title: Gut microbiota regulates tumor via circRNA/miRNA networks III

first: Zheyu

address: Yueyang Road

institute: CAS

summary: Increasing evidence indicates that gut microbiota plays an important role in cancer progression. We have employed RNA-seq or microarray for genome including mRNA, microRNA or circRNA profiling in an gut microbiota -dependent manner, as a discovery platform to identify target genes with the potential to involve in tumor regulation. The deep sequencing analysis reveals regulatory functions of microbiota-mediated circular RNA (circRNA)/microRNA networks that may contribute to cancer progression.

overall_design: Gut microbiota regulated mRNAs expression in tumor were measured in tumor samples of xenograft cancer model including germ-free mice with or without fecal microbiota transplantation (FMT) from specific pathogen free (SPF) mice or Probiotics (such as Bifidobacterium). Gut microbiota regulated no-coding RNAs (including circRNA and microRNA) expression in mice blood samples were measured in specific pathogen free (SPF) mice with or without broad-spectrum antibiotics (ABX) treatment, with or without fecal microbiota transplantation (FMT) from specific pathogen free (SPF) mice or Probiotics (such as Bifidobacterium, EcN) into germ-free mice.

first: Ziqiang

first: Zhuxian

last: Zhu


title: An enhancer cluster promotes NPCs formation from ESCs through maintaining HoxB activation by long-range chromatin interaction

status: Public on Oct 13 2020

city: Tianjin

first: Niannian

last: Li

state: Tianjin

address: No. 94 Weijin Road, Nankai District, Tianjin

department: college of Life Sciences

country: China

institute: Nankai University

type: Expression profiling by high throughput sequencing

summary: Homeobox B cluster genes (HoxB) are important marker genes for neural progenitor cells (NPCs) formation from embryonic stem cells (ESCs). However, mechanisms of HoxB activation in NPCs remain largely unknown. Here, we find an enhancer cluster (EnC) interacting with the HoxB locus by PLAC-seq analysis. CRISPR/Cas9-mediated EnC deletion significantly inhibited HoxB expression, indicating that the EnC is required for HoxB activation in NPCs. Transcriptome analysis revealed that differentiation-related master control genes and NPCs formation-related signaling pathways were significantly inhibited suggesting that the EnC is essential for NPCs formation. In summary, our results reveal a new mechanism about HoxB activation depending on EnC is crucial for NPCs formation.

overall_design: 3 biological replicates were analyzed for WT and enhancer cluster-KO by RNA-seq in NPC

first: Jian

last: Zheng

first: Guangsong

last: Su

first: Wenbin

last: Wang

first: Wange

last: Lu


title: Gut microbiota regulates tumor via circRNA/miRNA networks IV

city: Shanghai

last: Zhang

type: Non-coding RNA profiling by high throughput sequencing


title: Gut microbiota regulates tumor via circRNA/miRNA networks II


title: RNA-seq analysis of  differentially expressed genes between 2-week WT and Ngn3MettlsKO mice.

first: Yanqiu

address: 197 Rui-jin 2nd Road, Shanghai 20025, CHINA.

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.

summary: Using RNA-seq, we identified over 500 differentially expressed genes in KO islets, compared to WT. Among them, a cluster of genes involved in insulin secretion, ion transportation an prolferation were significantly changed.

overall_design: we isolated islets from 2-week KO and WT mice. Pulled more than 400 islets together for each sample and then islet total RNA was extracted using a RNeasy Micro kit (Qiagen) following the manufacturer’s protocol.Then, RNA high throughput sequencing was performed by Cloud-Seq Biotech (Shanghai, China).

first: Jiajun

last: Sun


title: MeRIP sequencing of 2-week primary mouse islets

summary: We report the first m6A RNA methylome of mouse islets using MeRIP sequencing. we recognized over 4000 methylation sites in 2-week islets.

overall_design: Examination of RNA modifications in islets


title: RNA-seq analyses of phase variation-dependent genes in Paenibacillus polymyxa E681

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

country: South Korea

institute: Pusan National University

summary: Paenibacillus polymyxa is a root-associated plant growth-promoting rhizobacterium. It was reported that many strains of P. polymyxa naturally exhibited the phenotypic variation. In the phase variation, the characteristics of the wild-type ‘B’ and the variant ‘F’ are very different in sporulation formation, motility, antibiotic ability and so on. For better understanding of the actual physiological changes, we performed RNA-seq analyses of P. polymyxa E681 to compare genome wide patterns of gene expression. As a result, we obtained 1,062 differentially expressed genes related to flagellar assembly and transport systems.

overall_design: Two libraries constructed: one wild-type ‘B’ and one variant ‘F’ in P. polymyxa E681

first: Younmi

last: Lee

first: Yongho

last: Jeon

first: Young-su

last: Seo


title: Gut microbiota regulates tumor via circRNA/miRNA networks

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

platform_organism:
Homo sapiens
Mus musculus
Rattus norvegicus

overall_design: Refer to individual Series


title: Chromatin States and their diverse protein occupancy drive genome organization in S. cerevisiae through heterogeneous Brownian motion

city: Cambridge

first: Steven

middle: William

last: Wingett

state: Cambs

address: Francis Crick Avenue, Cambridge Biomedical Campus

department: Cell Biology

country: United Kingdom

institute: MRC Laboratory of Molecular Biology

summary: We performed two full biological replicates Hi-C experiments of each temperature condition, with one 25°C sample and one 37°C sample each grown on the same day.

overall_design: Four samples: 2 biological replicates of Saccharomyces cerevisiae cultures grown at 25°C, and 2 biological replicates, grown at 25°C and shifted to 37°C for 15 minutes

first: Sven

last: Sewitz

first: Zahra

last: Fahmi

first: Latifa

last: Aljebali

first: Jeremy

last: Bancroft

first: Otávio

middle: B

last: Brustolini

first: Hicham

last: Saad

first: Isabelle

last: Goiffon

first: Csilla

last: Várnai

middle: W

first: Hua

last: Wong

first: Biola-Maria

last: Javierre

first: Stefan

last: Schoenfelder

first: Simon

middle: R

last: Andrews

first: Stephen

middle: G

last: Oliver

first: Peter

last: Fraser

first: Kerstin

last: Bystricky

first: Karen

last: Lipkow


title: Weighted gene coexpression network analysis-based identification of key modules and hub genes associated with drought sensitivity in rice

status: Public on Oct 12 2020

city: Nanning

first: Jijing

last: Luo

state: Guangxi

address: 100 Daxue Rd.(East)

institute: Guangxi University

summary: Drought stress is an adverse factor with deleterious effects on several aspects of rice growth. However, the mechanism underlying drought resistance in rice remains unclear. To understand the molecular mechanism of the drought response in rice, drought-sensitive CSSL (Chromosome Single-substitution Segment Line) PY6 was used to map QTLs of sensitive phenotypes and to reveal the impact of the QTLs on transcriptional profiling. The QTL dss-1 was mapped onto the short arm of chromosome 1 of rice. According to transcriptomic analysis, the identified differentially expressed genes (DEGs) exhibited a downregulated pattern and were mainly enriched in photosynthesis-related GO terms, indicating that photosynthesis was greatly inhibited under drought. Further, according to weighted gene coexpression network analysis (WGCNA), specific gene modules (designating a group of genes with a similar expression pattern) were strongly correlated with H2O2 (4 modules) and MDA (3 modules), respectively. Likewise, GO analysis revealed that the photosynthesis-related GO terms were consistently overrepresented in H2O2-correlated modules. Functional annotation of the differentially expressed hub genes (DEHGs) in the H2O2 and MDA-correlated modules revealed cross-talk between abiotic and biotic stress responses for these genes, which were annotated as encoding WRKYs and PR family proteins, were notably differentially expressed between PY6 and PR403. We speculated that drought-induced photosynthetic inhibition leads to H2O2 and MDA accumulation, which can then trigger the reprogramming of the rice transcriptome, including the hub genes involved in ROS scavenging, to prevent oxidative stress damage. Our results shed light on and provide deep insight into the drought resistance mechanism in rice.

overall_design: Examination of transcriptomic profiling in 3 timepoints of drought stress treatment in two rice materials, PY6 and PR403, respectively.

first: Baiyang

last: Yu

first: Jianbin

last: Liu


title: Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ [Mouse sn-RNA-Seq]

city: Nashville

first: E Michelle

last: Southard-Smith

state: TN

address: 2215 Garland Ave,

department: Medicine, Genetic Medicine

country: USA

institute: Vanderbilt University Medical Center

summary: Single-nucleus RNA-Seq of enteric neurons of adult mice, derived from the major regions of the intestine.

overall_design: Myenteric neurons were isolated from the duodenum, ileum, and colon of adult Phox2b-CFP mice (P42-52) using FACS. Nuclei were subjected to single-nucleus RNA-Seq

first: Aaron

last: May-Zhang

first: Michelle

middle: E


title: Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ [Mouse nuclei bulk RNA-Seq]

summary: The data provided here were used to generate a comprehensive transcriptome atlas for the enteric neurons and glia of adult mice.

overall_design: Myenteric neurons and glia were isolated from the duodenum, ileum, and colon of adult Phox2b-CFP mice (P42-52) using FACS. Nuclei were subjected to bulk RNA-Seq and differential Expression analysis was performed between enteric neurons and glia as well as those derived from different gut segments in order to identify neuron-specific genes in each gut region


title: H3 K27M and EZHIP impede H3K27-methylation spreading by inhibing allosterically stimulated PRC2 [nonM]

city: Madison

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by high throughput sequencing

summary: In this study, we report that EZHIP and H3 K27M preferentially interact with an allosterically activated form of PRC2 in vivo. The formation of H3 K27M- and EZHIP-PRC2 complexes occurs at CpG islands containing H3K27me3 and impedes PRC2 and H3K27me3 spreading. Moreover, we find that H3 K27M inhibits PRC2 in trans and can reduce H3K27me3 levels independent of chromatin incorporation. While EZHIP is not found outside of placental mammals, we find that expression of human EZHIP reduces H3K27me3 in Drosophila melanogaster through a conserved molecular mechanism.

overall_design: Profiling genomic enrichment of H3K27me3

first: Siddhant

middle: U

last: Jain


title: Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ [Human Enteric Ganglia]

summary: The data provided here were used to generate a comprehensive transcriptome atlas for the human myenteric plexus from healthy human adults

overall_design: Enteric ganglia were collected from the duodenum, ileum, and/or colon of 15 adult (18-35 y.o.) human organ donors, who had no documented history of drug abuse or GI /neurological disease.


title: H3 K27M and EZHIP impede H3K27-methylation spreading by inhibing allosterically stimulated PRC2 [S2_ATAC]

summary:
In this study, we report that EZHIP and H3 K27M preferentially interact with an allosterically activated form of PRC2 in vivo. The formation of H3 K27M- and EZHIP-PRC2 complexes occurs at CpG islands containing H3K27me3 and impedes PRC2 and H3K27me3 spreading. Moreover, we find that H3 K27M inhibits PRC2 in trans and can reduce H3K27me3 levels independent of chromatin incorporation. While EZHIP is not found outside of placental mammals, we find that expression of human EZHIP reduces H3K27me3 in Drosophila melanogaster through a conserved molecular mechanism.
ATAC-seq chromatin accessibility profiling in drosophila S2 cells

overall_design: ATAC-seq was performed in duplicate.


title: Combinatorial transcriptional profiling of mouse and human enteric neurons identifies shared and disparate subtypes in situ

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: H3 K27M and EZHIP impede H3K27-methylation spreading by inhibing allosterically stimulated PRC2 [EED_rescue]

overall_design: Profiling genomic enrichment of H3K27me3, EZH2


title: Gut microbiota regulates tumor via circRNA/miRNA networks I

first: Zheyu

last: Zhang

first: Ziqiang

first: Zhuxian

last: Zhu


title: H3 K27M and EZHIP impede H3K27-methylation spreading by inhibing allosterically stimulated PRC2 [S2_H3K27me3]

overall_design: Profiling genomic enrichment of H3K27me3 in drosophila S2 cells


title: RNA sequencing of whole Dorsal Root Ganglia (DRG) upon Environmental Enrichment and Sciatic Nerve Axotomy  (EE_SNA) or Sciatic Nerve Axotomy alone (SH_SNA) compared to Standard Housing Sham (SH_Sham)

city: Miami

first: Matt

middle: C

last: Danzi

state: FL

address: 1095 NW 14th Terrace, Lois Pope LIFE Center 4-26

institute: University of Miami

summary:
Purpose: compare the gene expression in whole DRG of mice: A) undergone to nerve axotomy vs control condition  B) pre-exposed to EE and undergone to nerve axotomy vs control condition
Results: we found that EE_SNA induces transcriptional changes strongly promoting axon regeneration. We call this "Enriched Conditioning"

overall_design: Method: RNA-seq from sciatic L4-L6 DRG extracted from mice housed for 10 days in Environmental Enrichment (EE) vs Standard Housing (SH). Each group of mice has either undergone SNA or sham injury, and DRG have been collected 24 hours afterwards. Pool of sciatic DRGs from 2 mice were used for each sample. DRG were collected in RNase later reagent, and crushed with RNase free micropestle for RNA extraction.

first: Francesco

last: De Virgiliis

first: Thomas

last: Hutson

first: Ilaria

last: Palmisano

first: Simone

last: Di Giovanni

first: Lazarevic

last: Dejan


title: Resilience and susceptibility in a mouse model of immune-mediated neurodevelopmental disorders

city: Zurich

first: giancarlo

last: russo

state: Schweiz

address: winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: ETH/University of Zurich

summary: We identify and characterize subgroups of isogenic mouse offspring exposed to identical maternal immune activation induced by gestational administration of the viral mimetic, poly(I:C). We demonstrate that offspring with manifest impairments in social behavior, sensorimotor gating and working memory (“susceptible” offspring) differ from asymptomatic (“resilient” offspring) in terms of their transcriptional profiles in cortical and subcortical brain regions, while displaying only subtle differences in brain morphometry

overall_design: We perfromed next-generation RNA sequencing in the medial prefreontal cortex and amygdala in subgroup of behvairally characterized offspring ( n=3 resilient, n=3 susceptible and n=3 control offspring)

first: Flavia

middle: S

last: Mueller

first: Ulrike

last: Weber-Stadlbauer

first: Urs

last: Meyer


title: MUC1-c is a target for suppressing stemness in the progression of colitis and colorectal cancer

city: Buffalo

first: Qiang

last: Hu

state: NY

address: Elm & Carlton Streets

institute: Roswell Park Cancer Institute

summary: Colitis is associated with the development of colorectal cancer (CRC) by largely undefined mechanisms that are critical for understanding the link between inflammation and cancer. Intestinal stem cells (ISCs) marked by LGR5 expression are of importance in both the inflammatory response to colitis and progression to colitis-associated colon cancer (CACC). Here, we report in human MUC1-transgenic mouse models of CACC that targeting the MUC1-C oncogenic protein, which is upregulated in inflammation, suppresses the (i) Lgr5+ ISC population, (ii) induction of Myc and core pluripotency stem cell factors, and (iii) severity and progression of colitis to dysplasia and cancer. By extension to human colon cancer cells, we demonstrate that MUC1-C drives MYC, forms a complex with MYC on the LGR5 promoter and activates LGR5 expression. We also show in CRC cells that MUC1-C induces the cancer stem cell (CSC) markers (BMI1, ALDH1, FOXA1, LIN28B) and the OCT4, SOX2 and NANOG pluripotency factors. Consistent with conferring the CSC state, targeting MUC1-C suppresses the capacity of CRC cells to promote wound healing, invasion, self-renewal and tumorigenicity. In analysis of human tissues, MUC1 expression associates with activation of inflammatory pathways, development of colitis and aggressiveness of CRCs. These results collectively indicate that MUC1-C is of importance for integrating stemness and pluripotency in colitis and CRC. Of clinical relevance, the findings further indicate that MUC1-C represents a previously unrecognized target that is druggable for treating progression of colitis and CRC.

overall_design: SW620 cells were cultured in RPMI1640 medium containing 10% FBS, streptomycin and penicillin, and were treated with vehicle control or doxycycline.

first: Wei

last: Li

first: Mark

last: Long


title: Pharmacological blockade of high-risk MYCN driven neuroblastoma using an orally-bioavailable CDK2/9 inhibitor

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary: The undruggable nature of oncogenic Myc transcription factors poses a therapeutic challenge in neuroblastoma, a paediatric cancer in which MYCN amplification is strongly associated with unfavourable outcome. Here, we show that CYC065, a clinical inhibitor of CDK2 and CDK9, selectively targets MYCN-amplified neuroblastoma via blockade of CDK9-dependent, MYCN-driven transcriptional elongation and CDK2-dependent proliferation. CYC065 also targets nascent transcription of short half-life genes including MYCN and MCL-1 leading to downregulation of MYCN-driven ‘adrenergic’ gene expression programs, growth inhibition, and apoptosis in vitro and in vivo. These data highlight the clinical potential of CDK2/9 inhibition in the treatment of MYCN-amplified neuroblastoma.

overall_design: ChIP-seq in SHEP and SHEP MYCN neuroblastoma cell lines for H3K27ac, MYCN

first: Tong

last: Liang

first: Evon

last: Poon

middle: Y

first: Louis

last: Chesler


title: mRNA expression of gastric cancer and paracancerous tissues

status: Public on Oct 11 2020

city: Shenyang

first: Ang

last: Wang

address: North Nanjing Street 155#, Heping District

department: Tumor Etiology and Screening Department of Cancer Institute and General Surgery

institute: First Hospital of China Medical University

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

summary: mRNA expression for gastric cancer and paracancerous tissues

first: Liang

last: Sang


title: DNA methylation in human pancreatic cancer vs. adjacent normal pancreatic tissue

city: Tainan City

first: Po-Hsien

middle: Joseph

last: Huang

address: 1 University Rd.

department: Biochemistry and Molecular Biology

country: Taiwan

institute: National Cheng Kung University

type: Methylation profiling by genome tiling array

summary:
HumanMethylation 450K microarrays were used to identify aberrant DNA methylation in pancreatic adenocarcinoma (n=14), juice-circulating cancer cells (n=4), cancer associated fibroblasts (n=3), against adjacent normal pancreatic tissues (n=7)
Bisulphite converted DNA from the 28 samples were hybridised to the Illumina HumanMethylation450 Beadchip v1.2

overall_design: Pancreatic tumor samples (n=14), pancreatic juice circulating cancer cells (n=4), cancer associated fibroblasts (n=3) and adjacent normal pancreatic tissues (n=7)

first: Yan-Shen

last: Shan


title: Role of androgen receptor splice variant 7 (AR-v7) in prostate cancer resistance to 2nd generation androgen receptor signaling inhibitors

city: Seattle

first: Ilsa

last: Coleman

state: WA

address: 1100 Fairview Ave N, E2-112

department: Human Biology

institute: Fred Hutchinson Cancer Center

summary: Since its discovery, there has been one central issue of significant clinical relevance related to expression of the truncated androgen receptor splice variant-7 (AR-v7), which lacks the C-terminal ligand binding domain and thus acquires ligand-independent transcriptional activity in castration-resistant prostate cancer (CRPC). That question is whether AR-v7 is simply a marker of enhanced AR transcriptional activity characteristic of resistance to 2nd generation androgen receptor signaling inhibitors (ARSi) like Abiraterone and Enzalutamide, or whether it drives lethal resistance to ARSi. To address this question, the present study utilized 4 independently derived CRPC patient-derived xenografts in which the genetic and phenotypic changes could be followed before and after the development of ARSi resistance. This allowed evaluation of the correlation between acquired resistance to ARSi and changes in the expression levels of full length AR (AR-FL) vs. AR-v7 during this process. The combined results document that elevated expression of AR-FL alone is sufficient for Abiraterone- but not Enzalutamide-resistance. This is true even if AR-FL has a gain-of-function mutation. Furthermore, Enzalutamide-resistance is consistently correlated with the acquisition of AR-v7 expression. To directly test the requirement for AR-v7 expression in ARSi-refractory CRPC, CRISPR-Cas9 knockout of AR-FL and/or AR-v7 in LNCaP-95 cells was performed to evaluate in vitro and in vivo growth responses. These results document that AR-v7 drives Enzalutamide-resistance and focuses the critical need to develop therapeutic options to prevent and/or inhibit AR-v7 driven lethal progression of CRPC.

overall_design: RNA sequencing of patient-derived xenograft (PDX) models using Illumina TruSeq Library prep and sequenced on Illumina HiSeq 2500.

first: Yezi

last: Zhu

first: Susan

last: Dalrymple

first: S

middle: L

last: Zheng

first: Jianfeng

last: Xu

first: Jody

last: Hooper

first: Emmanuel

last: Antonarakis

first: Angelo

middle: M

last: De Marzo

first: Alan

middle: K

last: Meeker

first: Michael

last: Haffner

first: Srinivasan

last: Yegnasubramanian

first: Peter

last: Nelson

first: William

last: Isaacs

first: Jun

last: Luo

first: W

middle: N

last: Brennen

first: John

middle: T


title: Hypothalamic REV-ERBs Control Circadian Food Intake and Leptin Sensitivity [ChIP-seq]

city: Philadelphia

first: Hoang

last: Nguyen

state: PA

address: 3400 Civic Center Boulevard

institute: University of Pennsylvania Perelman School of Medicine

summary: Obesity occurs when energy expenditure is outweighed by food intake. Tuberal hypothalamic nuclei, including the arcuate nucleus (ARC), ventromedial nucleus (VMH), and dorsomedial nucleus (DMH), regulate feeding amount as well as energy expenditure. Here we report that mice lacking circadian nuclear receptors REV-ERBa and b in the tuberal hypothalamus (HDKO) gain excessive weight on an obesogenic diet due both to decreased energy expenditure and increased food consumption during the light phase. Moreover, rebound food intake after fasting is markedly increased in HDKO mice. Integrative transcriptomic and cistromic analyses revealed that such disruption in feeding behavior is due to perturbed REV-ERB-dependent leptin signaling in the ARC. Indeed, in vivo leptin sensitivity is impaired in HDKO mice on an obesogenic diet in a circadian manner. Thus, REV-ERBs play a crucial role in hypothalamic regulation of food intake and circadian leptin sensitivity in diet-induced obesity.

overall_design: Chromatin immuno-precipitation followed by high throughput sequencing  (ChIP-seq) of REV-ERBalpha genomic occupancy in hypothalamic nuclei (ARC/VMH) using HA-tagged REV-ERBalpha mice as previously described in Adlanmerini, PNAS 2019 with anti-HA magnetic beads (Pierce, 888367)

first: Marine

last: Adlanmerini

first: Mitchell

middle: A

last: Lazar


title: Development of LHX6-inducible system in PK-1 and PK-9 cells

city: Sendai

first: Shinichi

last: Fukushige

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Diabetes, Metabolism and Endocrinology

country: Japan

institute: Tohoku University Graduate School of Medicine

summary: Epigenetic gene silencing by aberrant DNA methylation leads to loss of key cellular pathways in tumorigenesis. DNA methylation-mediated silenced genes in pancreatic cancer were searched by methyl-CpG targeted transcriptional activation (MeTA) method and LHX6 (LIM homeobox 6), a transcription factor involved in embryogenesis and head development, was selected as one of candidate genes. LHX6 was downregulated in most pancreatic cancer cell lines (83%: 10/12) mainly through promoter hypermethylation and histone deacetylation. Furthermore, LHX6 was also methylated in primary pancreatic cancers in a tumor-specific manner (57%: 16/28). In order to assess the biological significance of LHX6 in pancreatic tumorigenesis, we first performed colony formation assay and found that LHX6 re-expression inhibited colony formation in pancreatic cancer cell lines. Similarly, inducible expression of LHX6 inhibited cell proliferation and migration in LHX6 low-expressing pancreatic cancer cell lines. On the other hand, knockdown of LHX6 accelerated cell proliferation in LHX6 high-expressing pancreatic cancer cell lines. Our present results suggest that epigenetic inactivation of LHX6 plays an important role in pancreatic tumorigenesis by promoting cell proliferation.

overall_design: Two pancreatic cancer-derived cell lines, PK-1_LHX6#13 and PK-9_LHX6#4, that allow tetracycline-regulated LHX6 expression were constructed. The RNAs from PK-1_LHX6#13 and PK-9_LHX6#4 with (4 days treatment) or without tetracycline were prepared and analyzed by using Agilent whole human genome microarray (4×44K) v2.

first: Yakefujiang

last: Abudurexiti


title: Multi-colour lineage tracing reveals intra-stage proliferative heterogeneity during mammary tumour progression

city: Basel

first: Ravi Kiran Reddy

last: KALATHUR

state: Basel

address: Mattenstrasse 28

department: Departement Biomedizin

institute: University of Basel

summary: We have assessed clonal heterogeneity within individual primary tumours and metastasis and also during the distinct stages of malignant tumour progression using the Confetti lineage reporter in the background of the MMTV-PyMT mouse model of metastatic breast cancer. Comparative gene expression analysis of the clonal populations reveals a substantial level of heterogeneity across and also within the various stages of breast carcinogenesis. This intra-stage heterogeneity is manifested by differences in cell proliferation, where the fast-proliferating subclass is further enriched in oxidative phosphorylation and cell death.

overall_design: Outgrowth of clonal cell populations was analysed when the maximum tumour volume comprising all tumour stages (normal mammary gland, hyperplasia, adenoma, carcinoma, pulmonary metastases) had been reached in colour-induced MMTV-PyMT; R26-CBW; K8-CreERT2 mice. Zonal patches of clonal populations of the primary tumour as well as metastases were isolated by Laser Capture Microdissection (encircled regions) and samples obtained were subjected to RNA sequencing. n = 3.

first: Stefanie

last: Tiede

first: Ravi

last: Kalathur


title: Construction of IRX4-inducible system in pancreatic cancer cell lines, PK-1 and PK-9

summary: Epigenetic gene silencing by aberrant DNA methylation is one of the important mechanisms leading to the loss of key cellular pathways in tumorigenesis. We have previously reported that IRX4 (Iroquois homeobox 4) was highly downregulated by promoter hypermethylation in pancreatic cancer cell lines as well as in resected primary pancreatic cancers. Based on these data, we have constructed a tetracycline-inducible IRX4 expressing system using pancreatic cancer cell lines PK-1 and PK-9. IRX4 induction significantly suppressed cell growth and caused apoptosis in both PK-1 and PK-9. Because IRX4 is a sequence-specific transcription factor, we tried to analyze IRX4 downstream events by performing microarray analyses using IRX4 inducible PK-1 cells with or without tetracycline. We found that IRX4 induction upregulated several genes that had tumor suppressive functions such as PRDM1, CRYAB, and IL32, and downregulated several genes that had oncogenic functions such as PTCH1, CD36, TFAP2C, and MUC4. These results suggest that DNA methylation-mediated silencing of IRX4 may contribute to pancreatic tumorigenesis through aberrant transcriptional regulation of cancer-related genes.

overall_design: Two pancreatic cancer-derived cell lines, PK-1_IRX4#28 and PK-9_IRX4#23, that allow tetracycline-regulated IRX4 expression were constructed. The RNAs from PK-1_IRX4#28 and PK-9_IRX4#23 with (4 days treatment) or without tetracycline were prepared and analyzed by using Agilent whole human genome microarray (4×44K) v2.


title: High-throughput RNA sequencing analysis of human nasopharyngeal carcinoma cell line HK1 transfected with E2F1 siRNA or E2F3 siRNA

city: Changsha

first: Jian

last: Ma

state: Hunan

address: 110 Xiangya Road

department: Cancer Research Institute

institute: Central South University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are using  RNA sequencing analysis to evaluate the effects of si-E2F1 (or E2F3) on the mRNA of human nasopharyngeal carcinoma cell line HK1.
Methods: Human nasopharyngeal carcinoma cell line HK1 was transfected with a control non-targeting siRNA to cells or transfected with siRNA targeting E2F1 (or E2F3) for 48 hours in DMEM medium (with 10% serum). Total RNA were extracted and detected by Illumina high-throughput RNA sequencing data analysis. 3 independent biological replicates were plated, transfected in parallel for each control and siRNA.
Results: Log-fold changes of up- or down-regulated mRNAs between the control and experiment group were selected with a significance threshold of p<0.05.
Conclusions: Our study describes the mRNA changes of human nasopharyngeal carcinoma cell line HK1 transfected with E2F1 (or E2F3) siRNA.

overall_design: Human nasopharyngeal carcinoma cell line HK1 mRNA profiles of “control” (cells was transfected with a control non-targeting siRNA) and “si-E2F1”(cells was transfected with E2F1 siRNA)  and “si-E2F3”(cells was transfected with E2F3 siRNA) were generated by RNA sequecning, using Illumina high-throughput sequencing service (Microanaly, Shanghai, China).

first: Peishan

last: Liu


title: H3 K27M and EZHIP impede H3K27-methylation spreading by inhibing allosterically stimulated PRC2 [K27M]

last: Lewis

first: Siddhant

last: Jain


title: CX3CL1 and IL-15 Promote CD8 T Cell Chemoattraction in HIV and in Atherosclerosis

city: Cleveland

first: Mark

last: Cameron

state: OH

address: 10900 Euclid Ave

department: Population and Quantitative Health Sciences

institute: Case Western Reserve University

summary: Atherosclerotic cardiovascular disease (ASCVD) remains an    important cause of morbidity in the general population and risk for ASCVD    is increased approximately 2-fold in persons living with HIV infection    (PLWH). This risk is linked to elevated CD8 T cell counts that are abundant    in atherosclerotic plaques and have been implicated in disease pathogenesis    yet the mechanisms driving T cell recruitment to and activation within    plaques are poorly defined. Here we investigated the role of CD8 T cells in    atherosclerosis in a non-human primate model of HIV infection and in the    HIV-uninfected elderly; we sought to identify factors that promote the    activation, function, and recruitment to endothelium of CX3CR1+ CD8 T    cells. We measured elevated expression of CX3CL1 and IL-15, and increased    CD8 T cell numbers in the aortas of rhesus macaques infected with SIV or    SHIV, and demonstrated similar findings in atherosclerotic vessels of    HIV-uninfected humans. We found that recombinant TNF enhanced the    production and release of CX3CL1 and bioactive IL-15 from aortic    endothelial cells, but not from aortic smooth muscle cells. IL-15 in turn    promoted CX3CR1 surface expression on and TNF synthesis by CD8 T cells, and    IL-15-treated 60 CD8 T cells exhibited enhanced CX3CL1-dependent    chemoattraction toward endothelial cells in vitro. Finally, we show that    CD8 T cells in human atherosclerotic plaques have an activated, resident    phenotype consistent with in vivo IL-15 and CX3CL1 exposure. In this    report, we define a novel model of CD8 T cell involvement in    atherosclerosis whereby CX3CL1 and IL-15 operate in tandem within the    vascular endothelium to promote infiltration by activated CX3CR1+ memory    CD8 T cells that drive further endothelial activation via TNF. We propose    that these interactions are prevalent in aging and in PLWH, populations    where circulating activated CX3CR1+ CD8 T cell numbers are often expanded.

overall_design: Sorted CD8 T cells from 5 donors were sequenced under 4 stim conditions and a control (CD3.CD28, CD2, IL15, oxLDL and Medium) across two timepoints (6 and 24 hours).

first: S

last: Panigrahi

first: B

last: Chen

first: M

last: Fang

first: D

last: Potashnikova

first: A

last: Komissarov

last: Lebedeva

first: G

last: Michaelson

first: J

last: Wyrick

last: Morris

last: Sieg

last: Paiardini

first: F

last: Villinger

first: K

last: Harth

first: V

last: Kashyap

first: C

first: E

last: Vasilieva

first: L

last: Margolis

last: Younes

first: N

last: Funderburg

last: Zidar

last: Lederman

last: Freeman


title: H3 K27M and EZHIP impede H3K27-methylation spreading by inhibing allosterically stimulated PRC2 [EZHIP]

first: Peter

last: Lewis

overall_design: Profiling genomic enrichment of H3K27me3, EZH2 and EZHIP

last: Jain


title: The Folate Cycle Enzyme MTHFR is a Critical Regulator of Cell Response to MYC-Targeting Therapies

city: Paris

first: Camille

last: Lobry

address: 16 rue de la Grange aux Belles

department: IRSL Inserm U944 / CNRS UMR7212

country: France

institute: Inserm

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

overall_design: Refer to individual Series


title: Real-time quantitative PCR analysis of human perhiperal blood mononuclear cells following mind-body interventions

city: Nijmegen

first: Ivana

last: Buric

address: Montessorilaan 3

country: Netherlands

institute: Donders Institute for Brain, Cognition and Behaviour, Raboud University

summary: This study was the first randomized controlled trial to test if mind-body interventions can improve self-regulation in prisoners with different personality disorders, using a combination of gene expression, neural, and behavioral measures.Thirty prisoners with personality disorders who score high on psychopathy were assigned to a mindfulness intervention (n=10), a yoga intervention (n=10), or a wait-list control group (n=10) using stratified random sampling. Both mindfulness and yoga interventions were held at the same time and lasted three hours per day on five consecutive days. At baseline and after the intervention, we measured inflammation-related gene expression; resting state brain activit with electroencephalography (EEG); risk-taking and attention with cognitive tasks; event-related potentials (ERPs) related to the attention task; and stress, emotion regulation and mindfulness with questionnaires. We expected that both yoga and mindfulness would improve self-regulation (i.e., executive attention, emotion regulation and self-awareness), reduce stress and risk-taking behavior, downregulate inflammatory-related gene  expression and increase alpha and theta power. Blood was collected for the analysis of changes in gene expression of 38 genes related to inflammation and the immune system (IL-1 signaling pathway). Venipuncture samples were collected into 10ml EDTA tubes, lysed and frozen at -80°C. Peripheral blood mononuclear cells were isolated by density gradient centrifugation. Ribonucleic acid (RNA) was extracted (QiaAmp RNA Blood Mini kit; Qiagen) and tested for suitable mass and integrity (NanoDrop One, Acclaro Sample Intelligence; Thermo Scientific). RNA was then converted to fluorescent cRNA for hybridization to IL-1 signaling pathway plate H96 (Bio-Rad Labs Ltd, UK). Gene expression data were expressed as cycle threshold (CT) values by calculating 2−ΔΔCT, and referencing to the geomean of all genes because endogenous control genes that are supposed to have constant levels of expression were not stable in this case. After normalizing 2−ΔΔCT to the wait-list control group median, the data were imported into SPSS and analyzed by group allocation based on change scores of each normalized 2−ΔΔCT. Intent-to-treat (ITT) principles were used for all the analyses. Post-intervention missing  data was handled by running multiple imputations. A p-value of <0.05 was considered significant and Bonferroni correction was implemented to adjust for multiple comparisons (i.e., <.02 was considered significant in individual 2-group comparisons). The data were analyzed with the IBM SPSS 24.0 software (Statistical Package for Social Sciences, SPSS Inc., 237 Chicago, IL). The effectiveness of interventions was tested by calculating changes scores and running non-parametric Kruskal-Wallis test for K independent samples because the assumptions for ANOVA were not met. If there was a significant difference detected, it was followed with Mann-Whitney U test 240 and Kolmogorov-Smirnov Z test to determine specific group differences. Additionally, eta squared was used as a measure of effect size to determine the proportion of variability in outcomes that can be explained by group membership.We found no significant changes in gene expression or any other measures.

overall_design: qPCR gene expression profiling

first: Christopher

last: Mee


title: DCAF1 regulates Treg senescence via the ROS axis during immunological aging

status: Public on Oct 10 2020

city: Chapel Hill

first: Zengli

last: Guo

state: NC

address: 125 Mason Farm Road

department: Lineberger Comprehensive Cancer Center

institute: University of North Carolina at Chapel Hill

summary: Total RNA of regulatory T (Treg) cells and conventional CD4 T (Tconv) cells from young WT (2 months), aged WT (>18 months) and young Dcaf1-deficient mice was extracted and RNA-seq libraries were generated. Reads (32-45 Million reads per sample) were analyzed with Salmon software to align and quantify the transcript expression. R packages in Bioconductor, tximport and tximportData were used to aggregate transcript-level quantifications to the gene level, with the R package biomaRt for gene and transcripts mapping. The option "lengthScaledTPM" for countsFromAbundance in tximport was used to obtain the estimated counts at the gene level using abundance estimates scaled based on the average transcript length over samples and the library size.  The option "lengthScaledTPM" for countsFromAbundance in tximport was used to obtain the estimated counts at the gene level using abundance estimates scaled based on the average transcript length over samples and the library size. For the differential expression (DE) analysis of RNA-seq data, gene-level count matrix was passed into by DESeq2 package as input directly from the tximport package. The normalized gene expression data was retrieved from DESeq2 analysis after regulated log (rlog) transformation (‘rlog’ in DESeq2). The z-score at gene-level average of normalized expression matrix was used to generate heatmap in Gene-E from Broad Institute (www.broadinstitute.org/ /GENE-E/).  Gene Set Enrichment Analysis was performed using the Java application available from Broad Institute (www.broadinstitute.org/gsea/). Gene set databases including Hallmarks (h.all.v6.1.symbols.gmt) and KEGG (c2.cp.kegg.v6.1.symbols.gmt) from the Molecular Signatures Database (MSigDB) were used in the analysis. The aging-program gene set was from DEMAGALHAES_AGING_UP in MSigDB. One thousand gene set permutations were performed. FDR<0.05 was used for enriched terms, as is recommended when performing permutations by gene set.

overall_design: Examination of differential gene expression in regulatory T (Treg) cells and conventional CD4 T (Tconv) cells from young WT (2 months), old WT (>18 months) and young (2 months) Dcaf1-deficient mice.

first: Di

last: Wu

first: Yisong

last: Wan

first: Jitong

last: Lou


title: Application of MeTA-array to nine pancreatic cancer cell lines

first: Shinichi

last: Fukushige

summary: Aberrant DNA hypermethylation, the most well defined epigenetic changes in cancer, is associated with inappropriate gene silencing and this feature is utilized to search for tumor-specific DNA methylation biomarkers. Methyl-CpG binding domain (MBD) proteins (MBPs) can elicit the repressive potential of methylated DNA and play a major role in gene silencing mechanisms. Therefore, if the genes governed by MBPs are specifically reactivated, it should be possible to uncover them. We developed a method termed “methyl-CpG targeted transcriptional activation (MeTA)” that employs a fusion gene comprised of the MBD from MBD2 and the NFkB transcriptional activation domain. Microarray coupled with MeTA (MeTA-array) provides not only the information about methylated genes but also the one about transcriptional repression in a single experiment. We applied MeTA-array to 12 pancreatic cancer cell lines along with HPDE (normal pancreatic ductal epithelial cell line) and identified 31 candidate tumor-specific hypermethylated genes; 26 of them have never been reported previously using the conventional DNA demethylating agents. Seven genes, IRX4, LHX6, NEFH, NEFL, NEFM, NPTX2 and TMEM204 were further examined their methylation statuses by MSP, and we found that 100% (21/21) of IRX4, 62% (13/21) of LHX6, 100% (21/21) of NEFH, 100% (21/21) of NEFL, 100% (21/21) of NEFM, 100% (21/21) of NPTX2 and 95% (20/21) of TMEM204 were methylated in our series of pancreatic cancer cell lines. Furthermore, 68% (15/22) of IRX4, 55% (12/22) of LHX6, 55% (12/22) of NEFH, 59% (23/22) of NEFL, 82% (18/22) of NEFM and 82% (18/22) of NPTX2 were also hypermethylated in primary pancreatic cancer specimens in a tumor-specific manner. Our results suggest that MeTA-array is a highly efficient method to identify methylation-mediated transcriptionally silenced genes in human cancer.

overall_design: Nine pancreatic cancer cell lines, PK-1, PK-8, PK-9, PK-45P, PK-45H, PK-59, PCI-6, PCI-35, and BxPC-3 were transfected with the plasmid containing NFkB (AD)-MBD or the vector alone. These RNAs were prepared and analyzed by using Agilent whole human genome microarray (4×44K) .


title: Hypothalamic REV-ERBs Control Circadian Food Intake and Leptin Sensitivity [RNA-seq]

first: Hoang

last: Nguyen

overall_design: Transcriptomic profiling (RNA-seq) of punched-out hypothalamic nuclei (ARC or VMH) harvested from control or REV-ERBS (alpha and beta) DKKO mice on control treated with either normal chow, high fat diet (HFD), fasting, refeeding, or treated with leptin. Library was prepared with Illumina Truseq kit and sequenced on  Illumina Hiseq 4000 sequencer.

first: Marine

last: Adlanmerini

first: Mitchell

last: Lazar


title: Comparative gene expression of CD34+ human hematopoietic progenitor cells upon knockdown of STAT5

first: Franck

last: Letourneur

address: 22 rue mechain

institute: INSERM

summary: The objective of the study is to identify the genes regulated by STAT5 in very primitive human hematopoietic stem progenitor cells (HSPCs). We used Affymetrix Human Genome U133 Plus 2.0 microarrays to investigate gene expression in human CD34+CD38- HSPC upon expression of STAT5 or control luciferase shRNA-encoding vectors.

overall_design: Human cord bloods were collected and CD34+ cells were isolated and immediately frozen. CD34+CD38- were sorted from thawed cells and cultured for one day in four-cytokine (IL3, 10 ng/ml; Flt3L, 100 ng/ml; SCF, 100 ng/ml; TPO, 20 nM) minimal cocktail medium before being transduced at multiplicity of infection of 20 with Ctl luciferase- or STAT5-shRNA encoding lentiviral vectors that co-express GFP marker. A few hours later, cells were seeded on MS5 stromal layer and allowed to grow for 5 days. CD34+/GFP+ cells were then sorted and RNA were prepared using Trizol reagent according to manufacturer’s instructions.

first: Séverine

last: Martin-Lanneree

first: Isabelle

last: Dusanter-Fourt


title: RNA-Sequencing for pancreatic cancer cells with scramble-shRNA and GPx1-shRNA

city: Shanghai

first: Qingcai

last: Meng

address: No. 270 Dong'An Road

department: Department of Pancreatic Surgery

institute: Fudan University Shanghai Cancer Center

summary: We reported glutathione peroxidase-1 (GPx1) was negatively associated with overall survival in pancreatic ductal adenocarcinoma patients. Silencing GPx1 in pancreatic cancer cells showed epithelial–mesenchymal transition phenotype and increased chemoresistance to gemcitabine in vitro and in vivo. Next, to search for a putative molecular mechanism, we used a high-throughput gene expression profiling array in scramble-shRNA and GPx1-shRNA pancreatic cancer cells (MiaPaCa-2). This study provides the differentially expressed genes and altered signaling pathways towards characterization of gemcitabine resistance cell populations.

overall_design: The mRNA profiles of scramble-shRNA and GPx1-shRNA pancreatic cancer cells were generated by RNA-sequencing, in triplicate, using Illumina HiSeq 4000 Sequencing System.

first: Xianjun

last: Yu


title: A high glycemic burden drives functional and metabolic alterations of human monocytes in patients with type 1 diabetes

status: Public on Oct 09 2020

city: Wageningen

first: Guido

last: Hooiveld

address: HELIX, Stippeneng 4

department: Div. Human Nutrition & Health

institute: Wageningen University

summary: Diabetes mellitus is associated with serious long-term complications, including increased cardiovascular risk and a higher occurrence of infections. These diabetes-related complications are suggestive of altered responses of the innate immune system. Recent studies have shown that energy metabolism of monocytes is a crucial determinant of their functionality. Here we investigate whether metabolism and function of monocytes are changed in patients with diabetes and aim to identify diabetes-associated factors driving these alterations. Patients with type 1 diabetes (T1D) and healthy age-, sex- and BMI-matched nondiabetic controls were recruited and detailed characteristics related to disease status including diabetes duration and glycemic burden (HbA1c levels) were collected. Monocytes were isolated from peripheral blood to determine immune functionality, metabolic responses and to perform transcriptome analyses. Upon ex vivo stimulation with TLR-4 agonist LPS or TLR-2 agonist P3C, monocytes of patients with T1D secreted lower levels of various cytokines (TNFα, IL-1β and IL-1Ra) and had lower glycolytic rates in comparison to monocytes isolated from matched controls. Stratification based on HbA1c levels revealed that a lower cytokine secretion was coupled to a higher glycolytic rate of monocytes in patients with a higher glycemic burden. Gene expression signatures of circulating monocytes displayed an enhanced inflammatory expression pattern that was associated with this high glycemic burden. A high glycemic burden in patients with T1D promotes expression of inflammatory genes of monocytes in vivo and is coupled to an impaired relationship between metabolism and inflammatory function upon activation ex vivo.

overall_design: Microarray analysis was performed on CD14+ monocytes isolated from peripheral blood mononuclear cells obtained from patients with type 1 diabetes and healthy nondiabetic control subjects

first: Kathrin

last: Thiem

first: Xanthe

last: van Dierendonck

first: Rinke

last: Stienstra


title: Hypothalamic REV-ERBs Control Circadian Food Intake and Leptin Sensitivity


title: CRISPR-induced deletion of honey bee orco gene

city: Princeton

first: Ian

middle: Michael

last: Traniello

state: NJ

address: Princeton University

department: Lewis-Sigler Insitute for Genomic Biology

institute: Princeton University


title: Cytoplasmic Miz1 Suppresses TNF-α-Induced NF-κB Activation and Hepatocellular Carcinoma Progression via the Interaction with Metadherin

first: Guangyan

last: Zhangyuan

state: Shanghai

address: 197 Ruijin Er Road

department: Department of General Surgery, Pancreatic Disease Center

institute: Ruijin Hospital, Shanghai Jiao Tong University School of Medicine

summary: Previous studies have revealed that nuclear Miz1 is implicated in the regulation of several cancers mainly relying on its POZ domain. Current study, however, uncovers an unexpected function of cytoplasmic Miz1 in hepatocellular carcinoma (HCC). In vivo HCC models in Miz1 and Miz1(POZ) KO mice along with RNA-sequencing experiments show that hepatocyte specific ablation of Miz1 exacerbates TNF-α-induced NF-κB activation and promotes the progression of HCC independent of its transcriptional activity. Ubiquitination and proteosomal degradation of cytoplasmic Miz1 liberates its novel partner Metadherin (MTDH), and its site specific phosphorylation is critical to NF-κB activation. These findings reveal a brand new role of cytosolic Miz1 as a suppressor of HCC, and provide profound insights into liver cancer diagnosis and treatment.

overall_design: Miz1fl/fl and Miz1(POZ)fl/fl mice were crossed with Alb-Cre transgenic mice (C57BL/6 background) to generate an hepatocyte specific knock out of Miz1 and Miz1(POZ) respectively(Miz1△Hep, Miz1(POZ)△Hep). For different groups of mice (Miz1fl/fl, Miz1△Hep, Miz1(POZ)fl/fl, Miz1(POZ)△Hep), HCC was induced by the combination of DEN (25 mg/kg i.p.) given at Week 2 postpartum followed by weekly injections of CCl4 (0.5 ml/kg i.p., dissolved in corn oil). Mice were sacrificed at the age of 5 months and pure tumors from Miz1fl/fl, Miz1△Hep, Miz1(POZ)fl/fl, Miz1(POZ)△Hep mice were subjected to RNA sequencing, in triplicate. All animal experimental protocols were approved by the Animal Ethics Committee of Nanjing Medical University.

first: Wenjie

last: Zhang

first: Kangpeng

last: Jin

first: Fei

last: Wang

first: Xiaochen

first: Weiwei

first: Ruyi

last: Huang

first: Xiaoliang

last: Xu

first: Haiyuan

last: Shen

first: Mulong

last: Du

first: Haitian

first: Yin

last: Yin

first: Guisheng

last: Zhong

first: Anning

last: Lin

first: Beicheng

last: Sun


title: Effects of temporal segmentation of meal composition on human adipose tissue transcriptome

city: Mannheim

first: Carsten

last: Sticht

address: Theodor-Kutzer-Ufer

department: ZMF

country: Germany

institute: University Heidelberg

summary: There is few data about effects of temporal segmentation of meal composition on the metabolic response in humans. The meal-induced hormonal secretion in humans strongly depends on the meal composition and on the day time and may be involved in the circadian entrainment of metabolic gene expression. Our study investigated effects of two different diurnal patterns of meal composition (carbohydrate-rich meals in the morning and fat-rich meals in the evening or vice versa) on the gene expression in human subcutaneous adipose tissue (SAT).

overall_design: 15 non-diabetic non-obese men participated in the cross-over study. We compared effects of two 4-week isocaloric diets – (1) HC/HF diet consisted of a carbohydrate-rich breakfast and lunch (65 EN% carbohydrates, 20 EN% fat, 15 EN% protein) and a fat-rich snack and dinner (35 EN% carbohydrates, 50 EN% fat, 15 EN% protein) and (2) HF/HC diet consisted of a fat-rich breakfast and lunch and a carbohydrate-rich snack and dinner. At the end of each intervention period, subcutaneous adipose tissue biopsies were collected three times during the investigation day (at 8.40, 12.20 and 19.00).

first: Olga

last: Pivovarova

first: Katharina

last: Kessler

first: Silke

last: Hornemann

first: Norbert

last: Gretz

first: Achim

last: Kramer

first: Andreas

middle: F

last: Pfeiffer


title: Potentiating the activity of berberine for Staphylococcus aureus in a combinatorial treatment with thymol

city: Istanbul

first: Cemile

middle: Selin

last: Aksoy

address: Marmara Uni, Bioengineering Dep., No:404 Kadıköy

department: Bioengineering

country: Turkey

institute: Marmara University

summary: In the current study, RNA sequencing based transcriptional profiling was used to elaborate the combinatorial effect of berberine, a well-known antibacterial alkaloid, and thymol, a monoterpenic phenol, on the Staphylococcus aureus transcriptome.

overall_design: Staphylococcus aureus cells treated with 32 μg/mL berberine and 64 μg/mL thymol combination for one-hour were compared with the control (DMSO treated) cells.

first: Berna

last: Sariyar-Akbulut


title: Nucleosome assembly protein-1 (NAP-1) is regulator of histone H1 acetylation

city: Nagasaki

first: Mitsuhiro

last: Yoneda

address: 1-12-4 Sakamoto

institute: Nagasaki University

summary: We identified NAP-1 as regulator of histone H1 acetyation.

overall_design: mRNA expression profile of control-, NAP-1-, and CBP- knockdown in Drosophila S2 cells were generated by deep sequencing in duplicate, using illumina MiSeq.

first: Masamichi

last: Doiguchi

first: Takashi

last: Ito


title: Transcriptomic analyses of different Tetranychus urticae strains that differ in their resistance to the acaricide pyflubumide

city: Gent

first: Nicky

last: Wybouw

address: Coupure Links 653

department: Department of Crop Protection

country: Belgium

institute: University of Ghent

summary:
No major transcriptomic differences were observed between JPR-R1/2 and JPR when strains were not exposed to pyflubumide. Only three genes (tetur13g01730, tetur14g03160, and tetur14g01700) were consistently up-regulated in JPR-R1/2, but none coded for enzymes that are known to be associated with xenobiotic metabolism. As a next step, we used the original and susceptible JPO strain, the parent of JPR, as a reference to investigate transcriptomic changes. Compared to JPO, 16 cytochrome P450s were up-regulated in JPR, whereas two CCE genes were down-regulated. In both JPR-R1/2, 13 cytochrome P450s were up-regulated compared to JPO, of which 11 genes already showed significant up-regulation in JPR (CYP392D2, CYP392D6, and CYP392E8 had the highest average transcriptional increase).
As only limited constitutive gene expression differences were observed between JPR and the JPR-R1/2 strains, the plastic, environmentally dependent, transcriptomic changes were characterized to shed light on the molecular basis of pyflubumide resistance. After nine hours of exposure to a non-lethal dose of pyflubumide (100 mg/L), no DEGs were detected in JPR-R1 upon pyflubumide exposure, whereas only a single DEG (tetur04g04350, log2FC of 1.17) was observed in JPR. After 24 hours of exposure to pyflubumide (100mg/L), large transcriptomic responses were observed in JPR-R1/2. Eight cytochrome P450s were part of the positively correlated response, of which five (CYP385C4, CYP385C4v2, CYP392D2, CYP392E8, and CYP392A4) showed up-regulation after exposure to pyflubumide.

overall_design: Three major experimental set-ups were performed and differed in the exposure of T. urticae strains to pyflubumide. The studied strains were: JPO, JPR, JPR-R1, and JPR-R2. JPO is the parental, sensitive strain. JPR, JPR-R1, and JPR-R2 are all resistant to pyflubumide. First, four replicates were collected from JPO, JPR, JPR-R1, and JPR-R2 that were maintained for one generation on non-sprayed plants. Second, four replicates were collected from JPR and JPR-R1 that were either exposed to pyflubumide (100 mg/L) or water for 9h. Third, four replicates were collected from JPR-R1 and JPR-R2 that were either sprayed with pyflubumide (100 mg/L) or water 24 h before collection.

first: Seyedeh

last: Masoumeh Fotoukkiaii

first: Thomas

last: Van Leeuwen


title: Transcriptome analysis reveals regulation of gene expression during photoacclimation to high irradiance levels in Dunaliella salina (Chlorophyceae)

city: Qingdao

first: Yuanxiang

last: Li

address: Nanhai Road 7

institute: Institute of Oceanology, Chinese Academy of sciences

summary: The unicellular green alga Dunaliella salina is an attractive model organism for studying photoacclimation responses. Changes in irradiance levels during cell growth affect the organization and structure of the photosystem and the pigments composition. We sequenced the RNA of D. salina to investigate the transcriptomic response of the organism after transitioning from normal light conditions to higher light intensity. Specific transcripts encoding for enzymes involved in photosynthesis were down-regulated, whereas genes involved in the metabolism of carotenoid and triacylglycerol were up-regulated. Genes encoding for photoprotective enzymes related to reactive oxygen species (ROS) scavenging and to the xanthophyll cycle were also up-regulated at higher irradiance levels. The present transcriptomic study would assist in the comprehensive understanding of photoacclimation mechanisms of D. salina.

overall_design:
9 biological samples, each condition in triplicates.
Please note that the microalgae Dunaliella Salina used in our study was conserved at Institute of Oceanology, Chinese Academy of Sciences. It has been identified, and its related research results have been published in Algal Research (Zheng, Zhenbing, et al. 'The enhancement of the oxidative pentose phosphate pathway maybe involved in resolving imbalance between photosystem I and II in Dunaliella salina.' Algal Research 26(2017).)

first: Guangce

last: Wang


title: Pilot study of transcriptomic responses to IL13 and HRV-A and their interaction

status: Public on Oct 08 2020

city: Denver

first: Satria

last: Sajuthi

state: Colorado

address: 1400 Jackson St.

institute: National Jewish Health

summary: We seek to determine how IL-13 modifies airway cell responses to HRV infection

overall_design:
Bulk RNA-seq,: 5 control + 5 HRV-A + 5 IL13
scRNA-seq: 1 paired Mock + IL13 and 1 in-vivo nasal brush

middle: P

first: Peter

last: Deford

first: Yingchun

first: Nathan

middle: D

last: Jackson

first: Michael

last: Montgomery

first: Jamie

last: Everman

first: Cydney

last: Rios

first: Elmar

last: Pruesse

first: James

last: Nolin

first: Elizabeth

middle: G

last: Plender

last: Wechsler

first: Angel

last: Mak

first: Celeste

last: Eng

first: Sandra

last: Salazar

first: Vivian

last: Medina

first: Eric

last: Wohlford

first: Scott

last: Huntsman

first: Deborah

last: Nickerson

first: Soren

last: Germer

last: Zody

first: Goncalo

last: Abecasis

first: Hyun

last: Kang

first: Kenneth

last: Rice

first: Rajesh

last: Kumar

first: Sam

last: Oh

first: Jose

last: Rodriguez-Santana

first: Esteban

last: Burchard

first: Max

last: Seibold


title: Identification of adult endothelial stem cells with endothelial and haemopoietic reconstitution potential

city: St. Lucia

first: Othmar

last: Korn

state: Queensland

address: University of Queensland

country: Australia

institute: Australian Institute for Bioengineering and Nanotechnology

summary: Hemopoietic stem cells (HSC) reside in marrow niches, producing circulating blood cells. Interfacing blood and the niche are sinusoidal endothelial cell lined vessels. Bone marrow (BM) sinusoids have been identified as critical stem cell regulators and a key niche component. However, little is known about the characteristics or functional capacity of marrow endothelial cells. We have identified, prospectively isolated and characterized marrow scavenging sinusoidal endothelial cells with immense endocytic capacity, demonstrating a hierarchical organization and a sub-population highly enriched for endothelial sinusoidal stem cells (BM-ESSC) in endosteal BM with long-term serial transplant potential and revascularization of recipient marrow. In addition, we also demonstrate that BM-ESSC have hemogenic potential: giving rise to long-term multi-lineage reconstituting HSC. These findings represent a paradigm shift and a major advance in the understanding of marrow sinusoidal endothelial cells and HSC in vivo. Identification of human endothelial counterparts and their use in transplantation may lead to improved clinical outcomes.

overall_design: Total RNA obtained from cells isolated from mouse bone marrow endosteal region by flow cytometry

first: Peter

last: McCourt

first: Ana

last: Oteiza

first: Melonie

middle: J

last: Storan

first: Brenda

last: Williams

first: Chad

last: Heazlewood

first: Karen

last: Sørensen

first: Songhui

last: Li

first: Christian

last: Nefzger

first: Yoshiaki

last: Kubota

last: Polo

first: Susan

last: Nilsson


title: Three-dimensional human alveolar stem cell culture models reveal infection response to SARS-CoV-2

city: Daejeon

first: Young Seok

last: Ju

address: Daehak-ro 293

institute: KAIST

summary: Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2), which is the cause of a present global pandemic, infects human lung alveolar type 2 (hAT2) cells. Characterizing pathogenesis is crucial for developing vaccines and therapeutics. However, the lack of models mirroring the cellular physiology and pathology of hAT2 cells limits the study. Here, we develop a feeder-free, long-term three-dimensional (3D) culture technique for hAT2 cells, and investigate infection response to SARS-CoV-2. By imaging-based analysis and single-cell transcriptome profiling, we reveal rapid viral replication and the increased expression of interferon-associated genes and pro-inflammatory genes in infected hAT2 cells, indicating robust endogenous innate immune response. Further tracing of viral mutations acquired during transmission identifies full infection of individual cells effectively from a single viral entry. Our study provides deep insights into the pathogenesis of SARS-CoV-2, and the application of defined 3D hAT2 cultures as models for respiratory diseases.

overall_design: Of total, six of SARS-CoV-2 infected Vero cells were deposited here. Two biological replicates were sequenced at post infection day 0, 1, and 2, respectively.

first: Young

middle: S

first: Joo-Hyeon

last: Lee

first: Byeong-Sun

last: Choi

first: Gou

last: Koh

last: Kim


title: Easy characterization of transcription by Chromatin-Associated Transcript sequencing

first: Violaine

last: Saint-Andre

address: 26 rue d'Ulm

institute: Institut Curie

summary: In the last decade, new high-throughput sequencing techniques have revealed the complexity of the human transcriptome, allowing the characterization of long non-coding (lnc)RNAs. Since their expression has been reported as very specific to tissue, developmental stage and pathological variations, some lncRNAs have been proposed as biomarkers for diagnosis as well as prognosis of tumors. In this project, we investigate a role for the poorly characterized class of lncRNAs, antisense lncRNAs, and their association to the epithelial-to-mesenchymal transition (EMT), a biological process that promotes metastasis. In order to measure the transcription and properly describe the gene-structure of unannotated lncRNAs at the genome-wide level, we adapted a protocol of subcellular fractionation from Gagnon et al. (2014) to isolate nascent chromatin-associated transcript. This was performed on an in vitro model (Castro Vega et al, 2015) in which primary HEK cells naturally undergo EMT. Cells were immortalized prior and after EMT, therefore giving rise to the Epi (HA5-Early) and Mes (HA5-Late) cell-lines, which respectively display epithelial and mesenchymal phenotypes. In addition to the chromatin fraction, the cytoplasmic fraction of the cells was also sequenced in order to decipher the complexity of the transcriptome and assess the composition of mature transcripts.

overall_design: The experiment was performed in biological duplicates on each cell-line (Epi and Mes) and RNA from both cytoplasmic and chromatin fraction was sequenced.

first: Marina

last: Pinskaya

first: Julien

last: Jarroux

first: Antonin

last: Morillon


title: Density dependent gene expression change in RAW264.7 cells stimulated without or with LPS.

city: Kalyani

first: Partho

middle: Sarothi

last: Ray

state: West Bengal

address: Mohanpur

department: Department of Biological Sciences

country: India

institute: Indian Institute of Science Education and Research Kolkata

summary: Quorum sensing mechanisms that sense the density of macrophages at the site of inflammation, to initiate inflammation resolution, have recently been demonstrated as a major determinant of the inflammatory response. We observed a density-dependent increase in expression of the inflammatory tumor suppressor protein programmed cell death 4 (PDCD4) in mouse macrophage cells. Conditioned medium from high density cells upregulated PDCD4 expression, revealing the presence of a secreted factor(s) acting as a macrophage quorum sensor. Secreted gelsolin (GSN) was identified as the quorum sensor and alteration of GSN levels changed PDCD4 expression. LPS induced the expression of microRNA miR-21 which downregulated GSN expression and reversed the high density phenotype. The high density phenotype was correlated with an anti-inflammatory gene expression program, which was counteracted by inflammatory stimulus. Together, our observations establish the miR-21-GSN-PDCD4 regulatory network as a central mediator of a macrophage quorum sensing mechanism for the control of inflammatory responses.

overall_design: The analysis performed on single sample of highly dense, low dense and high dense cells treated with LPS to examine the change of gene expression in high dense cell (HD) with respect to low dense cells (LD). Alteration of gene expression after treatment with LPS to high dense cells also checked.

first: Reshma

last: Sharma

first: Sukhen

last: Mandal


title: Screening for functional circular RNAs using the CRISPR-Cas13 system

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Deep sequencing datasets are used for gRNA library analysis for large-scale screens. Using a lentiviral library that targets sequences across back-splicing sites of highly expressed human circRNAs, we show that a group of circRNAs are important for cell growth mostly in a cell-type specific manner and that a common oncogenic circRNA, circFAM120A, promotes cell proliferation in vitro and in vivo.

overall_design: To screen circRNAs that are important for cell proliferation, the gRNA lentiviral library-infected HT29T, 293FT and HeLa cells harvested in day 1 and day 30 were used for DNA extraction, gRNA enrichment by PCR amplification and deep sequencing.

first: Ling-Ling

last: Chen

first: Siqi

last: Li

first: Xiang

first: Wei

last: Xue


title: Gene expression for circFAM120A knockdown by RfxCas13d/BSJ-gRNA or shRNA in human 293FT cells

summary: Deep sequencing datasets are used for gene expression analysis. Knockdown of circFAM120A by BSJ-gRNA or shRNA revealed that the BSJ-gRNA-mediated knockdown showed a much higher correlation with gene expression compared to shRNA.

overall_design: Poly(A)+ RNA-seq of 293FT circFAM120A knockdown cells by BSJ-gRNA or shRNA are used for gene expression analysis.


title: Repeated sampling facilitates within- and between-subject modeling of the human sperm transcriptome to identify dynamic and stress-responsive sncRNAs

city: Baltimore

first: Christopher

last: Morgan

state: MD

address: 670 W Baltimore St

department: Pharmacology

institute: University of Maryland School of Medicine

summary: Epidemiological studies from the last century have drawn strong associations between paternal life experiences and offspring health and disease outcomes. Recent studies have demonstrated sperm small non-coding RNA (sncRNA) populations vary in response to diverse paternal insults. However, for studies in retrospective or prospective human cohorts to identify changes in paternal germ cell epigenetics in association with offspring disease risk, a framework must first be built with insight into the expected biological variation inherent in human populations. In other words, how will we know what to look for if we don’t first know what is stable and what is dynamic, and what is consistent within and between men over time? From sperm samples from a ‘normative’ cohort of healthy human subjects collected repeatedly from each subject over six months, 17 healthy male participants met inclusion criteria and completed donations and psychological evaluations of perceived stress monthly. sncRNAs (including miRNA, piRNA, and tRNA) isolated from mature sperm from these samples were subjected to Illumina small RNA sequencing, aligned to subtype-specific reference transcriptomes, and quantified. The repeated measures design allowed us to define both within- and between-subject variation in the expression of 254 miRNA, 194 tRNA, and 937 piRNA in sperm over time. We developed screening criteria to identify a subset of potential environmentally responsive ‘dynamic’ sperm sncRNA. Implementing complex modeling of the relationships between individual dynamic sncRNA and perceived stress states in these data, we identified 5 miRNA (including let-7f-5p and miR-181a-5p) and 4 tRNA that are responsive to the dynamics of prior stress experience and fit our established mouse model. In the current study, we aligned repeated sampling of human sperm sncRNA expression data with concurrent measures of perceived stress as a novel framework that can now be applied across a range of studies focused on diverse environmental factors able to influence germ cell programming and potentially impact offspring development.

overall_design: Six sperm samples were collected monthly from 17 healthy male participants. sncRNA (including miRNA, piRNA, and tRNA) were isolated from mature sperm from these samples,  subjected to Illumina small RNA sequencing, aligned to subtype-specific reference transcriptomes, and quantified.

first: Amol

middle: C

last: Shetty

first: Tracy

last: Bale


title: CRISPR-induced deletion of honey bee orco gene [DNA]

first: Ian

last: Traniello

summary: Honey bee embryos were injected either with a CRISPR contruct targeting the orco gene or an injection buffer control. RNA-Sequencing was performed on the antennal mRNA from adult bees within 24 hours of eclosion.

overall_design: 76 orco-knockout and 7 buffer-injected control samples


title: in vivo mRNA display: Large-scale Proteomics by Next Generation Sequencing

city: New York

first: Panos

last: Oikonomou

state: New York

address: 1150 St. Nicholas Ave

department: Biological Sciences

institute: Columbia University

summary: We introduce in vivo mRNA display, a technology that converts a variety of proteomics applications into a DNA sequencing problem.

overall_design: In vivo expressed proteins are coupled with their encoding mRNAs via a high-affinity stem-loop RNA binding domain interaction, enabling high-throughput identification of proteins with high sensitivity and specificity by next-generation DNA sequencing.

first: Roberto

last: Salatino

first: Saeed

last: Tavazoie


title: SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs

city: Cambridge

first: Shira

last: Weingarten-Gabbay

state: MA

address: 75 Ames St

institute: The Broad Institute

summary: T cell-mediated immunity seems to play a critical role against SARS-CoV-2 infection and establishing protective memory. Yet the repertoire of viral epitopes responsible for activation of T cell responses remains mostly unknown. Identification and characterization of viral peptides presented on class I human leukocyte antigen (HLA-I) will reveal the viral signatures as seen by cytotoxic T cells that can then be harnessed for the development of effective vaccines. Here, we report the first HLA-I immunopeptidome of SARS-CoV-2 in two human cell lines at different times post-infection using mass spectrometry. We found HLA-I peptides derived not only from canonical ORFs, but also from internal out-of-frame ORFs in Spike and Nucleoprotein not currently captured by vaccine approaches. Whole proteome analysis revealed that expression of ubiquitination pathway proteins, and the proteasome maturation protein, POMP, were significantly altered in infected cells. Retrospective analysis of computational predictions highlighted shortcomings of in silico-only approaches in recovering the observed viral epitopes. Finally, given the experimental evidence for endogenous processing and presentation of the viral peptides we detected, we estimated that at least one HLA-A, -B, or -C allele is covered by at least one peptide for 99% of the population. These biological insights and the list of naturally presented SARS-CoV-2 peptides will facilitate data-driven selection of peptides for immune monitoring and vaccine development.

sample_organism: Severe acute respiratory syndrome coronavirus 2

overall_design:
RNA-seq of human lung A549 cells and human kidney HEK293T infected with SARS-CoV-2 12h, 18h and 24h post infection
RNA-seq was used to evaluate viral and human transcripts abundance, and the processed file contains the % human and viral of reads in each cell line and time point.

last: Weingaren-Gabbay

first: Susan

last: Klaeger

first: Siranush

last: Sarkizova

first: Nir

last: Hacohen

first: Steven

last: Carr

first: Jennifer

last: Abelin

first: Mohsan

last: Saeed

first: Pardis

last: Sabeti


title: ext Generation Sequencing Facilitates Quantitative Analysis of Wild Type and MAP4K1-/- tumor inflitrating T cell Transcriptomes

city: Guangzhou

first: Lingyun

last: Zheng

state: Guangdong

address: 280 Wai Huan Dong Lu, Guangzhou Higher Education Mega Center

department: School of Life Sciences and Biopharmaceutics

institute: Guangdong Pharmaceutical University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis
Methods: Tumor inflitrating T cell mRNA profiles of 21-day after inoculated in wild-type (WT) and Hematopoietic progenitor kinase 1 (HPK1−/−) mice were generated by deep sequencing, in duplicate, using Illumina HiSeq 2500.

overall_design: Tumor inflitrating T cell mRNA profiles of 21-day after tumor inoculated in wild type (WT) and MAP4K1-/- mice

first: Jingwen

last: Si

first: Xuebin

last: Liao


title: Regeneration in sponge Sycon ciliatum partly mimics postlarval development

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

institute: Marine Biological Association of the UK

summary: We performed high-throughput sequencing on regenerating samples and compared the data with regular embryonic and postlarval development of Sycon ciliatum. Our comparative transcriptomic analysis illuminates that sponge regeneration is equally dynamic as embryogenesis.

overall_design: By using height throughput sequencing  to measured gene expression in regenerating samples at 7-time points spanning from 1 to 24 days including days 1, 2, 3-4, 6-8, 10-12, 16-18 (PJUV) and 21-24 (JUV)

first: Anael

last: SOUBIGOU

first: Ethan

last: Ross

first: V

last: Modepalli


title: Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes

city: Hyderabad

first: Divya Tej

last: Sowpati

state: Telangana

address: Habsiguda

institute: CSIR Centre for Cellular and Molecular biology

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

overall_design: Refer to individual Series


title: Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [5C]

summary: Transcription of genes residing within constitutive heterochromatin is paradoxical to the tenets of epigenetic code. Regulatory mechanisms of Drosophila melanogaster heterochromatic gene transcription remain largely unknown. We investigated the contribution of pericentromeric genome organization and heterochromatic factors in orchestrating heterochromatic gene expression. Using 5C-seq, we characterized the pericentromeric TADs in Drosophila melanogaster. Het TAD borders are enriched in nuclear matrix attachment regions while the intra-TAD interactions are mediated by various insulator binding proteins. Heterochromatic genes of similar expression levels cluster into Het TADs, indicating transcriptional co-regulation. HP1a or Su(var)3-9 RNAi results in perturbation of global pericentromeric TAD organization but the expression of the heterochromatic genes is minimally affected. A subset of active heterochromatic genes has been shown to have combination of HP1a/H3K9me3 with H3K36me3 at their exons. Consequently, knock-down of dMES-4 (H3K36 methyl transferase) downregulates expression of the heterochromatic genes. Furthermore, dADD1, present near the TSS of the active heterochromatic genes, is likely to regulate the heterochromatic gene expression in the presence of HP1a or H3K9me3 marks. Therefore, our findings provide mechanistic insights into the interplay of chromatin interactions and the combination of heterochromatic factors (HP1a, H3K9me3, dMES-4 and dADD1) in regulating heterochromatic gene expression.

overall_design: 5C analysis of pericentromeric heterochromatin in untreated and RNAi knockdown of HP1a and Su(Var)3-9 in Drosophila S2 cells.

first: Parna

last: Saha

first: Divya

first: Ishanee

last: Srivastava

first: Rakesh

last: Mishra


title: CRISPR-induced deletion of honey bee orco gene [RNA-Seq]

first: Ian

last: Traniello

address: Princeton University

institute: Princeton University

overall_design: 5 orco-knockout and 5 buffer-injected control samples


title: Expression data from eight patients with coronary heart disease before and after Tongmai Yangxin Pills treatment for eight weeks.

city: Tianjin

first: Ya-dong

last: Fan

address: No.10 PoYangHu Road, JingHai, District,

institute: Tianjin university of TCM

summary:
The Tongmai Yangxin Pill (TMYX), a patented medicine, has been widely used to treat coronary heart disease (CHD) in China for several decades. Though the anti-inflammatory effect has been preliminarily proposed as one of the potential mechanisms of TMYX for CHD treatment, the underlying mechanisms remain elusive.
We used microarrays to explain the genomic changes of Tongmai Yangxin Pills in the treatment of patients with coronary heart disease, in order to explore the potential mechanism of TCM in the treatment of diseases.

overall_design: Microarray gene expression analysis was used to identify the differentially expressed genes (DEGs) in peripheral blood mononuclear cells of patients before and after TMYX treatment.

first: Yu-hong

last: Bian


title: Loss of transcription factor EB action remodel lipid metabolism and cell death pathways in the cardiomyocyte

city: Saint John

first: Thomas

last: Pulinilkunnil

state: New Brunswick

address: 100 Tucker park road

department: Biochemistry and Molecular Biology

country: Canada

institute: Dalhousie University

summary: Loss of TFEB action, impaired lysosomal autophagy and increased proteotoxicity are observed in numerous metabolic diseases. Previous research from our laboratory demonstrated that glucolipotoxicity following nutrient-overload causes cardiomyocyte injury by inhibiting TFEB and suppressing lysosomal function. However, the identity of signalling and metabolic pathways engaged by the loss of TFEB action in the cardiomyocytes remain unknown. In cardiomyocytes subjected to nutrient-overload ex-vivo, saturated fatty acid, palmitate, but not polyunsaturated fatty acids decreased TFEB content in a concentration- and time-dependent manner. Hearts from high-fat high-sucrose diet-fed mice also exhibited a temporal decline in nuclear TFEB content with marked elevation of distinct lipid species suggesting that when myocyte threshold of lipid loading exceeds its metabolic capacity, loss of TFEB and cardiomyocyte stress is observed. Transcriptome analysis in murine cardiomyocytes with targeted deletion of myocyte TFEB (TFEB-/-) revealed enrichment of differentially expressed genes (DEG) representing pathways of nutrient metabolism, DNA damage and repair, cell death and cardiac function. Strikingly, genes involved in autophagy, proteolysis and lysosome function constituted a small portion of DEGs in TFEB-/- cardiomyocytes signifying that TFEB plausibly regulates non-canonical pathways of cardiac energy metabolism than the canonical pathway of autophagy. TFEB-/- myocytes exhibited higher lipid droplet accumulation and increased caspase-3 activation. Under nutrient-overload condition, restoration of constitutive localization of TFEB in the myocyte nucleus  abrogated increased lipid deposition and caspase-3 activity. Together, our data demonstrated that TFEB insufficiency and its loss of action in the cardiomyocyte remodels energy metabolism and renders the heart prematurely susceptible to nutrient overload-induced injury and failure.

overall_design:
Total RNA from wild-type (WT, n=3) and TFEB-/- (n=3) adult mouse cardiomyocytes were isolated using TRIzol. Sequencing libraries were prepared from 400 ng total RNA using the TruSeq Stranded mRNA Sample Preparation kit (Illumina, San Diego, CA).

Funding source: Diabetes Canada
Grant Title: Role of the lysosome nutrient sensor transcription factor EB in diabetic heart disease
Grant Number: NOD_OG_3-15-5037-TP

Funding source: Diabetes Canada
Grant Title: Lysosomal role of transcription factor EB in diabetic cardiomyopathy
Grant Number: NOD_SC_5-16-5054-TP


title: Interplay of pericentromeric genome organization and chromatin landscape regulates the expression of Drosophila melanogaster heterochromatic genes [RNA-seq]

overall_design: Whole transcriptome analysis of S2 cells in Control and RNAi conditions of HP1a and Su(var)3-9 in triplicates.


title: MERISTEM ACTIVITYLESS1 (MAL1) is involved in crown root development through the maintenance of meristem size in rice

city: Wuhan

first: shaoli

last: zhou

state: Hubei

address: shizishan street

department: National Key Laboratory of Crop Genetic Improvement

institute: Huazhong Agricultural University

summary: Rice MERISTEM ACTIVITYLESS1 (MAL1) is an RING-H2 finger domain (RFD) contained gene. To elucidate the molecular functions of MAL1 during crown root development, we generated MAL1 knock-down transgenic plants. MAL1 RNA interfering (RNAi) transgenic plants exhibited shorter crown root length and less crown root number phenotype accompanied by low cell division rate.Here we sought to find the downstream genes of OsMAL1 in rice crown root tip

overall_design: Genome-wide analysis of 5 day-after-germination crown root tip transcriptomes of MAL1 RNAi and corresponding wild type.

first: W

last: Jiang

first: S

last: Zhou

first: Y

last: Zhao


title: Next Generation Sequencing based mRNA sequencing of human mesenchymal stem cells from hair follicle outer root sheath

status: Public on Oct 07 2020

city: Leipzig

first: Hanluo

last: Li

address: Liebigstraße 12

department: Clinic and Policlinic for Oral-, Jaw- and Plastic Face Surgery

institute: University Hospital Leipzig

summary: Next Generation Sequencing (NGS) based mRNA sequencing (RNA-seq) has provided high-throughput measurements to analyze the transcriptome of cells. We report the comprehensive transcriptome profiling of primarily isolated human mesenchymal stem cells from hair follicle outer root sheath (MSCORS) in series cultivation passages using NGS-based RNA-seq method. Human anagen hair follicles were non-invasively plucked from scalp of healthy donors, cultivated on a Transwell membrane, from which the MSCORS were isolated and subcultured onto normal culture flask. Attached and proliferating MSCORS were cultivated and characterized as mesenchymal stem cells (MSC) according to the minimum criteria for defining multipotent MSC from the International Society for Cellular Therapy (ISCT). mRNA profiles of MSCORS in p0, p1 and p2 were quality controlled, and generated by deep sequencing, in triplicate, using Illumina PE150. Paired-end raw data were pre-processed using a published protocol. HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to align reference genome. HTSeq was used to calculate Reads Count, and gene abundence was determined by analyzing FPKM (fragments per kilobase of exon model per million reads mapped).

overall_design: mRNA profiles of human mesenchymal stem cells from hair follicle outer root sheath (MSCORS) in p0, p1 and p2

first: Ulrich

last: Sack

first: Simin

first: Jan

last: Simon

first: Bernd

last: Lethaus

first: Vuk

last: Savkovic


title: Next Generation Sequencing-based on mRNA sequencing of human adipose mesenchymal stem cells submitted to osteogenic differentiation

summary: Next Generation Sequencing (NGS)-based mRNA sequencing (RNA-seq) has provided high-throughput measurements to analyze the transcriptome of differentiating adipose mesenchymal stem cells. We are reporting  comprehensive transcriptome profiling of primarily isolated human adipose-derived mesenchymal stem cells (ADMSC) throughout consecutive culture passages using NGS-based RNA-seq method. ADMSC were isolated from human adipose tissue, cultured and characterized as mesenchymal stem cells (MSC) according to the minimum criteria for defining multipotent MSC from the International Society for Cellular Therapy (ISCT). After osteogenic differentiation of the ADMSC,  mRNA profiles of ADMSC differentiated for 1 week, 2 weeks and 3 weeks were quality controlled, and generated by deep sequencing using Illumina PE150 kits. Paired-end raw data were pre-processed using a published protocol. HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to align reference genome. HTSeq was used to calculate Reads Count, and gene abundence was determined by analyzing FPKM (fragments per kilobase of exon model per million reads mapped).

overall_design: mRNA profiles of differentiated human adipose-derived mesenchymal stem cells after 1 week, 2 weeks and 3 weeks osteogenic differentiation


title: Clinical and molecular characterization of patients with 16p11.2 microdeletion syndrome

city: Lublin

first: Monika

last: Szelest

address: ul. Antoniego Gębali 6

department: Laboratory of Genetic Diagnostics

country: Poland

institute: Medical University of Lublin

summary: The study presents three cases of patients with deletions within 16p11.2 regions. Every child had characteristic craniofacial dysmorphic features and hand or feet abnormalities. The first proband had additionally obesity, epilepsy, moderate intellectual disability, aphasia, motor delay, hyperinsulinism and café au lait spots. The second proband suffered from cardiac, pulmonary and hematological problems. The third proband had motor delay, bronchial asthma and umbilical hernia. Although each patient presented characteristic features of the syndrome, children differed in clinical pictures among themselves. The genetic diagnosis of the 16p11.2 deletion syndrome was made in children at different age, based on the multiplex ligation probe-dependent ampliﬁcation (MLPA) analysis and/or microarrays methods. This study highlights the impact of the size of deleted regions, as they may affect the clinical picture of patients with 16p11.2 microdeletion syndrome. Reported cases indicates the key role of the interdisciplinary approach in 16p11.2 microdeletion syndrome diagnostics, as the care of patients with this deletion is based on regular health assessment and adjustment of the nervous system development therapy

overall_design: In this study we report the cases of three patients with 16p11.2 microdeletions. Although every child had characteristic craniofacial and hand or feet dysmorphic features and presented motor or /and speech developmental delay, patients differed in clinical pictures among themselves. The multiplex ligation probe-dependent ampliﬁcation (MLPA) analysis and microarray test were used to confirm the cytogenetic aspect of the diagnosis. All three patients had genomic imbalance within the critical region for this microdeletion

last: Lejman


title: A small UTX stabilization domain of Trr is conserved within mammalian MLL3-4/COMPASS and is sufficient to rescue loss of viability in null animals

city: Chicago

first: Ali

last: Shilatifard

state: IL

address: 320 E Superior St

department: Department of Biochemistry and Molecular Genetics

institute: Northwestern University Feinberg School of Medicine

summary: Catalytic-inactivating mutations within the Drosophila enhancer H3K4 monomethyltransferase Trr and its mammalian homologs, MLL3/4, cause only minor changes in gene expression compared to whole-gene deletions for these COMPASS members. To identify essential histone methylatransferase-independent functions of Trr, we screened to identify a minimal Trr domain sufficient to rescue Trr-null lethality and demonstrate that this domain binds and stabilizes Utx in vivo. Using the homologous MLL3/MLL4 human sequences, we mapped a short ~80 amino acid UTX-Stabilization-Domain (USD) that promotes UTX stability in the absence of the rest of MLL3/4. Nuclear UTX stability is enhanced when the USD is fused with the MLL4 HMG-box. Thus, COMPASS-dependent UTX stabilization is an essential non-catalytic function of Trr/MLL3/MLL4, suggesting that stabilizing UTX could be a therapeutic strategy for cancers with MLL3/4 loss-of-function mutations.

overall_design: ChIP-seq for UTX and H3K27me3 and RNA-seq in MLL4 knockout HCT116 cells with and without doxycyclne-induced expression of a small rescue domain of MLL4.

first: Ryan

last: Rickels

first: Lu

last: Wang

first: Marta

last: Iwanaszko


title: Sexual differences in physiological and transcriptional responses to salinity stress of Salix linearistipularis

city: Harbin

first: Jian

address: 600 Changjiang Road

institute: Northeast Agricultural University

summary: RNA sequencing was performed to investigate the sexual differences of Salix linearistipularis salt tolerance

overall_design: mRNA profiles of salt-treated male and female roots of Salix linearistipularis were generated by RNA-Seq. The sequence reads that passed quality filters were analyzed at the transcript

first: Shuang

last: Feng

first: Shenkui

last: Liu


title: Next Generation Sequencing-based mRNA sequencing of human adipose mesenchymal stem cells

summary: Next Generation Sequencing (NGS)-based mRNA sequencing (RNA-seq) has provided high-throughput measurements to analyze the transcriptome of cells. We are reporting  comprehensive transcriptome profiling of primarily isolated human adipose-derived mesenchymal stem cells (ADMSC) throughout consecutive culture passages using NGS-based RNA-seq method. Human adipose tissue was obtained from operative remains and and digested in collagenase X. ADMSC were isolated, cultivated and characterized as mesenchymal stem cells (MSC) according to the minimum criteria for defining multipotent MSC from the International Society for Cellular Therapy (ISCT). mRNA profiles of ADMSC in p0, p1 and p2 were quality controlled, and generated by deep sequencing, in triplicate, using Illumina PE150 kits. Paired-end raw data were pre-processed using a published protocol. HISAT2 (Hierarchical Indexing for Spliced Alignment of Transcripts) was used to align reference genome. HTSeq was used to calculate Reads Count, and gene abundence was determined by analyzing FPKM (fragments per kilobase of exon model per million reads mapped).

overall_design: mRNA profiles of human adipose-derived mesenchymal stem cells in passage 0, passage 1 and passage 2


title: microRNA-630 regulates underglycosylated IgA1 production in the tonsils by targeting TLR4 in IgA nephropathy

city: Changsha

first: Chan

address: NO.139 of Renmin road

institute: The Second Xiangya Hospital

summary: IgA nephropathy (IgAN) is the most common primary glomerular disease. The characteristic pathology involves immune complexes formed by the deposition of IgA1 and underglycosylated IgA1 aggregates in the mesangial area, which may be accompanied by the deposition of IgG and/or IgM and complement components. However, the molecular mechanisms of IgAN remain unclear. In the present study, microarray analysis showed that the expression of miR-630 was significantly reduced in palatal tonsils from IgAN patients compared with chronic tonsillitis. Additionally, bioinformatic analysis showed that Toll-like receptor 4 (TLR4) was the predicted target gene of miR-630 and was regulated by miR-630. When miR-630 was overexpressed in palatal tonsil mononuclear cells from IgAN patients, the expression of TLR4 was reduced and the content of IgA1 in the cell culture supernatant was decreased, and the level of galactosylation in the IgA1 hinge region was increased. Moreover, immunohistochemical analysis showed that the expression of TLR4 in IgAN patients was significantly increased and. After knocking down the expression of TLR4, both the concentration of IgA1 and the binding force of IgA1 with broad bean lectin were significantly reduced  in IgAN. Furthermore, the mechanism study demonstrated that TLR4 might regulate the expression of IL-1β and IL-8 through NF-κB signaling pathway to modulate the concentration of IgA1 and the glycosylation level of IgA1. This interesting finding may offer new insight into the molecular mechanism of IgAN.

overall_design: To identify the differentially expression of microRNAs in tonsil of patients with IgA nephropathy. Tonsillar tissue specimens were obtained from 24 patients with IgA nephropathy (IgAN) whom had been diagnosed by renal biopsy, used as experimental group. The tonsillar tissue specimens which were obtained from20 patients with chronic tonsillitis (CT) lacking renal diseases were used as control group. Chose two specimens randomly from the above two groups respectively, and use the Agilengt Human miRNA microarrays V19 to detect the microRNAs (miRNAs) profile differentially expressed in tonsil of IgAN. The miRNA microarray differential analysis resulted in 29 significantly deregulated miRNAs after applying a fold change threshold >2, either up regulated or down regulated. Among the 29 significantly deregulated miRNAs, 7 miRNAs were up regulated and 22 miRNAs were down regulated. Tonsillar mononuclear cells (TMCs) were separated by density-gradient centrifugation using Lymphocyte Separation Medium, and we performed quantitative real-time PCR (qRT-PCR) to validate 4 deregulated miRNAs showed in the microarray results. The deregulated miRNAs were miR-630, miR-513b, miR-135a-3p, miR-642-3p respectively.

first: Youming

last: Peng


title: Cultured resident and thioglycolate-elicited mouse peritoneal macrophages

city: Kyoto city

first: Atsuhiko

last: Ichimura

state: Kyoto

address: 46-29, Yoshida Shimoadachi-cho, Sakyo-ku

department: Department of Biological Chemistry

institute: Kyoto University

summary:
In macrophage biology, resident peritoneal macrophages (RPMs) and thioglycolate-elicited peritoneal macrophages (TGPMs) have been traditionally utilized as primary cultured models. RPMs and TGPMs display distinct morphological and functional characteristics.
We analyzed altered gene expression between RPMs from control mice and TGPMs from thioglycolate-injected mice.

overall_design: C57BL/6J mice (8 weeks old) were i.p. injected with thioglycolate (Gibco). Peritoneal macrophages were prepared from thioglycolate-injected mice and non-treated mice and cultured in vitro from overnight. Total RNA preparations from the cultured macrophages were subjected to Affymetrix Mus musculus microarrays.

first: Hiroshi

last: Takeshima


title: TRAP-seq of newly generated olfactory sensory neurons from the open and closed sides of the mouse olfactory epithelium following unilateral naris occlusion

city: Aurora

first: Stephen

middle: William

last: Santoro

department: Department of Pediatrics, Section of Developmental Biology

institute: University of Colorado Denver - Anschutz Medical Campus

summary: The objectives of this study were to use unilateral naris occlusion (UNO) in order to characterize the effects of olfactory deprivation on the relative abundance of newly generated olfactory sensory neurons that express specific odorant receptors.

overall_design: Comparison of ribosome-bound transcripts of newly generated olfactory sensory neurons from the olfactory epithelia of PD35 Ascl1-CreERT2(+/-); Ribotag(+/+) mice that underwent UNO and tamoxifen treatment at PD14 and PD28, respectively.

middle: W