THSTI

summary: Our study reports that over-expression of NRf2 target genes causes reduction in the ROS accumulation in differentiating cells which ultimately enhances Dengue virus replication and we also report the suppression of cell adhesion molecules and platelet specific surface markers in Dengue virus infected K562-megakaryocyte cells.

overall_design: mRNA profiles of differentiated and undifferentiated K562 cells

first: Kaur

last: Jaskaran

first: Rawat

last: Yogita

first: Sood

last: Vikas

first: Periwal

last: Neha

first: Rathore

last: Deepak

first: Kumar

last: Shrikant

last: Niraj

first: Bhattacharyya

last: Sankar


title: Comprehensive analysis of differentially expressed profiles of mRNA N6-methyladenosine in colorectal cancer

city: Chengdu

first: Qin

last: Guo

address: Baoguang Road, Xindu district, Chengdu, Sichuan

department: Department of Gastroenterology

institute: chengdu medical college

type: Methylation profiling by high throughput sequencing

summary:
Purpose: To comprehensively profile the landscape of the mRNA N6-methyladenosine (m6A) modification in human colorectal cancer (CRC).
Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was explored to compare the difference in mRNA N6-methyladenosine (m6A)  methylation between CRC tissues and adjacent normal control (NC) tissue. RNA-sequencing (RNA-seq) was  performed to transcribe differentially expressed mRNAs. Conjoint analysis of MeRIP-seq and RNA-seq data was conducted to predict RNA-binding proteins (RBPs).
Results: MeRIP-seq identified 1110 differentially m6A methylated sites (DMMSs) and 980 differentially m6A methylated genes (DMMGs) in CRC, with 50.13% of all modified genes showing unique m6A-modified peaks in CRC. RNA-seq showed 915 upregulated genes and 1463 downregulated genes in CRC. QRT-PCR verified the RNA-seq results by detecting the expression of some mRNAs. Conjoint analysis of MeRIP-seq and RNA-seq identified 400 differentially m6A methylated and expressed genes (DEGs), and pathway analysis detected that DMMGs and DEGs were  closely related to cancer. After analyzing these DMMGs and DEGs through the GEPIA database, we found that the expression of B3GNT6, DKC1, SRPK1 and RIMKLB were associated with prognosis, and the  expression  of B3GNT6 and RIMKLB were associated with clinical stage. 17 RBPs were identified based on the DMMGs and DEGs, among which FXR1, FXR2, FMR1, IGF2BP2, IGF2BP3 and SRSF1 were obviously highly expressed in CRC, and FMR1, IGF2BP2 and IGF2BP3 were closely related to methylation, and might be involved in the development of CRC.
Conclusions: This study comprehensively profiled m6A modification of mRNAs in CRC, which revealed possible mechanisms of m6A-mediated gene expression regulation.

overall_design: Examination  differentially expressed profiles of mRNA N6-methyladenosine in five CRC patients. 2 = ChIP, 3 = Input.

last: Li

first: Qiao

last: Zhang

first: Bai-jun

last: Chen

first: Xiao-an

first: Yan

last: Zhou


title: Tracking immunoglobulin gene editing and transcriptomic changes in GC B cells by single-cell analysis

city: New York

first: Riccardo

last: Dalla-Favera

state: NY

address: 1130 St Nicholas Avenue

institute: Columbia University

summary: In response to T cell-dependent antigens, mature B cells are stimulated to form germinal centers, which are the place of B cell affinity maturation and selection. Here, we dissected the heterogeneity of germinal center B cells and reconstructed their pathway of differentiation by integrating single-cell transcriptomic data with the information on immunoglobulin gene editing associated with somatic hypermutation and class switch recombination.

overall_design: Dark zone and light zone B cells were isolated from two donors, and total germinal center B cells were isolated from three donors.

first: Katia

last: Basso

first: Antony

last: Baden Holmes


title: RNAseq analysis of genes differentially expressed in MDA-MB-231 and 231-BR

city: Beijing

first: Lulu

last: Wang

address: No. 10 You An Men Wai Xi Tou Tiao

department: Department of Human Anatomy

institute: Capital Medical University

summary: We used RNA sequencing to analyze gene expression profiles of MDA-MB-231 and its brain metastasis variant (231-BR).  The goal of this study is to explore genes that are differentially expressed in 231-BR and MDA-MB-231.

overall_design: Six samples obtained from 231-BR and MDA-MB-231 cells were analyzed. Three indipendent samples were analyzed for each cell line.

last: Gao

first: Dan

last: Zeng

first: Qi


title: The context of the ribosome binding site in mRNAs defines specificity of action of kasugamycin, an inhibitor of translation initiation

city: San Francisco

state: CA

address: 600 16th Street

department: Microbiology and Immunology

institute: UC San Francisco

summary: Kasugamycin (KSG) is an aminoglycoside antibiotic widely used in agriculture and exhibiting considerable medical potential. Previous studies suggested that KSG interferes with translation by blocking binding of canonical mRNA and initiator tRNA to the small ribosomal subunit thereby preventing initiation of protein synthesis. Here, by using genome-wide approaches, we show that KSG can interfere with translation even after the formation of the 70S initiation complex on mRNA, as the extent of KSG-mediated translation inhibition correlates with increased occupancy of start codons by 70S ribosomes. We also show that KSG inhibits protein synthesis in a gene- and context-specific manner as even saturating concentrations of KSG do not completely abolish translation of all Escherichia coli genes. Differential action of KSG significantly depends on the nature of the mRNA residue immediately preceding the start codon, with guanine in this position being the most conducive to inhibition by the drug.  In addition, the activity of KSG is attenuated by translational coupling as genes whose start codons overlap with the coding regions or the stop codons of the upstream cistrons tend to be less susceptible to drug-mediated inhibition. Altogether, our findings reveal KSG as the first example of a small ribosomal subunit-targeting antibiotic with a well-pronounced context specificity of action.

overall_design: Ribosome profiling (Ribo-seq) and mRNA-seq data collected from E. coli ΔgcvB cells grown in MOPS EZ rich defined media at mid-log phase, and the cells treated with 1 mg/ml an 10 mg/ml kasugamycin (KSG) for 2.5 min at 37˚C.

first: Nikolay

last: Aleksashin

first: Dorota

last: Klepacki

first: Caleb

last: Anderson

first: Nora

last: Vázquez-Laslop

first: Carol

last: Gross

first: Alexander

last: Mankin


title: MeRIP-seq of K1 PTC cells

city: Shenyang

first: JiaPeng

last: Huang

address: No. 155 in Nanjing North Street

department: Department of Thyroid Surgery

institute: The First Hospital of China Medical University

summary: Exploring the target genes of m6A modification downstream of FTO that play a regulatory role in glycolytic metabolism of PTC.

overall_design: To map the altered m6A modification caused by FTO, MeRIP-seq was performed in K1 cells with si-NC or si-FTO.

first: Jiapeng

first: Hao


title: Transcriptomes of de novo lab-adapted monomorphic Trypanosoma brucei (EATRO 1125) and naturally monomorphic T. evansi and T. equiperdum.

city: Guangzhou

first: Cai

last: Xiao-Li

state: Guangdong

address: Xingangxi Rd 135

department: School of Life Sciences

institute: Sun Yat-Sen University

summary: Here, we produced a series of monomorphic trypanosome stocks, creating snapshots of the transition from pleomorphism to monomorphism, by continuous rapid syringe-passage in mice using a pleomorphic T. brucei. We then compared  the transcriptomes of these artificial monomorphic trypanosomes, alongside several naturally monomorphic T. evansi and T. equiperdum strains, with the pleomorphic T. brucei, to analysis the causes of the monomorphism. Trypanosomes grown in  mice were harvested at different stage post infection depend on strains (Detailed information was descrided in overall design), and  mRNA profile of each sample was generated by deep sequencing, in triplicate.

sample_organism:
Trypanosoma equiperdum
Trypanosoma evansi
Trypanosoma brucei brucei

overall_design:
Three replicates each of three conditions (ascending A/slender, ascending B/stumpy,  ascending C/less stumpy) of pleomorphic T. brucei (Tbp1) were analysed, but only two replicates isolated from 'Ascending B' ( Tbp1B) were qualified for subsequent analysis. 'Ascend A' samples were derived from a pool of three infections , to generate sufficient material for analysis. 'Ascending B' and 'Ascending C' samples were each derived from infections in three individual mice, . All samples were analysed for their cell cycle status by scoring the number of kinetoplasts and nuclei in parasites and  the presence of morphological stumpy forms, as well as the sensitivity to differentiated stimulus signals.
Three replicates each of two conditions (ascending A(low parasitemia), ascending C(peak parastmia)) of passaged monomorphic T. brucei  (Tbp40) were analysed. 'Ascend A' samples were derived from a pool of three infections , to generate sufficient material for analysis.  'Ascending C' samples were each derived from infections in three individual mice.
Three replicates each of one condition (ascending C(peak parastmia)) of passaged monomorphic T. brucei  (Tbp80, Tbp120) were analysed.  'Ascending C' samples were each derived from infections in three individual mice.
T. evansi and T.equiperdum samples were each derived from infections in three individual mice.

first: Xiao-Li

last: Cai

first: De-Hua

last: Lai

first: Zhao-Rong

last: Lun


title: Clustering of Surrogates of Cardiovascular Risk Factors Results in Emergent Phenotypes in Endothelial Cells

city: Sao Paulo

first: Jose Eduardo

last: Krieger

state: Sao Paulo

address: 44 Av. Dr. Enéas de Carvalho Aguiar

department: Medical School

country: Brazil

institute: University of Sao Paulo

summary:
Global gene expression of human coronary artery endothelial cells (HCAEC) submitted surrogates of cardiovascular risk factors
Based on the analysis of global gene expression in human coronary artery endothelial cells (HCAEC), we identified gene pathways and inferred cellular processes that are modulated in response to chemical hypoxia, oxidized lipids, IL-1β and oscillatory flow or combined stimuli. Our results indicate that clustering of the surrogates of risk factors is different from the sum of the individual insults that give rise to emergent phenotypes such as cell proliferation. Altogether, we provide evidence of a hierarchical effect between risk factor surrogates and advent of emergent phenotypes in response to combined stimulation.

overall_design: 24 Total samples were analyzed. We evaluated the roles of chemical hypoxia (CoCl2), oxidized lipids (OxPAPC), inflammation (IL-1β) and oscillatory shear stress (OSS) and CoCl2+OxPAPC+Il1B+OSS in global gene expression using laminar shear stress (LSS) as reference

first: Iguaracy

last: Pinheiro-De-Sousa

first: Miriam

last: Fonseca-Alaniz

first: Samantha

middle: K

last: Teixeira

first: José

middle: E


title: IRF1 and IFNγ regulated gene expression in A549 lung epithelial cells

city: St. Louis

first: Sibley

last: David

state: Missouri

address: 660 S. Euclid, CB 8230

institute: Washington University in St. Louis

summary: Identification and comparison of genes induced by IRF1 ectopic expression versus IFNγ treatment in A549 lung epithelial fibroblasts.

overall_design: IRF1 or FLUC control were ectopically expressed in A549s using a lentiviral expression cassette. 72 h after transduction, FLUC expressing cells were further treated with or without 1000 U/mL IFNγ for 12 h. All samples were subsequently harvested for analysis. Three biological replicates were conducted per sample. For RNA-seq analysis, changes in gene expression with IRF1 ectopic expression or IFNγ treatment were determined via comparison to untreated cells ectopically expressing FLUC control.

first: Nicholas

last: Rinkenberger

first: David

last: Sibley


title: Genetic Activation and Suppression of the Canonical WNT Pathway in Cardiac Myocyte-Specific Dsp Deficient Mouse Model of Arrhythmogenic Cardiomyopathy

city: Houston

first: Hyun-Hwan

last: Jeong

state: TX

address: 7000 Fannin St

institute: UTHealth

summary: The cWNT pathway has been implicated in the pathogenesis of arrhythmogenic cardiomyopathy (ACM), including in cardiac dysfunction, apoptosis, and fibro-adipogenesis, the latter being the histological hallmark of ACM. The study was designed to determine effects of genetic activation or suppression of cWNT in a mouse model of arrhythmogenic cardiomyopathy. The data show that activation of the cWNT in ACM deleterious whereas it suppression is benefiial.

overall_design: The cWNT signaling pawathway was activated or suppressed post-nataly (P14) using tamoxifen-inducible cre and floxed beta catenin gene while concomittantly deleting the Dsp deficiency, all specificially in cardiac myocytes. The experimental groups include wild type (WT), Myh6-MerCreMer, , Myh6-MCM:DspF/F,  Myh6-MCM:Ctnnb1GoF  (Gain of function) , Myh6-MCM:Ctnnb1LoF (Loss of function), Myh6-MCM:DspF/F:Ctnnb1LoF , and Myh6-MCM:DspF/F:Ctnnb1GoF/F mice.  Phenotypic characterization and myocyte RNA sequencing were performed at 4 weeks of age.

first: Siyang

last: Fan

first: Leila

last: Rouhi

first: Sirisha

middle: M

last: Cheedipudi

first: Priyatansh

last: Gurha

first: Ali

middle: J

last: Marian

first: Zhongming

last: Zhao


title: Mapping Transcriptomic Vector Field of Single Cells

city: Cambridge

first: Xiaojie

last: Qiu

address: 455 Main St, Cambridge, MA

institute: Whitehead Institute

summary: Single-cell (sc)RNA-seq, together with RNA velocity and metabolic labeling, reveals cellular states and transitions at unprecedented resolution. Fully exploiting these data, however, requires kinetic models capable of unveiling governing regulatory functions. Here, we introduce an analytical framework dynamo, which infers absolute RNA velocity, reconstructs continuous vector fields that predict cell fates, employs differential geometry to extract underlying regulations, and ultimately predicts optimal reprogramming paths and perturbation outcomes. We highlight dynamo’s power to overcome fundamental limitations of conventional splicing-based RNA velocity analyses to enable accurate velocity estimations on a metabolically labeled human hematopoiesis scRNA-seq dataset. Furthermore, differential geometry analyses reveal mechanisms driving early megakaryocyte appearance and elucidate asymmetrical regulation within the PU.1-GATA1 circuit. Leveraging the least-action-path method, dynamo accurately predicts drivers of numerous hematopoietic transitions. Finally, in silico perturbations predict cell-fate diversions induced by gene perturbations. Dynamo, thus, represents an important step in advancing quantitative and predictive theories of cell-state transitions.

overall_design: This study contains three main experiments. The first two are about 10x scRNA-seq experiment and sequential lineage tracing of HL60 cell differentiation with static barcode and scSLAM-seq, respectively. The third one is about profiling human hematopoiesis in vitro with scNT-seq.

first: Jorge

middle: D

last: Martin-Rufino

first: Chen

last: Weng

first: Shayan

last: Hosseinzadeh


city: Shanghai

first: Jin

last: Zheng

state: Shanghai

address: 800 Dongchuan RD

institute: sjtu

summary: We demonstrated that Pyk2 is a novel fear memory suppressor molecule and Pyk2 null mice provide a model for understanding fear-related disorders.

overall_design: Study for Pyk2 suppresses contextual fear memory in an autophosphorylation-independent manner used RNA-seq experiments of hippocampus from WT,Pyk2 KO at basal conditioning before fear conditioning.

first: J

first: L

last: Suo

first: Y

last: Zhou

last: Jia

first: Q

last: Wu


title: Roles of PfAP2-EXP2 in Plasmodium falciparum blood-stage development [ChIP-seq]

first: Mei

last: Jiang

address: 1239 Siping Road

institute: Tongji University

summary: Genome-wide occupancy of  PfAP2-EXP2 at the schizont stage

overall_design: 2 biological ChIP-seq replicates for the AP2-EXP2-GFP parasite line using an antibody against GFP, and input DNA

first: Xiaomin

last: Shang


title: Roles of PfAP2-EXP2 in Plasmodium falciparum blood-stage development

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

overall_design: Refer to individual Series


title: Roles of PfAP2-EXP2 in Plasmodium falciparum blood-stage development [RNA-seq]

summary: Effects of PfAP2-EXP2 knockdown on gene expression at the ring, trophozoite, and schizont stages

overall_design: RNA-seq for the AP2-EXP2-KD parasite line treated with or without glucosamine (GlcN) at the ring (10–15 hpi), trophozoite (25–30 hpi), and schizont (40–45 hpi) stages, respectively


title: An S-phase checkpoint gated by Bms1 and Ttf1 at the rDNA loci

first: Yanqing

last: Zhu

address: No.866, Road Yuhangtang

department: College of Animal Science

summary: During S-phase, active rDNA transcription conflicts with rDNA replication along hundreds of copies of tandemly arrayed rDNA genes. Ttf1 prevents conflicting collisions by binding to specific ‘Sal-boxes’, thus forming replication-fork-barriers. However, understanding of how Ttf1 is displaced from ‘Sal-boxes’ to allow replication-fork progression remains elusive. Here we report that Bms1, a nucleolar GTPase, interacts with Ttf1 to disassociate the Ttf1-DNA complex. GTPase-activity compromised zebrafish Bms1 mutants display ‘Sal-boxes’ accumulation of Ttf1 and resultant replication-fork stall. However, genomic DNA undergo over-replication that in turn activates DNA-damage response and arrests cell cycle at the S-phase, causing a small liver in bms1 mutants. We propose that Ttf1 and Bms1 together impose a nucleolar checkpoint on cell cycle progression through balancing S-phase rDNA transcription and replication.

overall_design: Examination of Ttf1 binding site in 3dpf wildtype zebrafish embryo

first: Yong

last: Wang

first: Jinrong

last: Peng


title: RNA sequencing analysis for comparing gene expression of the corneal endothelium of Slc4a11-/- vs Slc4a11+/+  mice

city: Bloomington

first: Joseph

middle: A.

last: Bonanno

state: IN

address: 800 E Atwater Ave. , OPT 220

institute: Indiana University School of Optometry

summary:
Purpose: Slc4a11 KO mice show significant edema and altered corneal endothelial morphology at an early age with concomitant increased mitochondrial ROS and oxidative damage relative to wild type. Here we used RNA-Seq with the goal of finding pathways related to corneal endothelial metabolic, pump and barrier function alterations.
Methods: Corneal endothelium-Descemet’s membrane (CEDM) samples were from WT and Slc4a11 KO mice at 12 weeks of age.  RNA sequencing data was subjected to Ingenuity Pathway Analysis and QPCR for validation.
Results: The RNA sequencing IPA analysis predicted activation, inhibition or differential regulation of several pathways. We validated downregulation of Glycolytic enzymes, Mitochondrial complex components and Ion transporters. We observed upregulation of genes of cholesterol biosynthesis, GSH metabolism and tight and adherens junctions.
Conclusions: Slc4a11 KO induces a coordinated decrease in glycolysis, glutaminolysis, oxygen consumption, lactate transporters and Na-K-ATPase.  These changes together with the altered barrier function cause an accumulation of stromal lactate in Slc4a11 KO mice leading to chronic corneal edema.

overall_design: Corneal endothelium mRNA from Slc4a11-/- vs Slc4a11+/+  mice at 12 weeks of age.

first: Diego

last: Ogando


title: Thymus exports precursors of innate lymphoid cells to the blood and peripheral tissues

city: Norman

first: KAILI

last: LIU

state: Oklahoma

address: 173 Felgar St

institute: The University of Oklahoma

summary: Thymus has been shown to have a high capacity to support the differentiation of ILCs.  Whether it actually contributes to ILC pools in the body is not clear.  Single cell RNA sequencing analyses using wild type and athymic nude mice show a substantial amount of thymus-derived ILC precursors in the blood, along with differentiated ILC subsets which may or may not be generated in the thymus.  The precursors express CD3 intracellularly (ic) but not on the surface.  icCD3ε+ cells are primarily found in immature forms in peripheral tissues including the lung, small intestine and epidermis, and differentiate into ILC subsets in different tissue environments in steady state.  Helminth infection promotes their differentiation towards functional ILC2s.  Thus, the thymus exhibits a previously unappreciated role in replenishing ILC pools in different peripheral tissues through life.  This finding is of great significance in understanding age-related differences in immune responses and pathophysiology.

overall_design: transcriptional profiling of ILC2 from WT, Nude, dKO, ID1 strains performed by single-cell RNA sequencing

first: Sandra

last: Bajana

first: Aneta

last: Pankow

first: Kaili

last: Liu

first: Martyna

last: Michniowska

first: Wei

last: Chen

first: Xiao-Hong

last: Sun


title: Sequential azacitidine and carboplatin can prime high-grade serous ovarian cancer to respond to checkpoint inhibitor immunotherapy.

city: New Lambton Heights

first: Michelle

last: Brown

state: New South Wales

address: Hunter Medical Research Institute, Lot 1 Kookaburra Circuit

country: Australia

institute: University of Newcastle

summary: Platinum chemoresistance results in disease recurrence in patients with high-grade serous ovarian cancer (HGSOC). Recent advances in the treatment of solid tumours using checkpoint inhibitor immunotherapy has not benefited platinum-resistant HGSOC. Epigenetic silencing of genes involved in triggering cell death and apoptosis in HGSOC is known to occur via hypermethylation during development of platinum resistance. DNA methyltransferase (DNMT) inhibitors block methylation from occurring and allow silenced genes to be expressed. In ovarian cancer, DNMT inhibitors alter the epigenome and transcriptome of the tumours, which primarily affected expression of immune reactivation pathways. We aimed to determine the epigenome and transcriptome response to sequential treatment of HGSOC cells with DNMTi followed by standard-of-care carboplatin.

overall_design: High-grade serous ovarian cancer cell lines confirmed by genomic and proteomic profiling to be HGSOC cell lines were treated with 0.5 µM azacitidine every 24hr for 72hr, followed by 20µM carboplatin for 48hr. RNA was extracted from these cell lines after sequential azacitidine and carboplatin treatment.

last: Wong-Brown

first: Nikola

middle: A

last: Bowden

first: Andre

last: van der Westhuizen


title: Integrative analysis from the transcriptome to proteome uncovers brassinosteroid-mediated regulation of cambium initiation and patterning in woody stems

city: Qingdao

first: Congpeng

state: Shandong

address: Changcheng Road

institute: Qingdao Agricultural University

summary: Wood formation involves sequential developmental events, requiring the coordination of multiple hormones. Brassinosteroids (BRs) play a key role in wood development, but little is known about the cellular and molecular processes that underlie wood formation in tree species. Here, we generated transgenic poplar lines editing one or several members of PdBRI1s, the orthologs of Arabidopsis vascular-enriched BR receptors, and showed how inhibition of BR signaling influences wood development at the mRNA level. Six Populus PdBRI1 genes form three gene pairs and each exhibits high expression in the basal stems. Simultaneous mutation of PdBRI1-1, 2, 3 and 6, the orthologs of Arabidopsis vascular-enriched BR receptors BRI1, BRL1 and BRL3, resulted in a severe defect in growth. Particularly, the stems of these mutant lines displayed a discontinuous ring of cambium and patterning defects in derived secondary vascular tissues. Abnormal formation of cambia within cortical parenchyma was also observed in the stem of pdbri1-1;2;3;6. Transgenic poplars editing PdBRI1-1 or PdBRI1-1;2;6 had phenotypic alterations in stem development at 4.5 months of growth, indicating functional redundancy among these PdBRI1 genes. An integrated analysis of the transcriptome from pdbri1-1;2;3;6 stems revealed differential expression of a number of genes associated with wood development and hormones.

sample_organism: Populus deltoides x Populus x canadensis

overall_design: mRNA  of  stem profiles of 45-day old wild type (WT) and pdbri1-1;2;3;6 in Populus

first: Congpneg

first: Gongke

last: Zhou

first: Guohua

last: Chai


title: Brain macrophages adopt distinct profiles prior to demyelination in multiple sclerosis

city: Groningen

first: Emma

last: Gerrits

email: e.gerrits@rug.nl, e.gerrits@umcg.nl

state: Groningen

address: Antonius Deusinglaan 1

department: BSCS

country: Netherlands

institute: UMCG

summary: Multiple sclerosis is a disease of the central nervous system (CNS) that is characterized by inflammation and focal areas of demyelination, ultimately resulting in axonal degradation and neuronal death. Several lines of evidence point towards a role for microglia and other CNS-associated macrophages in disease initiation and progression, but exactly how lesion formation is triggered is currently unknown. Here, we characterized early changes in MS brains through transcriptomic analysis of normal appearing white matter (NAWM). We found that NAWM was already characterized by expression of inflammatory genes and that expression of genes associated with stress-response was increased, likely as a result of changes in the macrophage compartment. Single cell RNA sequencing analysis confirmed an early stress response in brain macrophages and identified specific macrophage subsets that associate with different stages of demyelinating lesions. These data provide insight into early changes in MS brains that may provide therapeutic targets in order to limit lesion development and demyelination.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Bulk RNA sequencing of 68 total tissue brain samples obtained from MS donors (normal appearing white matter and lesion) and control donors (white matter). Single-cell RNA sequencing of FACS sorted mouse brain macrophages from four treatment groups: control, cuprizone 3 weeks, cuprizone 5 weeks, remyelinated. Single-cell RNA sequencing of FACS sorted human brain macrophages from 5 donors, 3 brain regions per donor (normal appearing grey matter, normal appearing white matter and white matter lesion).

first: Anneke

last: Miedema

first: Nieske

last: Brouwer

first: Qiong

last: Jiang

first: Laura

last: Kracht

first: Michel

last: Meijer

first: Anna

middle: T

last: Pijnacker

first: Evelyn

last: Wesseling

first: Marion

last: Wijering

first: Hans-Joachim

last: Gabius

last: Amor

first: Bart

last: Eggen

first: Susanne

last: Kooistra


title: Sequential azacitidine and carboplatin can prime high-grade serous ovarian cancer to respond to checkpoint inhibitor immunotherapy

first: Michelle

last: Brown

type: Methylation profiling by genome tiling array

overall_design: Bisulfite-treated DNA from 8 samples were hybridised to the Infinium MethylationEPIC Beadchip (Illumina).

last: Wong-Brown

first: Nikola

last: Bowden

first: Andre


title: TFAP2A transcription factor ChIP-seq in HEPM cells (HEPM ATCC CRL-1486)

city: Bonn

first: Karharina

last: Ruff

address: Venusberg-Campus 1

institute: Institute of Human Genetics, University of Bonn, School of Medicine & University Hospital

summary: We performed a transcription factor (TF) ChIP-seq in human embryonal palatal mesenchyme (HEPM;  HEPM ATCC ® CRL-1486™) cells with a polyclonal anitbody against TFAP2A ((ab52222, abcam®, Great Britain) in two replicates.

overall_design: TFAP2A ChIP-seq in HEPM cells

first: Kerstin

last: Ludwig

first: Katharina


title: 3'mRNA-seq in HEPM cells (HEPM ATCC CRL-1486)

summary: We performed 3'mRNA-seq in human embryonal palatal mesenchyme (HEPM) cells to identify genes expressed in this cellular modell of the developing palate.

overall_design: Gene expression analysis in HEPM cells, performed in 3 replicates


title: MAGT1 is involved in HeLa cell proliferation through regulating p21 expression, S-phase progress and ERK/p38 MAPK MYC axis

city: Nangjing

first: Ming

last: Fang

state: jiangsu

address: 2 Sipailou Road

institute: Southeast University

summary:
Background: Magnesium transporter subtype 1 (MAGT1) is involved in animal development and cell differentiation. Thus far, researches on MAGT1 are mainly focused on Cardiomyocyte regulation and differentiation, but rare research has been reported on cell proliferation, especially concerning the underlying molecular mechanisms.
Methods: HeLa cells were transiently knock down with different SiRNAs and processed for RNA sequencing and bioinformatics analysis, western blot, real-time PCR as well as cell cycle assays.
Results: We showed that cell proliferation was significantly restricted with S-phase arrest in MAGT1 knock down cells, which was further confirmed by the up expression of p21, CCNA1 and CCNB1, while down expression of CCND1, CCNE1 and CDK4. Knocking down MAGT1 also resulted in significant transcriptional expression changes of 1599 target genes analyzed by RNA sequencing. The bioinformatics analysis showed that MAGT1 was related to MAPK signaling pathway. Western blot analysis confirmed that the phosphorylation of ERK1/2 and p38 exhibited a remarkable reduction in MAGT1 downregulated group.
Conclusion: MAGT1 is critical in HeLa cell proliferation, S-phase progress and ERK/p38 MAPK signaling pathway, indicating that MAGT1 might be a novel target of anticancer research.

overall_design: mRNA profiles of HeLa cells treated with MAGT1 and negative Control SiRNAs

first: Hongcan

last: Shi

first: Caili

last: Bi


title: Novel human-derived RET fusion NSCLC cell lines have heterogeneous responses to RET inhibitors and differential regulation of downstream signaling

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: The goal of this study was to understand RET signaling dynamics and regulation of response to RET inhibitors

overall_design: RNAsequencing was preformed to determine differences in gene expression between RET-rearranged cell lines as well as changes after treatment with RET inhibitors

first: Laura

last: Schubert

first: Anh

last: Le

first: Adriana

last: Estrada-Bernal

first: Andrea

last: Doak

first: Minjae

last: Yoo

first: Sarah

last: Ferrara

first: Fumi

last: Kinose

first: Uwe

last: Rix

first: Aik-Choon

last: Tan

first: Robert

middle: C

last: Doebele


title: Single-cell RNA-sequencing of murine breast tumor infiltrating immune cells isolated from the site of metastasis in wild-type and short-form Ron knockout mice

city: Salt Lake City

first: Alana

last: Welm

address: 2000 Circle of Hope

institute: University of Utah

summary: Metastatic breast cancer is the overwhelming cause of breast cancer mortality and is still incurable. Development of immunotherapy is an exciting new area of research in metastatic breast cancer; however, the extreme immunosuppressive tumor environment poses a major challenge. Here we provide evidence that a particular isoform of Ron kinase, short-form Ron (SF-Ron), strongly suppresses anti-tumor immune responses and promotes metastatic outgrowth of mammary tumors. We used single-cell RNA-sequencing to identify the CD45+ immune cell populations within the common site of breast cancer metastasis, lung, from either wild-type (WT) or SF-Ron knockout (Ron SF-/-) in the MMTV-PyMT experimental metastasis model. SF-Ron was required for breast cancer metastasis develoment and the skewing of the lung immune microenvironment toward the immune-suppressive pro-tumor microenvironment. Lack of SF-Ron not only enhanced tumor-specific immune response, but also led to accumulation of less differentiated TCF1+ CD4+ T cells in the metastatic lungs that were endowed with type I helper T cell-like (Th1-like) differentiation potential. Mice treated with a small molecule Ron kinase inhibitor produced significantly more tumor-specific CD8+ T cells and reduced metastatic outgrowth. Our study indicates that blocking Ron, specifically SF-Ron, remodels the metastatic lung microenvironment to enhance anti-tumor immunity and clear metastatic lesions, providing strong pre-clinical evidence for Ron kinase inhibitors to augment immunotherapy for treatment of metastatic breast cancer.

overall_design: MMTV-PyMT tumor cells were injected via the lateral tail vein into wild-type and short-form Ron knockout mice (n>8). Lung metastasis were allowed to develop for 28 days. At the end point, lungs occupied by metastases were harvested and pooled in each group, and processing into single cell suspension. The DAPI(-)CD45(+) live tumor metastases infiltrating immune cells were sorted via flow cytometry and processed for single-cell RNA-sequencing via 10x platform.

first: S

last: Lai

first: H

last: Gundlapalli

last: Ekiz

first: A

last: Jiang

first: E

last: Fernandez

middle: L


title: Transcriptomic analysis revealed increased expression of genes involved in keratinization in the tears of COVID-19 patients

city: Messina

first: Emanuela

last: Mazzon

address: STRADA STATALE 113 - C.DA CASAZZA

country: Italy

institute: IRCCS Centro Neurolesi "Bonino-Pulejo"

summary:
Purpose: Recent studies have focused their attention on conjunctivitis as one of the symptoms of  coronavirus disease 2019 (COVID-19). Therefore, tear samples were taken from COVID-19  patients and the presence of SARS-CoV-2 was evidenced using Real Time reverse transcription  polymerase chain reaction.
Methods: The main aim of this study was to analyze mRNA expression in the  tears of patients with COVID-19 viral infection compared with healthy subjects using Next  Generation Sequencing (NGS).
Results: The functional evaluation of the transcriptome highlighted 25  genes that differ statistically between healthy individuals and patients affected by COVID-19  disease. In particular, the NGS analysis identified the presence of several genes involved in B cell  signaling and keratinization. In particular, the genes involved in B cell signaling were  downregulated in the tears of COVID-19 patients, while those involved in keratinization were  upregulated.
Conclusions: The results indicated that COVID-19 may induce a process of ocular keratinization  and a defective B cell response.

overall_design: Tears mRNA profiles of patients suffering from COVID and healthy individuals

first: Leonardo

last: Mastropasqua

first: Lisa

last: Toto

first: Luigi

last: Chiricosta

first: Francesca

last: Diomede

first: Agnese

last: Gugliandolo

first: Serena

last: Silvestro

first: Guya

last: Marconi

first: Bruna

last: Sinjari

first: Jacopo

last: Vecchiet

first: Francesco

last: Cipollone

first: Damiano

last: D'Ardes

first: Antonio

last: Auricchio

first: Manuela

last: Lanzini

first: Segio

last: Caputi

first: Rossella

last: D'Aloisio

first: Oriana

last: Trubiani


title: Expression data of PDGFRα- and PDGFRα+ mesenchymal stem cells isolated  from mouse periosteum

city: Baltimore

first: Aaron

last: James

state: MD

address: 600 North Wolfe Street

department: Pathology

institute: Johns Hopkins University School of Medicine

summary: The outer coverings of the skeleton, or periosteum, are arranged in concentric layers and act as a reservoir for tissue specific bone progenitors.  Cellular heterogeneity within this tissue depot is increasingly recognized.  Here, Pdgfra reporter animals were used to highlight a subset of periosteal progenitor cells with high osteogenic potential.  Pdgfra+ periosteal progenitor cells enhanced osteogenic differentiation in vitro and improved fracture healing and bone regeneration in vivo.  Depletion of Pdgfra-expressing progenitor cells interferes with cortical appositional bone, periosteal bone formation in response to mechanical load, and during fracture repair.  Pdgfra+ periosteal progenitors give rise to Nestin+ periosteal cells overtime, after fracture and upon transplantation.

overall_design: 4 Total samples were analyzed. The cells in each sample were isolated from 3-6 male mice.  Two samples of PDGFRα+ FACS-sorted cells were compared to two samples of PDGFRα- cells.

first: Jiajia

last: Xu


title: Hsa-miR-144-3p is down-regulated in serum from drug-naïve and advanced Parkinson’s disease patients.

city: Verona

first: Alessandra

last: Dal Molin

address: Via Roveggia 43B

institute: Personal Genomics

summary: Advanced age represents one of the major risk factors for Parkinson’s Disease. Recent studies posit a role for microRNAs in Parkinson’s Disease and it is well established that microRNAs are remodelled during ageing, but the relationship between the two processes have not been clarified yet. The aim of the present study is to unravel the relevance of microRNAs as biomarkers of Parkinson’s Disease within the ageing framework. We used Next Generation Sequencing to profile serum microRNAs from samples informative for Parkinson’s Disease (recently diagnosed, drug-naïve Parkinson’s Disease patients) and healthy ageing (centenarians) plus healthy controls age-matched with Parkinson’s Disease patients. Potential candidates, emerging from the combination of differential expression and network analyses, were further validated in an independent cohort including both drug-naïve and advanced Parkinson’s Disease patients together with healthy siblings of Parkinson’s Disease patients at higher genetic risk for Parkinson’s Disease. While we did not find evidences of microRNAs co-regulated in Parkinson’s Disease and ageing, we report that hsa-miR-144-3p is consistently down-regulated in early and advanced Parkinson’s Disease and in Parkinson’s Disease siblings. Interestingly, functional analysis revealed that hsa-miR-144-3p is involved in the regulation of coagulation, a process known to be altered in Parkinson’s Disease.  Our results consistently show the down-regulation of hsa-mir144-3p in early and advanced Parkinson’s Disease, robustly confirmed across a variety of analytical and experimental analyses. These results are promising, and additional research is needed to unveil the functional details of its relevance and involvement in Parkinson’s Disease.

overall_design: miRNA-seq of drug-naïve Parkinson’s Disease patients, healthy ageing centenarians and healthy controls

first: Elisa

last: Zago

first: Giovanna

last: Dimitri

first: Luciano

last: Xumerle

first: Chiara

last: Pirazzini

first: Maria

last: Bacalini

last: Maturo

first: Tiago

last: Azevedo

first: Simeon

last: Spasov

first: Pilar

last: Gómez-Garre

first: María

last: Periñán

first: Silvia

last: Jesús

first: Luca

last: Baldelli

first: Luisa

last: Sambati

last: Calandra-Buonanuora

first: Paolo

last: Garagnani

first: Federica

last: Provini

first: Pietro

last: Cortelli

first: Pablo

last: Mir

first: Claudia

last: Trenkwalder

first: Brit

last: Mollenhauer

first: Claudio

last: Franceschi

last: Liò

first: Christine

last: Nardini


title: Activation and acetylation of tumor-intrinsic PD-L1 via HBXIP accelerates breast cancer growth

city: Tian jin

first: xu

last: feifei

address: weijinlu

institute: nankai univesity

summary: Programmed death ligand-1 (PD-L1) is a well-known transmembrane protein, which antibodies present effective clinical therapy in multiple human cancers. However, the function of tumor cell-intrinsic PD-L1 and its related mechanism in breast cancer remains incompletely studied.   Programmed death ligand 1 (PD-L1) on the membrane of tumor cells strengthens tumor immune escape. Tumor cell-intrinsic PD-L1 is also involved in tumorigenesis and development, but the mechanism in regulating PD-L1 expression remains incompletely studied. Here, we report a novel mechanism for PD-L1 that can be induced by hepatitis B X-interacting protein (HBXIP), an oncogenic transcriptional coactivator, promoting breast cancer growth. Overexpression of PD-L1 increases breast cancer proliferation in vitro and in vivo. Transcriptomic analysis also reveals that PD-L1 plays a critical role in cancer development. Furthermore, we find that the expression of PD-L1 is positively associated with HBXIP in breast cancer clinical tissues as well as in cell lines, PD-L1 and HBXIP expression have higher levels in tumor. Mechanistically, HBXIP predominantly stimulates the promoter activity of PD-L1 through coactivating transcription factor ETS2. Especially, HBXIP induced PD-L1 acetylation with the acetyltransferase p300 at lysine 270 (K270), enhancing PD-L1 protein stability. Functionally, depletion of HBXIP markedly attenuates PD-L1-induced breast tumor growth in vitro and in vivo. Moreover, aspirin decreased breast cancer growth via targeting PD-L1 and HBXIP. Taken together, our results extend a new mechanism of PD-L1 functions, expound non-immune effects of PD-L1 and imply broader uses for PD-L1 as a target in breast cancer therapy.

overall_design: Examination of PD-L1 overexpression functions in breast cancer cells.

first: Feifei

last: Xu

first: Weiying

last: Zhang

first: Lihong

last: Ye


title: Mechanism for Cortical Bone Stem Cell-Derived Exosomes' Therapeutic Effect on Myocardial Ischema Reperfusion and Remodeling

city: Philadelphia

first: Steve

middle: R

last: Houser

state: PA

address: 3500 N Broad Street

institute: Temple University

summary: The goal of this study was to understand the effect of human cortical bone stem cells on human cardiac fibroblast activation. We treated normal human cardiac fibroblasts +/-  50 ng/mL TGFBeta +/- 2,000,000 human cortical bone stem cell-derived exosome particles per fibroblast treated for 72 hours and then isolated RNA for RNA-sequencing.

overall_design: Normal Human Cardiac Fibroblasts +/- TGFBeta +/- human cortical bone stem cell-derived exosomes

first: Giana

last: Schena

first: Emma

last: Murray

first: Steven


first: Yuxiao

last: Zhou

address: Dongchuan Road NO.800

institute: Shanghai Jiaotong University

summary: We demonstrated that Pyk2 is a novel fear memory suppressor molecule and Pyk2 null mice provide a model for understanding fear-related disorders.

overall_design: Study for Pyk2 suppresses contextual fear memory in an autophosphorylation-independent manner used RNA-seq experiments of hippocampus from WT,  Pyk2 KO and Pyk2 Y402F mutant.

first: Jin

last: Zheng

first: Lun

last: Suo

first: Liling

last: Jia

first: Qiang

last: Wu


title: mRNA sequencing  of WT, ∆MTA and ∆MTB cells in Starvation, costimulation and early Conjugation of Tetrahymena thermophila.

city: wuhan

first: Wei

last: Miao

state: hubei

address: donghu south road #7

institute: Institute of hydrobiology, CAS

summary: The goals of this study is to investigate the function of MTA and MTB of Tetrahymena thermophila.

overall_design: Compare the expression of genes amnong WT, ∆MTA and ∆MTB cells in Starvation, costimulation and early Conjugation.


title: Uninterrupted Mutant Huntingtin CAG-repeat but Not Polyglutamine Length Predicts Striatal Nuclear Pathogenesis and Transcriptionopathy in HD Mice

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

summary: Huntington’s disease (HD) is caused by CAG repeat expansion at the N-terminal region of huntingtin (HTT) gene and characterize by neuronal cell loss and neuroinflammation transcriptional profile change in striatum, cortex and other brain regions.  Here we reported generation and characterization of BAC-CAG, a novel full length human HD mouse model host over 120 uninterrupted CAG repeats. we performed RNA-seq analysis of the striatum and cortex of BAC-CAG mice at 2m, 6m and 12m of age (N=6 per genotype, sex balanced). We observed an age-dependent transcriptionopathy in the striatum of BAC-CAG mice, with only 7 and 36 significant DE genes in 2m and 6m striatum respectively (FDR<0.1), but 820 DE genes (538 downregulated and 282 upregulated genes) at 12m of age (FDR<0.1). The transcriptomic deficits in this model are highly striatum-selective, as we only detected 4, 3 and 14 DE genes (FDR<0.1) at 2m, 6m and 12m respectively in BAC-CAG cortices compared to WT controls. Remarkably, we found a highly significant positive transcriptome-wide correlation (r=0.62) of DE Z statistics between BAC-CAG vs WT at 12m and Q140 vs WT at 6m (p<1e-200). This result demonstrates a high concordance of both upregulated and downregulated genes in the BAC-CAG striatum compared to that of allelic series KI mice; but RNA-seq studies of BACHD mice at 12m and found only 50 genes significantly differentially expressed (DE) genes (FDR<0.1) in the striatum at 12m of age compared to WT littermates, 31 downregulated and 19 upregulated genes. In the cortex at 12m of age, BACHD only showed 6  significantly downregulated genes and 7 upregulated genes comapred to WT controls (FDR<0.1).

overall_design: Three males and three females BAC-CAG mice and their WT littermates from 2, 6 and 12m age groups, respectively, were perfused with PBS and striatum, cortex and cerebellum were dissected out immediately. The samples were fresh frozen and kept at -80°C. Total RNA was extracted using Qiagen (Valencia, CA) RNeasy kit with QIA shredder columns. cDNA libraries were generated using Illumina TruSeq RNA Library Prep Kit v2 and sequenced using an Illumina Illumina HiSeq 4000 sequencer with strand-specific, paired-end, 69-mer sequencing protocols to a minimum read depth of 37.5 million reads per sample. In another experiment, 4 BACHD and 4 WT littermate control mice (both 2 males and 2 females) at 12 months age were used. Their cortical and striatal tissues were dissected and assayed as above.

first: Xiaofeng

last: Gu

first: Jeff

last: Richman

first: Peter

last: Langfelder

last: Wang

first: Lalini

last: Ramanathan

last: Cantle

first: Fuying

last: Gao

first: Chang

last: Park

first: Giovanni

last: Coppola

last: Horvath

first: X

last: Yang


title: H2AK121ub and H3K27me3 marks have different effects on nucleosome organization in Arabidopsis

city: Sevilla

first: Myriam

last: Calonje

address: Americo Vespucio 49

country: Spain

institute: Institute for Plant Biochemistry and Photosynthesis (CSIC -  University of Sevilla)

summary: Background: Nucleosome organization within chromatin can be altered through the incorporation of histone modifications that in turn affects gene expression. Accordingly, the Polycomb Group (PcG) complexes PRC1 and PRC2 through the incorporation of H2AK121ub and H3K27me3 marks, respectively, maintain the repression of target genes; however, little is known about the exact function of these modifications in shaping nucleosome array at target genes, especially in plants.    Results: By using two different MNase-seq datasets we analyzed the nucleosome occupancy profile of different PcG target genes in Arabidopsis. We found that PcG targets strongly differ in their nucleosome organization depending on the marks that they carry. Our data indicate that H2AK121ub marks play a role in fine-tuning +1 nucleosome position, while H3K27me3 marks impact nucleosome spacing and chromatin accessibility at both promoter and gene regions. Furthermore, analyzing the nucleosome profile of transcriptionally active PcG target genes in WT seedlings we found that their apparent activated state may be actually due to transcriptional heterogeneity across different cells.   Conclusion: Our findings show that H2AK121ub and H3K27me3 marks differentially affect nucleosome organization in Arabidopsis, displaying additive effects when co-localizing at target genes.

overall_design: Nucleosome landscapes of 7DAG  Arabidopsis seedlings Col-0 and triple mutants atbmi1a/b/c


title: GDF5+ chondroprogenitors derived from human pluripotent stem cells, which  resemble embryonic teno/ligamento-genic cells, preferentially form permanent chondrocytes

city: Houston

first: Guangsheng

last: Pei

state: Texas

address: 7000 Fanin

institute: UTHealth

summary:
Background: Human pluripotent stem cells (hPSCs) give rise to chondrogenic activity in culture. Such activity was found in mesodermal and neural crest like progeny of hPSCs, and readily expanded as SOX9+ msenchymal cells in a medium containing FGF2.  However, once expanded, the type of chondrocytes they perfer to form is growth plate-ike transient chondrocytes that are destined to form bone. However, we have recently developed a method to generate GDF5+ mesenchymal cells from such SOX9+ cells which ehibit activity to preferentially form articular-like permanent chondrocytes.  The aim of the present prospective follow-up study was to reveal the cell-type and developmental origin of the GDF5+ cells as well as the SOX9+ cells.
Methods: Paraxial mesoderm was generated from human PSCs, purified by FACS, and expanded to generate SOX9+ chondroprogenitors.  Then, the SOX9+ cells were further differentiated into joint progenitor-like GDF5+ chondroprogenitors.  These two chondroprogenitors were subjcted to bulk RNA-seq.
Results: Based on the transcriptomic data, we examined differentially expressed genes, cell-type deconvolution analysis, and cell-type correlation analysis. The results suggested that GDF5+ cells might contain a teno/ligamento-genic potential (e.g., SCX+ cells), while SOX9+ cells were related to (neural crest-derived) ectomesenchymal chondroprogenitors. The followup biological analyses indicated as follows. The fast-growing SOX9+ cells formed cartilage that expressed chondrocyte hypertrophy markers and was readily mineralized after ectopic transplantation. In contrast, the slowly-growing GDF5+ cells were derived from SOX9+ cells. They formed cartilage that tended to express low to no chondrocyte hypertrophy markers, while expressing PRG4, a marker of embryonic articular chondrocytes, and to remain largely unmineralized in vivo.
Conclusions: Our results imply that GDF5+ cells specified to generate permanent-like cartilage are likely to emerge in association with the commitment of SOX9+ cells to the tendon/ligament lineage.

overall_design: Bulk RNA-seq data of 4 SOX9+ chondogenic cells and 4 GDF5+ chondrogenic cells generated independently from human pluripotent stem cells were generated by deep sequencing.


title: In vivo selection reveals long non-coding RNAs implicated in colon to liver metastasis

first: Carl

middle: Robert

last: Rankin

state: CA

address: 3615 Watseka Ave Unit 204

department: Medicine

institute: UCLA

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

summary: A microaaray containing both lncRNAs and mRNAs expression data in LS-PAR and LS-3B cells.

overall_design: 2 groups, 3 independent samples per group

first: David

last: Padua