title: Transcriptomic profiling of drug-naïve or proteasome inhibitor-resistant myeloma cell lines

city: Adelaide

first: John

last: Toubia

address: Frome Rd

institute: Centre for Cancer Biology

summary: RNA was extracted from myeloma cell lines that were either drug-naïve or resistant to bortezomib or carfilzomib and the transcriptome was characterised using RNA sequencing.

overall_design: 5TGM1 or RPMI-8226 cells were cultured in increasing concentrations of bortezomib (for bortezomib-resistant) or carfilzomib (for carfilzomib resistant) over a period of several months in order to generate resistant cell lines. Resistant cell lines were given a drug holiday for 5 days prior to RNA extraction. RNA was extracted from 1x10^7 cells per sample using the Qiagen RNeasy mini kit and RNA-seq was performed.

first: Melissa

middle: K

last: Bennett


title: Nicotinamide promotes human pluripotent stem cells differentiation into cardiomyocytes [2]

status: Public on Dec 01 2021

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

country: China

institute: University of Macau

summary: Nicotinamide, the amide form of vitamin B3, is essential to maintain the human fetal development. It benefits the ectoderm and endoderm development, but its influence in mesoderm differentiation is elusive. In this study, we reported that nicotinamide regulated the gene expression of cardiovascular system, and it induced functional cardiomyocytes which was independent of canonical WNT signaling. Through a kinase screening, we found that nicotinamide inhibited the activity of P38δ to promote cardiomyocyte differentiation. Furthermore, we compared the gene expression of cardiomyocytes induced by WNT inhibitor IWP-2, nicotinamide or P38 inhibitor SB202190. The results showed that the cardiomyocytes induced by nicotinamide had similar gene expression profile compared with P38 inhibitor, which indicated nicotinamide promoted cardiac differentiation via the inhibition of P38.

overall_design: Total RNA was harvested from the differentiated cells induced by IWP-2 (3 μM), SB202190 (10 μM), nicotinamide (10 mM) or none treated control at day 10 of cardiac differentiation.

first: Guokai

last: Chen


title: Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation

city: Los Angeles

first: Tom

last: Vondriska

state: CA

address: 650 Charles E Young Dr, BH553

country: USA

institute: UCLA

type: Genome binding/occupancy profiling by high throughput sequencing

type: Expression profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: RNA-seq of mouse spleen samples from Alginate oligosaccharides and/or busulfan treatment groups

city: Qingdao

first: Yong

last: Zhao

state: Shandong

address: 700 Changcheng Road

department: College of Life Sciences

institute: Qingdao Agricultural University

summary: The goat of this project is to exploreAlginate oligosaccharides (AOS) effect on the recovery of spleen function. RNA-seq of spleen samples from different groups: Con, busulfan(B), AOS, B+AOS.

overall_design:
RNA-seq of spleen samples from different groups: Con, busulfan(B), AOS, B+AOS. .
A0 means the treatment group is control (without any treatment). A10 means the animals were treated with Alginate oligosaccharides 10mg/kg for 5 weeks. B0 means the animal treated with busulfan at 40mg/kg once. BA10 means the animals were treated with busulfan once then dosed with Alginate oligosaccharides 10mg/kg for 5 weeks.

first: Xiangping

last: Ma


title: RNA-seq of mouse kidney samples from Alginate oligosaccharides and/or busulfan treatment groups

summary: The goat of this project is to exploreAlginate oligosaccharides (AOS) effect on the recovery of kidney function. RNA-seq of kidney samples from different groups: Con, busulfan(B), AOS, B+AOS.

overall_design:
RNA-seq of kidney samples from different groups: Con, busulfan(B), AOS, B+AOS. .
A0 means the treatment group is control (without any treatment). A10 means the animals were treated with Alginate oligosaccharides 10mg/kg for 5 weeks. B0 means the animal treated with busulfan at 40mg/kg once. BA10 means the animals were treated with busulfan once then dosed with Alginate oligosaccharides 10mg/kg for 5 weeks.


title: Extracellular traps released by antimicrobial TH17 cells contributes to host defense

first: Alice

last: Mouton

address: 610 Charles E. Young Dr. East

department: Ecology and Evolutionary Biology

summary: Herein, we used C. acnes as a model to elucidate the antimicrobial machinery of the TH17 subset. We generated C. acnes-specific antimicrobial TH17 clones (AMTH17) with varying antimicrobial activity against C. acnes, to enable us to study mechanisms by which TH17 cells kill bacteria. We show that C. acnes-induced AMTH17 clones represent a subset of CD4+ TEM and TEMRA cells. RNA-seq analysis of AMTH17 indicate transcripts encoding antimicrobial molecules such as GNLY, GZMB, PRF1 and histone H2B, whose expression correlates with killing activity. Additionally, we validated that AMTH17-mediated killing is a general mechanism that can target C. acnes and other bacterial species. Scanning electron microscopy reveal that AMTH17s can release T cell extracellular traps composed of lysine and arginine-rich histones such as H2B and H4 that entangle C. acnes. This study identifies a functionally distinct subpopulation of TH17 cells with an ability to secrete antimicrobial proteins and form extracellular T cell traps to capture and kill bacteria.

overall_design: Fifteen AMTH17 and five n-AMTH17 clones (control) generated from six healthy donors were stimulated with α-CD3/α-CD28 (BD) in T cell media.

first: George

middle: W

last: Agak


title: RNA-seq of mouse heart samples from Alginate oligosaccharides and/or busulfan treatment groups

summary: The goat of this project is to exploreAlginate oligosaccharides (AOS) effect on the recovery of heart function. RNA-seq of heart samples from different groups: Con, busulfan(B), AOS, B+AOS.

overall_design:
RNA-seq of heart samples from different groups: Con, busulfan(B), AOS, B+AOS. .
A0 means the treatment group is control (without any treatment). A10 means the animals were treated with Alginate oligosaccharides 10mg/kg for 5 weeks. B0 means the animal treated with busulfan at 40mg/kg once. BA10 means the animals were treated with busulfan once then dosed with Alginate oligosaccharides 10mg/kg for 5 weeks.


title: RNA-seq of F1 mouse testis samples from different lncRNA8276 modification groups

summary: The goat of this project is to explore lncRNA8276  regulation spermatogenesis. We tried to search the mechanism oflncRNA8276 regulation spermatogenesis. RNA-seq of F1 mouse testis samples from different groups: 5NC,  lncRNA8276 overexpression, 3NC, lncRNA8276 knockdown.  The testes of mouse were transfected with virus with 5NC, lncRNA8276 overexpression, 3NC, lncRNA8276 knocdown letivirus.

overall_design: RNA-seq of F1 mouse testes samples from different groups: 5NC,  lncRNA8276 overexpression, 3NC,  lncRNA8276 knockdown. The F1 mouse testes  were transfected with virus with overexpression or  inhibition of  lncRNA8276.

first: Xiao

last: Han


title: RNA-seq of mouse lung samples from Alginate oligosaccharides and/or busulfan treatment groups

summary: The goat of this project is to exploreAlginate oligosaccharides (AOS) effect on the recovery of lung function. RNA-seq of lung samples from different groups: Con, busulfan(B), AOS, B+AOS.

overall_design:
RNA-seq of lung samples from different groups: Con, busulfan(B), AOS, B+AOS. .
A0 means the treatment group is control (without any treatment). A10 means the animals were treated with Alginate oligosaccharides 10mg/kg for 5 weeks. B0 means the animal treated with busulfan at 40mg/kg once. BA10 means the animals were treated with busulfan once then dosed with Alginate oligosaccharides 10mg/kg for 5 weeks.


title: GFI1 maintains a chromatin state that is essential in human endothelial-to-hematopoietic transition [ATAC-seq]

city: Guangzhou

first: qianyu

last: chen

address: 190 Kai Yuan Avenue, Science Park

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

summary: During early embryonic hematopoiesis, hematopoietic stem/progenitor cells (HSPCs) are considered to develop from hemogenic endothelial cells (HECs) though endothelial to hematopoietic transition (EHT). However, little is known about how EHT is regulated in human. Here, we report that GFI1 plays an essential role in ensuring EHT during hematopoietic differentiation of human embryonic stem cells (hESCs). GFI1 deletion in hESCs showed a complete EHT defect due to a closed chromatin state of hematopoietic genes in HECs. Further analysis revealed that GFI1 directly binds and maintains the open chromatin state of genes important for EHT, such as PI3K signaling. Together, our findings reveal an essential role of GFI1 mediated epigenetic mechanism underlying human EHT during hematopoiesis.

overall_design: We compared GATA2/eGFP+ endothelial cells of WT and GFI1-KO by ATAC-Seq

first: Baoqiang

last: Kang

first: Guangjin

last: Pan


title: Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [ATAC-seq]

summary: Heart failure can be induced or ameliorated by regulation of chromatin modifying enzymes. Because so many chromatin factors regulate gene expression, we used ATAC-seq to report the status of a given locus at any time—the sum total of all epigenetic modifiers—in a mouse model of pressure overload hypertrophy. Early compensation of pressure overload at 3 days was associated with widespread changes in chromatin accessibility and DNA methylation, the majority of which persisted to the decompensated phase (3 weeks), revealing the temporal nature of epigenomic compensation to pathologic stimuli. A cardiac-specific CTCF depletion model was used to examine how this protein maintains basal cardiac chromatin function and revealed that loss of CTCF causes widespread changes in accessibility and methylation that are distinct from those in pressure overload. Less than half of the gene expression changes occurring at either time point after pressure overload were explained by the actions of DNA methylation alone and accessibility was likewise an imperfect predictor of transcription. Distal enhancers were paired with genes based on chromatin structural data and the regulatory actions of these elements examined in the context of DNA methylation and accessibility: enhancer actions require specific combinations of transcription factors and histone modifications at different stages of disease and to execute a specific transcriptional event (methylation and accessibility alone were insufficient to predict the behavior). In summary, these studies characterize the logic employed at different coding, regulatory, and noncoding regions to regulate chromatin accessibility and transcription, providing a resource of epigenomic data at distinct temporal stages of heart failure.

overall_design: Diferences in chromatin accessibility, DNA methylation and gene expression at early (3 days) and late (3 weeks) stage of cardiac disease, and during cardiac-specific CTCF depletion. TAC (transverse aortic constriction) samples represent mice with diseased hearts.

first: Douglas

middle: J

last: Chapski

first: Thomas

middle: M

first: Manuel

last: Rosa-Garrido


title: RNA-seq of F0 mouse testis samples from different lncRNA8276 modification groups

summary: The goat of this project is to explore lncRNA8276  regulation spermatogenesis. We tried to search the mechanism oflncRNA8276 regulation spermatogenesis. RNA-seq of F0 mouse testis samples from different groups: 5NC,  lncRNA8276 overexpression, 3NC, lncRNA8276 knockdown.  The testes of mouse were transfected with virus with 5NC, lncRNA8276 overexpression, 3NC, lncRNA8276 knocdown letivirus.

overall_design: RNA-seq of F0 mouse testes samples from different groups: 5NC,  lncRNA8276 overexpression, 3NC,  lncRNA8276 knockdown. The F0 mouse testes  were transfected with virus with overexpression or  inhibition of  lncRNA8276.


title: Temporal Analyses of Cardiac Chromatin Accessibility, DNA Methylation and Epigenomic Structure Reveal Locus-Specific Regulation [RRBS]


title: Transcriptome analysis of gene expression in scramble and METTL3 Knockdown HUVEC cell lines

city: Chongqing

first: Huang

last: Wu

address: 10 Changjiang Access Road

department: Department of Blood Transfusion

institute: Daping Hospital, Army Medical University

summary: We have used RNA-seq to explore  gene expression profiles in scramble and METTL3 Knockdown HUVEC cell lines.

overall_design: Three biological replicates for scramble and METTL3 Knockdown HUVEC cell lines.

first: Qin

last: Bai


title: Single Cell Profiling of DNMT3A-Mutant Progenitors  Novel Pre-Leukemia Marker and Potential Therapeutic Target

city: Houston

first: Mira

last: Jeong

address: One Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: To identify early events involved in pre-leukemic transformation, we have performed single-cell RNA-sequencing (scRNA-seq) in WT and Dnmt3a KO mice. Flow cytometry sorted wild-type and pre-leukemic Dnmt3a KO HSPC cells were captured using 10X genomics chromium platform.

overall_design: We performed single cell RNA sequencing  of hematopoietic precursor cells from wild type and Dnmt3a knockout mice at 2 and 6 months.

first: Margaret

last: Goodell


title: RNA-seq of C18-4 cells samples from different lncRNA8276 modification groups

summary: The goat of this project is to explore lncRNA8276  regulation spermatogenesis. We tried to search the mechanism oflncRNA8276 regulation spermatogenesis. RNA-seq of C18-4  cells samples from different groups: 5NC,  lncRNA8276 overexpression, 3NC, lncRNA8276 knockdown.  The cell were transfected with virus with 5NC, lncRNA8276 overexpression, 3NC, lncRNA8276 knocdown letivirus.

overall_design: RNA-seq of C18-4  cells samples from different groups: 5NC,  lncRNA8276 overexpression, 3NC,  lncRNA8276 knockdown. The C18-4 cells  were transfected with virus with overexpression or  inhibition of  lncRNA8276.

first: Cong

last: Zhang


title: small RNA sequencing of goat mamamary gland cells samples from cirRNA modification groups

type: Non-coding RNA profiling by high throughput sequencing

summary: The goat of this project is to explore cirRNA28250  efffect on small RNA to regulation goat mammary gland lipid metabolism. We tried to search the mechanism of cirRNA28250 regulation lipid metabolism through miRNA. small RNA seqencing of goat mamamary gland cells samples from different groups: 5NC, cirRNA28250 overexpression, 3NC,cirRNA28250 knockdown. The goat mammary gland cells were cultured in 3D condition. The cell were transfected with virus with cirRNA28250 gene (overexpression), or inhibition of cirRNA28250A expression (cirRNA28250 gene knockdown).

overall_design: small RNA sequencing of goat mamamary gland cells samples from different groups: 5NC,  cirRNA28250 overexpression, 3NC, cirRNA28250 knockdown. The goat mammary gland cells were cultured in 3D condition. The cell were transfected with virus with cirRNA28250 gene (overexpression), or inhibition of cirRNA28250 expression (cirRNA28250 gene knockdown).

first: Yishan

last: Gao

first: Lingjiang

last: Min


title: RNA-seq of goat mamamary gland cells samples from different cirRNA modification groups

first: Yong

last: Zhao

summary: The goat of this project is to explore cirRNA28250  regulation goat mammary gland lipid metabolism. We tried to search the mechanism of cirRNA28250 regulation lipid metabolism. RNA-seq of goat mamamary gland cells samples from different groups: 5NC,  cirRNA28250 overexpression, 3NC,  cirRNA28250 knockdown. The goat mammary gland cells were cultured in 3D condition. The cell were transfected with virus with  cirRNA28250 gene (overexpression), or inhibition of  cirRNA28250 expression ( cirRNA28250 gene knockdown).


title: RNA sequencing (RNA-SEQ) of FOXM1 knockdown by siRNA in ovarian cancer cells

city: jinan

first: David

last: Li

address: 44 Wenhua Xi Road,Jinan

institute: Shandong University

summary: Purpose：Forkhead box M1 (FOXM1) transcription factor is ubiquitously expressed in embryonic tissues but rare in differentiated cells. Increased expression of FOXM1 is observed in a variety of human malignancies. Here, we sought to characterize the expression and tumorigenic roles of FOXM1 in high-grade serous ovarian carcinoma (HGSOC).  Experimental Design：TCGA dataset were analyed to identify potential master transcriptional regulators in HGSOC. Immunohistochemistry was performed to evaluate the clinical signiﬁcance of FOXM1 in HGSOC. Invasion, clonogenic assays were conducted to determine to functional role of FOXM1. ChIP-seq and luciferase analyses were utilized to identify FOXM1 direct target genes in HGSOC. Association between mutant p53 and FOXM1 expression was investigated through TCGA data analysis, immunohistochemistry stainingand western blot.  Results: We identified FOXM1 as a potential key transcription factor in ovarian cancer. FOXM1 was markedly increased in HGSOCs and high FOXM1 expression correlated with poor prognosis in HGSOC patients. Mechanistically, FOXM1 regulated CCNF and KIF20A at transcriptional level through binding on their promoters. Consistently, CCNF and KIF20A were elevated in HGSOCs and correlated with poor prognosis. Importantly, mutant p53 contribute to the high expression of FOXM1 in HGSOCs.  Conclusions: These data reveal FOXM1 as a driver oncogenic transcription factor that promotes ovarian cancer malignancy which might be a potential drug target in HGSOC.

overall_design: The assay was performed on three biological triplicates as well as three experimental triplictes of FOXM1 knockdown and control cells.

first: Yingwei

first: Zhaojian

last: Liu

first: Beihua

last: Kong


title: RNA-seq  analysis of angiotensin II-induced myocardial fibrosis in rats treated with and without sodium butyrate

first: Yaowen

last: Wang

state: Chongqing

address: No. 74 Linjiang Road, Yuzhong District

department: Cardiology

institute: the Second Affiliated Hospital of Chongqing Medical University, Chongqing Cardiac Arrhythmias Therapeutic Service Center

summary: Analysis of sodium butyrate（NaBu） on angiotensin II（Ang II-induced cardiac fibrosis at gene expression level. The hypothesis tested in the present study was that NaBu influence the balance of gene expression of Ang II-induce cardiac fibrosis. Results provide important information of the response of NaBu to cardiac fibrosis, such as specific  genes, up- or down-regulated specific cardiac cellular functions.

overall_design: Total RNA obtained from isolated tendon fascicles subjected to 1 or 24 hours in vitro cyclic tensile strain compared to unstrained control fascicles.

first: Yuehui

last: Yin


title: Gene expression profiles of mice dendritic cell infected by Enterovirus 71

city: Tianjin

first: yang

middle: yue

last: jie

address: No. 7 South Sudi Road, Nankai District,

department: Infectious Diseases

institute: Tianjin Second People's Hospital

summary: Investigate the changes of Gene expression profiling in mice infected with Enterovirus 71 dendritic cell in vitro

overall_design: Human Rhabdomyosarcoma cells (RD cells) were used to amplify EV71 virus infection, and the model of EV71 virus infection with DCs was established. The immunophenotypic changes of DCs were detected by Flow cytometry, and the gene expression changes were detected by Agilent gene chip

first: yuejie

last: yang


title: RT² Profiler™ PCR Array Human Senesence

city: Newark

first: Pranela

last: Rameshwar

state: NJ

address: 185 South Orange Avenue

department: Medicine

institute: Rutgers NJ Medical School

summary:
In vivo restoration of aged bone marrow mononuclear cells by micrRNA: effect on cellular senesence
Treatment groups were (1) no microRNA, (2) microRNA-619 (miR-619), (3) a combination of microRNAs-619, -1303, 4497 (miR-combo), or (4) a control microRNA expected to have no effect (control RNA)

overall_design: Female NSG mice were humanized (huNSG) with mobilized bone marrow mononuclear cells from aged donors. Prior to humanization, cells were transfectedw ith specific microRNAs to partially reprogram the hematopoietic cells towards a young phenotype.

first: Steven

last: Greco

first: Seda

last: Ayer

first: Lauren

last: Sherman


title: The pathogenic role of stem cell-like memory T cells in rheumatoid arthritis

city: Seoul

first: Eun Bong

last: Lee

address: 101 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University College of Medicine

summary:
Objective: Stem cell-like memory T cells (Tscm) are a subset of memory T cells that have the characteristics of stem cells. The role of Tscm cells in rheumatoid arthritis (RA) is unknown.
Methods: The transcriptomes of Tscm cells from RA patients were compared with those from HCs.
Results: Transcriptome analysis revealed that Tscm cells from RA patients showed patterns distinct from those of HCs.
Conclusion: The percentage of transcriptionally distinct and potentially pathogenic Tscm cells are higher in RA patients than in HCs; these cells may be a continuous source of pathogenic T cells, which perpetuate RA.

overall_design: mRNA profiles of Tscm cells sorted from PBMCs of healthy controls or severe rheumatoid arthritis patients or rheumatoid arthritis in remission were generated by RNA sequencing.

first: Eun

middle: B

first: Ye


title: RT² Profiler™ PCR Array Human Aging

summary:
in vivo restoration of aged bone marrow mononuclear cells by microRNA: effect on cellular aging
Treatment groups were (1) no microRNA, (2) microRNA-619 (miR-619), (3) a combination of microRNAs-619, -1303, 4497 (miR-combo), or (4) a control microRNA expected to have no effect (control RNA)

overall_design: Female NSG mice were humanized (huNSG) with mobilized bone marrow mononuclear cells from aged donors. Prior to humanization, cells were transfected with specific microRNAs to partially reprogram the hematopoietic cells towards a young phenotype.


title: Transcriptome data of Hyphopichia burtonii when exposed to high osmosterss condtion

first: Dong Wook

address: 84, Heukseok-ro, Dongjak-gu

institute: Chung-Ang university

summary: Hyphopichia burtonii has much stronger osmotolerance than model Saccharomyces cerevisiae and other yeast. The transcriptomic changes by RNA-seq analysis in several hyperosmotic stresses and YPD condition as control were investigated, expecting changes in the expression patterns of genes that do not exist or change in other yeast.

overall_design:
4 conditions were analyzed duplicate: total 8 samples for one yeast species;
The sequencing data of RNAs obtained from yeast cells cultured in YPD + 1M NaCl, KCl, sorbitol at 1 hour were analyzed using YPD conditions as acontrol

first: DongWook

first: Hyunah

last: Kang


title: Transcriptome of pig whole blood microRNAs provides insight into immune system development

city: Chengdu

first: Xuebin

last: Lv

state: SiChuan

address: Niusha Road

institute: Sichuan, Animal Science Academy

summary: Blood is body fluid that contains multiple types of immune cells. Gene expression profiles of blood can reflect physiopathological status of the immune system. This study was to explore the dynamic expression of whole blood microRNAs across different developmental stages, and how such differential expression relates to immune system development.

overall_design: Peripheral blood samples at five different developmental stages (the 0-day newborn pigs, the 30-day weaning pigs, the 60-day childhood pigs, the 180-day and the 360-day pigs with sexual maturity) were utilized to construct 15 microRNA libraries with three biological replicates for each stage.

first: Zhijun

last: Zhong

first: Xingxing

last: Zhu

first: Qianzi

last: Tang

first: Liang

last: Hong

first: Yiren

last: Gu

first: Zhiping

last: He

first: Xuan

last: Tao

first: Xuemei

last: Yang

first: Yan

last: Liang

first: Linyuan

last: Shen

first: Ya

last: Tan

first: Kai

last: Zeng

first: Sancheng

last: Ying

first: Yuekui

first: Yunfeng

last: Lei

first: Jianjun

last: Gong

first: Xiaohui

last: Chen

first: Li


title: Next Generation Sequencing Facilitates Quantitative Analysis of CRC cells with low DUOX2 expression compared with the control group

city: Shijiazhuang

first: Xue

last: Zhang

state: Hebei

address: 12 Jiankang Road

department: Department of Medical Oncology

institute: Hebei Medical University Fourth Affiliated Hospital

summary:
Purpose: The purpose of this study was to analyze changes in the cell genome along with the downregulation of DUOX2, as well as changes in gene enrichment pathways, so as to find the downstream target genes of DUOX2
Conclusions: Our study is the first detailed analysis of DUOX2's effect on the genome of CRC cells.We concluded that changes in DUOX2 gene levels can lead to activation of multiple tumor-related signaling pathways, and that NGS provides a more comprehensive and accurate method for quantitative and qualitative assessment of cell mRNA content.

first: Guiying

last: Wang


title: Characterization of small RNAs in the different developmental stages of carcinogenic parasite-Clonorchis sinensis

city: Xuzhou

first: Chao

last: Yan

state: Jiangsu

address: 209 of Tongshan Road

institute: Xuzhou Medical University

summary: Clonorchiasis is a foodborne zoonotic disease caused by Clonorchis sinensis which belongs to trematodes with a complex lifecycle, there are increasing evidences that small RNAs including microRNAs and PIWI-interacting RNAs can participate in regulation of embryonic development. However, there is little information about the small RNAs in the different developmental stages of C. sinensis. In the present study, we investigated profiles of miRNAs and piRNAs in the different developmental stages including eggs, metacercaria and adults of C. sinensis using high-throughout sequencing technology. We found that 152 miRNAs for adults, 147 miRNAs for metacercariae and 161 miRNAs for eggs were identified, of these miRNAs, 52 miRNAs were universally expressed in these three developmental stage. For piRNAs, we also found that there were a total of 4573 piRNAs in adult worms, 3189 piRNAs in eggs and 3853 piRNAs in metacercariae, respectively, and 1127, 426, 756 piRNAs were absolutely expressed only in adults, eggs and metacercariae, respectively. These stage-specific small RNAs might be involved in various biological process and environmental adaption for parasitism as showed by GO and KEGG pathway analysis. The data of present study may provide a basis for future targeting at these stage-specific small RNAs for prevention and control clonorchisias.

overall_design: In the present study, the profiles of miRNAs and piRNAs in the different developmental stages including eggs, metacercaria and adults of C. sinensis were systemically investigated using high-throughout sequencing technology, and stage-specific miRNAs and piRNAs were identified; their poteintial roles in the embryonic development of C. sinensis were further ananlyzed by GO and KEGG pathway.

first: Ying

last: Du


title: miRNA expression data from neonatal and adult human livers

city: Gainesville

first: Stephan

last: Jahn

state: FL

institute: University of Florida

summary: The liver is a major site of drug metabolism and many of these hepatic enzymes are differentially expressed with age.  Since many of these changes have unknown mechanisms, we wanted to idenfity miRNAs that may be controlling the expression of these proteins.

overall_design: We obtained liver samples from 10 young (<1 year) and adult (>32 years) adult donors.  Total RNA was extracted and analyzed using the GeneChip miRNA 4.0 array.  We sought to identify miRNAs that were differentially regulated with age.

middle: C

first: Margaret

middle: O

last: James


title: Aged, Young and Restored Samples from Mobilized Peripheral Blood [mRNA]

first: Pranela

last: Rameshwar

summary: We report the gene expression changes in mobilized peripheral blood in aged, young, and aged/young samples cocultured in transwell. Restored samples refer to aged MPB co-cultured with young MPB in the transwell culture

overall_design: RNA sequencing on aged, young, and restored samples to find differentially expressed genes

first: Seda

last: Ghazaryan

first: Markos

middle: H

last: El-Far

first: Lauren

middle: S

last: Sherman


title: Aged, Young and Restored Samples from Mobilized Peripheral Blood [miRNA]

summary: We report the miRNA expression in each CD34+ cells and their exosomes in mobilized peripheral blood in aged, young, and aged/young samples cocultured in transwell.  Restored samples refer to aged MPB co-cultured with young MPB in the transwell culture.

overall_design: miRNA sequencing on each cells and exosomes from aged, young, and restored samples to find differentially expressed miRNAs

first: Steven

last: Greco


title: TBC1D3 Associates with the Histone Lysine N-methyltransferase G9a to Affect the Promotion of Neural Progenitors and Cortical Expansion in an Epigenetic Way [RNA-Seq]

city: shanghai

first: qiongqiong

last: hou

address: huanke road 199

institute: shanghaitech university

summary: we conducted RNA sequencing using human cerebral organoids treated with TAT peptides

overall_design: Human cerebral organoids were treated with TAT peptides for two groups, that is, TAT-Scrambled (Short for TAT-Scr) with the sequence of YGRKKRRQRRR-FRVRYWFQGCHSEDPWR and TAT-465-481, a special peoptide designed for inhibition of TBC1D3, with the sequence of YGRKKRRQRRR-EGPWFRHYDFRQSCWVR. After 4 days incubation, human cerebral organoid tissues were extracted at cultured day 16 and bulk RNA from TAT-Scr group or TAT-465-481 group was extracted to be sequenced.

first: Qiongqiong

last: Hou

first: Zhen-Ge

last: Luo


title: Aged, Young and Restored Samples from Mobilized Peripheral Blood

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

overall_design: Refer to individual Series


title: miRNA-9 regulates axon regeneration through the transcriptional regulator REST and the epigenetic factor UHRF1 [miRNA array]

city: Saint Louis

first: Valeria

last: Cavalli

state: Missouri

address: 660 S. Euclid Ave.

department: Anatomy and Neurobiology

institute: Washington University in St. Louis

summary: Injured sensory neurons successfully activate a pro-regenerative transcriptional program to enable axon regeneration and functional recovery, but the roles of genes that are inactivated after injury remain poorly understood. Analysis of the miRNA expression profile triggered by axon injury revealed down-regulation of the neural development associated miRNA, miR-9. A target of miR-9 is the critical epigenetic regulator involved in DNA methylation, ubiquitin-like containing PHD ring finger 1 (UHRF1), which increased after injury to promote axon regeneration. UHRF1 is known to repress the transcription of tumor suppressor genes through DNA methylation and we show that UHRF1 interacts with DNMT1 to methylate the promoter region of the tumor suppressors PTEN and CDKN1A, thereby triggering their inactivation. We also reveal that UHRF1 represses the transcriptional regulator REST. Our findings define an epigenetic mechanism that silences the transcription of axon growth suppressors to promote axon regeneration in sensory neurons.

overall_design: miRNA expression profiling of spot cultures collected at Day in Vitro (DIV) 7, axotomized spot cultures at DIV7 collected at 1 hour, 3 hour, or 8 hours post injury.

first: Young

last: Oh

first: Marcus

last: Mahar

first: Doug

last: Larson

first: Eric

middle: E

last: Ewan


title: Transcriptome sequencing of thalidomide treated limb bud of chick embryo

city: Cochin

first: Ravi

last: Gupta

state: Kerala

address: Plot no: 43A,SDF, 3rd floor, A Block,CSEZ, Kakkanad

department: Bioinformatics

country: India

institute: SciGenom Labs Pvt. Ltd.

summary:
Purpose: The aim of this study was to compare the differentially expressed genes under thalidomide treatment in limb buds.
Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 81 database. Alignment was performed using STAR (version 2.4.2a ). Expression estimation carried out using cufflinks program (version 2.2.1).Differential expression analysis carried using the cuffdiff program in cufflinks(version 2.2.1). Heat maps were generated for gene expression analysis using R statistical software.

overall_design: The mRNA profiles of thalidomide and vehicle control  treated  limb buds isolated from HH22 stage chick embryo  were generated by deep sequencing, using Illumina HiSeq 2500 platform.

first: Pavitra

last: kumar

first: Suvro

last: Chatterjee


first: Yong

last: Zhao

address: 700 Changcheng Road

institute: Qingdao Agricultural University

summary: Single-cell RNA-seq (10x) of the goat ovarian granulosa cells samples from high fertility group (>three babys per birth) and low fertility group (< two babys per birth). The goal of this project is to explore the role of ovarian granulosa cells on the fertility of goat at single cell level. We would like to investigate the role of ovarian granulosa cells on the ovulation rate which indicates fertility. Therefore the ovarian granulosa cells from different population (hihg or low fertility groups animals) were analyzed.

overall_design: We totally analyzed ~12,000 single cell transcriptome profile from goat ovarian granulosa cells from the two groups.

first: Zengkuan

last: Li

first: Lingjiang

last: Min


title: Loss of PD-1 aggravates plaque pathology by disrupting microglial phagocytosis in APP/PS1 mice

city: Bonn

first: Joachim

last: Schultze

state: NRW

address: Carl-Troll-Strasse 31

department: Genomics and Immunoregulation

country: Germany

institute: LIMES (Life and Medical Sciences Center Genomics and Immunoregulation)

summary: Astrocytic secretion of soluble B7-H1 and subsequent engagement with microglial PD-1 regulates microglial clearance of Ab by modulating the expression of CD36.

overall_design: Wild type and PD-1 KO mice brains at 0, 2, and 8 hours. Some treated with Amyloid-beta and some without.

middle: L

first: Kathrin

last: Klee

first: Marc

last: Beyer


title: TBC1D3 Associates with the Histone Lysine N-methyltransferase G9a to Affect the Promotion of Neural Progenitors and Cortical Expansion in an Epigenetic Way [ChIP-Seq]

first: qiongqiong

last: hou

summary: we conducted chromotin Immunoprecipitation sequencing (ChIP-seq) using mouse cortical tissues from TBC1D3-transgenic mice and wild-typed mice

overall_design: Mouse cortical tissues were extracted at about embryonic day 15.5 and DNA from ChIP samples was purified to be sequenced


title: ROS control in human iPS cells reveals early events in spontaneous carcinogenesis

city: Fukuoka

first: Sugako

last: Oka

address: 2-15-1, Tamura, Sawara-ku

country: Japan

institute: Fukoka Dental College

summary: We developed a system to control the intracellular level of reactive oxygen species (ROS) in human iPS cells. By introducing a specific substitution (I69E) into the SDHC protein, a component of the mitochondrial respiratory chain complex, the intracellular ROS level considerably increased. This caused an abnormal development of iPS cells, and these abnormalities were reverted by the overproduction of mitochondria-targeted catalase. When ROS-overproducing iPS cells (ChiPSC12-M cells) were used for subcutaneous inoculation on the backs of nude mice, the mice exhibited tumor formation. The expression of tumor-related FOXC1 transcription factor increased as early as 4 h after the the development of ROS-overproducing iPS cells was initiated. An RNA-seq analysis revealed that 27 transcript clusters among the more than 20,000 transcrips that were examined were highly expressed at 4 h after the initiation of tumor development in ChiPSC12-M cells. Some of these overexpressed transcripts might make networks to activate protooncogenes for spontaneous carcinogenesis.

overall_design: ChiPSC12-M was cultured with Day 0 endoderm differentiation medium and the medium was replaced with Day 1 differentiation medium with or without Tet-Express solution and the cells were cultured for 4 h. Total RNA from each cell was isolated using Isogen (Nippon Gene Co., Ltd, Toyama, Japan) and was subjected to RNA-Sequencing (Cell Innovator, Kyushu Univ., Fukuoka, Japan).

first: Michio

last: Hayashi

first: Kenichi

last: Taguchi

first: Teruhisa

last: Tsuzuki

first: Mutsuo

last: Sekiguchi


title: TBC1D3 Associates with the Histone Lysine N-methyltransferase G9a to Affect the Promotion of Neural Progenitors and Cortical Expansion in an Epigenetic Way

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Effect of Nitric oxide on heart development and its transcriptome analysis.

summary: Scope: To understand the effect of nitric oxide on cardiogenesis in reference to first heart beat.

overall_design: Methods: The trancriptome sequencing was performed using Illumina HiSeq 2500 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 81 database using STAR (version 2.4.2a ). Expression estimation carried out using cufflinks program (version 2.2.1).Differential expression analysis carried using the cuffdiff program in cufflinks(version 2.2.1). Heat maps were generated for gene expression analysis using R statistical software.

last: Kumar


title: Reduced representation bisulphite sequencing of two chickpea genotypes to identify differential DNA methylation patterns associated with drought tolerance and sensitivity

city: Melbourne

first: Nitin

last: Mantri

state: Victoria

address: 264 Plenty Rd, Bundoora VIC 3083

department: Biosciences and Food Technology

country: Australia

institute: RMIT University

summary: In this study, to obtain a clear picture of drought mechanism involved in two distinctive chickpea genotype, the aim was to identify the DNA methylation patterns which potentially regulate drought tolerance/sensitivity of these selected genotypes.  The leaf tissues from the shoot apical meristem from drought sensitive and drought tolerant genotypes were used for RRBS (Reduced representation bisulphite sequencing) under drought stress. The sequencing data was analysed using Bismark and methylkit to recall the methylation levels in control and samples for both genotypes and identify differentially methylated regions.

overall_design: In our present study, RRBS sequencing was employed to identify drought-responsive differentiaton in differential methylation in chickpea leaf tissue of two genotypes ICC8261 and ICC283 to identify Differentially methylated regions related to biological, cellular and molecular pathways related to drought tolerance under drought stress. The significant methylation level difference observed between the two genotypes in shoot apical meristem leaves indicates how drought stresses affect the different mechanisms in both genotypes. In this study the emphasis was on how the regulation of epignetic modification such as DNA methylation were influenced by drought stress in the two genotypes as well as role of methylation in different context CpG,CHH,CHG.

first: Sapna

last: Badhan


title: Down-regulation of atherosclerosis signaling in patients treated with on-line haemodiafiltration may contribute to lower cardiovascular risk in hemodialysis

city: Bari

first: Paola

last: Pontrelli

address: Piazza G.Cesare 11

department: Dept. of Precision and Regenerative Medicine and Ionian Area (DIMEPRE-J)

country: Italy

institute: University of Bari

summary: Recent studies suggest that on-line hemodiafiltration (OL-HDF) may reduce the progression of dialysis-related cardiovascular diseases, but the molecular mechanisms underlying this effect are unclear. The aim of our study was to identify, through a high-throughput approach, differences in gene expression profiles in peripheral blood mononuclear cells (PBMCs) associated with OL-HDF and bicarbonate dialysis (BHD).  The transcriptomic profile was investigated in PBMCs isolated from 8 patients on OL-HDF and 8 patients on BHD by microarray analysis. The results were evaluated by statistical and functional pathway analysis and validated by qPCR in an independent cohort of patients (OL-HDF N=20, BHD n=20, testing group).   Eight-hundred and sixty-eight genes were differentially expressed in the comparison between OL-HDF and BHD. Thirty-seven functional gene networks were identified and atherosclerosis signaling was the top canonical pathway regulated by OL-HDF. Among the genes modulated by OL-HDF in this pathway there were PDGF A chain (FC=-2.13), Clusterin (FC=-2.14), Monoamine Oxidase A (MAO-A, FC=-2.43), IL-6 (FC=-1.56), VEGF C (FC=-1.83) and Apolipoprotein E (Apo-E) (FC=+1.69). qPCR, performed in the testing-group, confirmed the microarray data. In the same set of patients PDGF AA, IL-6 and VEGF C serum levels were significantly lower in the OL-HDF group. Finally, 10 BHD patients were switched to OL-HDF and PBMC were harvested after 6 months. The qPCR results from this perspective group further confirmed the modulation of atherosclerotic genes observed in the cross-sectional analysis.   In conclusion, OL-HDF might contribute to cardiovascular risk reduction through the modulation of specific proteins involved in atherosclerotic disease

overall_design: We performed microarray experiments in PBMCs isolated from 8 patients on OL-HDF  and 8 patients on BHD. BHD subjects were treated three times per week with 240-min ultrapure bicarbonate based dialysate, using a synthetic high-flux membrane. OL-HDF was performed using a blood flow rate of >300 mL/min and a dialysate flow rate of 500 mL/min and synthetic high-flux dialysers, plus the on-line production of ultrapure bicarbonate-buffered substitution volume in post-dilution mode with a target convective volume of ≥22 L. Eight patients/treatment group were randomly selected and assigned to the microarray analysis group.

first: Simona

last: Simone

first: Annarita

last: Chieti

first: Federica

last: Rascio

first: Giuseppe

last: Castellano

first: Roberto

last: Corciulo

first: Giovanni

last: Stallone

first: Barbara

last: Infante

first: Loreto

last: Gesualdo

last: Grandaliano

first: Giovambattista

last: Pertosa


title: RNA sequencing of Frischella perrara

status: Public on Nov 30 2021

city: Lausanne

first: Philipp

last: Engel

address: Biophore Building

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

summary: RNA sequencing of Frischella perrara PEB0191 during in vitro growth and gut colonization

overall_design: In vitro experiment: RNA sequencing of Frischella perrara PEB0191 wild type and ihfA* mutant after 16h of growth on modified TYG agar. In vivo experiment: RNA sequencing of Frischella perrara PEB0191 during gut colonization. Sampling after 5 days and 10 days post-inoculation. RNA sequencing of Frischella perrara PEB0191 after 16h of growth on modified TYG agar was used as reference condition.

first: Konstantin

last: Schmidt


title: The role of ZNF32 in modulating transcriptoion of MCF-7

first: Ping

last: Lin

address: No.1, Keyuan 4th Road, Chengdu

institute: Sichuan University

summary: Zinc finger protein 32 (ZNF32), is regarded as a transcription factor that regulates gene transcription. But the function of ZNF32 in breast cancer metastasis remains unknown. Here,  the MCF-7 was transfected with the pENTER-ZNF32 or empty vector to search the target genes with ChIP-seq.

overall_design: The MCF-7 was transfected with the pENTER-ZNF32 or empty vector to search the target genes with ChIP-seq.

first: Di

last: Gong


title: Quantitative Analysis of differentially expressed genes between HH10-HH13 stages of chick embryo

first: Ravi

last: Gupta

summary:
Purpose: The aim of this study is to analyse and compare the differentially expressed genes between the developmental stages and to construct heat maps with the data generated.
Methods: The trancriptome sequencing was performed using Illumina HiSeq 2000 ® platform. The sequence reads were aligned to the reference genome of chicken (Galgal4) downloaded from Ensembl Release 75 database. Alignment was performed using TopHat (v2.0.8) program to the Ensembl Release 75 gene model of chicken with default parameter settings. After alignment, Cuffdiff (v2.2.0) program was used for performing differential expression analysis. Pathway analysis of differentially expressed genes was performed using DAVID program.
Results: Comparison of HH11 vs HH10 showed that gas transport, vascular and blood vessel development, extracellular matrix organization and tube morphogenesis biological processes (BPs) are differentially expressed. Among these, the up-regulated genes are related to extracellular matrix whereas gas transport, vascular and blood vessel development and others are related to down-regulated. Comparison of HH12 vs HH11 revealed that gas transport, iron ion transport and PPAR signaling pathway are enriched for differentially expressed genes. Only up-regulated genes show enrichment of these processes and pathway. It is interesting to note that while gas transport group genes are down-regulated from HH10 stage to HH11 stage, this group of genes are up-regulated while moving from HH11 to HH12. Comparison of HH13 vs HH12 indicated a large number of differentially expressed biological processes and pathways including blood vessel development, vasculature development, cell adhesion, heart development and morphogenesis, extracellular matrix organization, morphogenesis of a branching structure, PPAR signaling pathway, vascular smooth muscle contraction. Overall, we observe a large number of changes occurring between HH12 and HH13 stage.
Conclusions: Our study represents the first detailed analysis of differential expression of genes within a stipulated period of time (30-45 hours of egg incubation). Switching on and off of genes happenieng during early vasculogensis is clearly generated by RNA-sequencing. The data analysis reported here will serve as a reference for future investigations on the expression of genes in various other stages . Our results from NGS were in accordance with our experimental data, strongly validating the expression profile. We conclude that genome wide RNA-seq explored the differential expression of genes and pathway interlinked between the stages which permitted us to understand the early vasculogenesis process.

overall_design: Analyzing the mRNA profiles of HH10-13 stages of chick embryo were generated by deep sequencing, using Illumina HiSeq 2000 platform.

first: Saranya

last: Rajendran

first: Suvro

last: Chatterjee


title: miRNA-9 regulates axon regeneration through the transcriptional regulator REST and the epigenetic factor UHRF1 [RNA-seq]

first: Valeria

last: Cavalli

overall_design: Examining transcriptional changes after knockdown of UHRF1 in uninjured neurons

first: Young

last: Oh

first: Marcus

last: Mahar

first: Douglas

last: Larson

first: Eric

last: Ewan


title: Mitochondrial Plasticity Promotes Resistance to Sorafenib and Vulnerability to STAT3 Inhibition in Human Hepatocellular Carcinoma

city: Bellinzona

first: Giada

last: Sandrini

address: Via Chiesa 5

institute: IOR

summary: Enhanced expression of mitochondrial ribosomal proteins and marked reprogramming of the mitochondrial network are associated with sorafenib resistance in human cell lines and hepatocarcinoma patients, providing novel actionable targets for increasing therapeutic efficacy.

overall_design: Comparison between  2 conditions (3 replicates for each condition)

first: Carlo

middle: V

last: Catapano


title: Transcriptomic and Epigenomic Profiles of CIC-knockout and IDH1 mutant cells

city: Vancouver

first: Marco

middle: A

last: Marra

state: BC

address: 675 W 10th Ave, 7th Floor

country: Canada

institute: Canada's Michael Smith Genome Sciences Centre


title: RNAseq for cultured Control and TgAPPsweOCN BMSCs (sorted Ai9+ Osteoblast-linage cells)

city: cleveland

first: Wen-Cheng

last: Xiong

state: OH

address: 2210 circle drive, robbins building E765

institute: Case western reserve university

summary:
Purpose: To investigate if and how APPswe in OCN-Cre+ OB-lineage cells gives rise to the brain and behavior phenotypes, we purified OCN-Cre+ BMSCs (marked by tdTomato+, believed to be OB progenitors) from both the 6-MO control (OCN-Cre; Ai9) and TgAPPsweOCN; Ai9 mice using fluorescence-activated cell sorting (FACS) and then subjected them to RNA-seq analysis
Methods:  (1)the whole bone marrow cells of  6-month-old OCn-Cre;Ai9 andTgAPPswe;OCn-Cre;Ai9  flushed out from long bones of mice with DMEM were filtered through a 70-mm filter mesh, washed, re-suspended, and then plated in 100-mm dishes with growth medium (DMEM plus 10% FBS), which were incubated at 37oC with 5% CO2. The non-adherent cells were removed 72 hours after changing the medium. The attached bone marrow cells were cultured with the growth medium for 7 days. These cells were then resuspended and plated at culture dishes and cultured for another 3-6 days with the same growth medium. These cells, so called BMSCs. (2)Then cell media were removed from culture dishes and cells were rinsed with PBS. Trypsin solution was added to incubate at 37°C for 2 min. The detached adherent cells were centrifuged, and the pellet cells were washed with 1 ml cold PBS, and finally resuspended in 0.5 ml PBS with 1% FBS for flow cytometry analysis.  Flow cytometric analysis was performed by use of a flow cytometer in CWRU core facility. Acquisition and analysis were performed by using FACSDiva 8.0.1 software (BD).(3)Total RNAs were extracted from purified Td+ OB-progenitor cells from OCN-Cre; Ai9 and TgAPPsweOCN; Ai9 mice by flow cytometer.  RNA Integrity Number (RIN) was accessed for every sample, and the samples were considered qualified with RIN> 2. These RNA samples were then subjected to RNA-seq analyses by BGI America (Cambridge, MA) using the DNBseq platform.  Firstly, we removed the reads mapped to rRNA and obtained the raw data with 52.47 Mb reads. After filtering low-quality, adaptor-polluted and high content of unknown base reads in the sequencing reads, 51.9 Mb clean reads were obtained per sample on average. Then clean reads were mapped to reference genome using HISAT2. On average 92.91% reads were mapped and the uniformity of the mapping result for each sample suggests that the samples were comparable. Comparisons to RNAseq were normalized to fpkm
Results: 917 up- and 1825 down-regulated genes were identified in APPswe+ OB progenitors. Among these genes, 154 up- and 269 down-regulated genes encode secreted proteins. Interestingly, go analysis showed that most up-regulated genes are involved in inflammatory response, cytokine production, and cytokine/chemokine-mediated signaling pathways; and most down-regulated genes are implicated in cell cycle, cell proliferation, and bone mineralization.
Conclusions: Increased cytokines and chemokines in APPswe+ OB-progenitors, indicating that APPswe+ OB progenitors may undergo cellular senescence.

overall_design: cultured BMSCs mRNA profiles of 6-month-old OCn-Cre;Ai9 andTgAPPswe;OCn-Cre;Ai9 mice

first: Jin-Xiu

last: Pan

first: Dong

last: Sun

first: Daehoon

last: Lee

first: Lei

first: Xiao

last: Ren

first: Hao-han

last: Guo

first: Ling-Ling

last: Yao

first: Yuyi

last: Lu

first: Caroline

last: Jung


title: Gut microbiota interplay with COVID-19 reveals links to host lipid metabolism among Middle Eastern populations

city: Abu Dhabi

first: Habiba

last: Alsafar

address: Al Saada St. Muroor Road

department: Center of Biotechnology

country: United Arab Emirates

institute: Khalifa University

summary: We discovered an enrichment of linoleic acid, ether lipid, glycerolipid, and glycerophospholipid metabolism among the SARS-CoV-2 infected group, suggesting a link to SARS-CoV-2 entry and replication in host cells.The identified differences provide a new insight to enrich our understanding of SARS-CoV-2-related changes in gut microbiota, their metabolic capabilities, and potential screening biomarkers linked to COVID-19 disease severity.

overall_design: This case-control study involved 86 participants with previously confirmed COVID-19 infection and 57 healthy participants as controls. This study performed 16S rRNA gene-based microbial profiling of 143 subjects. However, after assessing the sample quality, only 128 samples passed quality control and were adequate to assess the gut microbiota diversity and composition. Of those, 78 participants had a previously confirmed COVID-19 infection and 50 healthy participants as controls.

first: Mohammad

middle: T

last: Al Bataineh

first: Andreas

last: Henschel

first: Mira

last: Mousa

first: Marianne

last: Daou

first: Fathimathuz

last: Waasia

first: Hussein

last: Kannout

first: Mariam

last: Khalili

first: Mohd

last: Kayasseh

first: Abdulmajeed

last: Alkhajeh

first: Maimunah

last: Uddin

first: Nawal

last: Alkaabi

first: Guan

last: Tay

first: Samuel

middle: F

last: Feng

first: Ahmed

last: Yousef


title: Epigenetic analysis of the low- and high-grade tumor component in a biphasic SMARCB1/INI1-deficient brain tumor (CNS LGDIT-INI1/ ATRT-MYC).

city: Hamburg

first: Julia

middle: Elisabeth

last: Neumann

address: Martinistrasse 52

department: ZMNH

institute: University Hospital Hamburg Eppendorf

type: Methylation profiling by genome tiling array

summary: The newly proposed entity CNS LGDIT-INI1 represents a low-grade tumor composed of inconspicuous SMARCB1-deficient tumor cells diffusely infiltrating the brain. Progression of CNS LGDIT-INI1 to ATRT(-MYC) has been reported. We published the first case report on a child harboring CNS LGDIT-INI1, which also featured a high-grade ATRT component. Moreover, we present the results of extensive spatial molecular profiling of this tumor.

overall_design: We subjected both the low- and the high-grade tumor areas to global DNA methylation analysis (850K).

first: Matthias

last: Dottermusch

first: Yannis

last: Schumann

first: Uwe

last: Kordes

first: Martin

last: Hasselblatt


title: Transcriptome analysis reveals key genes and pathways that the ligand insB:9-23 acts on pancreatic islets

city: Jinan

first: Jin-Peng

last: Sun

address: 44 Wenhua Xi Rd

institute: Shandong University

summary: Our research is helpful to understand the physiological and pathological level changes caused by the ligand insB acting on the receptor Olfr109 on the islets, to find the mechanism of the signaling pathway downstream of Olfr109 under the action of the ligand, and to determine which signaling pathway is mediated by Olfr109

overall_design: In this study, we isolated pancreatic islets from wild mice that were treated with control vehicle or the ligand insB:9-23 stimulation. The control group and the ligand stimulation group (3 samples each) were subjected to RNA sequencing.

first: J

middle: P

last: Cheng


title: Single-cell transcriptional analysis of lens placode development in Mab21l1 knockout mice

city: Bunkyo

first: Ryuichi

last: Yamada

state: Tokyo

address: Yayoi 1-1-1

department: Veterinary Anatomy

institute: The Univerisity of Tokyo

summary: In mouse early organogenic stages, a Mab21l1-null mutation causes severe defects in invagination of the lens placode toward optic cup due to its severe defects in both cell proliferation and survival, which subsequently results in severe microphthalmia after birth. In human, loss of function variants in MAB21L1 have recently been described in Cerebello-Oculo-Facio-Genital syndrome (COFG syndrome). The close similarity between mouse and human phenotypes including microphthalmia indicates the importance of Mab21l1 function in human lens placode. To approach the molecular function of MAB21L1 in eye morphogenesis, we examined single cell transcriptomes in lens placode and its surrounding surface ectoderm at 26 somite stage (E9.25), just prior to the onset of lens defects in Mab21l1-null embryos. Here we demonstrate the identification of several key genes immediately downstream of Mab21l1 function, together with the early lens placode-/surface ectoderm-specific single cell transcriptomes during murine lens placode specification.

overall_design: Ocular area scRNA-seq profiles of 26 somite stages wild type (WT) and Mab21l1-null (KO) mice were generated using a 10× Chromium system.

first: Katsunori

last: Fujiki

first: Hirotaka

last: Takezoe


title: Gene repression by DNA methylation promotes axon regeneration

first: Valeria

last: Cavalli

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

platform_organism:
Mus musculus
synthetic construct

overall_design: Refer to individual Series


title: Mapping cis-regulatory elements in the midgestation mouse placenta

city: Ames

first: Geetu

last: Tuteja

state: IA

address: 2106 Molecular Biology Building

department: Genetics, Development and Cell Biology

institute: Iowa State University

summary: We generated and analyzed ChIP-seq data for H3k4me3, H3k4me1, and H3k27me3. We annotated active and poised promoters and enhancers, as well as regions associated with repressed gene expression and found that poised promoters were associated with neuronal development genes, while active promoters were largely associated with housekeeping genes. Active and poised enhancers were associated with placental development genes, though only active enhancers were associated with genes that have placenta-specific expression.

overall_design: Examine histone modifications of the midgestation mouse placenta

first: Rebekah

middle: R

last: Starks

first: Haninder

last: Kaur


title: Alternative splicing of NF-YA promotes prostate cancer aggressiveness and represents a new molecular marker for clinical stratification of patients

city: Modena

first: Carol

last: Imbriano

address: Via Campi 213/D

department: Life Sciences

institute: University of Modena and Reggio Emilia

summary: Background: Approaches based on expression signatures of prostate cancer (PCa) have been proposed to predict patients’ outcomes and response to treatments. The transcription factor NF-Y participates to the progression from benign epithelium to both localized and metastatic PCa and is associated with aggressive transcriptional profile. The gene encoding for NF-YA, the DNA-binding subunit of NF-Y, produces two alternatively spliced transcripts, NF-YAs and NF-YAl. Bioinformatic analyses pointed at NF-YA splicing as a key transcriptional signature to discriminate between different tumor molecular subtypes. In this study, we aimed to determine the pathophysiological role of NF-YA splice variants in PCa and their association with aggressive PCa subtypes. Methods: Data on the expression of NF-YA isoforms were extracted from the TCGA (The Cancer Genome Atlas) database of tumor prostate tissues and validated in prostate cell lines. Through lentiviral transduction and CRISPR-Cas9 technology, we modulated the expression of NF-YA splice variants in prostate cancer cells. We investigated cellular and molecular effects on cancer programs through 2D/3D in vitro assays and RNA-seq profilings. The rank-rank hypergeometric overlap approach (RRHO) was used to identify concordant/discordant overlap between gene expression signatures of NF-YAs/NF-YAl cells and human PCa patients. We performed in vivo studies in SHO-SCID mice to determine pathological and molecular phenotypes of NF-YAs/NF-YAl xenograft tumors. Results: NF-YA depletion affects the tumorigenic potential of prostate cancer cells in vitro and in vivo. Elevated NF-YAs levels are associated to aggressive prostate cancer specimens, defined by Gleason Score and TNM classification. NF-YAl overexpression in prostate cancer cells increases cell motility, while NF-YAs enhances both cell proliferation and invasive properties in 3D cultured spheroids and xenograft tumors. NF-YAs-transcriptome of multi-cellular spheroids has an extensive overlap with both localized and metastatic human PCa signatures. The ratio between NF-YAs and NF-YAl transcripts is higher in LumB PAM50 subtype, characterized by poor prognosis, and stratification of patients based on NF-YAs expression is predictive of clinical outcome. Conclusions: Altogether, our results indicate that the modulation of NF-YA isoforms affects prostate pathophysiological processes and contributes to cancer-relevant phenotype, in vitro and in vivo. Evaluation of NF-YA splicing may represent a new molecular strategy for risk assessment of PCa patients.

overall_design: RNA-seq of PC-3 cell line over-expressing NF-YA alternative isoforms.

first: Silvia

last: Belluti


title: Nicotinamide promotes human pluripotent stem cells differentiation into cardiomyocytes

city: Macau

first: Ren

last: Zhili

address: Avenida da Universidade

institute: University of Macau


title: Pathogenic mechanisms implied by plasma exosomal miRNA profile of preeclampsia with severe features

city: Wuhan

first: zhi

middle: rui

last: chen

state: Hubei

address: jianshe street

institute: Huazhong University of Science and Technology

summary: Preeclampsia is a common complication of pregnancy that affects 4-5% of pregnant women around the world. At present,  there is a lack of early identification of high-risk patients of preeclampsia in clinical practice, which restricts the development of disease prevention and treatment. Previous studies have indicated that plasma exosomal miRNAs in pregnant women could serve as biomarkers of preeclampsia, but few is focused on exosomal miRNAs from preeclampsia pregnancy with severe features(sPE). Therefore, we detected and compared the plasma exosomal miRNA profiles between normal pregancy and sPE to explore potential biomarkers and pathogenic mechanisms of sPE.

overall_design: Blood samples were collected from pregnant women in control group (normotensive pregnant women, n=3) and sPE group (patients with sPE, n=3). After exosome isolation and RNA extraction, exosomal miRNAs were profiled using next generation seqeuencing.

first: Luo

last: Qingqing

first: Chen

last: Zhirui

first: Zhang

last: Wen


title: SMAD4 is dispensable for execution of epithelial-mesenchymal transition downstream of SNAIL1 in colorectal cancer cells

status: Public on Nov 29 2021

city: Freiburg

first: Antoine

last: Devisme

address: Breisacherstr. 153

institute: Institute of Medical Bioinformatics and Systems Medicine

summary:
Transforming growth factor beta (TGFβ) superfamily signaling is a prime inducer of epithelial-mesenchymal transitions (EMT) that foster cancer cell invasion and metastasis, a major cause of cancer-related deaths. Yet, TGFβ signaling is frequently inactivated in human tumor entities including colorectal cancer (CRC) and pancreatic  adenocarcinoma (PAAD) with a high proportion of mutations incapacitating SMAD4, which codes for a transcription factor (TF) central to canonical TGFβ and bone morphogenetic protein (BMP) signaling. Beyond its role in initiating EMT, SMAD4 was reported to crucially contribute to subsequent gene regulatory events during EMT execution. It is therefore widely assumed that SMAD4-mutant (SMAD4mut) cancer cells are unable to undergo EMT. Here, we scrutinized this notion and probed for potential SMAD4-independent EMT execution using SMAD4mut CRC cell lines. We show that SMAD4mut cells exhibit morphological changes, become invasive, and regulate EMT marker genes upon induction of the EMT-TF SNAIL1. Furthermore, SNAIL1-induced EMT in SMAD4mut cells was found to be entirely independent of TGFβ/BMP receptor activity. Global assessment of the SNAIL1‑dependent transcriptome confirmed the manifestation of an EMT gene regulatory program in SMAD4mut cells highly related to established EMT signatures. Finally, analyses of human tumor transcriptomes showed that SMAD4 mutations are not underrepresented in mesenchymal tumor samples and that expression patterns of EMT‑associated genes are similar in SMAD4mut and SMAD4 wild-type cases. Altogether, our findings reveal considerable plasticity of gene regulatory networks operating in EMT execution and establish that EMT is not categorically precluded in SMAD4mut tumors, which is relevant for their diagnostic and therapeutic evaluation.
To identify genes regulated during EMT execution in HT29 cells, two clonal HT29 cell populations (4F5 and 3C2) overexpressing Snail1-HA in a doxycycline (Dox)-inducible manner, as well as control cells were treated with Dox for different periods of time.

overall_design: 24 samples of total RNA from HT29-Snail1-HA clones 4F5 and 3C2, as well as HT29-ctrl cells, treated with Dox for four different periods of time (0 h, 24 h, 72 h, 144 h) in two biological replicates.

first: Patrick

last: Frey

first: Monika

last: Schrempp

first: Geoffroy

last: Andrieux

first: Melanie

last: Boerries

first: Andreas

last: Hecht


title: ENVIRONMENTAL STRESSORS IMPACT PLACENTATION THROUGH ACTIONS ON TROPHOBLAST, IMMUNE , AND ENDOTHELIAL CELL DYNAMICS [scRNA-Seq]

city: Kansas City

first: Khursheed

last: Iqbal

state: Kansas

address: 3901 Rainbow Blvd

department: Pathology

institute: University of Kansas Medical Center

summary: Our environment is replete with chemicals that can affect embryonic and extraembryonic development. Dioxins, such as 2,3,7,8-tetrachlorodibenzodioxin (TCDD), are compounds affecting development through the aryl hydrocarbon receptor (AHR). TCDD exposures can lead to placental adaptations and at higher doses pregnancy termination. Deep intrauterine endovascular trophoblast cell invasion was a prominent placentation site adaptation to TCDD. TCDD-mediated placental adaptations were dependent upon maternal AHR signaling but not placental or fetal AHR nor the presence of a prominent AHR target, cytochrome P450 1A1 (CYP1A1). At the placentation site, TCDD stimulated CYP1A1 transcription within endothelial cells but not trophoblast cells. Immune and trophoblast cell behaviors at the uterine-placental interface were guided by the actions of TCDD on endothelial cells. In summary, we have identified an AHR regulatory pathway activated by environmental stressors affecting uterine and trophoblast cell dynamics and the formation of the hemochorial placenta.

overall_design: Pregnant rats treated with TCDD and Oil at gestational day (gd) 6.5 and uterine-placental interface tissue was collected at gd 13.5.

first: Michael

middle: J

last: Soares


title: ENVIRONMENTAL STRESSORS IMPACT PLACENTATION THROUGH ACTIONS ON TROPHOBLAST, IMMUNE , AND ENDOTHELIAL CELL DYNAMICS


title: Effects of fetal sex on maternal immune activation (MIA)-induced transcriptional responses at the placenta

city: Charlottesville

first: David

middle: Michael

last: Johanson

state: VA

address: 200 Jeanette Lancaster Way

department: Department of Neuroscience

institute: UVa School of Medicine

summary: Pregnant dams at embryonic day 11.5 and 12.5 were injected i.p. with saline or polyI:C to induce activation of the maternal immune response. Placentas from each embryo were harvested at several time points relative to the E12.5 injection over the course of gestation to evaluate the placental transcriptome after MIA.

overall_design:
NextGen RNA sequencing of total RNA isolated from bulk placental tissue homogenate by phenol/chloroform extraction. Sequencing performed at UVa Genome Analysis & Technology Core,
Office of Research Core Administration.
University of Virginia Health System,
P.O. Box 800741,
Charlottesville, VA 22908-0741

first: Elizabeth

last: Frost

first: John

last: Lukens

middle: M

first: Morgan

last: Wall


title: cLoops2: a full-stack comprehensive analytical tool for chromatin interactions

city: Bethesda

first: Yaqiang

last: Cao

state: Maryland

address: 9000 Rockville Pike

department: System Biology Center

institute: NHLBI

summary: Investigating chromatin interactions between regulatory regions such as enhancer and promoter elements is pivotal for a deeper understanding of gene expression regulation.  The emerging 3D mapping technologies focusing on enriched signals such as Hi-TrAC/Trac-looping and HiChIP, compared to Hi-C, reduce the sequencing cost, and provide higher interaction resolution for cis-regulatory elements and more comprehensive information such as chromatin accessibility. A robust pipeline is needed for the comprehensive interpretation of these data, especially for loop-centric analysis. Therefore, we have developed a new versatile tool named cLoops2 for the full-stack analysis of the 3D chromatin interaction data. cLoops2 consists of core modules of peak-calling, loop-calling, differentially enriched loops calling and loops annotation. Additionally, it also contains multiple modules to carry out interaction resolution estimation, data similarity estimation, features quantification and aggregation analysis, and visualization. cLoops2 with documentation and example data are open source and freely available at GitHub:  https://github.com/YaqiangCao/cLoops2

overall_design: ChIC-seq data in GM12878 for antibodies of IgG, CTCF, H3K4me3 and H3K27ac were generated to benchmark cLoops2 peak-calling performance.

first: Shuai

last: Liu

first: Gang

last: Ren

first: Qingsong

last: Tang

first: Keji

last: Zhao


title: miR profiling of apoptotic murine neurons and their supernatent

city: Faro

first: Matthias

last: Futschik

address: Campus de Gambelas

country: Portugal

institute: Universidade do Algarve

summary:
miRNAs were recently discovered to directly activate receptors thereby extending their original role beyond post-transcriptional gene expression regulation. In particular, Here, conducting a systematic screening approach we identified miRNAs that in extracellular form can serve as receptor ligands, and elaborated the consequences of such an interaction in CNS injury.
Primary cortical neurons isolated from C57BL/6 mice were first exposed to staurosporine, a potent, non-selective kinase inhibitor, which is widely used to model neuronal apoptosis, for 8 h. While neurons remained morphologically intact within this time period, efficient apoptosis induction through activation of neuronal caspase-3 signaling was verified by western blot. Next, neurons and corresponding supernatant (S/N) were separately harvested and processed for miRNA detection. After enrichment and isolation of the small RNA fractions from neurons and their corresponding S/N, they were analyzed by GeneChip miRNA 4.0 array technology. Microarray data were processed using the robust multi-array average (RMA) method on the R/Bioconductor platform. Most of subsequent analysis was restricted to miRNA probes that were specific for Mus musculus.

overall_design: Replicate samples were taken from neurons and their supernatant after induction of apoptosis. As control,  samples were extracted from neurons and their supernatant without induced apoptosis. The abundance levels of miRNA were compared between apoptotic and control neurons as well as between the  supernatents of  apoptotic and of control neurons, respectively

first: Rui

last: Machado

first: Thomas

last: Wallach

first: Seija

last: Lehnard


title: Identification and characterization of miRNAs during flag leaf senescence in rice by high-throughput sequencing.

city: New Delhi

first: Jyothish

last: S

state: Delhi

address: Benito Juarez road

department: Department of Plant Molecular Biology

institute: University of Delhi

summary: Senescence is the ultimate stage of plant development. Among the different levels of senescence processes, flag leaf senescence plays a crucial role in determining grain quality in rice.  In the present study, efforts are made to identify the possible involvement of miRNAs in flag leaf senescence. Four small RNA libraries were generated from different stages of flag leaf senescence and sequenced by Illumina deep sequencing.  A total of 29 known miRNA families and 494 novel miRNAs were identified in the senescing flag leaves. 21 known and 116 novel miRNAs exhibited differential expression pattern. Computational prediction and analysis of putative targets of detected miRNAs revealed that miRNAs regulate the flag leaf senescence mainly by regulating transcription factors and hormone metabolism genes. The present study gives a clue about the senescence-associated miRNAs which can be used as a tool for manipulating flag leaf senescence in rice and other crops.

overall_design: Total four small RNA libraries of flag leaf senescence (US, ES, MS and LS) were constructed and high-throughput sequencing was performed using Illumina GA Iix system .

last: Sasi

first: Cheeni

last: Kumar

first: Balaji

last: Mani

first: Ankur

last: Bhardwaj

first: Manu

last: Agarwal

first: Surekha

last: Katiyar-Agarwal


title: Protein-RNA-Chromatin Interactions Reveal Nuclear RNA Architecture Functions in Transcriptional Condensation and Chromatin Folding

city: Farmington

first: Zhongyuan

last: Tian

state: CT

address: 10 Discovery Drive

institute: The Jackson Laboratory for Genomic Medicine

summary: It has been proposed that nucleome organization and genome function involve interplays between protein, RNA and chromatin architectures. However, how chromatin interactions are cooperatively mediated by nuclear proteins and RNAs have not been fully explored. Here, we report the multivalent interplays in Drosophila cells involving RNA Polymerase II (RNAPII), nuclear RNAs and chromatin interactions. Using a novel genomic approach (pRChIA-PET) for protein-RNA-chromatin interactions, we discovered that extensive combination of nuclear RNAs cooperatively act in trans and co-localize with RNAPII and associated protein cofactors at chromatin interaction loci of active promoters and enhancers. Nuclear perturbation by aliphatic alcohol and RNase-A revealed that chromatin associated nuclear RNAs (canRNAs) are likely integral components in phase-separation for transcriptional condensation, and may act to maintain open chromatin accessibility and long-range chromatin interactions. These findings suggest a significant architectural role for combinatorial canRNAs as potential scaffolding elements in 3D genome organization and transcriptional regulation.

overall_design: Investigation of protein-RNA-chromatin interactions by pRChIA-PET.

first: Meizhen

last: Zheng

first: Oscar

last: Luo

first: Simon

middle: Z

first: Yijun

last: Ruan


title: Mouse kidney-specific genes

city: Aurora

first: Makoto

last: Miyazaki

state: CO

address: 12700 E 22nd PL Denver CO

institute: University of Colorado

summary: Analysis of RNAs from multiple mouse tissues to find kidney-specific genes

overall_design: Total RNA obtained from isolated C57BL/6J mice, various tissues.


title: Genome-Wide Host Methylation Profiling of Anal and Cervical Carcinoma [cervical]

city: Tampa

first: Kieran

last: Smalley

state: Fl

address: 12902 USF Magnolia Drive,

institute: Moffitt cancer Center

summary: HPV infection results in changes in host gene methylation which, in turn, are thought to contribute to the neoplastic progression of HPV-associated cancers. The objective of this study was to identify joint and disease-specific genome-wide methylation changes in anal and cervical cancer as well as changes in high-grade pre-neoplastic lesions. Formalin-fixed paraffin-embedded (FFPE) anal tissues (n=143; 99% HPV+) and fresh frozen cervical tissues (n=28; 100% HPV+) underwent microdissection, DNA extraction, HPV genotyping, bisulfite modification, DNA restoration (FFPE) and analysis by the Illumina HumanMethylation450 Array.

overall_design: 143 FFPE anal samples (121 invasive tumor, 13 adjacent AIN3 and 9 adjacent normal mucosae) and 28 fresh frozen cervical samples (normal (n=10), CIN3 (n=9) and Cervical cancer  (n=9))

first: David

last: Shibata

first: Anders

last: Berglund

first: Erin

last: Siegel


title: T1 aptamer targets intratumoral myeloid cells with immunosuppression functions

status: Public on Nov 24 2021

city: Houston

first: Thomas

last: Welte

state: TX

address: 6670 Bertner Ave

department: Nanomedicine

institute: Houston Methodist Research Institute

summary: Intratumorally, immunosuppressive myeloid subsets are difficult to distinguish from mature, non-suppressive counterparts. T1 aptamer specifically targets the former subset and was used here to isolated the subsets for transcriptomic profiling.

overall_design: T1 aptamer-binding Ly6G(+) myeloid cells, T1-binding Ly6G(low) myeloid cells and T1-non-binding Ly6G(+) myeloid cells were isolated from tumors of mouse colon cancer model CT26 by FACS sorting and submitted to RNAsequ highthroughput analysis.

first: Haifa

last: Shen


title: Genome-Wide Host Methylation Profiling of Anal and Cervical Carcinoma [anal]


title: Genome-Wide Host Methylation Profiling of Anal and Cervical Carcinoma


title: Expression data form mouse partial hepatectomy in Kras mutant and Bap1 deleted / Kras mutant mice

city: New York

first: Anirban

last: Maitra

state: NY

address: Smilow 910, 522 1st Ave

department: Perlmutter Cancer Center

institute: New York University Grossman School of Medicine

summary:
BAP1 is a nuclear deubiquitinating enzyme in the ubiquitin carboxyterminal-hydrolase subfamily that is involved in chromatin remodeling.  It has been demonstrated to function as a tumor suppressor gene in multiple human malignancies.  Molecular studies have found recurrent somatic mutations in BAP1 in intrahepatic cholangiocarcinoma.  We have characterized the role of BAP1 in ICC development through a combination of whole genome ChIP-on-chip and transcriptional profiling of the mouse hepatic tumors.
In this dataset, we include the expression data obtained from dissected mouse livers containing tumors using a gain-of-function mutation in KRAS (G12D), as well as loss-of-function mutation in BAP1. These data are used to obtain genes that are differentially expressed in response to Bap1 loss.

overall_design: Total of 6 samples from mouse partial hepatectomy were processed and subjected to transcriptome analysis. 3 of these samples are replicates for Kras mutant mice and rest of the three are from Bap1 deleted / Kras mutant mice.

first: Rebecca

last: Marcus

first: Sonal

last: Gupta

first: Kimal

last: Rajapakshe


title: Time-restricted feeding prevents deleterious metabolic effects of circadian disruption through epigenetic control of β-cell function

city: Cambridge

first: Matthew

last: Brown

state: MA

address: 75 Ames St

institute: Broad Institute

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus


title: MiRNA Deregulation Distinguishes Anaplastic Thyroid Carcinoma (ATC) and Supports Upregulation of Oncogene Expression

status: Public on Nov 23 2021

city: Halle (Saale)

first: Danny

last: Misiak

address: Kurt-Mothes-Str. 3a

department: Molecular Cell Biology

institute: Martin Luther University Halle-Wittenberg

summary:
Anaplastic thyroid carcinoma (ATC) is the most fatal and rapidly evolving endocrine malignancy invading the head and neck region and accounting for the majority of thyroid cancer-associated deaths. Deregulation of microRNA (miRNA) expression promotes thyroid carcinoma progression by modulating reorganization of the ATC transcriptome. Here, we applied comparative miRNA-/mRNA-sequencing in a cohort of 28 thyroid carcinomas to unravel the association of deregulated miRNA and mRNA expression. This identifies 85 miRNAs significantly deregulated in ATC. By establishing a new analysis pipeline we unravel 85 prime miRNA-mRNA interactions supporting the downregulation of candidate tumor-suppressors and upregulation of bona fide oncogenes like survivin (BIRC5) in ATC. This miRNA-dependent reprogramming of the ATC
transcriptome provides a mRNA signature comprising 65 genes sharply distinguishing ATC from other thyroid carcinomas. Validation of deregulated protein expression in an independent thyroid carcinoma cohort demonstrates that miRNA-dependent oncogenes comprised in this signature, the transferrin receptor TFRC (CD71) and the E3-ubiquitin ligase DTL, are sharply upregulated in ATC. This upregulation is even sufficient to distinguish ATC from partially differentiated thyroid carcinomas (PDTC). In sum, these findings provide new diagnostic tools and a robust resource to explore key miRNA-mRNA regulation underlying the progression of thyroid carcinoma.

overall_design: Small RNA sequencing of the miRNA-transcriptome from 28 primary thyroid tumor samples

first: Marcus

last: Bauer

first: Jana

last: Lange

first: Jacob

last: Haase

first: Juliane

last: Braun

first: Kerstin

last: Lorenz

first: Claudia

last: Wickenhauser

first: Stefan

last: Hüttelmaier


title: Drug repurposing in rare diseases: an integrative study of drug screening and transcriptomic analysis in nephropathic cystinosis

status: Public on Nov 26 2021

city: Rome

first: Francesco

last: Bellomo

address: Viale di S. Paolo, 15

department: Genetic and Rare Diseases

institute: Bambino Gesù Children's Hospital, IRCCS

summary: We combined a mechanism-based and a cell-based drug screening coupled to a computational analysis, which allowed to identify potential drugs and metabolic pathways relevant for the pathophysiology of nephropathic cystinosis. This result was achieved by comparing gene-expression signature of lead compounds that share common mechanisms of action or that involve similar pathways with the disease gene-expression signature revealed by RNA-seq.

overall_design: In this project 6 samples (triplicate for two biological conditions) was sequenced by using DNBseq platform. Samples are conditionally immortalized proximal tubular epithelial cells (ciPTECs), from healthy donor and patient with cystinosis bearing the classical homozygous 57-kb deletion.

first: Ester

last: De Leo

first: Anna

last: Taranta

first: Laura

last: Giaquinto

first: Gianna

last: Di Giovamberardino

first: Sandro

last: Montefusco

last: Rega

last: Pastore

first: Diego

last: Medina

last: Di Bernardo

first: Maria

last: De Matteis

last: Emma


title: Chronic sleep deprivation impaired bone formation in growing rats via down-regulating PI3K/AKT Signaling

city: Beijing

first: Xiaoye

last: Duan

state: dongcheng

address: Beijing hospital

institute: beijing hospital

summary: Background: This study aimed to assess the effects of chronic sleep deprivation (CSD) on bone metabolism in growing rats and the likely underlying mechanism. Methods: Twenty 5-week-old male Wistar rats and randomly divided into the CSD and normal control (NC) groups after one-week acclimatization. After a 6-week intervention of sleep deprivation, the left distal femurs of both groups were harvested for micro-computed tomography scans and histological analysis. Meanwhile, the right femur were measured the mRNA and protein expression via RNA sequencing and western blot. Serum bone turnover markers were evaluated at 0, 2, 4, and 6 weeks. Result: CSD impaired the bone growth, showing an imbalance of bone turnover status, dysphasia in the metaphysis growth plate, and deterioration of bone microarchitecture. Further, CSD suppressed bone formation, showing that the expression of osteogenesis-related proteins (col1α1 and osteocalcin) and mRNA (igf1, bglap, runx2, col1α1, pth1r) are down-regulated. Meanwhile, the potential of osteoblast differentiation of bone marrow-derived mesenchymal stem cells decreased in the CSD group. Differentially expressed genes were detected, and functional enrichment analyses revealed that the PI3K/AKT pathway was significantly down-regulated in the CSD group, which was further verified by the protein expression levels.Conclusion: These results suggest that CSD can significantly impaired bone health, and it may exert these effects in part by suppressing bone formation and osteoblast differentiation, and inactivating the PI3K/AKT signaling pathway.

overall_design: bone mRNA profiles of 12-week Wistar rats from normal control group and chronic sleep deprivation

first: Linxin

last: Guo

first: Qi

last: Pan


title: Regulation of TET2 gene expression and 5mC oxidation in breast cancer cells by estrogen signaling [hMeDIP-seq]

status: Public on Nov 28 2021

city: Shanghai

first: Ruitu

last: Lyu

address: 138 Yixueyuan Road Xuhui District

institute: Institutes of Biomedical Sciences Fudan University

summary: Estrogen signaling plays important roles in diverse physiological and pathophysiological processes. However, the relationship between estrogen signaling and epigenetic regulation is not fully understood. Here, we explored the effect of estrogen signaling on the expression of Ten-Eleven Translocation (TET) family genes and DNA hydroxylmethylation in estrogen receptor alpha positive (ERα+) breast cancer cells. By analyzing the RNA-seq data, we identified TET2 as an estradiol (E2)-responsive gene in ERα+ MCF7 cells. RT-qPCR and Western blot analyses confirmed that both the mRNA and protein levels of TET2 gene were upregulated in MCF7 cells by E2 treatment. ChIP-seq and qPCR analyses showed that the enrichment of ERα and H3K27ac on the upstream regulatory regions of TET2 gene was increased in MCF7 cells upon E2 treatment. Moreover, E2 treatment also led to a significant increase in the global 5-hydroxymethylcytosine (5hmC) level, while knockout of TET2 abolished such E2-induced 5hmC increase. Conversely, treatment with ICI 182780, a potent and selective estrogen receptor degrader (SERD), inhibited TET2 gene expression and down-regulated the 5hmC level in MCF7 cells. Taken together, our study identified an ERα/TET2/5hmC epigenetic pathway, which may participate in the estrogen-associated physiological and pathophysiological processes.

overall_design: Examination of 5-hydroxymethylcytosine (5hmC) in EtOH and E2 treated MCF7 cells.

first: Lijun

last: Xiong

first: Xuguo

last: Zhu

first: Li

last: Tan


title: Retinoic Acid Signaling Drives Differentiation towards Enterocytes in Colorectal Cancer

city: Nijmegen

first: Michiel

last: Vermeulen

state: Gelderland

address: Geert Grooteplein 28

department: Molecular Biology

country: Netherlands

institute: Radboud University

summary: Retinoic Acid (RA) signaling is an important and conserved pathway that regulated cellular proliferation and differentiation. Furthermore, perturbed RA signaling is implicated in cancer initiation and progression. However, the mechanisms by which RA signaling contributes homeostasis malignant transformation and disease progression in the intestine, remain incompletely understood. Here, we show that activation of the Retinoic Acid Receptor and the Retinoid X Receptor results in enhanced transcription of enterocyte-specific genes in mouse small intestinal organoids. Conversely, inhibition of this pathway results in reduced expression of genes associated with the absorptive lineage. Strikingly, this latter effect is conserved in a human organoid model for colorectal cancer (CRC) progression. We further show that the epigenome in metastatic organoids is less permissive for RXR binding compared to pre-metastatic organoids, resulting in reduced sensitivity for RA signaling perturbations. Finally, we show that reduced RXR target gene expression correlates with worse CRC prognosis, implying RA signaling as a putative therapeutic strategy in CRC.

overall_design: RNA-seq analysis of mouse small intestinal organoids treated with several compounds that affect retinoic acid signaling. RNA-seq analysis of human colorectal cancer organoids treated with several compounds that affect retinoic acid signaling. ATAC-seq of human colorectal cancer organoids with either 3 or 4 prevalent cancer driving mutations.

first: Roelof

last: Wester

first: Lisa

last: van Voorthuijsen

first: Hannah

last: Neikes

first: Jelmer

last: Dijkstra

first: Siebren

last: Frölich

first: Maarten

last: van der Sande

first: Colin

last: Logie

first: Rik

middle: G

last: Lindeboom


title: The transcription factor FEZF1, a direct target of EWSR1-FLI1 in Ewing sarcoma cells, regulates the expression of neural-specific genes

status: Public on Nov 22 2021

city: MAJADAHONDA

first: Javier

last: Alonso

state: MADRID

address: CTRA. MAJADAHONDA-POZUELO KM 2

department: AREA DE GENÉTICA HUMANA

country: Spain

institute: INSTITUTO DE SALUD CARLOS III - IIER

summary: Transcriptomic analysis of the well-characterized Ewing sarcoma cell line A673 indicated that one of the genes more strongly upregulated by EWSR1-FLI1 was FEZF1 (FEZ family zinc finger protein 1), a transcriptional repressor involved in brain development and neural cell identity. FEZF1 was highly expressed in Ewing sarcoma cells but not in other bone tumors such as osteosarcoma or chondrosarcoma. FEZF1 promoter contains a large GGAA-microsatellite and the number of GGAA repeats correlated positively with FEZF1 expression levels in Ewing sarcoma cell lines. To characterize the functional role of FEZF1 in Ewing sarcoma we analyzed the effect of FEZF1 knockdown in three Ewing sarcoma cell lines (A673, SKNMC, SKES1). FEZF1 knockdown inhibited clone formation in clonogenic assays and cell proliferation. Finally, we analyzed the FEZF1-dependent expression profile in A673 cells by RNAseq. Interestingly, several neural genes regulated by FEZF1 were concomitantly regulated by EWSR1-FLI1. In summary, FEZF1 is a transcriptional target of EWSR1-FLI1 in Ewing sarcoma cells involved in the regulation of neural-specific genes which could explain, at least in part, the neural-like phenotype observed in several Ewing sarcoma tumors and derived cell lines.

overall_design: FEZF1-dependent expression profile in A673 Ewing sarcoma cells by RNAseq

first: Laura

last: Garcia-Garcia

first: Enrique

last: Fernández-Tabanera

first: Saint

last: Cervera


title: Spatial transcriptome analysis defines heme as a hemopexin-targetable inflammatoxin in the brain

status: Public on Nov 25 2021

city: Zürich

first: Raphael

middle: Matthias

last: Buzzi

address: Rämistrasse 100

department: Division of Internal Medicine

institute: Universitätsspital and University of Zurich

summary: After intracranial hemorrhages, heme is released from cell-free hemoglobin. This red blood cell toxin may drive secondary brain injury at the hematoma-brain interface. This study aimed to generate a spatially resolved map of the transcriptome-wide gene expression changes in the heme-exposed brain and define the potential therapeutic activity of the heme-binding protein hemopexin.

overall_design: Spatial transcriptome analysis of mouse brain using the 10X genomics Visium spatial gene expression kit after stereotactic injections.

first: Kevin

last: Akeret

first: Michael

last: Hugelshofer

first: Dominik

last: Schaer


title: RNA-seq of HPV-negative Oral Squamous Cell Carcinoma Patients

city: Camperdown

first: Dario

last: Strbenac

state: NSW

address: City Road

department: School of Mathematics and Statistics

institute: University of Sydney

summary: Strand-specific, paired-end, total RNA-sequencing data for fifteen Australian, HPV-negative, young oral squamous cell carcinoma patients of primary tumour and adjacent normal.

overall_design: 30 samples belonging to 15 patients (tumour-normal pairs)

first: Laveniya

last: Satgunaseelan

first: Ruta

last: Gupta

first: Jonathan

last: Clark


title: A novel miRNA screen identifies miRNA-4454 as a candidate biomarker for ventricular fibrosis in patients with hypertrophic cardiomyopathy

status: Public on Nov 20 2021

city: Hamburg

first: Tilo

last: Thottakara

address: Martinistr 52

department: Kardiologie

institute: Universität Hamburg

summary:
Left ventricular hypertrophy, myocardial disarray and interstitital fibrosis are the hallmarks of hypertrophic cardiomyopathy (HCM). Access to the myocardium for diagnostic purposes is limited. Circulating biomolecules reflecting the myocardial disease processes could improve early detection of HCM. Circulating miRNAs have been found to reflect disease processes in several cardiovascular diseases.
Circulating miR-1, miR-495-3p and miR-4454 levels are elevated in plasma of HCM patients. miR-4454 is suggested as a potential biomarker for fibrosis in these patients.

overall_design: A total of 800 miRNA were screened in plasma of 24 patients with hypertrophic cardiomyopathy and 11 healthy controls using nCounter technology and qPCR analyses.

first: Elisabeth

last: Krämer

first: Natalie

last: Lund

first: Paulus

last: Kirchhof

first: Lucie

last: Carrier

first: Monica

last: Patten


title: The JAK2-STAT pathway epigenetically regulates tolerized genes during the first encounter to bacterial antigens [RNA-seq]

city: Badalona, Barcelona

first: Esteban

last: Ballestar

state: N/A = Not Applicable

address: Ctra de Can Ruti, Camí de les Escoles s/n

institute: Josep Carreras Research Institute (IJC)

summary: Microbial challenges, such as widespread bacterial infection, induce endotoxin tolerance. This state of hypo-responsiveness to subsequent infections is mainly displayed by monocytes and macrophages. Endotoxin tolerance is generally acquired following a septic episode. In this study, we investigated DNA methylation changes during the acquisition of in vitro tolerance. We identified a set of TET2-mediated demethylation events that are specific to toll like receptor (TLR) 2 and 4 stimulation. Lipopolysaccharide (LPS)-specific demethylation occurs at genomic sites that have low accessibility in quiescent monocytes, concomitantly with the transcriptional activation of many inflammation-related genes, and they are enriched in binding motifs for several signal transducer and activator of transcription (STAT) family members. Indeed, STAT1, STAT3 and STAT5, elements of the JAK2 pathway, are phosphorylated in association with the acquisition of endotoxin tolerance. Inhibition of the JAK2 pathway impairs the activation of tolerized genes at the first encounter with LPS. This supports a crucial role of this pathway in determining the initial response of these genes to bacterial antigens and provides a pharmacological target to prevent exacerbated responses, allowing regulated responses upon subsequent challenges. Finally, we prove the pathological relevance of the JAK2 pathway in monocytes from patients with sepsis.

overall_design: RNA were isolated from 12 samples from 3 different donors. 4 conditions: non-cultured monocytes, non-treated monocytes, LPS monocytes and P3C monocytes

first: Clara

last: Lorente-Sorolla

first: Octavio

last: Morante-Palacios

first: Antonio

last: Garcia-Gomez

first: Laura

last: Ciudad

first: Francesc

last: Català-Moll

first: Adolfo

last: Ruiz-Sanmartín

first: Mónica

last: Martínez-Gallo

first: Ricard

last: Ferrer-Roca

first: Juan

middle: C

last: Ruiz-Rodríguez

first: Damiana

last: Álvarez-Errico


title: Expression data from ASPC1-GFP PDAC cells treated with fluvastatin

city: Essen

first: Barbara

last: Grüner

address: Hufelandstr. 55

institute: University Hospital Essen

summary:
Drug treatments often result in dramatic changes in gene expression.
Thus, we used microarray to uncover gene expression effects of fluvastatin treatment on ASPC1-GFP PDAC cells.

overall_design: ASPC1-GFP cells treated in triplicate for 48 hours with fluvastatin to detect gene expression changes. ASPC1-GFP cells treated in triplicate with DMSO served as control.

first: Madeleine

last: Dorsch


title: Transcriptome-wide profile of 25-hydroxyvitamin D3 in primary immune cells from human peripheral blood

status: Public on Nov 27 2021

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: In this study, we used PBMCs of five healthy individuals participating in the VitDHiD intervention trial (NCT03537027) and investigated in a transcriptome-wide approach the gene regulatory potential of 25(OH)D3 and D3 in reference to 1,25(OH)2D3 (GSE156124).

overall_design: In the first experimental series (S1), PBMCs of five individuals (#05,#09,#12,#13,#14) were exposed for 24 h to either solvent (0.1% EtOH, GSE156124), 250 nM vitamin D3 (D3), 250 nM 25(OH)D3 (25D) or 10 nM 1,25(OH)2D3 (GSE156124), while in the second series (S2) PBMCs of individuals #05, #09 and #14 were stimulated for 24 h with either solvent, 100, 1000 or 10,000 nM 25(OH)D3. All experiments were performed in three repeats.

first: Carsten

last: Carlberg


title: The JAK2-STAT pathway epigenetically regulates tolerized genes during the first encounter to bacterial antigens [array]

overall_design: Total DNA were isolated from 12 samples from 3 different donors. 4 conditions: non-cultured monocytes, non-treated monocytes, LPS monocytes and P3C monocytes


title: Whole transcriptome profiling of macrophage-DC progenitors (MDPs) and common monocyte progenitors (cMoPs) from Dnmt1+/+ and Dnmt1c/chip mice

city: Bad Nauheim

first: Sweta

last: Talyan

address: Ludwigstraße 43

institute: MPI

summary: Dendritic cells (DCs) are critical immune regulators involved in autoimmune diseases, but exploiting them clinically requires a detailed picture on the mechanisms orchestrating their development. DNA methylation is attractive in this regard because it is reversible and as such allows therapeutic manipulation. Combining single cell transplantation assays with whole-genome methylation assessment and with mice expressing reduced DNA methyltransferase 1 levels, we show that conventional and plasmacytoid DCs arise from myeloid-restricted hematopoietic stem cells (HSCs), suggesting that both subsets can develop independently of the lymphoid pathway. DC commitment by these HSCs requires an intrinsically high methylation threshold to establish expression of DC genes, particularly the Flt3 cytokine receptor. Reducing methylation depleted DCs and ameliorated systemic lupus erythematosus in mice. These studies shed novel light on the DC origin, show how lineage- and subset-specific methylation dynamics regulate DC fate and provide a potential rationale for targeting DCs in autoimmunity by hypomethylating agents.

overall_design: MDPs (Lin-cKithiCD115+CD11b-Ly-6C-) and cMoPs (Lin-cKithiCD115+CD11b-Ly-6C+) were sorted from 8-12 weeks old Dnmt1+/+ and Dnmt1c/chip mice, total RNA was extracted using the RNeasy Micro kit (Qiagen) and gDNA was digested with the RNase-free DNAse provided in the Kit. Sample processing and hybridization on Affymetrix GeneChIPs (Mus musculus) MG 430 PM was carried out according to standard procedures at the Center of Excellence for Fluorescent Bioanalytics (KFB, University of Regensburg).

first: Miguel

last: Andrade-Navarro

first: Frank

last: Rosenbauer

first: Melinda

last: Czeh