title: Correlation between immune lymphoid cells and plasmacytoid DCs in colon cancer

city: Changchun

first: Jing

state: Jilin

address: 519 Dongminzhu Ave

institute: 1st Hospital of Jilin University

summary:
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to use RNA-seq to compare ILC3s and pDCs gene expression in colon cancer.
Results: Using an optimized data analysis workflow, More than >60  million clean reads were obtained from each sample group after elimination of low-quality reads. A total of 14,943 in ILC3s and 10,840 in pDCs DEGs were found up-regulated and 4,213 in ILC3s and 11,549 DEGs in pDC s down-regulated on comparison of ILC3s and pDCs from tumor samples and controls samples transcripts with TopHat workflow. RNA-seq data confirmed stable expression of 25 known housekeeping genes, and 12 of these were validated with qRT–PCR. RNA-seq data had a linear relationship with qRT–PCR for more than four orders of magnitude and a goodness of fit (R2) of 0.8798. Approximately 10% of the transcripts showed differential expression between the WT and Nrl−/− retina, with a fold change ≥1.5 and p value <0.05. Altered expression of 25 genes was confirmed with qRT–PCR, demonstrating the high degree of sensitivity of the RNA-seq method. Hierarchical clustering of differentially expressed genes uncovered several as yet uncharacterized genes that may contribute to retinal function. Data analysis with BWA and TopHat workflows revealed a significant overlap yet provided complementary insights in transcriptome profiling.
Conclusion: These findings highlighting the important roles of ILC3s and pDCs in the processes of tumor progression and inhibition in colon cancer promote the development of new strategies for inducing antitumor immune responses in metastatic and recurrent colon cancer.

overall_design: Methods: ILC3s and pDCs mRNA profiles of tumor sample and those of control were generated by deep sequencing, using Hiseq Xten.The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

first: Jingtao

last: Chen


title: Next Generation Sequencing Facilitates Analysis of Wild Type and glioma Transcriptomes

status: Public on Mar 16 2021

city: ShanTou

first: juan

middle: juan

last: Luo

address: Xinling street 22

country: China

institute: ShanTou University

type: Expression profiling by high throughput sequencing

summary: Methods: Brain mRNA profiles of 90-day-old wild-type (WT) and glioma were generated by deep sequencing, in triplicate, using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows–Wheeler Aligner (BWA) followed by ANOVA (ANOVA) and TopHat followed by Cufflinks.

overall_design: Brain mRNA profiles of 90-day old wild type (WT) and glioma were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Luo

last: Juanjuan

first: Yang

last: Xiaojun


title: Modeling Preeclampsia using human induced pluripotent stem cells

status: Public on Mar 15 2021

city: La Jolla

first: Robert

middle: E

last: Morey

state: CA

address: 2880 Torrey Pines Scenic Dr

department: Pathology

country: USA

institute: UCSD

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

overall_design: Refer to individual Series


title: Development of gene expression signatures for MCF10A cell lines carrying HER2 and WT or H1047R PIK3CA oncogenes.

city: Greater Noida

first: Anindita

last: Chakrabarty

state: UP

address: NH91 Tehsil Dadri

department: Life Sciences

country: India

institute: Shiv Nadar University

summary:
We wanted to know how introduction of H1047R oncogenic mutation of PIK3CA (p110a subunit of PI3K) in HER2-overexpressing MCF10A human non-transformed mammary epitheial cell lines introduces change in gene expression levels. Our control was HER2-overexpressing MCF10A cell line with wild-type (WT) PIK3CA.
Mutated oncogene-induced gene expression signature was measured and compared with that induced by the WT oncogene from cell lines harvested at 70-80% confluency.

overall_design: MCF10A/HER2/WT [C] and MCF10A/HER2/HR [T] PIK3CA cell lines from two different passages (p18 and p20) were grown in media containing DMEM/F12, 5% horse serum, 20ng/ml EGF, 100ng/ml cjolera toxin, 10mg/ml insulin, 0.5mg/ml hydrocortisone. Total RNA was isolated by TRIzol  method when cells were 70-80% confluent.


title: Modeling Preeclampsia using human induced pluripotent stem cells [methylation]

summary: Preeclampsia (PE) is a hypertensive disorder, which affects up to 10% of pregnancies worldwide. The primary etiology is considered to be abnormal development and function of placental cells called trophoblasts. We previously developed a two-step protocol for differentiation of human pluripotent stem cells, first into cytotrophoblast (CTB) progenitor-like cells, and then into both syncytiotrophoblast (STB)- and extravillous trophoblast (EVT)-like cells, and showed that this protocol can be used to model both normal and abnormal trophoblast differentiation. We have now applied this protocol to differentiate induced pluripotent stem cells (iPSC) derived from placentas of pregnancies with or without PE.  While we did not note any differences in CTB induction, PE-iPSC-derived CTB showed a defect in syncytialization, and had a >180-fold reduction in expression of PSG4, a mature STB marker (p<0.02). While EVT formation did not appear to be altered, the invasive capacity of PE-iPSC-derived EVT was non-responsive to a decrease in oxygen tension, while that of non-PE-iPSC-derived EVT was enhanced 3.8-fold. RNA sequencing analysis showed gene expression changes consistent with defects in STB formation and response to hypoxia in PE-iPSC derived trophoblast. However, differences in DNA methylation were minimal, with only documented differences consistent with part of the response to hypoxia. Overall, PE-associated iPSC recapitulated multiple defects associated with placental dysfunction, with their lack of response to decreased oxygen tension emphasizing the importance of the interface with the maternal microenvironment in normal placentation.

overall_design: 36 samples were run on the Illumina Epic methylation array. The 36 samples include three day 0 samples from each of the 6 patients, for a total of 18 samples. Each patient has one day +4 2% sample and day +4 21% sample from the same iPSC clone for a total of 12 samples. The remaining six samples are the MSC patient samples from which the iPSCs were derived.

first: Mariko

last: Horii


title: PEGylated AdipoRon Analogs Improve Glucose Homeostasis and Lipid Metabolism in Mice under Insulinopenic and High Fat Diet Conditions

city: Dallas

first: Toshiharu

last: Onodera

state: TX

address: 5323 Harry Hines Boulevard

department: Touchstone diabetes center

institute: UT Southwestern medical center

summary: Since the first report of AdipoRon as an orally active adiponectin receptor (AdipoR1/2) agonist, several studies have investigated its protective, metabolic and anti-cancer effects in the liver, kidney, heart, central nervous system and ovaries. Despite that, the effects of AdipoRon on pancreatic -cell function are yet to be addressed. Furthermore, the various AdipoRon actions reported to date have only been assessed at a rather high oral dosage without attempts to enhance its affinity and/or bioavailability. To examine how structural modifications can affect AdipoRon-induced multifaceted actions, we describe a series of AdipoRon analogs that contain amphiphilic ethylene glycol chains. Among these, we propose AdipoRonPEG5 as a more potent derivative of AdipoRon in exerting pleiotropic actions in mice under insulinopenic and high fat diet (HFD) conditions. While both AdipoRon and AdipoRonPEG5 substantially attenuate palmitate-induced lipotoxicity in INS-1 cells in a dose-dependent manner, only AdipoRonPEG5 treatment is accompanied by a marked expression of genes involved in maintaining the functional state of β-cells along with a significant reduction in ceramides. Similarly, AdipoRonPEG5 can induce a substantial reduction of pancreatic, hepatic and serum ceramide species, with a concomitant increase in the corresponding sphingoid bases, and improves insulin sensitivity of mice under HFD feeding conditions. Furthermore, hyperglycemia in STZ-induced insulinopenic adiponectin null mice is also attenuated upon AdipoRonPEG5 treatment. Our results suggest that AdipoRonPEG5 is more effective in reducing lipotoxicity in the pancreas and liver of HFD-fed mice than AdipoRon at 5 mg/Kg dosage and is consistent with adiponectin cytoprotective effect of β-cells. Additionally, these results indicate that the beneficial effects AdipoRonPEG5 can be partially attributed to improved pharmacokinetics compared to AdipoRon, thus providing the opportunity for further derivatization to achieve improved affinity and tissue-specific targeting.

overall_design: Comparison of the effect of PEGylated AdipoRon, AdipoRon and vehicle on the liver.

first: Ebrahim

middle: G

last: Zadeh

first: Scherer

last: Philipp

first: Wen-hong

last: Li


title: Role of NEIL3 in aortic Vascular Smooth Muscle cells

city: Oslo

first: Kuan

last: Yang

address: Sognsvannsveien 20

department: Research Institute of Internal Medicine

country: Norway

institute: Oslo University Hospital

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Generation of cortical neurons through large-scale expanding neuroepithelial stem cell from human pluripotent stem cells

city: Kunming

first: Tianqing

state: Yunnan

address: 727 South Jingming Road, Chenggong District

department: Yunnan Key Laboratory of Primate Biomedical Research & Institute of Primate Translational Medicine

institute: Kunming University of Science and Technology

summary: We developed a serum-free, defined, and low-cost culture system for large-scale expansion of NESCs in stirred suspension bioreactors. The stable and controllable 3D system supports long-term expansion of highquality and homogeneous NESC-spheres. These NESC-spheres can be used to efficiently give rise to cortical neurons for cell therapy, disease modeling, and drug screening in future.

overall_design: The NESC medium was first optimized, and the suspension culture system was then enlarged from plates to stirred bioreactors for large-scale production of NESC-spheres by a stirring speed of 60 rpm. During the expansion, the quality of NESC-spheres was evaluated. The differentiation potential of NESC-spheres into cortical neurons was demonstrated by removing bFGF and two pathway inhibitors from the NESC medium. Cellular immunofluorescence staining, global transcriptome, and single-cell RNA sequencing analysis were used to identify the characteristics, identities, purities, or homogeneities of NESC-spheres or their differentiated cells, respectively

first: Shumei

last: Zhao


title: Modeling Preeclampsia using human induced pluripotent stem cells [RNA-seq]

summary: Preeclampsia (PE) is a hypertensive disorder, which affects up to 10% of pregnancies worldwide. The primary etiology is considered to be abnormal development and function of placental cells called trophoblasts. We previously developed a two-step protocol for differentiation of human pluripotent stem cells, first into cytotrophoblast (CTB) progenitor-like cells, and then into both syncytiotrophoblast (STB)- and extravillous trophoblast (EVT)-like cells, and showed that this protocol can be used to model both normal and abnormal trophoblast differentiation. We have now applied this protocol to differentiate induced pluripotent stem cells (iPSC) derived from placentas of pregnancies with or without PE.  While we did not note any differences in CTB induction, PE-iPSC-derived CTB showed a defect in syncytialization, and had a >180-fold reduction in expression of PSG4, a mature STB marker (p<0.02). While EVT formation did not appear to be altered, the invasive capacity of PE-iPSC-derived EVT was non-responsive to a decrease in oxygen tension, while that of non-PE-iPSC-derived EVT was enhanced 3.8-fold. RNA sequencing analysis showed gene expression changes consistent with defects in STB formation and response to hypoxia in PE-iPSC derived trophoblast. However, differences in DNA methylation were minimal, with only documented differences consistent with part of the response to hypoxia. Overall, PE-associated iPSC recapitulated multiple defects associated with placental dysfunction, with their lack of response to decreased oxygen tension emphasizing the importance of the interface with the maternal microenvironment in normal placentation.

overall_design: Total RNA-seq of iPSC-derived trophoblast cell lines from mesenchymal stem cells from umbilical cord tissue from placentas of patients with (3 patients and 3 lines per patient)  and without (3 patients and 3 lines per patient) severe early-onset preeclampsia

first: Mana

middle: M

last: Parast


title: Drosophila CRTC promotes starvation resistance by modulating one-carbon metabolism and insulin signaling

city: San Diego

first: Ezra

last: Wiater

address: 10010 N Torrey Pines Rd

department: PBL

institute: Salk Institute For Biological Studies

summary: CRTC modulates one-carbon metabolism and insulin signaling during fasting

overall_design: RNA-Seq from RNA of adult fly, ad-lib fed or fasted for 16 hours, head only or body without head samples

first: Tian

last: Wang

first: Xinmin

last: Zhang

first: John

last: Thomas

first: Marc

last: Montminy


title: Transcriptome profiling of murine aortic Vascular Smooth Muscle cells from ApoE knockout and ApoE/Neil3 double knockout mice

summary: We performed high-throughput RNA sequencing to characterize possible differences in the transcriptome of murine aortic Vascular Smooth Muscle cells from both 26 weeks-old ApoE knockout and ApoE/Neil3 double knockout mice fed a regular diet.

overall_design: RNA-sequencing performed in aortic Vascular Smooth Muscle cells from two (2) ApoE knockout and three (3) ApoE/Neil3 double knockout mice, using Illumina NovaSeq 6000

first: Ana

last: Quiles-Jiménez


title: Analyse the differently expressed genes in tamoxifen resistant breast cancer cells

city: Guangzhou

first: Yinghua

last: Zhu

address: 107 Yanjiang West Road

institute: Sun Yat-Sen University

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

summary: Tamoxifen resistance has been a major clinical problem and is accountable for relapse in about one third of ER positive breast cancer patients. Most of the recurrent patients will eventually receive chemotherapy. However, the chemosensitivity of these tamoxifen-resistant breast cancer patients has never been explored. In this study, we demonstrate that tamoxifen-resistant breast cancer cells express significantly more BARD1 and BRCA1, which results in the resistance to DNA-damaging chemotherapy including cisplatin and adriamycin , but not to paclitaxel. Silencing BARD1 or BRCA1 expression or inhibition of BRCA1 phosphorylation by Dinaciclib restored the sensitivity to cisplatin in tamoxifen-resistant cells. In addition, we identified that activated PI3K/AKT pathway in tamoxifen-resistant cells was responsible for the upregulation of BARD1 and BRCA1. PI3K inhibitors, BKM120 and BYL719, decreased the expression of BARD1 and BRCA1 in tamoxifen-resistant cells and re-sensitized them to cisplatin both in vitro and in xenografted mice. Higher BARD1 and BRCA1 expression was associated with poor prognosis of early breast cancer patients, especially the ones received radiotherapy, indicating the potential use of PI3K inhibitors to reverse chemoresistance and radioresistance in ER positive breast cancer patients.

overall_design: MCF7 parent cells and MCF7 tamoxifen resistant cells growthed for 48 hours, then extracted the total RNA for analyzation of the gene expression profile.

first: Yujie

last: Liu

first: Qiang


title: Effect of FENDRR  on genetic expressions of primary liver cancer based on next generation sequencing

first: Shui

state: Jilin Province

address: Ziqiang Stree No.218

department: The Second Hospital of Jilin University

institute: Jilin University

summary: Primary liver cancer (PLC) is the third largest contributor to cancer mortality in the world. PLC is a heterogeneous disease that encompasses several biologically distinct subtypes including hepatocellular carcinoma (HCC), intrahepatic cholangiocarcinoma (ICC) and combined hepatocellular-cholangiocarcinoma (CHC). The cells were cultured in DMEM medium supplemented with 10% fetal bovine serum and 1% antibiotic-antimitotic solution. The HCC cell line LM3 and ICCA cell line RBE were transfected using Lipofectamine 3000 reagent following the manufacturer’s protocol and incubated for 48h for further analysis. The gene expression profiles were analyzed of LM3 and RBE cells transfected with si-FENDRR or si-NC to assess effect of FENDRR on genetic expressions of PLC.

overall_design: High-throughput sequencing raw data for 4 samples, A1(LM3) and A2(RBE) are two samples from experimental group (cells with si-FENDRR transfection), C1(LM3) and C2(RBE) are two samples from negative control group (cells with si-NC transfection).


title: Survey of Functional Genes in the Arctic Soil of Whapmagoostui-Kuujjuarapik

city: Tachikawa-shi,

first: Shu-Kuan

last: Wong

state: Tokyo

address: 10-3, Midori-cho,

country: Japan

institute: National Polar Research Institute

summary: The objective of this study was to identify the different functional genes involved in key biogeochemical cycles in the sub- Arctic regions. Understanding the microbial diversity in the Arctic region is an important step to determine the effects of climate change on these areas.

overall_design: Soil samples were collected from the sub-Arctic region of Whapmagoostui-Kuujjuarapik . At each sampling site five biological replicates were collected and DNA and RNA were subsequently extracted. The DNA and cDNA (synthesized from RNA samples) samples were shipped to the University of Oklahoma, where it was analyzed with the GeoChip microarray.

first: M

last: Uchida

first: S

middle: K


title: Comparative gene expression profiling of cornea macrophages, retinal and brain microglia and bone marrow-derived monocytes

city: Freiburg

first: Ori

last: Staszewski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University Medical Center Freiburg

summary: Resident tissue macrophages such as microglia in the retina and the brain inhabit tissues providing specific environmental cues. We therefore intened to compare the expression profiles of these two microglial subpopulations. Additionally, we included other resident tissue macrophages from the eye, like the cornea, that are supposed to underly a turnover with peripheral monocytes. Overall, we compared two long-lived microglial populations with two short-lived populations, cornea macrophages and bone marrow-derived monocytes. The gene expression profiles between retinal and brain microglia were comparable to each other while cornea macrophages showed more similarities to monocytic expression signatures underlining their short-lived nature and closer relation to peripheral myeloid cells.

overall_design: mRNA signatures from CD45+CD11b+ retinal and brain microglia, CD45+CD11b+CD64+F4/80+ cornea macrophages and CD45+CD11b+CD115+Ly6C+ bone marrow monocytes

last: Staszewksi

first: Peter

last: Wieghofer


title: The m6A reader IGF2BP2 regulates macrophage phenotypic activation and inflammatory diseases by stabilizing TSC1 and PPARγ

city: wuhan

first: dong

last: chen

state: Hubei

address: GaoXin 2nd Road

institute: ablife

summary: Phenotypic polarization of macrophages is regulated by a milieu of cues in the local tissue microenvironment. Currently, little is known about how the intrinsic regulators modulate pro-inflammatory (M1) versus pro-healing (M2) macrophages activation. Here, we observed that insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) -deleted macrophages exhibited enhanced M1 phenotype and promoted DSS induced colitis development. However, the IGF2BP2-/- macrophages were refractory to IL4 induced activation and alleviated cockroach extract induced pulmonary allergic inflammation. Molecular studies indicated IGF2BP2 switched M1 macrophages to M2 activation by targeting tuberous sclerosis 1 (TSC1) via an N6-methyladenosine-dependent manner. Additionally, we also showed a signal transducer and activators of transcription 6 (STAT6) - high mobility group AT-hook 2 (HMGA2) -IGF2BP2-peroxisome proliferator activated receptor-γ (PPARγ) axis involves in M2 macrophages differentiation. These findings highlight a key role of IGF2BP2 in regulation of macrophages activation and imply a potential therapeutic target of macrophages in the inflammatory diseases.

overall_design: IRIP-seq analysis of IGF2BP2 versus input in BMDMs

first: Wang

last: Xia


title: Plasma samples from pregnant who developed preeclampsia and remained healthy along pregnancy (controls)

city: Belo Horizonte

first: Izabela

middle: Mamede Costa Andrade

last: Conceição

state: Minas Gerais

address: Av. Pres. Antônio Carlos, 6627

department: Genetics

country: Brazil

institute: UFMG

summary:
Preeclampsia (PE) is a major health problem in pregnancy, and miRNAs play a role in the pathophysiology of PE. However, the expression of circulating miRNAs was not analyzed in the second trimester of pregnancy, a period of major relevance to identify predictive biomarkers for PE. Therefore, we examined the expression profiles of 84 circulating miRNAs using PCR-array in plasma collected between 20 and 25 weeks of gestation from pregnant who subsequently developed PE and from those who remained healthy along pregnancy randomly selected from a prospective cohort of pregnant. miR-204-5p (P=0.0082) and other 22 miRNAs were upregulated (fold change > 2.0, while miR-24-3p, miR-22-3p, miR-143-3p, and miR-376c-3p had fold change > 4.0) and six miRNAs were downregulated (fold change < 0.5) in plasma from pregnant who developed PE. Target genes for differentially expressed miRNAs were extracted from the miRTarBase of experimentally validated miRNA-target interactions and used in gene set functional enrichment and REACTOME pathway analysis. The 20 pathways with the lowest false discovery rate for the upregulated and downregulated miRNAs are related to pathophysiology of PE, such as apoptosis, angiogenesis, and signal transduction, including signaling by receptor tyrosine kinases, VEGF and TGFB family members. Moreover, we explored the 37 target genes and pathways for miR-204-5p, including MMP-9, MALAT1, TGFBR2, and SIRT1. The circulating miRNAs differentially expressed in the second trimester of pregnancy are related to target genes and pathways of pathophysiological relevance during the early development of PE, and our findings provide for potential circulating predictive biomarkers in PE.
For the PCR array, total RNA isolated was converted into cDNA using the miScript II RT Kit (Qiagen®, Leusden, Netherlands), according to the manufacturer’s instructions

overall_design: PCR-array expression profile from five plasma samples of pregnant who developed preeclampsia (cases) and four women who remained healthy during pregnancy (controls)

first: Valéria

middle: C

last: Sandrim

first: Marcelo

middle: R

last: Luizon


title: Expression data for participants in iWITH study at screening visit, primary endpoint (yr2)/For-cause biopsy visit, 5year visit

city: Bethesda

first: Sai

last: Kanaparthi

state: MD

address: 7500 Old Georgetown Rd

department: BiG

institute: Immune Tolerance Network

summary:
A longitudinal study using data collected at the time of liver biopsy, the final eligibility assessment for participation in iWITH (NCT01638559), an immunosuppression withdrawal trial.
Microarrays were used to understand the gene expression profile differences between IS withdrawal outcomes (Tolerant and Non-tolerant)

overall_design: RNA samples (n=222) were extracted from cryopreserved liver tissue samples using TRIzol and hybrid-ized onto Affymetrix Human Genome U219 96-array plates.

first: A

last: Sanchez-Fueyo

last: Feng


title: Transcriptomic profiling of CRISPR/Cas9-generated mutant of Marchantial polymorpha BES1 transcription factor (Mpbes1)

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

country: Spain

institute: Center for Research in Agricultural Genomics (CRAG)

summary: Brassinosteroid hormones are essential for growth and development in seed plants. In Arabidopsis, transcriptional factors from the AtBES1 (BRI1-EMS-SUPPRESSOR1)/AtBZR1 (BRASSINAZOLE-RESISTANT 1) family, are main regulators of steroid phytohormone Brassinosteroids, which finely coordinate gene expression. While genome sequence analysis in Marchantia polymorpha failed to identify BR receptors homologues to the BRI1-family, a homologue of downstream BR-regulated BES1/BZR1 transcription factors is present.  Here, we decipher the biological function of MpBES1 in liverwort. Mpbes1 knock out plants have impaired thallus development, pointing up the conservation of BES1 function in organ development. RNAseq analysis of Mpbes1 reveals a prominent deregulation of oxidation processes, responses to stress and carbohydrate metabolism. Furthermore, in the Arabidopsis orthologs of Mpbes1 deregulated genes, described targets of AtBES1/BZR1 are overrepresented, suggesting a major conservation in the signaling module. In conclusion, this study unravels the origin of BES1/BZR1 family of transcriptional factors in plant cell division.

overall_design: A single-factor (genotype) design was followed:  M. polymorpha  wild type plants (ecotype Tak-1) were compared to Mpbes-1 mutant plants. Thalli of three different plants per genotype were sampled, constituting three independent biological replicates. Total RNA was extracted but only mRNA was used for sequencing.

first: Martin

last: Mecchia

first: Ana

middle: I

last: Caño-Delgado


title: Acute myeloid leukemia cells resist chemotherapy through a transient senescence-like state [Array]

status: Public on Mar 14 2021

city: New York

first: Matt

last: Teater

state: NY

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: In acute myeloid leukemias (AML), chemotherapy is frequently followed by disease relapse, yet the mechanism by which AML reemerges is not fully understood. We hypothesized that chemotherapy induces senescence-like dormancy that facilitates survival to genotoxic exposure, allowing AML cells to endure treatment in a transiently dormant state while retaining potential for leukemic repopulation. Here, we show that primary AML cells exhibit hallmark senescence features following treatment with cytarabine (AraC), including growth arrest, increased cellular granularity, senescence-associated-β-galactosidase (SA-β-gal) activity, and senescence-associated transcriptomic alterations. Induction of AraC-induced premature senescence was regulated by the ATR kinase activity and mediated stress-survival. High-throughput single cell RNA (scRNA)-seq analysis of primary AML cells ex vivo and in vivo following chemotherapy suggest active transcriptional programming towards senescent-like dormancy instead of enrichment for leukemia stem cells (LSCs). scRNA-seq of sorted AraC-induced premature senescent AML cells demonstrated a heterogenous population including a fraction of cells with simultaneous expression of dormancy- and senescence-associated gene signatures. Xenotransplantation of AraC-induced premature senescent AML cells into mice demonstrated that senescent-like AML cells maintain leukemia-repopulating potential. Altogether, we propose a mechanism of AML relapse whereby AML cells tolerate chemotherapy via acquisition of a transient senescent-like state.

overall_design: Gene expression in AraC treated AML ex vivo culture, primary xenografts

first: Duy

last: Cihangir

first: Ari

last: Melnick


title: Acute myeloid leukemia cells resist chemotherapy through a transient senescence-like state [PDX]


title: Transcriptome profiling of primary human aortic Vascular Smooth Muscle cells abrogated of NEIL3 mRNA via antisense oligonucleotides targeting NEIL3 exon 4

first: Kuan

last: Yang

summary: We performed high-throughput RNA sequencing to characterize possible differences in the transcriptome of primary human aortic Vascular Smooth Muscle cells abrogated of NEIL3 mRNA via antisense oligonucleotides targeting NEIL3 exon 4, compared with control cells treated with a scramble version of the same antisense oligonucleotide

overall_design: RNA-sequencing performed in primary human aortic Vascular Smooth Muscle cells from three (3) NEIL3 mRNA-abrogated, and two (2) treated with the scramble control, using Illumina NovaSeq 6000

last: Quiles-Jiménez


title: HMJSL C. Neoformans splicing factor knockout RNA-seq

status: Public on Mar 13 2021

city: San Francisco

first: Hiten

last: Madhani

department: Biochemistry

institute: UCSF

summary: We determined that over 60 spliceosomal proteins are conserved between many fungal species and humans but were lost during the evolution of S. cerevisiae, an intron-poor yeast with unusually rigid splicing signals.  We analyzed null mutations in a subset of these factors, most of which had not been investigated previously, in the intron-rich yeast Cryptococcus neoformans.  We found they govern splicing efficiency of introns with divergent spacing between intron elements.  Importantly, most of these factors also suppress usage of weak nearby cryptic/alternative splice sites.  Among these, orthologs of GPATCH1 and the helicase DHX35 display correlated functional signatures and copurify with each other as well as components of catalytically active spliceosomes, identifying a conserved G-patch/helicase pair that promotes splicing fidelity.  We propose that a significant fraction of spliceosomal proteins in humans and most eukaryotes are involved in limiting splicing errors, potentially through kinetic proofreading mechanisms, thereby enabling greater intron diversity.

overall_design: Examination of 13 splicing factor knockouts, and 1 exosome factor knockout in Cryptococcus neoformans.

first: Jade

last: Sales-Lee


title: RNA-sequencing shows the changes on transcriptomes after deletion of Setd2 in mice.

city: Shanghai

first: Hanyu

last: Rao

address: Huashan Rd, No. 1954

institute: Shanghai Jiao Tong University

summary: To explore a possible role of SETD2 in kidney development and tumorigenesis in vivo, we generated Setd2-floxed mice and deleted the Setd2 gene in tubular epithelial cells using a transgenic Ksp1.3/Cre mouse line. Then, we established our own c-MYC-transgene mouse line by overexpressing the human c-MYC under the control of the Ksp promoter to generate kidney disease mouse model. To get an insight into the mechanism of how SETD2 ablation promotes ccRCC formation in a c-MYC-generated PKD model, we performed RNA-seq using the renal tubules isolated from Wild Type, Setd2-KO, MYC-OE and MYC-OE; Setd2-KO mice.

overall_design: Renal primary tubular epithelial cells mRNA profiles of three Wild Type mice, three Setd2-KO mice, three MYC-OE mice and three MYC-OE; Setd2-KO mice were generated by deep sequencing, in triplicate.

first: Wei-Qiang

last: Gao

first: Li

last: Li


title: Acute myeloid leukemia cells resist chemotherapy through a transient senescence-like state [scRNA-seq]


title: TLR7 ligation augments hematopoiesis in Rps14 deficiency via paradoxical inflammatory signalling

status: Public on Mar 12 2021

city: London

first: Elspeth

last: Payne

email: a.lubin@ucl.ac.uk, e.payne@ucl.ac.uk

address: 72 Huntley Street

department: Department of Haematology

country: United Kingdom

institute: UCL Cancer Institute

summary: Myelodysplastic syndrome (MDS) is a haematological malignancy characterised by blood cytopenias and predisposition to acute myeloid leukaemia. We developed a model of MDS using zebrafish using knockout of Rps14, the primary mediator of the anaemia associated with del (5q) MDS. These mutant animals develop bone marrow failure with dysplastic features. We conducted an in vivo small molecule screen to identify compounds that ameliorate the MDS phenotype, identifying imiquimod, an agonist of TLR7. We conducted RNA-seq analysis of both treated and untreated animals to define the mechanism of imiquimod in alleviating anaemia. We find imiquimod alleviates anaemia by promoting haematopoietic stem and progenitor cell expansion and erythroid differentiation, the mechanism of which is dependent on TLR7 ligation. TLR7 activation in this setting paradoxically promoted an anti-inflammatory gene signature suggesting crosstalk between pro-inflammatory pathways endogenous to Rps14 loss and TLR7 pathway activation.

overall_design: RNA-seq analysis of HSPCs (Tg(Itga2b:GFPlo) cells) from pooled rps14+/- or wildtype zebrafish embryos, which were phenylhydrazine (Phz) stressed or unstressed, and then treated with imiquimod or vehicle control. A minimum of three replicates per condition were analysed.

first: Alexandra

last: Lubin


title: RT-PCR profiling analysis of microRNA expression in cisplatin-resistant cancer

city: Shenyang

first: Wei

address: 36 Sanhao street

institute: Shengjing hospital of China Medical University

summary:
Chemotherapy remains the primary treatment of advanced solid cancer, including lung cancer. As first line treatment, cisplatin-based therapy is restricted by frequent development of drug resistance. Increasing data showed that programmed cell death protein ligand 1 (PD-L1) plays a vital role in regulating cisplatin resistance. However, the mechanisms underlying are not fully understood. We found miR-526b-3p expression declined while PD-L1 elevated in cisplatin-resistant lung cancer compared to that in cisplatin-sensitive lung cancer by analyzing clinical samples. Importantly, miR-526b-3p was associated with response to cisplatin negatively. We further demonstrated that miR-526b-3p reversed cisplatin resistance, suppressed metastasis, and activated CD8+ T cells in a STAT3/PD-L1-dependent manner. Our findings extended the knowledge of PD-L1-mediated cisplatin resistance of lung cancer. In addition, the introduction of miR-526b-3p provided a new clue to improve the anti-tumor effects of the combination of immunotherapy and chemotherapy.
miProfileTM Cancer miRNA qPCR Array

overall_design: Three primary patients with primary cancer were recruited in the present study. MicroRNA expression profiles were obtained.


title: A knockout mutation associated with juvenile paroxysmal dyskinesia in Markiesje dogs indicates SOD1 pleiotropy

city: Utrecht

first: Frank

last: van Steenbeek

state: Select State/Province

address: Yalelaan 104

country: Netherlands

institute: Utrecht University

type: Genome variation profiling by high throughput sequencing

summary: A juvenile form of paroxysmal dyskinesia segregated in the Markiesje dog breed. Affected pups exhibited clinical signs of a severe tetraparesis, dystonia, cramping and falling over when trying to walk. In most cases the presentation deteriorated within weeks and elective euthanasia was performed. Pedigree analysis indicated autosomal recessive inheritance. Genome-wide association and homozygosity mapping of 5 affected dogs from 3 litters identified the associated locus on chromosome 31 in the region of SOD1. The DNA sequence analysis of SOD1 showed that the patients were homozygous for a frameshift mutation in the fourth codon. None of the other analyzed dogs of the breed was homozygous for the mutation, indicating full penetrance of the genetic defect. Mutations in SOD1 are known to cause recessive degenerative myelopathy in middle-aged dogs with low penetrance and dominant amyotrophic lateral sclerosis in humans with variable age of onset. Our findings are similar to recent observations in human patients that a loss of function mutation in SOD1 leads to a juvenile neurologic disease distinct from amyotrophic lateral sclerosis.

overall_design: Targeted resequencing of 3 cases and 2 controls.

first: P

middle: J

last: Mandigers

first: F

first: W

last: Bergmann

first: M

last: Vos-Loohuis

middle: A

last: Leegwater


title: Antitumor effects of the hydralazine-valproate combination in lymphoma

city: México City

first: Daniel

middle: Ortega

last: Bernal

state: México City

address: Calzada del Hueso 1100

department: Atención a la Salud

country: Mexico

institute: Universidad Autónoma Metropolitana, Unidad Xochimilco

summary:
Epigenetic alterations are common in both B cell and T cell lymphomas. These contribute to lymphomagenesis and treatment resistance, hence epigenetic therapy is being investigated.
We evaluated the effects of the DNA-methyltrasferase inhibitor hydralazine and the histone deacetylase inhibitor valproate in T-cell lymphoma HuT78 cells and B-cell lymphoma Raji cells.

overall_design: HuT78 and Raji cells were treated with hydralazine and valproate, and then total RNA was isolated. A total of 200 ng RNA from each experimental cell group was evaluated.

first: Harold

last: Salamanca-Ortiz

first: Guadalupe

last: Domínguez-Gomez

last: Ortega-Bernal

first: Alfonso

last: Dueñas-González


title: Inflammatory gene expression profiling in peripheral blood from patients with Alzheimer’s disease reveals key pathways and hub genes with potential diagnostic utility

city: Thuwal

first: Antonio

last: Adamo

state: Makkah

address: Thuwal 23955-6900 KAUST

department: iological, Environmental Sciences and Engineering

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: Late-onset Alzheimer disease (LOAD) is the most common neurodegenerative disorder worldwide. Recent studies have shown that differential expression in genes (DEG) related to inflammatory response may result associated with disease onset and progression. This study aimed to explore the molecular pathogenesis of LOAD-related inflammation through next-generation sequencing, to assess RNA expression profiles in Alzheimer's disease patients and healthy controls.

overall_design: RNA was isolated from whole blood from 5 LOAD cases and 10 controls (all female. Mean age 76.3±3.5). The amplicon sequencing approach using 20812 probes sets specific to human mRNA was applied to assess gene expression profiles, and functional annotation was performed.

first: Kelly

middle: Y

last: Cardona-Londoño

first: J

last: Medina-Salcedo

first: Mary

last: Orrego-Cardozo

first: Francia

last: Restrepo de Mejía

first: Xabier

last: Elcoroaristizabal Martín

first: Carlos

last: Naranjo-Galvis


title: The diatom Thalassiosira pseudonana grown in mesocosms at contemporary and elevated CO2 over the diel cycle

city: Seattle

first: Jacob

last: Valenzuela

state: Washington

address: 401 Terry Ave. N

institute: Institute for Systems Biology

summary: To test whether elevated CO2 , which drives seawater below pH 7.9, would shift the dynamical expression patterns diatoms in a more natural environment, we designed a controlled mesocosm study at Friday Harbor Laboratories (FHL) Ocean Acidification Environmental Laboratory (OAEL). Briefly, four independent mesocosm tanks were set up with continuous flow (10-12 mL/min) of filtered seawater from the Puget Sound to simulate mid-century (pH 7.9) and acidified oceanic conditions (pH 7.6) in duplicate. Mesocosm reservoirs were supplemented with nutrients and inoculated with T. pseudonana acclimated in FHL seawater. Mesocosms were outfitted with custom enclosures to simulate a 12:12 light:dark diel cycle. Cells for RNA extraction were sampled in the middle of the light and dark cycle and sequenced on Illumina NextSeq 500 platform.

overall_design: Duplicate mesocosms at mid-century (pH 7.9) and acidified oceanic conditions (pH 7.6) were  inoculated with T. pseudonana and grown over a 12:12 diel cycle (275 μM photons/m2/s). Cells were collected for gene expression analysis in the middle of the light and dark cycle over 2 days. Result: 16 total transcriptomes (n=4 at pH 7.9 in the light, n=4 at pH 7.9 in the dark, n=4 at pH 7.6 in the light, and n=4 at pH 7.6 in the dark).

first: Monica

middle: V

last: Orellana

first: Nitin

middle: S

last: Baliga


title: Gene expression changes in breast cancer cells upon USP1 knockdown [RNA-Seq]

city: shanghai

first: aihui

last: ma

address: 800, Dongchuan Road

institute: shanghai cancer institute

summary: To explore the function of deubiquitinase USP1 in breast cancer cells, we performed RNA sequencing to analyze the expression pattern changes by knockdown of USP1 in MCF7 cells.

overall_design: RNA-seq was preformed in breast cancer MCF7 cells transfected with control or USP1-specific siRNAs.

first: Aihui

last: Ma

first: Yongzhong

last: Liu


title: Multi-influential interactions controls behaviour and cognition through a limited number of pathways in Down syndrome mouse models (Affymetrix reanalysis)

status: Public on Mar 17 2021

city: Strasbourg

first: maria

middle: del mar

last: muñiz moreno

state: Alsace

address: 1 Rue Laurent Fries

department: Translational medicine and neurogenetics

country: France

institute: IGBMC

type:
Expression profiling by array
Third-party reanalysis

summary: Down syndrome (DS) is the most common genetic form of intellectual disability with additional clinical features, caused by the presence of an additional copy of human chromosome 21 (Hsa21). A few number of patients with DS features, carry partial duplication of Hsa21 and their study provided novel insights into genotype–phenotype correlations. Despite the progress of genome analysis, the rareness of patients with partial duplication, and the human genetic heterogeneity, makes difficult to achieve a more detailed phenotypic map at present. As a complementary approach, we screened the in vivo DS mouse library with highly standardized behavioural tests, magnetic resonance imaging (MRI) and digged into hippocampal gene expression to go further in dissecting the genotype–phenotype correlations and in deciphering misregulated genes, functional pathways and biological cascades in DS models. Altogether this approach bring novel insights into the field. First, we unravelled the complexity of the genetic interactions between different regions of the chromosome 21 and how they play an important role in modulating the outcome of the behavioural and molecular phenotypes. Then, in depth analysis of misregulated expressed genes involved in synaptic dysfunction highlitghed six biological cascades centered around DYRK1A, GSK3beta, NPY, RHOA, NPAS4 and the SNARE complex. Finally, we provide a novel vision of the existing altered gene-gene crosstalk and molecular mechanisms that could be at play for both the DS clinical features and the rescue mechanisms by targeting specific hubs or well connected nodes that may be central to advance in our understanding of DS  and therapies development.

relation:
Reanalysis of: GSM123277
Reanalysis of: GSM123276
Reanalysis of: GSM123271
Reanalysis of: GSM123274
Reanalysis of: GSM123278
Reanalysis of: GSM123272
Reanalysis of: GSM123275
Reanalysis of: GSM123273
Reanalysis of: GSM123265
Reanalysis of: GSM123270
Reanalysis of: GSM123269
Reanalysis of: GSM123267
Reanalysis of: GSM123268
Reanalysis of: GSM123266
Reanalysis of: GSM123264
SubSeries of: GSE149470

overall_design:
I downloaded and re-analysed the gene expression profile of the human derived dataset of 8 euploid and 7 Down syndrome adults published by Lockstone et al., (2007) with GEO accession number GSE5390. The re-analysis was performed using our bioinformatics pipeline, developed over the R environment the full description is on the supplementary material of our manuscript Duchon A., Muñiz MM et al., under revision. As a brief sumup, the pipeline consisted in seven major steps: Quality control (QC), pre-processing and normalization of the raw data, analysis of the structure and homogenicity of the data, differential expression analysis (DEA), differential functional analysis (DFA), Network connectivity analyses of pathways and genes and finally network topology and centrality analyses.   Data quality control: The quality control (QC) workflow was implemented in two steps. The first step consisted in analysing the quality of the raw data, and the second in the analysis of the quality after the pre-processing and normalization steps. Data pre-processing and annotation: The raw intensity measurements of the arrays where normalized using limma RMA normalization algorithm producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific R package pd.hugene.1.0.st.v1. Data structure and homogeneity: We performed a study of i) the gene expression correlation across models and ii) the structure of the data and the separation between experimental groups using hierarchical clustering, PCA, tSNE and OPLS. Differential expression analysis (DEA): We carried on the differential expression analysis in R environment using FCROS (Dembele  et al., 2014). FCROS is a fold change (FC) rank based method that works well with noisy datasets and gives strong reproducible results. FCROS computes for each pair of test/control samples (K pairs), a statistic associated with the k ranks of the FC values for each gene, and the obtained probability (f-value) is used to identify the differential expressed genes (DEGs) within an error level fixed by the analyst. Our fixed error level corresponds to a 5% False Discovery Rate (FDR), and is attained by setting the Ɑ parameter within this range 0.025<Ɑ>0.975.Differential functional analysis (DFA): To identify the altered functions due to the changes in gene expression and possibly get new insights into the mechanistic changes along the pathways between the two conditions trisomic vs. wild type on each model we used the generally applicable gene set enrichment for pathway analysis (GAGE, Luo et al., 2009) R package  to carry on the functional expression analysis.The main aim of re-analysing this data was to get new insights into DS gene deregulation first in humans applying a more updated computational pipeline and  secondly, by applying a comparative genomic approach with rodent Down syndrome datasets identify the conserved gene and functional deregulated profiles.
I downloaded and re-analysed the gene expression profile of human foetal derived datasets published by Mao et al., (2003) with ArrayExpress accession number E-GEOD-1397. We re-analysed 2 samples coming from cerebrum-derived astrocytes, 3 samples of cerebellum, 4 samples of cerebrum and 2 samples of heart of Down syndrome individuals compared to 2 samples coming from cerebrum-derived astrocytes, 3 samples of cerebellum, 7 samples of cerebrum,2 samples of heart of euploid individuals .The re-analysis was performed using our bioinformatics pipeline, developed over the R environment the full description is on the supplementary material of our manuscript Duchon A. & Muñiz MM et al., under revision. As a brief sumup, the pipeline consisted in seven major steps: Quality control (QC), pre-processing and normalization of the raw data, analysis of the structure and homogenicity of the data, differential expression analysis (DEA), differential functional analysis (DFA), Network connectivity analyses of pathways and genes and finally network topology and centrality analyses.   Data quality control: The quality control (QC) workflow was implemented in two steps. The first step consisted in analysing the quality of the raw data, and the second in the analysis of the quality after the pre-processing and normalization steps. Data pre-processing and annotation: The raw intensity measurements of the arrays where normalized using limma RMA normalization algorithm producing the summaries at the probe/transcript level. The probes were gene and transcript annotated using the specific R package pd.hugene.1.0.st.v1. Data structure and homogeneity: We performed a study of i) the gene expression correlation across models and ii) the structure of the data and the separation between experimental groups using hierarchical clustering, PCA, tSNE and OPLS. Differential expression analysis (DEA): We carried on the differential expression analysis in R environment using FCROS (Dembele  et al., 2014). FCROS is a fold change (FC) rank based method that works well with noisy datasets and gives strong reproducible results. FCROS computes for each pair of test/control samples (K pairs), a statistic associated with the k ranks of the FC values for each gene, and the obtained probability (f-value) is used to identify the differential expressed genes (DEGs) within an error level fixed by the analyst. Our fixed error level corresponds to a 5% False Discovery Rate (FDR), and is attained by setting the Ɑ parameter within this range 0.025<Ɑ>0.975.Differential functional analysis (DFA): To identify the altered functions due to the changes in gene expression and possibly get new insights into the mechanistic changes along the pathways between the two conditions trisomic vs. wild type on each model we used the generally applicable gene set enrichment for pathway analysis (GAGE, Luo et al., 2009) R package  to carry on the functional expression analysis.The main aim of re-analysing this data was to get new insights into DS gene deregulation first in humans applying a more updated computational pipeline and  secondly, by applying a comparative genomic approach with rodent Down syndrome datasets identify the conserved gene and functional deregulated profiles.

first: Maria

last: Muñiz Moreno


title: Mitochondria-Rough-ER Contacts in The Liver Regulate Systemic Lipid Homeostasis

city: Quebec

first: Luca

last: Pellegrini

address: 1050 Rue de la Médecine

department: Department of Molecular Biology

country: Canada

institute: Université Laval

summary: Contacts between organelles create microdomains that play major roles in regulating key intracellular activities and signaling pathways, but whether they also regulate systemic functions remains unknown. Here, we report the ultrastructural organization and dynamics of the inter-organellar contact established by rough-Endoplasmic Reticulum closely wrapped around the mitochondria (wrappER). To elucidate the in vivo function of this contact, mouse liver fractions enriched in wrappER-associated-mitochondria are analyzed by transcriptomics, proteomics and lipidomics. The biochemical signature of the wrappER points to a role in the biogenesis of very-low-density lipoproteins (VLDL). Altering wrappER-mitochondria contacts curtails VLDL secretion and increases hepatic fatty acids, lipid droplets and neutral lipid content. Conversely, acute liver-specific ablation of Mttp, the most upstream regulator of VLDL biogenesis, recapitulates this hepatic dyslipidemia phenotype and promotes remodelling of the wrappER-mitochondria contact. The discovery that liver wrappER-mitochondria contacts participate in VLDL biology suggests an involvement of inter-organelle contacts in systemic lipid homeostasis.

overall_design:
mRNA profiles of liver postnuclear lysates and of the corresponding wrappER-associated mitochondria (WAM) fraction were generated by deep sequencing (n=6 per sample type).
The transcriptomic analysis shown in this study were performed by the Genomics Center of the CHU de Québec-Université Laval Research Center, Québec City, Canada

first: Irene

last: Anastasia

first: Nicolò

last: Ilacqua


title: Development of omic biomarkers for Fathead minnow larva (Pimephales promelas) exposed to ethinyl estradiol

city: Cincinnati

first: Gregory

middle: Peter

last: Toth

state: OH

address: 26 W ML King Jr. Dr.

department: CCTE

institute: USEPA/ORD

type: Non-coding RNA profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Acute myeloid leukemia cells resist chemotherapy through a transient senescence-like state

first: Matt

last: Teater


title: Development of omic biomarkers for Fathead minnow larva (Pimephales promelas) exposed to ethinyl estradiol [non-coding small RNA]

summary: This work aimed to expand the panel of gene expression-based biomarkers to include estrogens, to identify training strategies that maximize the range of applicable concentrations, and to evaluate the potential for two classes of small non-coding RNAs (sncRNAs), microRNA (miRNA) and piwi-interacting RNA (piRNA), as biomarkers.

overall_design: SmallRNA reads from fathead minnow (FHM) larvae (48 h post-hatch) exposed to 10 ng ethinyl estradiol for 48 hours were mapped against known FHM miRNA sequences or Danio rerio piRNA sequences, followed by identification of differentially expressed miRNAs or piRNAs.

middle: P

first: John

last: Martinson

first: David

last: Bencic

last: Lattier

first: Mitchell

last: Kostich

first: Weichun

last: Huang

first: Adam

last: Biales


title: Loss-of-function mutations in the histone methyltransferase EZH2 promote chemotherapy resistance in AML

city: Munich

first: Sabrina

last: Weser

address: Marchioninistraße 15

department: Department of Medicine III

institute: University Hospital, LMU

summary: We report that loss of EZH2 provides leukaemia cells with a selective growth advantage, which mediates chemotherapy resistance. This resistance is conferred by up regulation of direct and indirect EZH2 target genes.

overall_design: Description of expression changes due to EZH2 knockout in K562 cells.

first: Julia

last: Kempf

first: Michael

middle: D

last: Bartoschek

first: Klaus

middle: H

last: Metzeler

first: Binje

last: Vick

first: Tobias

last: Herold

first: Kerstin

last: Völse

first: Raphael

last: Mattes

first: Manuela

last: Scholz

first: Lucas

middle: E

last: Wange

first: Moreno

last: Festini

first: Enes

last: Ugur

first: Maike

last: Roas

first: Oliver

last: Weigert

first: Sebastian

last: Bultmann

first: Heinrich

last: Leonhardt

first: Gunnar

last: Schotta

first: Wolfgang

last: Hiddemann

first: Irmela

last: Jeremias

first: Karsten

last: Spiekermann


title: Eliminating genome-wide and transcriptome-wide off-target mutations by base editor [tBE_target_genomic_seq]

first: Li

last: Yang

address: 131 Dong-An Road

department: Institutes of Biological Sciences

institute: Fudan University

summary: Conjugation of CRISPR-Cas9 with cytidine deaminases leads to base editors (BEs) for programmable C-to-T editing, which holds potentials in clinical applications, but suffers from off-target (OT) mutations. By taking advantage of a cleavable deoxycytidine deaminase inhibitor (dCDI) domain, a transformer BE (tBE) system is developed to induce efficient editing with only background levels of genome-wide and transcriptome-wide OT mutations. After being produced, tBE remains inactive at OT sites with the fusion of a cleavable dCDI, thus eliminating unintended mutations. Only when binding at on-target sites, tBE is transformed to cleave off the dCDI domain and catalyzes targeted deamination for precise base changes. After delivery into mice via a dual-AAV system, tBE created a premature stop codon in Pcsk9 and significantly reduced serum PCSK9 level, which resulted in ~30-40% decrease of total cholesterol. Together, the development of tBE establishes a highly-precise base editing system and its in vivo efficacy envisions potential therapeutic applications.

overall_design: Examination of base substitutions induced by the transformer base editor (tBE)

first: Jia

last: Chen

first: Hao

last: Yin

first: Bei

first: Lijie

last: Wang

first: Wei

last: Xue


title: Dual targeting of brain region-specific kinases potentiates neurological rescue in Spinocerebellar ataxia type 1

city: Houston

first: Won-Seok

last: Lee

address: One Baylor Plaza

department: MHG

institute: Baylor College of Medicine

summary:
We performed an shRNA screen to identify novel ATXN1 protein level regulators in hope of finding some that may improve brainstem function in SCA1. We found that two closely related BTB-ZF transcription factors, ZBTB7A and ZBTB7B, positively regulate ATXN1 levels in vitro and in vivo, with ZBTB7B displaying a more pronounced effect. ZBTB7B regulates ATXN1 by regulating the transcription of RSK3 (RPS6KA2). RSK3 in turn regulates ATXN1 by phosphorylating its serine 776 (S776), a residue critical for ATXN1 stability, which is similar to another one previously identified ATXN1 kinase, MSK1.
However, despite the convergent function of the two kinases, each kinase selectively regulates Atxn1 in a brain region-dependent manner; Msk1 predominantly regulates Atxn1 in the cerebellum, while Rsk3 is the predominant regulator of Atxn1 in the brainstem. Our results demonstrate that toxic protein levels can be modulated by different regulators in select brain regions, and hence targeting multiple regulators can expand therapeutic efficacy to rescue multiple degenerating brain areas.

overall_design: mRNA profiles of Daoy (human brain cancer) cells overexpressing either wild-type ZBTB7B or zinc-finger domain mutant (R363L) ZBTB7B.

first: Ying-Wooi

last: Wan


title: Comparison of gene expression profiles between SCD1/FADS2 knockdown and vector control of ovarian cancer cells  OVCA433 by RNA-sequencing

city: Hong Kong

first: Yang

last: XUAN

state: Please Select

address: L740 Laboratory Block LKS Faculty of Medicine,21 Sassoon Road, Pokfulam

department: Department of Obstetrics & Gynaecology

country: Hong Kong

institute: The University of Hong Kong

summary: To understand the dependence of ovarian tumor cells on fatty acid metabolism, we performed transcriptome analysis using OVCA433 ovarian cancer cells, in which SCD1/FADS2 was genetically ablated via CRISPER/Cas9.

overall_design: Gene Expression profiles of SCD1/FADS2 knock out OVCA433 cells , were generated by RNAseq using Illumina NovaSeq6000 sequencer.

first: Olivia

last: Xuan


title: GPR15+ vs GPR15- tumor-associated Tregs

city: Braunschweig

first: Robert

last: Geffers

address: Inhoffenstr. 7

department: Dep. Molecular Bacteriology

institute: HCI - Helmholtz Centre for Infection Research

summary: GPR15+ vs GPR15- tumor-associated Tregs were sorted from colorectal cancer mice (Foxp3-RFP x GPR15-GFP)

overall_design: To analyze the role of GPR15 on the phenotype of tumor-associated Tregs, gene expression analysis of sort-purified GPR15-GFP+ (1 GPR15P, 5 GPR15P, 6 GPR15P) and GPR15-GFP- (1 GPR15M, 5 GPR15M, 6 GPR15M) Tregs from the tumorous colonic lamina propria of Foxp3-RFP x GPR15-GFP double-reporter mice were performed.

first: A

last: Adamczyk

middle: M

last: Westendorf

first: R


title: The Anna Karenina model of β cell maturation in development and their dedifferentiation in type 1 and type 2 diabetes

city: Madison

first: Barak

last: Blum

state: Wisconsin

address: 4551 WIMR II, 1111 Highland Ave.

institute: University of Wisconsin-Madison

summary: Loss of mature β cell function and identity, or β cell dedifferentiation, is seen in all types of diabetes mellitus. Two competing models explain β cell dedifferentiation in diabetes. In the first model, β cells dedifferentiate in the reverse order of their developmental ontogeny. This model predicts that dedifferentiated β cells resemble β cell progenitors. In the second model, β cell dedifferentiation depends on the type of diabetogenic stress. This model, which we call the “Anna Karenina” model, predicts that in each type of diabetes, β cells dedifferentiate in their own way, depending on how their mature identity is disrupted by any particular diabetogenic stress. We directly tested the two models using a β cell-specific lineage-tracing system coupled with RNA-sequencing in mice. We constructed a multidimensional map of β cell transcriptional trajectories during the normal course of β cell postnatal development, and during their dedifferentiation in models of both type 1 diabetes (NOD) and type 2 diabetes (BTBR-Lepob/ob). Using this unbiased approach, we show here that despite some similarities between immature and dedifferentiated β cells, β cells dedifferentiation in the two mouse models is not a reversal of developmental ontogeny and is different between different types of diabetes.

overall_design: Mouse β cell mRNA profiles of E18.5 ICR embryos, P1 ICR neonates, P7 ICR neonates, P10 ICR neonates, ICR adult (wildtype), NOD adult (T1D model), BTBR ob/+, and BTBR ob/ob (T1D model)

first: Sutichot

last: Nimkulrat

first: Christina

last: Kendziorski

first: Zijian

last: Ni

first: Jared

last: Brown


title: tableNONMMUT140591.1 may serve as a ceRNA to regulate Gata5 in UT-B knockout-induced cardiac conduction block

city: Changchun

first: yanwei

last: du

state: Jilin

address: No. 218, Ziqiang Street, Nanguan District

department: Department of Respiratory and Critical Care Medicine

institute: The 2nd Hospital of Jilin University

summary:
Objective: We intended to explore the potential molecular mechanisms underlying cardiac conduction block inducted by UT-B deletion at the transcriptome level.
Methods: The heart tissues were harvested from UT-B null mice and age-matched wild-type mice for lncRNA sequencing analysis. Based on the sequencing data, the differentially expressed mRNAs (DEMs) and lncRNAs (DELs) between UT-B knockout and control groups were identified, followed by function analysis and mRNA-lncRNA co-expression analysis. The miRNAs were predicted, and then the competing endogenous RNA (ceRNA) network was constructed.
Results: UT-B deletion results in the aberrant expression of 588 lncRNAs and 194 mRNAs. These DEMs were significantly enriched in inflammation-related pathway. A lncRNA-mRNA co-expression network and a ceRNA network was constructed on the basis of the DEMs and DELs. C7 (complement C7)-NONMMUT137216.1 co-expression pair had the highest correlation coefficient in the co-expression network. NONMMUT140591.1 had the highest degree in ceRNA network and involved in ceRNA of NONMMUT140591.1-mmu-miR-298-5p-Gata5 (GATA binding protein 5).
Conclusion: UT-B deletion may promote cardiac conduction block via inflammatory process. The ceRNA NONMMUT140591.1-mmu-miR-298-5p-Gata5 may be a potential molecular mechanism of UT-B knockout-induced cardiac conduction block.

overall_design: Retinal mRNA profiles of 16 weeks old UT-B+/+ and UT-B-/- mice

first: Baoxue

last: Yang


title: DEG expression in primary human Cytotoxic T Lymphocytes (CTL, CD8+ T-cells) and Natural Killer cells (NK cells) [donor 3 & 4]

status: Public on Mar 11 2021

city: Homburg

first: Eva

last: Schwarz

address: Geb. 48

department: Biophysics

institute: Saarland University

summary:
Based on differential expression analysis of the transcriptome data and analysis of master regulator genes, we identified 31 candidates which potentially regulate Ca2+-homeostasis in CTL
Genes showing differential expression between NK cells and CTL were intersected with members of known Ca2+-signaling pathways and combined with putative key regulators

overall_design: Primary CD8+ T-cells and NK cells were bead-isloated (untouched) and CD8+ T-cells were stimulated with SEA or anti-CD3/CD28 beads, of each template, we analyzed 11 different donors, PBMC were purified from leukocyte reduction chambers (LRS) of healthy platelet donors

first: Mohamed

last: Hamed


title: Breast Milk Extracellular Vesicle miRNAs from a Population-Based Cohort in the Faroe Islands

city: New York

first: Allison

last: Kupsco

department: Environmental Health Sciences

institute: Columbia University Mailman School of Public Health

summary: Human breast milk (BM) plays a critical role in infant development and health, particularly in cognitive, immune, and cardiometabolic functions. BM contains extracellular vesicles (EVs) that can transport biologically relevant cargo from mother to infant, including microRNAs (miRNAs). However, to date, most studies on BMEVs have been limited in sample size. We aimed to investigate BMEV-miRNA profiles in a human population cohort, characterize BMEV-miRNAs patterns, and assess potential pathways and ontology. We thus conducted the first study to describe the EV miRNA profile of BM in 364 mothers from a population-based mother-infant cohort in the Faroe Islands using small RNA sequencing. We detected 1,523 miRNAs with ≥ one read in 70% of samples, and 447 miRNAs with ≥ one read in 100% of samples. Using hierarchical clustering, we determined five BMEV-miRNA clusters, the top three consisting of 15, 27 and 67 miRNAs. Correlation coefficients indicated that the expression of many miRNAs within the top three clusters was highly correlated. Top-cluster BMEV-miRNAs were involved in pathways enriched for the endocrine system, cellular community, neurodevelopment, and cancers. Future studies investigating determinants of BMEV-miRNAs and associated health outcomes are needed to elucidate the role of BMEV-miRNAs in health and disease.

overall_design: We leveraged 364 breast milk samples collected at two weeks postpartum from the Faroe Islands Birth Cohort, which recruited women between 1997 and 2000 from the National Hospital in Torshavn, Faroe Islands. Samples were centrifuged at 200g for 10 mins to remove fat globules, then 3,000g for 15 mins to pellet cellular debris. Extracellular vesicle (EV) RNA was isolated with the ExoEasy Maxi Kit and the miRNeasy RNA Isolation Kit (Qiagen) according to manufacturer instructions.  EV-miRNA libraries were prepared with the HTG Molecular Whole Transcriptome miRNA Assay (HTG Molecular, Tucson, AZ), which profiles 2,083 mature miRNAs via a targeted library prep method, and sequenced in four lanes on a HiSeq4000 (Illumina) with 50 nucleotide single-end reads. Three replicate EV-miRNA samples  and three human brain positive control samples were included in each sequencing run.

first: Andrea

last: Baccarelli


title: DEG expression in primary human Cytotoxic T Lymphocytes (CTL, CD8+ T-cells) and Natural Killer cells (NK cells) [donor 10 & 11]

overall_design: Primary CD8+ T-cells and NK cells were bead-isloated (untouched) and CD8+ T-cells were stimulated with SEA or anti-CD3/CD28 beads, of each template, overall, we analyzed 11 different donors, PBMC were purified from leukocyte reduction chambers (LRS) of healthy platelet donors


title: Acute myeloid leukemia cells resist chemotherapy through a transient senescence-like state [RNA-seq]

first: Matt

last: Teater

address: 445 E 69th St

institute: Weill Cornell Medical College

summary: In acute myeloid leukemias (AML), chemotherapy is frequently followed by disease relapse, yet the mechanism by which AML reemerges is not fully understood. We hypothesized that chemotherapy induces senescence-like dormancy that facilitates survival to genotoxic exposure, allowing AML cells to endure treatment in a transiently dormant state while retaining potential for leukemic repopulation. Here, we show that primary AML cells exhibit hallmark senescence features following treatment with cytarabine (AraC), including growth arrest, increased cellular granularity, senescence-associated-β-galactosidase (SA-β-gal) activity, and senescence-associated transcriptomic alterations. Induction of AraC-induced premature senescence was regulated by the ATR kinase activity and mediated stress-survival. High-throughput single cell RNA (scRNA)-seq analysis of primary AML cells ex vivo and in vivo following chemotherapy suggest active transcriptional programming towards senescent-like dormancy instead of enrichment for leukemia stem cells (LSCs). scRNA-seq of sorted AraC-induced premature senescent AML cells demonstrated a heterogenous population including a fraction of cells with simultaneous expression of dormancy- and senescence-associated gene signatures. Xenotransplantation of AraC-induced premature senescent AML cells into mice demonstrated that senescent-like AML cells maintain leukemia-repopulating potential. Altogether, we propose a mechanism of AML relapse whereby AML cells tolerate chemotherapy via acquisition of a transient senescent-like state.

overall_design: Gene expression in AraC treated AML ex vivo culture, primary xenografts

first: Duy

last: Cihangir

first: Ari

last: Melnick


title: Development of omic biomarkers for Fathead minnow larva (Pimephales promelas) exposed to ethinyl estradiol [mRNA]

first: Gregory

last: Toth

summary: This work aimed to expand the panel of gene expression-based biomarkers to include estrogens, to identify training strategies that maximize the range of applicable concentrations, and to evaluate the potential for mRNA and two classes of small non-coding RNAs (sncRNAs), microRNA (miRNA) and piwi-interacting RNA (piRNA), as biomarkers.

overall_design: mRNA reads from fathead minnow (FHM) larvae (48 h post-hatch) exposed for 48 h to a range of ethinyl estradiol concentrations (0, 0.12, 1.2, 2.5, 5.0 or 10 ng EE2/l) were mapped against 47K known FHM mRNA transcripts, followed by identification of differentially expressed miRNAs or piRNAs.

first: John

last: Martinson

first: David

last: Bencic

last: Lattier

first: Mitchell

last: Kostich

first: Weichun

last: Huang

first: Adam

last: Biales


title: Eliminating genome-wide and transcriptome-wide off-target mutations by base editor

city: Shanghai

first: Li

overall_design: Examination of whole transcriptome-wide off-target (OT) mutations induced by the transformer base editor (tBE)

first: Jia

last: Chen

first: Hao

last: Yin

first: Bei

first: Lijie

last: Wang

first: Wei

last: Xue


title: Single cell RNA profiles of bone marrow aspirate concentrate

city: La Jolla

first: Samuel

middle: Richard

last: Ward

state: CA

address: 9500 Gilman Drive (0863)

department: Orthopaedic Surgery, Radiology, and Bioengineering

institute: University of California San Diego

summary:
Background: There is a need to identify and quantify mesenchymal stromal cells (MSCs) in human bone marrow aspirate concentrate (BMAC) source tissues, but current methods to do so were established in cultured cell populations. Given that surface marker and gene expression change in cultured cells, it is doubtful that these strategies are valid to quantify MSCs in fresh BMAC.
Purpose: To establish the presence, quantity, and heterogeneity of BMAC-derived MSCs in minimally manipulated BMAC using currently available strategies.
Study Design: Descriptive Laboratory Study.
Methods: Five published strategies to identify MSCs were compared for suitability and efficiency to quantify clinical-grade BMAC-MSCs and cultured MSCs at the single cell transcriptome level on BMAC samples being used clinically from fifteen orthopedic patients and on one cultured MSC sample. Strategies included: 1) the guidelines by the International Society for Cellular Therapy (ISCT), 2) CD271 expression, 3) the Ghazanfari et al. transcriptional profile, 4) the Jia et al. transcriptional profile, and 5) the Silva et al. transcriptional profile.
Results: ISCT guidelines did not identify any MSCs in BMAC at the transcriptional level and only 1 in 9 million cells at the protein level. 9 of 12850 BMAC cells expressed the CD271 gene. Only 116 of 396 Ghazanfari genes were detected in BMAC, whereas no cells expressed all of them. No cells express all Jia genes, but 25 cells express at least 13 of 22. No cells express all Silva genes, but 19 cells express at least 8 of 23. Most importantly, the liberalized strategies tended to identify different cells and most of them clustered with immune cells.
Conclusion: Currently available methods need to be liberalized to identify any MSCs in fresh human BMAC and lack consensus at the single cell transcriptome and protein expression levels. These different cells should be isolated and challenged to establish phenotypic differences.
Clinical Relevance: This study demonstrated that improved strategies to quantify MSC concentrations in BMAC for clinical applications are urgently needed. Until then, injected minimally manipulated MSC doses should be reported as rough estimates or as unknown.

overall_design:
Single cell RNA profiles of nine clinical-grade bone marrow aspirate concentrate samples and one cultured mesenchymal stromal cell sample.

Library IDs and cell barcode suffixes in processed data:
Cultured MSCs (Lonza, Switzerland) JTW01 = -1
BMAC cells JTW03 = -3
BMAC cells JTW05 = -4
BMAC cells JTW06 = -5
BMAC cells JTW07 = -6
BMAC cells JTW08 = -7
BMAC cells JTW10 = -8
BMAC cells MG01 = -9
BMAC cells MG02 = -10
BMAC cells MG03 = -11

first: Severin

last: Ruoss

first: J

middle: T

last: Walker

first: Sonya

last: Ahmed

first: Chanond

last: Nasamran

first: Kathleen

last: Fisch

first: Conner

last: Paez

first: Jesal

middle: N

last: Parekh

first: Scott

last: Ball

first: Jeffrey

middle: L


title: DEG expression in primary human Cytotoxic T Lymphocytes (CTL, CD8+ T-cells) and Natural Killer cells (NK cells) [donor 9 & 2]

first: Eva

middle: C

last: Schwarz

first: Mohamed

last: Hamed


title: DEG expression in primary human Cytotoxic T Lymphocytes (CTL, CD8+ T-cells) and Natural Killer cells (NK cells) [donor 8 & 2, 3, 4]

overall_design: Primary CD8+ T-cells and NK cells were bead-isloated (untouched) and CD8+ T-cells were stimulated with SEA or anti-CD3/CD28 beads, of each template, we analyzed 11 different donors, PBMC were purified from leukocyte reduction system (LRS) chambers of healthy platelet donors


title: INPP4B regulates AR activity

city: Miami

first: Irina

last: Agoulnik

state: FL

address: 11200 SW 8th ST

department: Human and Molecular Genetics

institute: Florida International University, HWCOM

summary: Activation and transcriptional reprograming of AR in advanced prostate cancer frequently overlaps with the loss of two tumor suppressors, INPP4B and PTEN, which are highly expressed in human and mouse prostate epithelium. While regulation of AR signaling by PTEN has been described by multiple groups, it is not known whether the loss of INPP4B affects AR activity. Using prostate cancer cell lines we showed that INPP4B regulates AR transcriptional activity and oncogenic signaling pathways Akt and PKC. Analysis of gene expression in prostate cancer patient cohorts showed a positive correlation between INPP4B expression and both AR mRNA levels and AR transcriptional output. Using an Inpp4b-/- mouse model, we demonstrated that INPP4B suppresses Akt and PKC signaling pathways and modulates AR transcriptional activity in normal mouse prostate. It has been previously shown that the high fat diet activates Akt pathway in mouse prostate. We showed that the loss of INPP4B further increases Akt phosphorylation in dorsolateral and ventral lobes of mice fed with the high fat diet. Remarkably, PTEN protein levels and phosphorylation of S380 were the same in Inpp4b-/- and WT males, suggesting that observed changes were due exclusively to the loss of INPP4B. Our data show that INPP4B modulates AR activity in normal prostate and its loss contributes to the AR-dependent transcriptional profile in prostate cancer.

overall_design: Two groups were analyzed: control and INPP4B knockdown. Each group had 3 biological variables. Control: LNCAP-Cont2, LNCAP-Cont3, LNCAP-Cont4. INPP4B knockdown: LNCAP-INPP4B-2, LNCAP-INPP4B-3, LNCAP-INPP4B-4.

first: Manqi

last: Zhang

first: Lubov

last: Nathanson

first: Leif

last: Peterson

first: Kimal

last: Rajapakshe

first: Nancy

last: Weigel

first: Cristian

last: Coarfa

middle: U


title: DEG expression in primary human Cytotoxic T Lymphocytes (CTL, CD8+ T-cells) and Natural Killer cells (NK cells) [donor 1 & 5]


title: Genomic methylation signatures of idiopathic subglottic stenosis (iSGS)

first: Xudong

last: Shi

address: 1111 Highland ave

department: Surgery

summary: iSGS exhibits distinct genomic methylation signatures. These signatures expand current understanding of the iSGS phenotype and may inform the direction of future experimental studies.

overall_design: Molecular analysis of clinical biospecimens.  We collected subglottic tissue biopsies from 12 patients during direct laryngoscopy, immediately prior to surgical  treatment of iSGS; as well as from 4 age-, sex-, and race/ethnicity-matched control patients undergoing other direct laryngoscopic procedures.

first: Stephen

last: Schoeff

first: William

middle: G

last: Young

first: Chad

middle: W

last: Whited

first: Resha

last: Soni

first: Peng

last: Liu

first: Irene

last: Ong

first: Seth

last: Dailey

first: Nathan

last: Welham


title: DEG expression in primary human Cytotoxic T Lymphocytes (CTL, CD8+ T-cells) and Natural Killer cells (NK cells)

first: Eva

last: Schwarz

overall_design: Refer to individual Series


title: Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases  [ChIP-seq]

city: Amsterdam

first: Tesa

last: Severson

address: 121 Plesmanlaan

department: Molecular Carcinogensis

institute: Netherlands Cancer Institute

type: Genome binding/occupancy profiling by high throughput sequencing

summary: We performed transcriptional profiling and chromatin immunoprecipitation for the key oncogenic driver in prostate cancer, Androgen Receptor (AR) and FOXA1, H3K27ac, H3K27me3 and CTCF to chart the epigenomic landscape in four clonal metastatic tumors from a single prostate cancer patient whose clinical course was closely followed over 17 years.  The vast majority (~80% ) of all AR binding sites were shared among all samples and found in normal prostate tissue and primary prostate cancers signifying core binding events within the prostate lineage. Remarkably, active (H3K27ac marked) metastatic sample-specific AR binding sites showed no differential transcriptional output, indicating a robustness of transcriptional programming across different metastases samples.

overall_design: Examination of AR, FOXA1, CTCF, H3K27ac, H3K27me3 and RNA-seq in 4 separate metastases samples from a single metastatic castration resistant prostate cancer patient.

first: Yanyun

last: Zhu

first: Angelo

last: De Marzo

first: Tracy

last: Jones

first: Jonathan

last: Simons

last: Nelson

first: Srinivasan

last: Yegnasubramanian

first: Matthew

last: Freedman

first: Lodewyk

last: Wessels

first: Andries

last: Bergman

first: Michael

last: Haffner

first: Wilbert

last: Zwart


title: Age-Related Differences in Monocyte DNA Methylation and Immune Function in Healthy Kenyan Adults and Children

city: Cleveland

first: Katherine

middle: Rose

last: Dobbs

address: 10900 Euclid Ave.

institute: Case Western Reserve University

type: Methylation profiling by genome tiling array

summary:
Genome wide DNA methylation profiling of isolated monocyte samples from healthy Kenyan children, the same children during an episode of acute malaria, healthy Kenyan adults, and healthy  adults from the United States. The Illumina Infinium MethylationEPIC BeadChip microarray was used to obtain DNA methylation profiles across approximately 860,000 CpGs in negatively selected monocyte samples. Samples included monocytes from 8 children from western Kenya obtained while healthy and matching samples from the same 8 Kenyan children obtained during an episode of acute uncomplicated Plasmodium falciparum malaria, 8 healthy malaria-immune adults from western Kenya, and 8 healthy malaria-naive adults from the US.
Abstract -- Background: Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profiles in monocytes from young adults and children from western Kenya.  Results:  We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles. Conclusions:  These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.

overall_design: Bisulphite converted DNA from the 32 samples were hybridised to the Illumina Infinium MethylationEPIC BeadChip.

middle: R

first: Paula

last: Embury

first: Emmily

last: Koech

first: Sidney

last: Ogolla

first: Stephen

last: Munga

first: James

last: Kazura

first: Arlene

last: Dent


title: Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases

first: Tesa

last: Severson

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


title: Multi-omics analysis to examine gene expression and metabolites from multisite adipose-derived mesenchymal stem cells

city: Nanjing

first: Chuanxi

last: Yang

state: China

address: 300 Guangzhou Road, 210029, Nanjing, PR China

department: Department of Cardiology

institute: School of Medicine, Southeast University

summary: The aim of this study was to explore the gene expression and metabolites among multisite adipose-derived mesenchymal stem cells, and investigate the metabolic pathway of multisite adipose-derived mesenchymal stem cells using a multi-omics analysis. Subcutaneous adipose-derived mesenchymal stem cells (SASCs), perirenal adipose-derived mesenchymal stem cells (PASCs), and epididymal adipose-derived mesenchymal stem cells (EASCs) were isolated from Sprague Dawley rats. RNA and metabolites were extracted and sequenced using transcriptomics and metabolomics analyses, respectively. There were 720 differentially expressed genes (DEGs) in EASCs and 688 DEGs in PASCs compared with SASCs; there were 166 unique DEGs in EASCs, 134 unique DEGs in PASCs, and 554 common DEGs between EASCs and PASCs. Furthermore, there were 220 differential metabolites in EASCs, 249 differential metabolites in PASCs, 83 unique differential metabolites in EASCs, 112 unique differential metabolites in PASCs, and 137 common differential metabolites between EASCs and PASCs. The transcriptomics and metabolomics analyses identified four hub genes, one in EASCs and three in PASCs. There are functional differences among multisite adipose-derived mesenchymal stem cells that may be related to the hub genes Atac2, Rrm1, Rrm2, and Gla. The relevant signaling pathways are the Ras signaling pathway, HIF-1 signaling pathway, and the p53 signaling pathway.

first: Jing

last: Zhang

first: Tingting

last: Wu

first: Xiangqing

last: Kong


title: Dihydrotanshinone exerts antitumor effects and improves the effects of cisplatin in anaplastic thyroid cancer cells

city: Udine

first: Giuseppe

last: Damante

address: via chiusaforte, E

department: Medical Area

country: Italy

institute: University of Udine

summary:
Anaplastic thyroid cancer (ATC) is the most aggressive type of thyroid cancer and is responsible for 20-50% of thyroid-associated cancers deaths. The absence of response to conventional treatments makes the search for novel therapeutics an urgent clinical challenge. In the present study, the effects of 15,16-dihydrotanshinone I (DHT), a tanshinone extracted from Salvia miltiorrhiza Bunge (Danshen), which has been shown to possess anticancer activity, were examined on two human ATC cell lines.
DHT significantly reduced cell viability, coupled with an increase in apoptosis. DHT administration was also able to reduce the colony-forming ability and the growth in soft agar and downregulate the expression of certain epithelial-to-mesenchymal transition-related genes. In addition, DHT significantly reduced MAD2 expression, a target of HuR with a relevant role in ATC. Finally, cotreatment with cisplatin and DHT augmented their effects on cell viability compared with each compound alone.
In conclusion, to the best of our knowledge, the present study is the first to demonstrate that DHT exerts antitumor effects on ATC cells by reducing MAD2 expression levels. Moreover, a synergistic effect of DHT with cisplatin was shown, and thus further in vivo studies are required to assess this phytochemical compound as a potential adjuvant for the treatment of ATC.

overall_design: mRNA profiles of SW1736 and 8505C DHT treated or untreated cells

first: Lorenzo

last: Allegri

first: Federica

last: Baldan

first: Diego

last: Russo


title: No evidence for whole-chromosome dosage compensation or global transcriptomic expression differences in spontaneously-aneuploid mutation accumulation lines of Saccharomyces cerevisiae

city: Athens

first: Holly

last: McQueary

state: GA

address: 120 E Green St

department: Genetics

institute: University of Georgia

summary: Aneuploidy, the state in which an organism’s genome contains one or more missing or additional chromosomes, often causes widespread genotypic and phenotypic effects. Most often, aneuploidies are deleterious; the most common examples in humans being Down’s syndrome (Trisomy 21) and Turner’s syndrome (monosomy X). However, aneuploidy is surprisingly common in wild yeast populations. In recent years, there has been debate as to whether yeast contain an innate dosage compensation response on the whole-genome level, or if these natural isolates are robust to aneuploidy without such a mechanism. In this study, we tested for differential gene expression in 20 aneuploid and 18 euploid lines of yeast from two previous mutation accumulation experiments, where selection was low and therefore aneuploidies arose spontaneously. We found no evidence for whole-chromosome dosage compensation in aneuploid yeast but did find some evidence for attenuation of expression on a gene-by-gene basis. We additionally found that aneuploidy has no effect on the expression of the rest of the genome (i.e. “trans” genes), and that very few mutually exclusive aneuploid lines shared differentially expressed genes. However, we found a small common differential expression response in the euploid lines, suggesting an effect of mutation accumulation on gene expression. Our findings contribute to our understanding of aneuploidy in yeast and support the hypothesis that there is no innate dosage compensation mechanism at the whole-chromosome level.

overall_design: To determine the effects of aneuploidy on gene expression, we collected and analyzed RNA sequencing data from a selection of euploid and aneuploid lines from each experiment. For aneuploid samples, we chose all the MA lines that were monosomic for a chromosome (3 lines), those that shared common aneuploidies (21 lines), and those that had more than one aneuploidy event (4 lines). From the homozygous ancestor experiment, we selected 10 aneuploid and 12 euploid MA lines. From the heterozygous ancestor experiment, we selected 10 aneuploid and 6 euploid MA lines. Additionally, we collected RNA sequencing data for both ancestral lines.

first: Megan

last: Behringer

first: Sam

last: Demario

first: Alexander

middle: J

last: Canas

first: Brittania

last: Johnson

first: Ariella

last: Tsfoni

first: John

last: Chamberlin

first: David

last: Hall


title: DEG expression in primary human Cytotoxic T Lymphocytes (CTL, CD8+ T-cells) and Natural Killer cells (NK cells) [donor 6 & 7]

first: Eva

last: Schwarz

first: Mohamed

last: Hamed


title: Aberrant expression of long noncoding RNAs in exosomes in follicle fluid from PCOS patients

city: Yangzhou

first: Wang

last: Li-ping

state: Jiangsu

address: No. 98 West Nantong Road

department: Department of Biobank, Clinical Medical College,

institute: Yangzhou University

summary: Polycystic ovary syndrome (PCOS) is a common reproductive endocrine disease characterized by persistent anovulation and hyperandrogenism, affecting approximately 8%-10% of women of childbearing age and occupying an important position in the etiology of infertility. There is increasing evidence that lncRNAs are involved in the development of PCOS, but the potential regulatory mechanism is still unclear. This study performed high-throughput lncRNA sequencing of follicular fluid exosomes in non-PCOS infertility patients and PCOS infertility patients. The sequencing results led to the identification of 1253 upregulated and 613 downregulated lncRNAs from a total of 1866 detected candidates. There was no significant difference between the PCOS patients and non-PCOS patients in body mass index (BMI) or the fasting blood glucose (FBG) level. However, luteinizing hormone (LH), estradiol (E2), testosterone (T), serum prolactin (PRL) and anti-Mullerian hormone (AMH) levels were clearly upregulated in PCOS patients compared to those in non-PCOS patients. There was also an increase in LH/FSH (>2) in the PCOS patients. Functional analysis showed that the functions of lncRNAs were related to adenine metabolism, adenine biosynthesis and cytidine triphosphate biosynthesis. These results suggest that lncRNAs may play an important role in the pathogenesis of PCOS and may be potential targets for the diagnosis and treatment of PCOS.

first: Li-ping

last: Wang


title: Epigenetic and transcriptional analysis reveals a core transcriptional program conserved in clonal prostate cancer metastases [RNA-seq]

first: Tesa

last: Severson

summary: We performed transcriptional profiling and chromatin immunoprecipitation for the key oncogenic driver in prostate cancer, Androgen Receptor (AR) and FOXA1, H3K27ac, H3K27me3 and CTCF to chart the epigenomic landscape in four clonal metastatic tumors from a single prostate cancer patient whose clinical course was closely followed over 17 years. The vast majority (~80% ) of all AR binding sites were shared among all samples and found in normal prostate tissue and primary prostate cancers signifying core binding events within the prostate lineage. Remarkably, active (H3K27ac marked) metastatic sample-specific AR binding sites showed no differential transcriptional output, indicating a robustness of transcriptional programming across different metastases samples.

first: Yanyun

last: Zhu

first: Angelo

last: De Marzo

first: Tracy

last: Jones

first: Jonathan

last: Simons

first: William

last: Nelson

first: Srinivasan

last: Yegnasubramanian

first: Matthew

last: Freedman

first: Lodewyk

last: Wessels

first: Andries

last: Bergman

first: Michael

last: Haffner

first: Wilbert

last: Zwart


title: Transcriptome analysis of activated CD4+ T cells treated either with sodium butyrate or bufexamac

city: Munich

first: Alexander

last: Graf

address: Feodor-Lynen-Str. 25

department: Gene Center Munich

institute: Ludwig-Maximilians-Universität München

summary: Sodium butyrate and bufexamac treatment of activated CD4+ T cells impairs de novo HIV-1 infection. RNAseq was used to obtain information about the cellular changes upon treatment, which could explain the observed effects on HIV-1 infection

overall_design: CD4 T cells were isolated from PBMCs using Easy-SepTM Rosette Human CD4+ T cell enrichment kit (Stemcell Technologies, Canada). Isolated cells were activated with IL-2 and PHA for 5-7 days according to standard protocols. To minimize donor effects, activated T cells from four donors were pooled and activated CD4+ T cell-pools were treated either with 1.95 mM sodium butyrate or 0.04 mM bufexamac and cultured for 48 h. Untreated T cell-pools served as control. Subsequently, cells were harvested, washed with PBS, and RNA was isolated from trizol lysates of cells using Direct-zol RNA Miniprep Kit (Zymo Research) following manufacturer’s instructions. Isolated RNA was additionally purified using Agencourt RNAClean XP beads (Beckman Coulter) following manufacturer’s instructions.  In total 3 independent samples of untreated, sodium butyrate treated , and bufexamac treated cells were generated. After quantification (Nanodrop), the RNA was quality controlled using a Bioanalyzer (Agilent Technologies). Good quality RNA (RIN > 7) was used to generate sequencing libraries by using 500 ng total RNA in a Sense mRNA Seq Libarary Prep Kit V2 for Illumina platforms (Lexogen) following manufacture’s instructions. Libraries were quantified and subsequently sequenced on an Illumina HiSeq 1500 (sequencing mode: 100 nt, single-end). The sequencing data was preprocessed on a Galaxy server (hosted by LAFUGA, Gene Center, Munich). After demultiplexing, the data was trimmed according to Lexogen. The output was mapped to the human genome (hg19) using STAR (v. 2.5.2b-0). Abundant reads were further analyzed using HTSeq-count (v. 1.0.0) and a differential gene expression analysis was performed using DESeq (v. 1.0.19) setting the FDR < 0.01.

first: Lin

last: Chen

first: Ariane

last: Zutz

first: Julia

last: Phillippou-Massier

first: Tim

last: Liebner

first: Oliver

last: Keppler

first: Chunaram

last: Choudhary

first: Helmut

last: Blum

first: Christian

last: Schölz


title: The genomic, epigenomic and biophysical cues controlling the emergence of the gas exchange niche in the lung

city: Philadelphia

middle: Patrick

last: Morley

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Penn Cardiovascular Institute

institute: Perelman School of Medicine at the University of Pennsylvania

summary: The lung alveolus is the functional unit of the respiratory system required for gas exchange. During the transition to air breathing at birth, biophysical forces are thought to shape the emerging tissue niche. However, the intercellular signaling that drives these processes remain poorly understood. Applying a multimodal approach, we identify alveolar type 1 (AT1) epithelial cells as a distinct signaling hub. Lineage tracing demonstrates that AT1 progenitors align with receptive, force-exerting, myofibroblasts in a spatial and temporal manner. Through single cell chromatin accessibility and pathway expression (SCAPE) analysis, we demonstrate that AT1-restricted ligands are required for myofibroblasts and alveolar formation. These studies show that the alignment of cell fates, mediated by biophysical and AT1-derived paracrine signals, drives the extensive tissue remodeling required for postnatal respiration.

overall_design: All mouse experiments used CD-1 female mice with the age indicated in the libraries . Single-cell suspensions were prepared from whole mouse lungs. For all libraries, DAPI-negative cells were  were sorted by flow cytometry to obtain heterogeneous whole lung sample. Human tissue was derived from normal peripheral lung tissue. Single cell suspension was depleted of CD45-positive cells by bead selection. All of the murine post-natal timepoints also had CD45-positive cells removed from cell sort. Single-cell barcoded droplets were produced using 10X Single Cell 3’ v2 chemistry. Libraries generated were sequenced using HiSeq2500 instrument in High-output mode. Reads were aligned and gene level unique molecular identifier (UMI) counts were obtained using the Cell Ranger pipeline.

first: Jarod

middle: A

last: Zepp

first: Edward

last: Morrisey


title: Transcriptome profile of 3T3-L1 adipocytes after overexpression of miR-690-5p

first: Wei

last: Ying

address: 9500 Gilman Dr, Stein Clinical Research Building, Room 225

institute: UC San Deigo

summary: This project was designed to understand the regulation of miR-690-5p on genetic network of 3T3-L1 adipocytes

overall_design: 3T3-L1 adipocytes control vs miR-690oe

first: Jerrold

last: Olefsky


title: T cell receptor repertoire analysis of tumor-infiltrating T cells in non-small cell lung cancer [tet_sorted_PBLT_cells]

city: New Brunswick

first: Shin-Heng

last: Chiou

state: NJ

address: 195 Little Albany St, Room 3001

department: Medicine

institute: Rutgers Cancer Institute of New Jersey

summary: We analyzed 778,938 T cell receptor (TCR) CDR3b sequences from 178 non-small cell lung cancer (NSCLC) patients using GLIPH2 (Grouping of Lymphocyte Interactions with Paratope Hotspots 2). We identified over 66,000 TCR shared specificity groups, of which over 400 were enriched in tumor vs. adjacent lung. We focused on one tumor-enriched specificity group and used a yeast display library to identify the peptide epitopes. These include peptides from TMEM161A, which is an overexpressed antigen in NSCLC, and homologous peptides from Epstein-Barr virus (EBV) and E. coli, aligning with recent reports of virus-specific T cells in tumor infiltrates. Overall, we analyzed a very large dataset of TCR sequences from NSCLC patients and found thousands of specificities shared by three or more patients. This creates a database of TCR shared specificity groups in NSCLC, and also a template for mining and understanding the specificity of infiltrating T cells for any cancer.

overall_design: Single-cell RNA-Seq data collected with FACS sorted T cells from PBL of HLA-A*02+, healthy donors and HLA-A*02+ lung cancer patients.

first: Diane

last: Tseng