title: Introducing Differential RNAseq mapping to track the phage infection process for Pseudomonas virus ɸKZ

city: Würzburg

first: Falk

last: Ponath

address: Josef-Schneider-Straße 2

institute: Helmholtz Institute for RNA-based Infection Research (HIRI)

summary: Differential RNA-seq (dRNA-seq) was performed on Pseudomonas aeruginosa alone or shortly after iinfection with the jumbo phage phiKZ

sample_organism:
Phikzvirus phiKZ
Pseudomonas aeruginosa PAO1

overall_design: Pseudomonas aeruginosa PA01 was infected during the early exponential growth phase with phiKZ (MOI of 15). The infection was allowed to take place for 10min before cells were frozen in liquid nitrogen. RNA was extracted and after DNaseI treatment used for library construction according to the dRNA-seq protocol at Vertis Biotechnology (Germany).

first: Laura

last: Wicke

first: Lucas

last: Coppens

first: Milan

last: Gerovac

first: Rob

last: Lavigne

first: Jörg

last: Vogel


title: The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis [CTC lines vs tumors and CCLE lines RNA-Seq]

status: Public on Nov 13 2020

city: Boston

first: Ben

middle: S.

last: Wittner

state: MA

address: 149 13th Street

department: Center for Cancer Research

country: USA

institute: Massachusetts General Hospital

type: Expression profiling by high throughput sequencing

summary: Circulating tumor cells (CTCs) are shed by cancer into the bloodstream, where a viable subset overcomes oxidative stress to initiate metastatic outgrowth. Here we show that CTCs from patients with BRAF-mutant melanoma coordinately upregulate both lipogenesis and iron homeostasis pathways. In clonally-derived cultures of melanoma CTCs these pathways are correlated with both intrinsic and acquired resistance to BRAF inhibitors. The lipogenesis regulator SREBF2 directly induces transcription of the iron carrier Transferrin (TF), reducing intracellular iron pools, reactive oxygen species (ROS) and lipid peroxidation, and conferring resistance to both BRAF inhibitors and inducers of ferroptosis. Knockdown of endogenous TF impairs tumor formation by melanoma CTCs, and their tumorigenic defects are partially rescued by the lipophilic anti-oxidants Ferrostatin-1 and Vitamin E. In a cohort of patient-derived melanoma CTCs, single cell RNA-seq identifies a subset with high lipogenic, iron metabolic and proliferative signatures, which are correlated with adverse clinical outcome, irrespective of treatment regimen. Thus, SREBF2-driven iron homeostatic pathways contribute to cancer progression, drug resistance and metastasis.

overall_design: We generated five patient-derived CTC cultures following microfluidic enrichment of blood samples from four patients with metastatic melanoma. We generated RNA-Seq profiles of 13 biological replicates from the five cultures. We also generated two RNA-Seq profiles from archival primary tumor specimens from one of the four patients and generated six profiles from archival independent metastatic lesions from another of the four patients. We compared the 13 RNA-seq profiles to those of standard melanoma tumor-derived cell lines (Cancer Cell Line Encyclopedia; CCLE; PMID: 22460905), and primary and metastatic melanoma tumors (The Cancer Genome Atlas; TCGA; PMID: 26091043), all generated by the same computational pipeline. We also compared the profiles of the primary and metastatic tumor specimens with the profiles of the matched CTC culture samples.

first: Xin

last: Hong

first: Whijae

last: Roh

first: Ryan

middle: J

last: Sullivan

first: Keith

middle: H

last: Wong

middle: S

first: Hongshan

last: Guo

first: Taronish

middle: D

last: Dubash

first: Moshe

last: Sade-Feldman

middle: K

last: Wesley

first: Elad

last: Horwitz

first: Genevieve

middle: M

last: Boland

first: Dieuwke

middle: L

last: Marvin

first: Todd

last: Bonesteel

first: Chenyue

last: Lu

first: Francois

last: Aguet

first: Risa

last: Burr

first: Samuel

last: Freeman

first: Laxmi

last: Parida

first: Katherine

last: Calhoun

first: Michelle

last: Jewett

first: Linda

middle: T

last: Nieman

first: Nir

last: Hacohen

first: Anders

last: Naar

first: David

last: Ting

first: Mehmet

last: Toner

first: Shannon

last: Stott

first: Gad

last: Getz

first: Shyamala

last: Maheswaran

first: Daniel

middle: A

last: Haber


title: The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis [isogenic CTC lines RNA-Seq]

first: Ben

last: Wittner

overall_design: We established 13 single CTC-derived isogenic lines from the same patient. From each of those lines we generated biological replicates, which we submitted to RNA-Seq generating a total of 30 gene expression profiles.

first: Xin

last: Hong

first: Whijae

last: Roh

first: Ryan

last: Sullivan

first: Keith

last: Wong

first: Hongshan

last: Guo

first: Taronish

last: Dubash

first: Moshe

last: Sade-Feldman

last: Wesley

first: Elad

last: Horwitz

first: Genevieve

last: Boland

first: Dieuwke

last: Marvin

first: Todd

last: Bonesteel


title: Meninges from mice with different microbiomes

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

country: United Kingdom

institute: University of Cambridge

summary: RNA was extracted from the meninges of mice from either Specific pathogen free or Germ free facilities or from the offspring of mice reconstituted with different human microbiomes.

overall_design:
4 groups:
Specific Pathogen Free
Germ Free
Donor 3
Donor 7

first: J

middle: R

first: Z

last: Fitzpatrick

first: T

last: Lawley

first: S

last: Clare

first: M

last: Clatworthy


title: Characterisation of CD4+ T-cell subtypes using single cell RNA sequencing and the impact of cell number and sequencing depth

city: Manchester

first: Paul

last: Martin

state: Greater Manchester

address: Oxford Road

department: Centre for Genetics and Genomics Versus Arthritis

institute: Univeristy of Manchester

summary: CD4+ T-cells represent a heterogeneous collection of specialised sub-types and are a key cell type in the pathogenesis of many diseases due to their role in the adaptive immune system. By investigating CD4+ T-cells at the single cell level, using RNA sequencing (scRNA-seq), there is the potential to identify specific cell states driving disease or treatment response. However, the impact of sequencing depth and cell numbers, two important factors in scRNA-seq, has not been determined for a complex cell population such as CD4+ T-cells. We therefore generated a high depth, high cell number dataset to determine the effect of reduced sequencing depth and cell number on the ability to accurately identify CD4+ T-cell subtypes. Furthermore, we investigated T-cell signatures under resting and stimulated conditions to assess cluster specific effects of stimulation. We found that firstly, cell number has a much more profound effect than sequencing depth on the ability to classify cells; secondly, this effect is greater when cells are unstimulated and finally, resting and stimulated samples can be combined to leverage additional power whilst still allowing differences between samples to be observed. These results will inform future scRNA-seq studies to ensure the most efficient experimental design.

overall_design: Peripheral blood mononuclear cells (PBMCs) were extracted from a healthy human volunteer by ficoll density gradient centrifugation. CD4+ T-cells were then isolated and either stimulated with anti-CD3/CD28 or left unstimulated. Single cell RNA-seq libraries were prepared using the Chromium Single Cell 3′ Library & Gel Bead v2 kit. Samples were subsampled, in replicate, for both read depth and cell number.

first: James

last: Ding

first: Samantha

last: Smith

first: Gisela

last: Orozco

first: Anne

last: Barton

first: Steve

last: Eyre


title: Systems-level analysis of peripheral blood gene expression in dementia patients reveals an innate immune response shared across multiple disorders [ftd]

city: Los Angeles

first: Daniel

last: Nachun

state: CA

address: 695 Charles E Young Dr S

institute: UCLA

summary: The role of peripheral inflammation in dementia is an important but complex topic. We present here the largest cohort of peripheral blood gene expression data ever assembled from patients with dementia and matching controls.  Importantly, this cohort includes individuals from a diverse set of dementia disorders, including Alzheimer’s Disease (AD), mild cognitive impairment (MCI), and multiple disorders within the frontotemporal dementia (FTD) spectrum.  We found strong transcriptional evidence of an innate immune inflammatory response, mediated by monocytes and neutrophils, in AD, MCI, and two FTD subtypes, PSP and nfvPPA. This transcriptional inflammatory response is enriched for genetic risk for AD, in part because it is also enriched for microglial genes, which have previously been implicated in AD risk. Finally, we show that this transcriptional response is strongly enriched for binding of the transcription factors PU.1 and RELA, which have previously been linked to AD risk and progression.

overall_design: Total RNA obtained from peripheral blood in dementia patients was compared to controls.  bvFTD = behavioral variant frontotemporal dementia; svPPA = semantic variant primary progressive aphasia; nfvPPA = non-fluent variant primary progressive aphasia; PSP = progressive supranuclear palsy; CBS = corticobasal syndrome

first: Giovanni

last: Coppola


title: H4K20me3 methyltransferase SUV420H2 shapes the three-dimensional chromatin landscape of pluripotent embryonic stem cells

city: Detroit

first: Benjamin

last: Kidder

state: MI

address: 4100 John R St

department: Oncology

institute: Wayne State University

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells

summary: Heterochromatin, which is a densely packed chromatin state that is transcriptionally silent, is a critical regulator of gene expression. However, it is unclear how the repressive histone modification, H4K20me3, or the histone methyltransferase, SUV420H2, regulate embryonic stem (ES) cell fate by patterning the epigenetic landscape. Here, we report that depletion of SUV420H2 leads to a near complete loss of H4K20me3 genome-wide, dysregulated gene expression, and delayed ES cell differentiation. SUV420H2-bound regions are enriched with repetitive DNA elements, which are de-repressed in SUV420H2 knockout ES cells. Moreover, SUV420H2 regulation of H4K20me3-marked heterochromatin controls chromatin architecture, including fine-scale interactions between gene regulatory elements in pluripotent ES cells. SUV420H2 plays a critical role in stabilizing the three-dimensional (3D) chromatin landscape of ES cells, where loss of SUV420H2 results in A/B compartment switching, perturbed chromatin insulation, and altered chromatin interactions of pericentric heterochromatin, indicative of localized decondensation. In addition, depletion of SUV420H2 resulted in compromised interactions between H4K20me3 and gene regulatory regions. Together, these findings describe a novel role for SUV420H2 in regulating the chromatin landscape of ES cells.

overall_design: Hi-C of wild-type and SUV420H2 knockout undifferentiated murine ES cells


title: Transcriptomic profiling of melanomas treated with BRAF inhibitor

status: Public on Nov 14 2020

city: ChengDu

first: Jinen

last: Song

address: Renmin road

country: China

institute: Sichuan university

summary: Since tumor early response is a timing sensitive progress, accurate time points for biopsy collection will provide a fundament for the investigation of the correlation between angiogenesis and BRAFi resistance. To this end, we recapitulated the clinical therapeutic process with a mouse model. SMM102, a BRAFi sensitive mouse cell line, was subcutaneously inoculated on both flanks of C57BL/6 mice. Mice were treated with BRAFi and sacrificed at different time point.

overall_design: C57BL/6J mice (female, 6-8 weeks old) were subcutaneously injected with 1x105 SMM102 cells, two injections per mouse. Once tumors volumes reached 150-300 mm3, mice were treated with vehicle or PLX4032 (50 mg/kg, 5 days per week) by intraperitoneal injection (IP). Mice were sacrificed at day 3 and 6 for vehicle group. And for PLX4032 group, mice were sacrificed at day 3, 6, 18 and 27.

first: Guangchao

last: Xu

first: Ya

last: Luo

first: Wenshuang

last: Wu

first: Xiaowei

last: Liu

first: Xin

last: Yu

first: Yu

last: Bao

first: Xiujing

last: He

first: Jing

first: Yanna

last: Li

first: Jiqiao

last: Yang

first: Rongjie

last: Zhang

first: Chune

first: Hongying

last: Chen

first: Jie

first: Jianping

last: Hu

last: Jing

first: Hubing

last: Shi


title: Changes in the gene expression in the olfactory organ of Xenopus laevis

city: Göttingen

first: Carsten

last: Lueder

address: Kreuzbergring 57

country: Germany

institute: Institut für Medizinische Mikrobiologie

summary: We report changes of the olfactory receptor gene expression and other important gene over the timecourse of metamorphosis

overall_design: Comparison of larval and adult stages under normal conditions and after an injury

first: Katarina

last: Dittrich


title: H4K20me3 methyltransferase SUV420H2 shapes the three-dimensional chromatin landscape of pluripotent embryonic stem cells [RNA-seq]

first: Benjamin

last: Kidder

overall_design: RNA-Seq of undifferentiated and differentiated murine WT, SUV420H2 KO, and SUV420H1/H2 DKO ES cells.


title: Age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 in lung epithelium

city: Nashville

first: Jennifer

last: Sucre

state: TN

address: 2215 B Garland Ave, 1125 Light Hall

department: Division of Neonatology, Department of Pediatrics

institute: Vanderbilt University Medical Center

summary: The SARS-CoV-2 novel coronavirus global pandemic (COVID-19) has led to millions of cases and hundreds of thousands of deaths globally. While older adults appear at high risk for severe disease, hospitalizations and deaths due to SARS-CoV-2 among children have been relatively rare. Integrating single-cell RNA sequencing (scRNA-seq) of developing mouse lung with temporally-resolved immunofluorescence in mouse and human lung tissue, we found expression of SARS-CoV-2 Spike protein primer TMPRSS2 was highest in ciliated cells and type I alveolar epithelial cells (AT1), and TMPRSS2 expression increased with aging in mice and humans. Analysis of autopsy tissue from fatal COVID-19 cases detected SARS-CoV-2 RNA most frequently in ciliated and secretory cells in airway epithelium and AT1 cells in peripheral lung. SARS-CoV-2 RNA was highly colocalized in cells expressing TMPRSS2. Together, these data demonstrate the cellular spectrum infected by SARS-CoV-2 in lung epithelium and suggest that developmental regulation of TMPRSS2 may underlie the relative protection of infants and children from severe respiratory illness.

overall_design:
Single Cell RNAseq of dissociated mouse lungs at ages: E18, P0, P7, P14, and P64. Suspensions were enriched for cells that were CD45 negative, Ter119 negative, and viable.
These data are part of a larger investigation (data not provided here) examining age-determined expression of priming protease TMPRSS2 and localization of SARS-CoV-2 in lung epithelium.
[contributor]  Vanderbilt COVID-19 Consortium Cohort
[contributor]  Human Cell Atlas Biological Network

first: Bryce

last: Schuler

first: A

middle: C

last: Habermann

first: Erin

last: Plosa

first: Chase

last: Taylor

first: Christopher

last: Jetter

first: Nicholas

last: Negretti

first: Meghan

middle: E

last: Kapp

first: John

last: Benjamin

first: Peter

last: Gulleman

first: David

last: Nichols

first: Lior

middle: Z

last: Braunstein

first: Alice

last: Hackett

first: Michael

last: Koval

first: Susan

last: Guttentag

first: Timothy

last: Blackwell

first: Steven

last: Webber

last: Banovich

first: Jonathan

last: Kropski


title: RNA-seq of temperature sensitive alleles of splicing factors in fission yeast

city: Ithaca

first: Jeffrey

last: Pleiss

state: NY

address: 453 Biotech

institute: Cornell University

summary: To identify conditional alleles which disrupt the splicing pathway, we screened a collection of ~2000 chemically mutagenized temperature-sensitive fission yeast isolates for intron accumulation in three introns, including a naturally occurring U2-dependent AT-AC intron. We identified 54 strains which accumulate unspliced message at the non-permissive temperature. A combination of mutation effect prediction and genetic mapping techniques revealed missense mutations in core splicing genes which function at various steps of spliceosome assembly and activation including: prp10, prp28, sap61, ntr1, spp42, sap114, cwf22, and prp22. Interrogation of structural data and genome-wide analysis of the splicing defects in these mutations revealed intron-specific defects which suggest the biochemical basis for these mutations’ effects on splicing.

overall_design: pre-mRNA splicing profiles of various temperature sensitve strains

first: Benjamin

last: Fair

first: Amy

last: Larson

first: Zachary

middle: W

last: Dwyer


title: Anterograde Regulation of Nuclear-encoded Mitochondrial Genes and FGF21 Signaling by Hepatic Histone Demethylase LSD1 [RNA-seq]

status: Public on Nov 12 2020

city: Irvine

first: QIN

last: YANG

address: 825 Health Science Rd.

department: Physiology and Biophysics

institute: University of California, Irvine

summary: Mitochondrial biogenesis and function are controlled by anterograde regulatory pathways involving more than one thousand nuclear-encoded proteins. Transcriptional networks controlling the nuclear-encoded mitochondrial genes remain fully elucidated.  Here we show that histone demethylase LSD1 knockout from adult mouse liver (LSD1-LKO) reduces one-third of all nuclear-encoded mitochondrial genes and decreases mitochondrial biogenesis and function. ChIP-seq analysis shows that LSD1 and LSD1-targeted H3K4me2 modulate the expression of mitochondrial genes in liver.

overall_design: RNA-seq analysis of gene expression in liver of LSD1-LKO and controls. To generate LSD1-LKO mice, AAV8-TBG-cre was injected through tail vein into LSD1-lox/lox mice at 6-7 weeks of age. AAV8-TBG-GFP was injected to LSD1-lox/lox mice as controls. One week after the injections, the mice were fed a high fat diet for 12 weeks.

first: Yang

last: Cao

first: Qiushi

last: Sun

first: Qin

last: Yang


title: Variability within rare cell states enables multiple paths towards drug resistance [WM989_WM983b]

city: Philadelphia

first: Arjun

last: Raj

state: PA

address: 415 Curie Boulevard

institute: University of Pennsylvania

summary: Molecular differences between individual cells can lead to dramatic differences in cell fate, such as the difference between death versus survival of cancer cells upon treatment with anti-cancer drugs. Despite some progress, these originating differences have largely remained hidden due to the difficulty in determining precisely what variable molecular features lead to which cellular fates. Here, we trace drug-resistant cell fates back to differences in the molecular profiles of their drug-naive melanoma precursors, revealing a rich substructure of variability underlying a number of resistant phenotypes at the single cell level. We make these connections using Rewind, a methodology that combines genetic barcoding with an RNA-based readout to directly capture rare cells that give rise to cellular behaviors of interest. We performed extensive single cell analysis to identify differences in gene expression and MAP-kinase signaling that mark a rare population of drug-naive cells (initial frequency of ~1:1000-1:10,000 cells) that ultimately gives rise to drug resistant clones. We demonstrate that this rare subpopulation has rich substructure and is composed of several distinct subpopulations, and the molecular differences between these subpopulations predict future differences in phenotypic behavior, such as the ultimate proliferative capacity of drug resistant cells. Similarly, we show that treatments that modify the frequency of resistance can allow otherwise non-resistant cells in the drug-naive population to become resistant, and that these new populations are marked by the variable expression of distinct genes. Together, our results reveal the presence of hidden, rare-cell variability that can underlie a range of latent phenotypic outcomes upon drug exposure.

overall_design: 2 separate, clonal melanoma cell lines (WM989 A6-G3 and WM983b E9-C6). 2 sorted cell populations (primed vs. non-primed). 2 drug conditions (1 micromolar vemurafenib vs. no drug), 2 replicates each (separate sorts, separate library preps). For some non-primed samples, multiple technical replicates (same sort, separate libraries)

last: Emert


title: Loss of E-cadherin promotes extraembryonic fates accompanying multilineage differentiation

city: San Francisco

first: Todd

last: McDevitt

address: 1650 Owens St

department: GICD

institute: Gladstone Institutes

summary: Embryonic development involves a range of complex morphogenic events as the embryo generates various cell types that go onto form functional tissues. This process is heavily reliant on symmetry breaking events that control the emergence of separate lineages that then spatial organize and physically arranging themselves within the embryo often via regulation of cell-cell adhesions. This work examines how changing adhesions in 3D aggregates of human pluripotent stem cells (hPSCs) encapsulated in hydrogel mixed with extracellular matrix allows for emergent population and morphological behaviors reminiscent of early embryonic behaviors and morphologies. In this context, knockdown of the cell adhesion molecule CDH1 generated aggregates with protrusion morphologies that did not arise in aggregates cultured without encapsulation. Genomic analysis revealed that the combination of CDH1 knockdown and encapsulation promoted emergence of extra-embryonic lineages. Further the transcriptomes of encapsulated CDH1(-) hPSCs were comparable to previously published single cell RNA-sequencing data of human embryos. Overall, these results establish a hPSC culture system that resembles early embryonic fate decisions and morphologies. Additionally, these studies highlight a potential relationship between changing adhesions, microenvironment, and acquisition of specific lineage fates, progressing our understanding of early human embryonic biology.

overall_design: WTC hiPSC cells with DOX inducible CRISPRi targeting CDH1 were treated for 5 days, then mixed with WT cells at defined ratios and force aggregated. Aggregates were then either encapsulated in agarose or unencapsulated and cultured in suspension for 6 days. At days 1, 3, and 6, WT, CDH1-KD and mixed aggregates were dissociated and prepared for single cell RNA-seq.

first: Ashley

last: Libby

first: Ivana

last: Vasic

first: David

last: Joy

first: Martina

last: Krakora

first: Fredrico

middle: N

last: Mendoza-Camacho

first: Bruce

last: Conklin


title: SMALL EXTRACELLULAR VESICLE REGULATION OF MITOCHONDRIAL DYNAMICS REPROGRAMS A HYPOXIC TUMOR MICROENVIRONMENT

first: Priyankara

last: Wickramasinghe

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: The crosstalk between tumor cells and the adjacent normal epithelium contributes to cancer progression, but its regulators have remained elusive. Here, we show that breast cancer cells maintained in hypoxia release small extracellular vesicles (sEV) that activate mitochondrial dynamics, stimulate mitochondrial movements and promote organelle accumulation at the cortical cytoskeleton in normal mammary epithelial cells. This results in Akt activation, membrane focal adhesion turnover and increased epithelial cell migration. RNA-Seq profiling identified Integrin-Linked Kinase (ILK) as the most upregulated pathway in sEV-treated epithelial cells and genetic or pharmacologic targeting of ILK reversed mitochondrial reprogramming and suppressed sEV-induced cell movements. In a three-dimensional model of mammary gland morphogenesis, sEV treatment induced hallmarks of malignant transformation, with deregulated cell death/cell proliferation, loss of apical-basal polarity and appearance of epithelial-to-mesenchymal transition (EMT) markers. Therefore, sEV released by hypoxic breast cancer cells reprogram mitochondrial dynamics and induce oncogenic changes in a normal mammary epithelium

overall_design: RNA-seq analysis of MCF10A cells treated by extracellular vesicles obtained from tumor cells MCF7 under normal and hypoxic conditions

first: Irene

last: Bertolini

first: Dario

last: Altieri


title: Molecular signatures for Hairy cell leukemia

city: Geneva

first: Thomas

last: Matthes

address: Rue Gabrielle Perret-Gentil

department: Hematology

country: Switzerland

institute: Geneva University Hospital

summary: Analysis of the expression profile of 298 mRNA's, measured with the nCounter (Nanostring Technologies platform), in 13 samples from the peripheral blood of Hairy cell leukemia patients  Hairy cell leukemia (HCL) is a rare chronic B-cell malignancy, characterized by infiltration of bone marrow, blood and spleen by typical “hairy cells” that bear the BRAFV600E mutation. However, in addition to the intrinsic activation of the MAP kinase pathway as a consequence of the BRAFV600E mutation, the potential participation of other signaling pathways to the pathophysiology of the disease remains unclear.   Using mRNA gene expression profiling based on the Nanostring technology and the analysis of 290 genes with crucial roles in B-cell lymphomas, we defined a 17 gene expression signature specific for HCL. Our analysis revealed intrinsic activation of the non-canonical NF-B pathway with underexpression of BIRC2 and BIRC3, two specific non-canonical NF-B inhibitors. Western blots confirmed activation of this pathway with increased processing of p100 in primary HCL samples. Separate analysis of samples from classical and variant forms of hairy cell leukemia showed almost similar mRNA expression profiles apart from overexpression in vHCL of the immune checkpoints CD274 and PDCD1LG2 and underexpression of FAS.  Our results provide a better understanding of the pathogenesis of HCL and describe new and potential targets for treatment approaches and guidance for studies in the molecular mechanisms of HCL.

overall_design: 24 samples from peripheral blood: 13 CLL samples (11 cHCL, 2 vCHL); 8 samples from normal blood donors; 3 samples from purified B lymphocytes

first: Elsa

last: Maitre

first: Edouard

last: Cornet

first: Agathe

last: Delbiquis

first: Bernard

last: Drenou

first: Francois

last: Gravey

first: Didier

last: Chollet

first: Stephane

last: Cheze

first: Mylene

last: Docquier

first: Xavier

last: Troussard


title: CPT1A Over-expression Increases Reactive Oxygen Species in the Mitochondria and Promotes Antioxidant Defenses in Prostate Cancer

city: Aurora

first: Andrew

last: Goodspeed

state: CO

address: 12801 E 17th Ave, Mail Stop 8303

institute: University of Colorado Anschutz Medical Campus

summary: The goal of this study was to identify gene expression changes and pathways associated with CPT1A deficiency ( knockdown, KD) and overexpression (OE) of prostate cancer cells

overall_design: RNA-seq was used to define the effects of CPT1A knokdown (KD) or overexpression (OE)  on gene expression in LNCaP-C4-2 castration resistant prostate cancer cells

first: Molishree

last: Joshi

first: Jihye

last: Kim

first: Angelo

last: D'Alessandro

first: Emily

last: Monk

first: Kimberley

last: Bruce

first: Hanan

last: Elajaili

first: Eva

last: Nozik

first: James

last: Costello

first: Isabel

last: Schlaepfer


title: The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis [single cell RNA-Seq]

first: Ben

middle: S.

last: Wittner

overall_design: We undertook single cell RNA-Seq of individually picked melanoma CTCs following microfluidic enrichment from primary blood specimens (PMID: 23552373, PMID: 24577360). We picked 76 individual CTCs freshly isolated from 22 melanoma patients and validated them to be melanoma cells by their expression of melanoma lineage markers (PMID: 29453278). We also picked and performed single cell RNA-Seq on 20 single CTCs that had been incubated in culture medium for 4-8 weeks, a condition in which only viable CTCs persist, but before they initiate in vitro proliferation. We also performed single cell RNA-Seq on six individually selected leukocytes from a healthy donor.

first: Xin

last: Hong

first: Whijae

last: Roh

first: Ryan

last: Sullivan

first: Keith

last: Wong

first: Hongshan

last: Guo

first: Taronish

last: Dubash

first: Moshe

last: Sade-Feldman

last: Wesley

first: Elad

last: Horwitz

first: Genevieve

last: Boland

first: Dieuwke

last: Marvin

first: Todd

last: Bonesteel

first: Chenyue

last: Lu

last: Aguet

first: Risa

last: Burr

first: Samuel

last: Freeman

first: Laxmi

last: Parida

first: Katherine

last: Calhoun

first: Michelle

last: Jewett

first: Linda

last: Nieman

first: Nir

last: Hacohen

first: Anders

last: Naar

first: David

last: Ting

first: Mehmet

last: Toner

first: Shannon

last: Stott

first: Gad

last: Getz

first: Shyamala

last: Maheswaran

first: Daniel

last: Haber


title: The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis [TF KD RNA-Seq]

first: Ben

last: Wittner

overall_design: We performed in triplicate shRNA knock-down of Transferrin in cells from a culture grown from CTCs from a melanoma patient.

first: Xin

last: Hong

first: Whijae

last: Roh

first: Ryan

middle: J

last: Sullivan

first: Keith

last: Wong

first: Hongshan

last: Guo

first: Taronish

last: Dubash

first: Moshe

last: Sade-Feldman

last: Wesley

first: Elad

last: Horwitz

first: Genevieve

last: Boland

first: Dieuwke

last: Marvin

last: Bonesteel

first: Francois


title: The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis [ChIP-Seq]

overall_design: To identify SREBF2-regulated genes mediating tumor-enhancing effects of SREBF2 expression, we undertook chromatin immunoprecipitation followed by Next Generation Sequencing (ChIP-Seq), defining direct SREBF2 transcriptional targets in cultured melanoma CTCs.

middle: H

first: Todd

first: Chenyue

last: Lu

last: Aguet

first: Risa

last: Burr

first: Samuel

last: Freeman

first: Laxmi

last: Parida

first: Katherine

last: Calhoun

first: Michelle

last: Jewett

first: Linda

last: Nieman

first: Nir

last: Hacohen

first: Anders

last: Naar

first: David

last: Ting

first: Mehmet

last: Toner

last: Stott


title: The lipogenic regulator SREBF2 induces Transferrin in circulating melanoma cells and suppresses ferroptosis

first: Ben

last: Wittner


title: Targeted genomic sequencing of the TCRγ locus in ILC2s and γδT cells

city: Vancouver

first: Kelly

last: McNagny

state: BC

address: 2222 Health Sciences Mall

country: Canada

institute: University of British Columbia

summary: An in-depth examination of the TCRγ locus in ILC2s and γδT cells was performed to assess the functionality of rearranged TCRγ locus.

overall_design: TCRγ gene rearrangement profiles of ILC2 and γδT cells

middle: B

last: Shin


title: Plasma extracellular vesicle miRNAs as potential biomarkers for superstimulatory response in cattle

city: Fort Collins

first: Ahmed

last: Gad

state: Colorado

address: 3107 Rampart Rd

department: Biomedical Sciences

institute: Colorado State University

type: Non-coding RNA profiling by high throughput sequencing

summary: The objective of this study was to analyze the extracellular vesicle microRNA (EV-miRNA) expression profiles in the blood plasma of heifers with variable response to superstimulation.

overall_design: Oestrous cycles of crossbred beef heifers were synchronized. On Day 10 after standing oestrus (=Day 0), superstimulation was induced by the administration of decreasing doses of follicle stimulating hormone twice a day for 4 d with PG administered with the 6th FSH injection followed by artificial insemination. Blood samples were collected on Day 7 of the unstimulated (U) and superstimulated (S) cycle from each heifer. All heifers were slaughtered on Day 7 of the S cycle. A subset of high (H, n=3) and low (L, n=3) responder heifers was selected depending on the ovarian response to superstimulation. Small RNA libraries were constructed and miRNA profiles were sequenced.

first: José

last: Sánchez

first: John

last: Browne

first: Jozef

last: Laurincik

first: Radek

last: Prochazka

first: Pat

last: Lonergan


title: Cytocidal Macrophages Cause Acute Diabetes following Checkpoint Blockade of PD-1 in NOD Mice

city: St. Louis

first: Pavel

last: Zakharov

state: MO

address: 660 S Euclid Ave Box 8118

department: Pathology and Immunology

institute: Wash.Univ in St. Louis

summary: Blocking the action of the PD-1 protein in lymphocytes results in their activation leading to an effective immune response in cancers and in experimental viral infections. But such immunotherapy in clinical cases results in immune adverse effects among them the development of autoimmune diabetes. In the diabetes susceptible NOD mice, blockade of the PD-L1/PD-1 pathway during the pre-diabetic stage results in severe and acute diabetes. Single-cell RNA sequencing and flow cytometry analysis of islets following blockade of the PD-L1/PD-1 pathway identified a cascade of cellular interactions involving resident macrophages and diabetogenic T cells. Such reactions led to the recruitment of monocyte derived macrophages that caused diabetes. Elimination of the monocyte derived macrophages resulted in protection. The cytocidal activity was highly dependent on IFNγ signaling and the downstream release of nitric oxide by the monocyte derived macrophages. The activation of macrophages required both the participation of CD4 and CD8 T cells. Our studies call attention to macrophages as the major effector cell following blockade of PD-1. Targeting the monocyte-derived macrophage provides a new option to prevent and treat immune checkpoint blockade induced diabetes and perhaps other immune adverse reactions.

overall_design: 10X Single-cell RNASeq

first: Hao

last: Hu

first: Emil

last: Unanue


title: Effect of DSS Colitis on Meninges

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

summary: The Meninges of mice which were treated with DSS to induce colitus were compared to control mice.

overall_design: 12 mice, 6 were treated with DSS and 6 control mice

first: J

first: A

last: Ferro

first: G

last: Frazer

first: M

last: Clatworthy


title: PAW-plasma activated water-triggers plant defence responses

city: Godollo

first: Eva

last: Varallyay

address: 4 Szent-Györgyi Albert Street

department: Institute of Plant Protection

country: Hungary

institute: Hungarian University of Agriculture and Life Sciences

summary: Nowadays one of the main challenges is moving towards an eco-sustainable agriculture, able to preserve the food production through a reduced use of pesticides. The current global food sustenance by intensive agriculture mainly based on economic crop monocultures drastically reduces the biodiversity increasing the yield losses due to biotic and abiotic stress. To try to ensure yield stability also enhancing the plant resistance responses to promote an eco-sustainable management of plant diseases, a technology based on plasma activated water (PAW), characterized by the production of reactive oxygen and nitrogen species, was tested. Differential expression levels of selected genes involved in the plant defence pathways and the microRNAs composition in PAW treated- micropropagated periwinkle shoots and grapevines were analyzed. The results indicate that PAW treatment enhances plant defence responses at both, transcriptional and post-transcriptional level, leading to an increased synthesis in periwinkle of vinblastine and vindoline, anti-oxidant compounds employed in the pharmaceutical industry and in grapevine of resveratrol that is an important compound for human health.

overall_design: 6 libraries from paw treated (3 biological replicates) and water treated (control - 3 biological replicates) Catharanthus roseus

first: Yuri

last: Zambon

first: Nicoletta

last: Contaldo

first: Romolo

last: Várallyay

first: Alessandro

last: Canel

first: Matteo

last: Gherardi

first: Vittorio

last: Colombo

first: Assunta

last: Bertaccini


title: Genome-wide mapping of Hnf4a binding sites in the newborn mouse kidneys

city: Cincinnati

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: Hnf4a is specifically expressed in developing proximal tubule cells in the newborn mouse kidney. In order to identify direct target genes of Hnf4a in the developing proximal tubules, we performed ChIP-Seq of Hnf4a in the mouse kidneys at P0.

overall_design: The mouse kidneys at P0 were crosslinked with 1% PFA and Hnf4a ChIP was performed. Sequencing libraries were generated using Rubicon ThruPLEX DNA sequencing kit for Illumina and sequencing was performed using the Illumina HiSeq2500.

first: Sierra

last: Marable

first: Eunah

last: Chung


title: Systems-level analysis of peripheral blood gene expression in dementia patients reveals an innate immune response shared across multiple disorders

first: Daniel

last: Nachun

address: 695 Charles E Young Dr S

institute: UCLA

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

overall_design: Refer to individual Series


title: RNA-seq of human dendritic cells cultured with PSAB-liposomes and/or Liraglutide

city: Badalona

first: Lauro

last: Sumoy

state: Barcelona

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

department: High Content Genomics and Bioinformatics

country: Spain

institute: IGTP

summary: RNA-seq data of monocyte-derived human Dendritic cells (huDCs) cultured with PSAB-liposomes and/or Liraglutide

overall_design: Monocytes were in-vitro isolated from human PBMCs and then differentiatied into Dendritic Cells. DCs were co-cultured with PBS, Liraglutide, PSAB-liposomes or PSAB-liposomes + Liraglutide during 4h. Cells from four different individuals following the four treatment regimes were analyzed. Illumina based massively parallel sequencing of polyA+ RNA was perfomed on a  total 16 samples, and differential mRNA expression between all conditions was assessed controlling for interindividual variation.

first: Adrián

last: Villalba

first: Marta

last: Vives-Pi

first: Jose

middle: F

last: Sanchez Herrero


title: Hhex promotes NK cell homeostasis by repressing BIM-dependent apoptosis

city: Melbourne

first: Melissa

last: Davis

state: Victoria

address: 1G Royal Parade

department: Bioinformatics Division

country: Australia

institute: Walter and Eliza Hall Institute of Medical Research

summary: Hhex encodes a homeobox transcriptional regulator that plays a key role in embryonic development and hematopoiesis. Hhex is highly expressed in NK cells and germline deletion of Hhex results in significant defects in lymphoid development, including NK cells. However, whether Hhex is intrinsically required throughout NK cell development or for NK cell function remains unknown. To investigate this, we generated mice that specifically lack Hhex in NK cells. Hhex was intrinsically required for NK cell homeostasis, while NK cell differentiation, IL-15 responsiveness and cytotoxic function were largely normal in the absence of Hhex. Unexpectedly, increased IL-15 availability failed to rescue Hhex-deficient NK cell homeostasis, suggesting that Hhex regulates developmental pathways extrinsic to those dependent on IL-15. Gene expression and functional genetic approaches revealed that Hhex promoted NK cell survival by repressing BIM expression, a key apoptotic mediator in NK cells. This study identifies Hhex as a novel transcription factor essential for NK cell biology.

overall_design: 4 biological repliciates of Hhex-deficient and 3 biological replicates of Cre control splenic NK cells (viable C45+CD3-Nk1.1+NKp46+CD49b+) were isolated ex vivo by sorting and subjected to mRNA extraction, library preparation and sequencing on an Illumina NextSeq 500 sequencer

first: Wilford

last: Goh

first: Soroor

last: Hediyeh-Zadeh

first: Stephen

last: Nutt

first: Nicholas

middle: D

last: Huntington


title: H4K20me3 methyltransferase SUV420H2 regulates pluripotent embryonic stem cells [ChIP-seq]

city: Detroit

first: Benjamin

last: Kidder

address: 4100 John R St

institute: Wayne State University

summary: Heterochromatin, which is a densely packed chromatin state that is transcriptionally silent, is a critical regulator of gene expression. However, it is unclear how the repressive histone modification, H4K20me3, or the histone methyltransferase, SUV420H2, regulate embryonic stem (ES) cell fate by patterning the epigenetic landscape. Here, we observed a near complete genome-wide loss of H4K20me3 in SUV420H2 depleted ES cells, suggesting that SUV420H enzymes are paramount for establishing global H4K20me3 domains. We also found that SUV0420H2-bound regions are enriched with repetitive DNA elements. Together, these findings describe a novel role for SUV420H2 in regulating the chromatin landscape of ES cells.

overall_design: ChIP-Seq of undifferentiated murine ES cells


title: Illumina RNA-seq of Human rhabdomyosarcoma Rh36 cell mouse xenograft tumors: effect of RITA, GANT61 and RITA/GANT61 combination treatments on xenograft tumor growth

city: Huddinge

first: Ani

last: Azatyan

state: Stockholm

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

summary: Overactivation of the Hedgehog (HH) signaling pathway is implicated in many cancers. In this study, we demonstrate that the small molecule RITA, a p53 activator, effectively downregulates HH signaling in human medulloblastoma and rhabdomyosarcoma cells irrespective of p53. This is mediated by a ROS-independent activation of the MAP kinase JNK. We also show that in vitro RITA sensitized cells to the GLI antagonist GANT61, as co-administration of the two drugs had more pronounced effects on cell proliferation and apoptosis. In vivo administration of RITA or GANT61 suppressed rhabdomyosarcoma xenograft growth in nude mice; however, co-administration did not further enhance tumor suppression, even though cell proliferation was decreased. RITA was more potent than GANT61 in downregulating HH target gene expression; surprisingly, this suppressive effect was almost completely eliminated when the two drugs were administered together. Notably, RNA-seq demonstrated a broader response of pathways involved in cancer cell growth in the combination treatment, providing a plausible interpretation for tumor reduction in the absence of HH signaling downregulation.

overall_design: In vivo effects of RITA and GANT61 small molecular drug treatments on Rh36 cell xenograft tumor growth in nude mice.

first: Peter

middle: G

last: Zaphiropoulos


title: Tolerance to cocaine-induced motor effects in rats: transcriptomic regulations in the ventral striatum

city: PARIS

first: Stephane

last: Le Crom

address: 46 rue Ulm

department: Genomic Core Facility

country: France

institute: IBENS

summary: Comparison of gene expression in the dorsal striatum of rats after chronic binge or acute binge cocaine injections or saline treatment

overall_design: 8-week-old Sprague-Dawley rats received saline, chronic (5 days) or acute binge cocaine injections

first: Florence

last: Vorspan

first: Romain

last: Icick

first: Nawel

last: Mekdad

first: Cindie

last: Courtin

first: Vanessa

last: Bloch

first: Frank

last: Bellivier

first: Jean-Louis

last: Laplanche

first: Nathalie

last: Prince

first: Dmitry

last: Pishalin

first: Cyril

last: Firmo

first: Corinne

last: Blugeon

first: Bruno

last: Mégarbane

first: Cynthia

last: Marie-Claire

first: Nadia

last: Benturquia


title: Pattern of Extramammary Paget disease gene expression

city: Beijing

first: li

last: bu

address: NO.2 yuanmingyuan

institute: China Agricultural University

summary: To further understand different gene expression of Extramammary Paget disease skin and normal skin, we have employed whole skin microarray expression profiling as a discovery platform to identify different genes with Extramammary Paget disease skin and normal skin.comparision with normal skin, upgene is 4572 in disease group, downgene is 6473. mTOR pathway, RAS pathway, PI3K-AKT pathway, IL6-JAK-Stat3 pathway and so on are activated, WNT Pathway is inhibited.

overall_design: 3 normal human skin and 4 Extramammary paget disease scrotum skin were taken and Quickly put it into liquid nitrogen ,the samples were taken to lab with dry ice,RNA were extracted with trizol,Good quality RNA were explored as microarrary analysis in capitalBio technology.

first: Yongli

last: Song

first: Zhengquan

last: Yu


title: Different gene expression of Musashi1 gene overexpression in mouse skin

summary: To further understand expression patterns of musashi1 overexpression (DTG) in mouse skin,we have employed microarray expression profiling as a discovery platform to identify different genes expression with DTG mouse and Control mouse. Comparision with Control mouse,upgene is 3772 in DTG mouse, downgene is 5529. mTOR pathway, RAS pathway, PI3K-AKT pathway,IL6-JAK-Stat3 pathway and so on are activated, WNT Pathway is inhibited.

overall_design: 4 Control mouse skin and 4 DTG mouse skin were taken and immediately put it to -80 Refrigerator.Trizol was added to the samples,RNA were extracted with trizol according to instructions,Good quality RNA were explored as microarrary analysis in capitalBio technology.


title: Variability within rare cell states enables multiple paths towards drug resistance [WM989_DOT1Li]

first: Arjun

last: Raj

address: 415 Curie Boulevard

institute: University of Pennsylvania

summary: Molecular differences between individual cells can lead to dramatic differences in cell fate, such as the difference between death versus survival of cancer cells upon treatment with anti-cancer drugs. Despite some progress, these originating differences have largely remained hidden due to the difficulty in determining precisely what variable molecular features lead to which cellular fates. Here, we trace drug-resistant cell fates back to differences in the molecular profiles of their drug-naive melanoma precursors, revealing a rich substructure of variability underlying a number of resistant phenotypes at the single cell level. We make these connections using Rewind, a methodology that combines genetic barcoding with an RNA-based readout to directly capture rare cells that give rise to cellular behaviors of interest. We performed extensive single cell analysis to identify differences in gene expression and MAP-kinase signaling that mark a rare population of drug-naive cells (initial frequency of ~1:1000-1:10,000 cells) that ultimately gives rise to drug resistant clones. We demonstrate that this rare subpopulation has rich substructure and is composed of several distinct subpopulations, and the molecular differences between these subpopulations predict future differences in phenotypic behavior, such as the ultimate proliferative capacity of drug resistant cells. Similarly, we show that treatments that modify the frequency of resistance can allow otherwise non-resistant cells in the drug-naive population to become resistant, and that these new populations are marked by the variable expression of distinct genes. Together, our results reveal the presence of hidden, rare-cell variability that can underlie a range of latent phenotypic outcomes upon drug exposure.

overall_design: clonal melanoma cell line (WM989 A6-G3). 3 sorted cell populations (primed requiring DOT1L inhibition, primed not requiring DOT1L inhibition, and  non-primed). 4 drug conditions (4 micromolar pinometostat or DMSO X 1 micromolar vemurafenib or no vemurafenib treatment), 2 replicates each (separate sorts, separate library preps). For some non-primed samples, multiple technical replicates (same sort, separate libraries)

first: Benjamin

last: Emert


title: β-carotene conversion to vitamin A delays atherosclerosis progression by decreasing hepatic lipid secretion in mice

city: New York City

first: Alireza

last: Khodadadi-Jamayran

address: 550 1st Ave, MSB 304

department: Division of Advanced Research Technologies (DART)

institute: New York University, NYU Langone Medical Center

summary: Atherosclerosis is characterized by the pathological accumulation of cholesterol-laden macrophages in the arterial wall. Atherosclerosis is also the main underlying cause of cardiovascular diseases (CVDs), and its development is largely driven by elevated plasma cholesterol. Strong epidemiological data find an inverse association between plasma β-carotene with atherosclerosis, and we recently showed that β-carotene oxygenase 1 (BCO1) activity, responsible for β-carotene cleavage to vitamin A, is associated with reduced plasma cholesterol in humans and mice. In this study, we explore whether intact β-carotene or vitamin A affect atherosclerosis progression in the atheroprone low-density lipoprotein receptor (LDLR) - deficient mice. In comparison to control-fed Ldlr-/- mice, β-carotene-supplemented mice showed reduced atherosclerotic lesion size at the level of the aortic root and plasma cholesterol levels (P = 0.0003). These changes were absent in Ldlr-/-/Bco1-/- mice, despite accumulating β-carotene in plasma and atherosclerotic lesions. We discarded the implication of myeloid BCO1 in the development of atherosclerosis by performing bone marrow transplant experiments. Lipid production assays found that retinoic acid, the active form of vitamin A, reduced the secretion of newly synthetized triglyceride and cholesteryl ester in cell culture and mice. Overall, our findings provide insights into the role of BCO1 activity and vitamin A in atherosclerosis progression through the regulation of hepatic lipid metabolism.

overall_design: CD68+ cells accumulated in atherosclerotic lesions at the level of the aortic root were isolated by laser capture microdisection. Briefly, Eight-week-old male and female Ldlr-/-/Bco1-/- mice were lethally irradiated with a double dose of 550 rads (5.5 GY) from a cesium source four hours apart. Ten hours later, mice were transplanted with freshly isolated bone marrow from donor wild-type or Bco1-/- (ko) mice.

first: Felix

last: Zhou

first: Xiaoyun

last: Wu

first: Ivan

last: Pinos

middle: M

last: Abraham

first: Tessa

last: Barrett

first: Johannes

last: von Lintig

first: Edward

last: Fisher

first: Jaume

last: Amengual


title: Foxp3 imparts regulatory T cell epigenetic identity through a transcription factor relay

city: Shanghai

first: Yi

last: Zhong

address: 227 South Chongqing Rd.

institute: SJTU

summary: RNA-seq, ATAC-seq, and CUT&RUN analysis in Foxp3+ regulatory T cells, Foxp3- conventional CD4 T cells and Foxp3 reporter-null cells subdivided based on cell surface activation markers CD44 and CD62L

overall_design: Cell populations were isolated from pooled spleen and lymph nodes by flow cytometry and subject to RNA-seq, ATAC-seq, or CUT&RUN analysis

first: Joris

last: van der Veeken

first: Ariella

last: Glasner

first: Alexander

last: Rudensky


title: Variability within rare cell states enables multiple paths towards drug resistance.

city: Philadelphia


title: Developmental genetics of corolla tube formation in monkeyflowers (Mimulus): role of the tasiRNA-ARF pathway

city: Guangzhou

first: Rui

last: Xia

state: Guangdong

address: 483 Wushan Rd, Tianhe

department: Horticulture

institute: South China Agricultural University

summary: About one third of all angiosperm species produce flowers with petals fused into a corolla tube. As an important element of the tremendous diversity of flower morphology, the corolla tube plays a critical role in many specialized interactions between plants and animal pollinators (e.g., beeflies, hawkmoths, hummingbirds, nectar bats), which in turn drives rapid plant speciation. Despite its clear significance in plant reproduction and evolution, the corolla tube remains one of the least understood plant structures from a developmental genetics perspective. Through mutant analyses and transgenic experiments, here we show that the tasiRNA-ARF pathway is required for corolla tube formation in the monkeyflower species Mimulus lewisii. Loss-of-function mutations in the M. lewisii orthologs of ARGONAUTE7 and SUPRESSOR OF GENE SILENCING 3 cause a dramatic decrease in tasiARF abundance and a moderate up-regulation of Auxin Response Factor 3 (ARF3) and ARF4, which lead to inhibition of lateral expansion of the bases of petal primordia and complete arrest of the upward growth of the inter-primordial regions, resulting in unfused corollas. Integrating our molecular and phenotypic analyses of the tasiRNA-ARF pathway in Mimulus with historical insights from morphological and anatomical studies in various sympetalous species, we propose a new conceptual model for the developmental genetic control of corolla tube formation.

overall_design: The goal of this experiment is to determine tasiRNA abundance in the Mimulus lewisii mutants flayed1 and flayed2 compared to the wild-type (inbred line LF10). The six samples include two biological replicates of the wild-type LF10 (LF10A and LF10B), two biological replicates of the flayed1 mutant (flayed1A and flayed1B), and two biological replicates of the flayed2 mutant (flayed2A and flayed2B). All plants were grown under the same standard greenhouse environment (22 oC; light:dark = 16h:8h). For all samples, RNA was extracted from the same tissue at the same developmental stage (i.e., 5-mm floral buds)

first: Baoqing

last: Ding

first: Vandana

last: Gurung

first: Janelle

last: Sagawa

first: Lauren

last: Stanley

first: Matthew

last: Strobel

first: Qiaoshan

last: Lin

first: Pamela

middle: K

last: Diggle

first: Blake

last: Meyers

first: Yao-Wu

last: Yuan


title: Cortical single-cell RNA sequencing of the microglia specific TREM2 inducible mouse models

status: Public on Nov 11 2020

city: jacksonville

last: Zhao

address: 4500 San Pablo Rd S

institute: Mayo Clinic

summary: We induced TREM2 expression at 2 months of age in our TREM2 mouse models and harvested the animals at 4 months of age. The single cells from the cortex were isolated and subjected to the single-cell RNA seq to investigate the effects of TREM2 on the transcriptomic profiles at single cell level in healthy condition. Our data revealed that TREM2-WT expression triggered the downstream mTOR/EIF2 signaling pathways and activated microglia by elevating Apoe expression; whereas TREM2-R47H had no effects on mTOR/EIF2 signaling pathway and minor impact on activating microglia antigen presentation pathway.

overall_design: Four mice (2 males and 2 females) were analyzed for each of the four groups, including TREM2-WT-Ctrl, TREM2-WT-Induced, TREM2-R47H-Ctrl, and TREM2-R47H-Induced.

first: Wenhui

last: Qiao

first: Yuka

middle: A

last: Martens

first: Yingxue

last: Ren


title: Cortical bulk RNA sequencing of the microglia specific TREM2 inducible mouse models

summary: We performed brain bulk RNA-seq aiming to study how microglia TREM2-WT or TREM2-R47H expression affect the overall brain transcriptomic profiles. Using WGCNA gene network analysis, we found the presynaptic transmission pathway was dysregulated after TREM2-R47H expression, not TREM2-WT. This finding was consistent with the impaired presynaptic transmission detected by electrophysiological recording in TREM2-R47H expressing mice. In addition, dysregulated circadian pathways were also identified in TREM2-R47H mice, not in TREM2-WT mice. Altogether, our bulk RNA-seq results provide additional evidence at transcriptomics level that TREM2-R47H expression in microglia affects neuronal functions and brain networks.

overall_design: Six mice (3 males and 3 females) were analyzed for each of the four groups, including TREM2-WT-Ctrl, TREM2-WT-Induced, TREM2-R47H-Ctrl, TREM2-R47H-Induced.


title: Regulatory eosinophils triggered by innate lymphoid cells type 2 during asthma induce resolution of chronic arthritis

city: Bern

first: Philipp

last: Kirchner

address: Murtenstrasse 31

department: Pathology

institute: University of Bern

summary: Eosinophils possess distinct functions, being pro-inflammatory in asthma and worm infection on the one hand, while supporting resolution of inflammation and tissue repair on the other hand. We could demonstrate that the immunological pathways causing asthma in the lungs at the same time elicit resolution of arthritis in the joints in an eosinophil-dependent manner. It can be hypothesized that the pro-inflammatory action of eosinophils in the lungs and their homeostatic functions in the synovium are mediated by tissue-specific functional priming. Therefore, single cell RNA sequencing (scRNA-seq) was used to investigate whether distinct eosinophil subsets arise in the lungs and the joints of mice upon combined asthma/arthritis model.

overall_design: Single cell mRNA sequencing of sorted CD45+CD11b+Sigec-F+ granulocytes of lung and synovial tissue from mice with eosinophilic asthma (OVA), K/BxN serum-induced arthritis (SIA) and a comination of asthma and arthritis (OVA+SIA) at day 7 post-SIA

first: Aline

last: Bozec

first: Darja

last: Andreev

first: Mengdan

last: Liu

first: Arif

last: Ekici


title: RNA-seq Analysis of wildtype (N2) C. elegans at the L4 stage on diets from the laboratory environment and natural environment

city: Los Angeles

first: Sean

last: Curran

address: 3715 McClintock Ave

department: Davis School of Gerontology

institute: University of Southern California

summary: We analyzed RNA-seq data from C. elegans on six bacterial diets, 3 E. coli diets (OP50, HT115, HB101) found in the laboratory setting and 3 found in C. elegans natural environment (Methylobacterium, Xanthomonas, Sphingomonas). We compared gene expression between L4 worms on the OP50 diet to the other 5 bacterial diets. We found that diet influences many gene expression changes, leading to genes being both up regulated and down regulated in a diet-dependent manner.

overall_design: mRNA profiles of L4 wildtype C. elegans on 6 different bacterial diets

first: Nicole

middle: L

last: Stuhr

middle: P


title: Gene expression profiles of TRA2B4 or exon 2 overexpressing HCT116 cells

city: Toskushima

first: Yuki

last: Kuwano

address: Kuramoto-cho

department: Pathophysiology

country: Japan

institute: The University of Tokushima Graduate School

summary: The human transformer 2β gene (TRA2B) encodes a ultraconserved region (uc.138) in exon 2. TRA2B4 RNA is the transcript that contains the whole exon 2. To investigate the molecular mechanism underlying the influence of uc.138 expression in colon cancer cells, we established stable cell lines that overexpressed full-length TRA2B4 (ex 1–ex 10) or TRA2B exon 2. In this study, microarray-based global expression analysis were investigated using uc.138 overexpressing HCT116 cells.

overall_design: To investigate the molecular mechanism underlying the influence of uc.138 expression in colon cancer cells, we generated stable cell lines that overexpressed full-length TRA2B4 (ex 1–ex 10) or TRA2B exon 2 using HCT116 cells. Total RNA was extracted from cells using a RNeasy kit (Qiagen) and purified RNAs were labeled using a Low RNA Input Liner Amplification Kit and a succinimide-containing fluorescent dye (Cy3)-CTP according to the manufacturer’s protocol (Agilent). Expression profiles were measured using a whole human genome microarray (SurePrint G3 Human; Agilent).


title: TNF induced inflammatory transcription dynamics and epigenetic changes

first: Zhuqiang

last: Zhang

address: 15 Datun Road, Chaoyang District.

institute: Institute of Biophysics, CAS

type: Methylation profiling by high throughput sequencing

summary: TNF can induce inflammatory responses in cells, including transcriptional and epigenetic changes. To investigate the long-term influence of TNF stimulation on epigenetic modifications, we did transcriptomic and epigenomic profiling of TNF-treated cells with various time length or stages.

overall_design: HEK 293 cells were treated with short-term (12 h) and long-term (12 d) TNF, withdrawn TNF to recover 10 d (12 d + 10 d), and treated with 12 h TNF again (12 d + 10 d + 12 h). p65 ChIP-seq and RNA-seq were done for those samples, in WT and TET gene KO cells respectively. WGBS experiments were also performed to obtain DNA methylation data for these samples. H3K27ac ChIP-seq were used to profile histone modifications at p65 binding sites. ATAC-seq experiments were performed to measure chromatin accessibility under various types of treatments.

first: Zuodong

first: Jingjing

last: Li

first: Qiang

last: Dong

first: Jun

last: Xiong

first: Yingfeng

first: Mengying

last: Lan

first: Bing

last: Zhu


title: Transcriptome analysis of dorsal root ganglion in rats with knee rheumatoid arthritis

city: Zheng zhou

first: Qian

last: Bai

state: Henan

address: NO.2 Jingba Road

institute: The second afficated hospital of zhengzhou University

summary: To determine the LncRNA expression profile in dorsal root ganglia tissues of 7 days after rats received 150 μl of CFA (1 mg/ml Mycobacterium tuberculosis, Sigma, USA) through the patella tendon into the right knee joint.  CFA injection rats macthed saline injection rats, we uesed  LncRNA microArray analysis form Arraystar to examine the expression of LncRNAs and mRNAs  in dorsal root ganglia tissues of 7 days after rats received CFA through the patella tendon into the right knee joint  and  matched Saline through the patella tendon into the right knee joint.

overall_design: dorsal root ganglia tissues from 7 days after rats received injection through the patella tendon into the right knee joint, which were distributed into two experimental groups:  rats received CFA through the patella tendon into the right knee joint group  and  matched Saline through the patella tendon into the right knee joint group , then perform LncRNAs chips by Arraystar Rat LncRNAs chip (Arraystar)

first: Jing

last: Cao

first: Tieli

first: Feng

last: Tao


title: Transcription profiling of the Hnf4a mutant mouse kidney by Osr2Cre

first: Joo-Seop

last: Park

address: 3333 Burnet Avenue

institute: Cincinnati Children's Hospital Medical Center

summary: The goal of our study is to determine if Hnf4a is required for the formation of proximal tubules during kidney development.

overall_design:
Method: Hnf4a floxed allele was deleted in the mouse kidney using Osr2Cre. Mouse kidneys at P0 were collected and subjected to RNA-seq analysis
Examination of 4 groups; two controls (Hnf4a c/+ ; Osr2Cre) and two mutants  (Hnf4a c/c ; Osr2Cre)

first: Sierra

last: Marable

first: Eunah

last: Chung


title: Comparative RNAseq of Mouse Parp3+/+ and Parp3-/- Neural Stem Progenitor Cells (NPSC)

city: Illkirch

first: Françoise

last: DANTZER

address: 300 boulevard S. Brant

institute: CNRS

summary: To identify the biological pathways underlying impaired differentiation of Parp3-deficient NPSC to astrocytes, RNAseq of the Parp3+/+ and Parp3-/- astrocytes were performed 4 days upon differentiation. Briefly, NPSC were isolated from the forebrains of Parp3+/+ and Parp3-/- 8-day-old mice. Viable single cells were induced to differentiate into astrocytes for 4 days and samples were collected for total RNA isolation and RNA sequencing.

overall_design: The experiment includes 3 independent differentiations (biological replicates) of Parp3+/+ and Parp3-/- NPSC to 4 days astrocytes. The samples represent 3 Parp3+/+ 4d-astrocytes and 3 Parp3-/- 4d-astrocytes.

last: Dantzer


title: Tolerance to cocaine-induced motor effects in rats: transcriptomic regulations in the dorsal striatum

first: Stephane

last: Le Crom

first: Florence

last: Vorspan

first: Romain

last: Icick

first: Nawel

last: Mekdad

first: Cindie

last: Courtin

first: Vanessa

last: Bloch

first: Frank

last: Bellivier

first: Jean-Louis

last: Laplanche

first: Nathalie

last: Prince

first: Dmitry

last: Pishalin

first: Cyril

last: Firmo

first: Corinne

last: Blugeon

first: Bruno

last: Mégarbane

first: Cynthia

last: Marie-Claire

first: Nadia

last: Benturquia


title: Transcriptome profiling of Benign and Malignant Pancreatic Headmass

city: Kalyani

first: Bishnupriya

last: Chhatriya

state: West Bengal

address: PO NSS

country: India

institute: National Institute of Biomedical Genomics

summary:
Microarray was used to find out the differentially expressed genes  in Benign and Malignant Pancreatic Headmass
Resulting genes could be further used to understand the disease as well as to identify transcriptomic biomarker.

overall_design: Total 26 Pancreatic headmass tissue samples were used, 6 Chronic Pancreatitis samples, 11 Pancreatic Adenocarcinoma samples and 9 Adjascent Normal  samples were used.

first: Srikanta

last: Goswami


title: Profiling site specific TCR diversity of CD4+ T Cells  in mice undergoing cardiac dysfunction

city: Boston

first: Njabulo

last: Ngwenyama

state: MA

address: 136 Harrison Ave

department: Immunology

institute: Tufts University

summary:
Purpose: Despite the well-established association between T cell-mediated inflammation and non-ischemic heart failure (HF), the specific mechanisms triggering T cell activation during the progression of HF and the antigens involved are poorly understood. We hypothesized that clonal expansion of CD4+ T cell in response to cardiac neoantigens promote the progression of HF.
Methods: We used transverse aortic constriction (TAC) in mice to trigger HF and profiled the TCR repertoire by mRNA sequencing of CD4+ T cells from 3 pooled Nur77GFP reporter mice, which transiently express GFP upon TCR engagement. We performed TCR clonal analysis of 5000 TCR-activated GFP+CD4+ T cells sorted from the LV, and 5000 CD4+ T cells sorted from the thymus, the inguinal lymph nodes (iLNs) and the heart-draining mediastinal lymph nodes (mLNs) by bulk RNA sequencing of the TCR beta chain after 8wks of TAC surgery. Paired‐end 300 base pair reads were obtained by Illumina sequencing and aligned and assembled using MiXCR software.
Results: As expected, the greatest number of unique TCR beta clonotypes (4412 clones) – and therefore the highest TCR diversity – was identified in the thymus. The heart draining mLNs showed a much lower degree of TCR clonal diversity relative to the peripheral iLNs, suggesting that cardiac antigen-driven clonal expansion occurs at the mLNs that directly drain the heart. TCR-activated GFP+CD4+ T cells in the LV represented even lower TCR diversity relative to other sites.
Conclusion: Collectively, our study demonstrates that in response to cardiac pressure overload, CD4+ T cells clonally expand in the heart-draining mLN; whilst a limited repertoire of CD4+ T cell clones engage endogenous antigens in the heart.

overall_design: TCR profiling of CD4+ T cells in 3 pooled Nur77GFP reporter mice after 8 weeks of TAC surgery.

first: Pilar

last: Alcaide


title: Effects of TREM-1 pharmacological blockade within aortas of apoE KO mice

city: Paris

first: Hafid

last: Ait-Oufella

address: 56, Rue Leblanc

institute: Inserm

summary: mouse aorta

overall_design: RT-PCR gene expression profiling.  Aorta from three apoeKO donors were pooled in each samples. Mice were treated with Scramble (Samples 1 and 3) or LR12 (Samples 2 and 4) during 7 days. Equal amount total RNA from each donor was pooled prior to gene expression analysis.


title: Gene expression profile of dermis and epidermis from young and old age group

city: Daejeon

first: Seungwoo

last: Hwang

address: 52 Eoeun-dong Yuseong-gu

department: Korean Bioinformation Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary:
To uncover the genes related to nervous system increased in the process of intrinsic aging, microarray analysis was performed with the dermis and the epidermis of buttock skin obtained from the young and old volunteers.
We found that 23 genes related to the nervous system were upregulated more than two-fold in the dermis of the aged. Conclusively, our results suggest that hyperinnervation together with elevated factors related to SP (substance P) signaling may result in the erroneous sensitization (e.g., pruritus) in the aged skin.

overall_design: Skin samples from five young and five old individuals were separated into dermis and epidermis. Thus, the sample preparation gave rise to four different groups of tissue-age combinations: Dermis-Old, Epidermis-Old, Dermis-Young, and Dermis-Young. Each group consisted of five samples, totaling twenty microarray altogether.

first: Jin

last: Chung


title: Transcriptome and epigenomics characteristics of LPS induced CD127 expressing human monocytes

status: Public on Nov 10 2020

first: Bin

last: Zhang

address: Zheng Yutong Building room D311

institute: Tsinghua University

summary: We performed the transcriptomic and epigenetic analysis for both CD127high and CD127low monocytes under LPS stimulation, and RNA-seq and ATAC-seq were performed accordingly for this purpose.

overall_design: PBMC were isolated from buffy coat of healthy blood donors by Ficoll gradients, and CD14+ monocytes were isolated from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec). CD14+ monocytes were treated with LPS for 6 h and then were collected for FACS-based sorting of CD127high and CD127low monocytes. Sorted cells were either directly used for ATAC-seq or TRIzol lysed for RNA extraction.

first: Yuan


title: Next Generation Sequencing Facilitates Quantitative Analysis of  Transcriptomes in negative control and miR-1290 knockdown HCT116 cells

city: Nanjing

first: Shukui

last: Wang

address: No.68, Changle Road, Nanjing

institute: Nanjing First Hospital

summary: Colorectal cancer (CRC) ranks third in incidence and second in mortality among cancers worldwide. Emerging researches showed that microRNAs (miRNAs) play an important role in CRC progression. Here, we aimed to investigate the expression and regulatory mechanism of miR-1290 in CRC. miR-1290 is significantly overexpressed in CRC primary tissues and metastatic tissues compared to that in normal tissues, and up-regulated miR-1290 is correlated with poor overall survival (OS) of CRC patients. Functional experiments showed that miR-1290 can promote the proliferation, migration, invasion and inhibit apoptosis of CRC cells. Mechanistically, miR-1290 directly targets KLF9 and promotes the malignancy progression of CRC cells through regulating MMP9 and p53 expression, subsequently. In addition, high H3K4me3 levels in miR-1290 promoter region activate its transcription in CRC. In summary, our study demonstrated the expression and regulatory mechanism of miR-1290 in CRC which supports the notion that therapeutic targeting of miR-1290 may be a promising treatment approach for CRC patients.

overall_design: mRNA profiles of negative control and miR-1290 knockdown HCT116 cells

first: Jian

last: Qin

first: Xiangxiang

last: Liu


title: Low-input tagHi-C in GM12878 and HeLa cells to validate the feasibility of the tagHi-C approach

city: Kunming

first: Chao

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: The spatiotemporal chromatin reorganization during hematopoietic differentiation has not been well characterized, which partly limited by the large amounts of starting cells for the current high-throughput chromatin conformation capture approaches. Here, we introduce a low-input Hi-C method, tagHi-C, to capture the chromatin structures in hundreds of cells. We proved tagHi-C was a feasible and reproducible approach

overall_design: We applied tagHi-C in GM12878 and HeLa cells to validate the feasibility of the tagHi-C approach.

first: Cheng

last: Li

first: Tao

last: Cheng

first: Hui


title: ChIP-chip from Arabidopsis with AtHMGB15

city: Kolkata

first: Shubho

last: Chaudhuri

address: P1/12 C.I.T Scheme VII M

institute: Bose Institute

type: Genome binding/occupancy profiling by genome tiling array

summary:
AtHMGB15 belongs to the ARID-HMG group of proteins in Arabidopsis thaliana. AtHMGB15 mutation results in defective pollen tube germination,however other roles of the protein remains unexplored.The expression of AtHMGB15 increases with the exposure to cold stress in 22 days old seedlings.
Chromatin immunoprecipitation (ChIP) of AtHMGB15 together with chromatin profiling by ChIP-on-chip analysis revealved AtHMGB15 binding site and demonstrated AtHMGB15 genome wide putative targets under both control and cold condition.

overall_design: Identification of genome wide binding sites of AtHMGB15 in control and cold 2hrs stressed sample


title: Long non-coding RNA and mRNA expression profile in the parotid gland of mouse with type 2 diabetes

city: Beijing

first: Yan

last: Huang

address: No.22 Zhong Guan Cun South Street

institute: Peking University School and Hospital of Stomatology

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

summary: To identify long non-coding RNA and mRNA expression profile in the parotid gland of mouse with type 2 diabetes, and predict the potencial role of differently expressed lncRNA in the dysfunction of diabetic PG

overall_design: Four 16-week-old male leptin receptor-deficient db/db mice weighting 40-55 g (a model of spontaneous type 2 DM) and age-matched db/m mice weighting 25-30 g were purchased from Changzhou Cavens Laboratory Animal Ltd. After anesthesia with an intraperitoneal injection of chloral hydrate (0.4 g/kg body weight), the fresh PG samples were extracted and frozen with liquid nitrogen for 1-2 min, then stored at ‑80°C.

first: Ruo-Lan

last: Xiang

first: Guang-Yan

last: Yu


title: Next generation sequencing of transcripts associated to five selected RNA-binding proteins in Leishmania infantum

city: Jaboatão dos Guararapes

first: LUDMILA

last: ASSIS

state: PE

address: Rua Coronel Dário Ferraz De Sá, 5357, Casa 1

department: Microbiologia

country: Brazil

institute: Instituto Aggeu Magalhães

summary: We report the sequencing of mRNAs associated with three Leishmania infantum Poly (A) binding proteins (PABP1, PABP2 and PABP3) and two of their partner RNA binding proteins (RBP23 and DRBD2). PABP1 and RBP23 preferentially associate with mRNAs that encode ribosomal proteins, absent from DRBD2-associated transcripts, and differently from PABP2 and PABP3 that bind to an overlapping set of mRNAs.

overall_design: mRNAs co-precipitated with HA-tagged RNA-binding proteins from cytoplasmic extracts of transfected Leishmania infantum cells

first: Ludmila

last: Assis

first: Moezio

middle: V

last: Santos Filho

first: Maria

last: Bezerra

first: Antônio

last: Rezende

first: Osvaldo

last: de Melo Neto


title: A rat epigenetic clock recapitulates phenotypic aging and co-localizes with heterochromatin-associated histone modifications

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: Aging has been shown to be a strong driver of DNA methylation changes, leading to the development of robust biomarkers in humans and more recently, in mice. This study aimed to generate a novel epigenetic clock in rats—a model with unique physical, physiological, and biochemical advantages for studying mammalian aging. Additionally, we incorporated behavioral data, unsupervised machine learning, and network analysis to identify epigenetic signals that not only track with age, but also relate to phenotypic aging and reflect higher-order molecular aging changes. We used DNAm data from reduced representation bisulfite sequencing (RRBS) to train an epigenetic age (DNAmAge) measure in Fischer 344 CDF (F344) rats. In an independent sample of n=32 F344 rats, we found that this measure correlated with age at (r=0.93), and related to physical functioning (5.9e-3), after adjusting for age and differential cell counts. DNAmAge was also found to correlate with age in C57BL/6 mice (r=0.79), and was decreased in response to caloric restriction (CR), such that the longer the animal was on a CR diet, the greater the decrease in DNAm. We also observed resetting of DNAm when kidney and lung fibroblasts when converted to induced pluripotent stem cells (iPSCs). Using weighted gene correlation network analysis (WGCNA) we identified two modules that appeared to drive our DNAmAge measure. These two modules contained CpGs in intergenic regions that showed substantial overlap with histone marks H3K9me3, H3K27me3, and E2F1 transcriptional factor binding. In moving forward, our ability to unravel the complex signals linking DNA methylation changes to functional aging would require experimental studies in model systems in which longitudinal epigenetic changes can be related to other molecular and physiological hallmarks of aging.

overall_design: Examination of DNA methylation via RRBS in n=134 Fischer 344 CDF (F344) rats ages 1-27 months.

first: Morgan

last: Levine

first: Rafael

last: de Cabo

first: Luigi

last: Ferrucci


title: iPSC-derived NK cells and anti-PD-1 antibody synergize to enhance T cell cytokine and cytolytic responses against multiple tumors

city: San Diego

first: Dave

last: Robbins

state: CA

address: 3535 General Atomics Court Ste. 200

institute: Fate Therapeutics

summary:
We have developed a robust and efficient manufacturing system for the differentiation and expansion of high-quality NK cells (iNKs) derived from induced pluripotent stem cells (iPSCs).
We used GeneChip microarrays to compare the whole transcriptome of iNK cells to the transcriptomes of primary T cell and NK cell populations, K562 feeder cell-expanded primary NK cells, fibroblasts, iPSCs and iCD34+ cells.

overall_design: Total RNA was extracted from in vitro cultured iNKs, primary NKs, fibroblasts, iPSCs and iCD34+ cells as well as sorted primary human T and NK cell populations.  Each sample was processed with triplicate donors (or samples) when possible and gene expression was compared.

first: D

first: R

last: Bjordahl

first: F

last: Cichocki


title: Prognosis prediction model for Alzheimer’s disease conversion from mild cognitive impairment by integrative analysis of multi-omics data

city: Obu

first: Daichi

last: Shigemizu

state: Aichi

address: 7-430 Morioka-cho

institute: National Center for Geriatrics and Gerontology

summary: Mild cognitive impairment (MCI) is a clinical precursor of Alzheimer’s disease (AD). Many MCI subjects convert to AD, although others remain stable as MCI or sometimes return to cognitive normal. Currently, there are no curative treatments for patients who are already in AD, and therefore biomarkers for early detection of high risk MCI-to-AD conversion subjects are rapidly required. Here, we investigated potential biomarkers from blood-based miRNA (miR) expression profiles and genomic data of 197 Japanese MCI patients. Using the candidate biomarkers, we constructed a prognosis prediction model based on a Cox proportional hazard model. The final prediction model, composed of 24 miR-eQTLs (i.e. SNP-miRNA pairs) and three clinical factors (age, sex and ApoE ε4 carriers), successfully classified MCI patients into two groups, low and high, in terms of risk of MCI-to-AD conversion (log-rank trend test P=3.44×10^(-4)), and achieved a concordance index of 0.702 on an independent test set. Network-based meta-analysis using target genes of the miR-eQTLs further revealed four important hub genes (SHC1, FOXO1, GSK3B, and PTEN) associated with the pathogenesis of AD. Statistically significant differences were observed in PTEN expression between MCI and AD and SHC1 expression between cognitively normal elder subjects (CN) and AD when examining RNA-seq data from 610 blood samples (PTEN, P=0.023; SHC1, P=0.049), although FOXO1 and GSK3B showed low levels of expression in blood. Accurate prediction of MCI-to-AD conversion enables earlier appropriate intervention for those MCI patients and can lead to a reduction of MCI patients that convert to AD with high risk. We believe that further investigation with larger sample sizes will contribute to practical clinical use of our approach in MCI-to-AD conversion in the near future.

overall_design: 197 serum Mild Cognitive Impairment (MCI) samples (83 MCI converters: MCI-C and 114 MCI non-converters: MCI-NC)

first: Shintaro

last: Akiyama

first: Sayuri

last: Higaki

first: Taiki

last: Sugimoto

first: Takashi

last: Sakurai

first: Keith

last: Boroevich

first: Alok

last: Sharma

first: Tatsuhiko

last: Tsunoda

first: Takahiro

last: Ochiya

first: Shumpei

last: Niida

first: Kouichi

last: Ozaki


title: Human yolk sac-like haematopoiesis generates RUNX1-, GFI1- and/or GFI1B-dependent blood and SOX17-positive endothelium

city: Melbourne

first: Freya

middle: Faith

last: Bruveris

state: VICTORIA

address: 50 Flemington Rd, Parkville

department: Cell Biology

institute: Murdoch Children's Research Institute

summary: The genetic regulatory network controlling early fate choices during human blood cell development are not well understood. We use human pluripotent stem cell reporter lines to track the development of endothelial and haematopoietic populations in an in vitro model of human yolk-sac development. We identified SOX17-CD34+CD43- endothelial cells at day 2 of blast colony development, as a haemangioblast-like branch point from which SOX17-CD34+CD43+ blood cells and SOX17+CD34+CD43- endothelium subsequently arose. Most human blood cell development was dependent on RUNX1. Deletion of RUNX1 only permitted a single wave of yolk sac-like primitive erythropoiesis, but no yolk sac myelopoiesis or aorta-gonad-mesonephros (AGM)-like haematopoiesis. Blocking GFI1/1B activity with a small molecule inhibitor abrogated all blood cell development, even in cell lines with an intact RUNX1 gene. Together, our data defines the hierarchical requirements for both RUNX1 and GFI1/1B during early human haematopoiesis arising from a yolk sac-like SOX17- haemogenic endothelial intermediate.

overall_design: mRNA profiling of 16 samples for 6 different cell populations

first: Andrew

last: Elefanty


overall_design: mRNA profiling of 24 samples were obtained from 2 different human embryonic cell lines and 2 different treatments.


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

overall_design: Refer to individual Series


title: RNA seq dataset of parental and reserve cells (FRCs Cycle 1 and SRCs Cycle 3)

city: Rotterdam

first: Gerben

last: Schaaf

address: Wytemaweg 80

country: Netherlands

institute: Erasmus MC

summary: Loss of regenerative capacity during ex vivo expansion of muscle stem cells hampers the development of cell-based therapies for skeletal muscle disorders. Here, we developed a method to isolate regenerative reserve cell fractions from expanded murine primary cultures using differential adhesion properties and the induction of subsequent cycles of proliferation and differentiation. Fast-adhering reserve cells (FRCs) were enriched for cells expressing myogenin and contributed efficiently to muscle regeneration following transplantation in immunodeficient hosts. Slow adhering reserve cells (SRCs) generated higher number of PAX7+ cells under differentiating conditions and predominantly regenerated muscle after a secondary injury, suggesting engraftment as muscle stem cells. Transcriptomic analysis revealed that FRCs were enriched for markers of myogenic differentiation, while SRCs were characterized by a distinctive set of cell-adhesion genes. Overall, reserve cells provide a valuable source for the study and identification of molecular determinants of regeneration using ex vivo-expanded muscle cells.

overall_design: Reserve cell populations were passaged twice after isolation in proliferation conditions before harvesting. Samples were harvested using RLT buffer. RNA was extracted using the RNeasy minikit with DNase treatment. Total RNA for triplicates of PAR, FRCs Cycle 1, and SRCs Cycle 3 were checked for quality on an Agilent Technologies 2100 Bioanalyzer using a RNA nano assay. All samples had RIN value of 10. Triplicate RNA-Seq libraries were prepared according to the Illumina TruSeq stranded mRNA protocol. Sequencing-by-synthesis was performed using the HiSeq 2500 with a single read 50-cycle protocol followed by dual index sequencing

first: Rodrigo

last: Canibano-Fraile

first: Wesley

last: Huisman

first: Jip

last: Zonderland

first: Faidra

last: Karkala

first: Claudia

last: Milazzo

first: Tom

last: van Gestel

first: Wilfred

last: van Ijcken

first: Ans

middle: T

last: van der Ploeg

first: W

last: Pim Pijnappel


title: Single cell RNA-seq for LPS-treated human monocytes

first: Bin

last: Zhang

summary: The heterogeneous characteristics of activated monocytes are much unknown. We performed the single cell transcriptomic analysis of LPS-treated human monocytes from healthy blood donor, and CD127 expression associated expression pattern of inflammatory genes was identified in LPS-treated monocytes.

overall_design: PBMC were isolated from buffy coat of healthy blood donor by Ficoll gradients, and CD14+ monocytes were isolated from PBMC with anti-CD14 magnetic beads (Miltenyi Biotec). CD14+ monocytes were treated with LPS for 6 h and then frozen for preservation to sent out for scRNA-seq library construction by using 10x genomics platform.

first: Yuan


title: Gene expression of endothelial cells isolated from pancreatic cancer tissues and from chronic pancreatitis tissues

city: Tokyo

first: Nobuyoshi

last: Hiraoka

address: 5-1-1 Tsukiji, Chuo-ku

department: Pathology Division

institute: National Cancer Center Research Institute

summary: Endothelial cells existed in the cancer tissue have unique biological characteristics that are different from those found in the noncancerous tissue of the same organ. In order to investigate molecular mechanisms involved in the unique biological phenotypes of endothelial cells in the cancer tissue, we compared gene expression profiles of endothelial cells isolated from pancreatic cancer tissues with those from chronic pancreatitis tissues.

overall_design: Gene expression profiles of endothelial cells of three pancreatic cancer tissues and three chronic pancreatitis tissues were measured using Agilent SurePrint G3 Human GE v2 8x60K Microarray.

first: Kosei

last: Nakajima

first: Yoshinori

last: Ino

first: Rie

last: Yamazaki-Itoh


title: Adipose tissue from metabolic syndrome mice induces an aberrant miRNA signature highly relevant in prostate cancer development

status: Public on Nov 09 2020

city: Ciudad Autónoma de Buenos Aires

first: Cintia

middle: Lorena

last: Massillo

state: Buenos Aires

address: Vuelta de Obligado 2490

country: Argentina

institute: Instituto de Biología y Medicina Experimental

summary:
We developed a MeS-like disease model using C57BL/6J mice chronically fed with high fat diet (HFD) that were inoculated with TRAMP-C1 prostate cancer (PCa) cells to investigate the interaction between white adipose tissue (WAT) and PCa cells through miRNAs, in MeS mice.
In this dataset, we include the expression data obtained from co-culture medium between TRAMP-C1 cells with HFD-gonadal WAT (gWAT) versus TRAMP-C1 cells with CD-gWAT. For differential expression analysis we used the Rank Product Method.

overall_design: TRAMP-C1 cells were co-cultured in 24-transwell plates with gWAT obtained from CD or HFD C57BL/6J mice. Culture medium was collected for RNA isolation followed by miRNA microarrays hybridization. As a control, TRAMP-C1 cells were cultured without the addition of gWAT.


title: Human umbilical cord tissue is a robust source for mesenchymal stem cells with enhanced myogenic differentiation potential compared to cord blood

city: Faridabad

first: Suchitra

last: GOPINATH

address: NCR Biotech Science Cluster, 3rd Milestone,

institute: Translational Health Science and Technology Institute

summary: We report that mesenchymal stem cells isolated from umbilical cord tissue differentiate more robustly into the myogenic lineage compared to mesenchymal stem cells from cord blood isolated from the same individual

overall_design: MSCs isolated from cord tissue (UCT) and cord blood (UCB) were induced to differentiate in myogenic differentiation medium and enhanced adhesion for 7 days.

last: Gopinath


title: Genome-wide BRD4 occupancy upon expression of YFV capsid in Huh-7 cells

city: New York

first: Diego

last: Mourão

state: NY

address: 1230 York Avenue

country: USA

institute: Rockefeller University

summary: We generated genome-wide ChIP-seq binding profiles of BRD4 to analyze the role of YFV capsid lysine residues in the levels of BRD4 on chromatin

overall_design: Examination of BRD4 levels in Huh-7 cells expressing an Empty vector, YFV capsid or YFV mutant capsid

last: Mourao

first: Uwe

last: Schafer

first: Alexander

last: Tarakhovsky


title: Histone methyltransferase G9a governs the mutant Kras-driven pancreatic carcinogenesis

first: Keisuke

last: Tateishi

address: 7-3-1 Hongo, Bunkyo-ku

department: Department of Gastroenterology

institute: Graduate School of Medicine, The University of Tokyo

summary: ATAC-seq of mouse pancreas organoids (K,KC,KC+UNC)

overall_design: Pancreatic organoid cells from the LSL-KrasG12D/+ (K) , Ptf1aCre/; KrasG12D (KC) mice were examined by ATAC-seq. Organoids were cultured either with fresh media or with 5µM UNC0638 for 24hours prior to experiments. Harvested organoids were gently digested into single cell suspension using TrypLE and DNase1, and 50,000 cells were processed for ATAC-seq. Sequence reads were trimmed and aligned to the mouse genome (mm10) using BWA. For visualization, ATAC-seq signals were normalized to RPKM and smoothed by 150bp sliding windows with 20bp bin size using bamCoverage.

first: Hiroyuki

last: Kato

first: Kazuhiko

last: Koike


title: RNA-seq of human induced pluripotent stem cell differentiation into cardiomyocytes using Wnt inhibition

city: Farmington

first: Marina

last: Yurieva

state: Connecticut

address: 10 Discovery dr

department: Computational Sciences

institute: Jackson Laboratory

summary: RNA-sequencing data from human iPSC PGP1 cells (n=4) differentiated into mesoderm (day-2) (n=4) or cardiomyocytes (days 25-30) (n=4) through modulation of Wnt/β-catenin signaling as previously described (Cohn et al., 2019; Hinson et al., 2017; Hinson et al., 2015; Lian et al., 2012).

overall_design: RNA-seq of iPSC, iPSC derived mesoderm and iPSC derived cardiomyocyte

first: Ketan

last: Thakar

first: John

last: Hinson

first: Nathan

last: Leclair

first: Olga

last: Anczukow


title: Gene expression analysis of wild type and Lats1/2-mutated uveal melanoma

city: Worcester

first: Julie

last: Zhu

address: 364 Plantation Street

department: Molecular Cellular and Cancer Biology

institute: UMass Medical School

summary: Lats1/2 kinases are the core Hippo pathway kinases. In this study, we use RNAseq to analyze the gene expression profiles of adult mouse uveal tract cells and mouse uveal melanoma generated by Lats1/2 deletion induced by AAV-based Cre injection into mouse uveal tract.

overall_design: Total RNA obtained from freshly isolated wild type uveal tissue and eye tumors from AAV-Cre-injected Lats1/2 fl/fl mice

first: Huapeng

last: Li

first: Junhao

last: Mao


title: Emergent pro-metatastatic heterogeneity is shaped by clone interactions and restricted by VSIG1 VII

city: Geneva

first: Celine

last: Delucinge

address: 1 rue Michel Servet

department: iGE3 Genomics Platform

institute: University of Geneva

summary: Our study prompeted us to assign, through spiked single cell RNAseq, metastatic  function to transcriptomic cluster of colon cancer cells. Interactions between clones also uncover a restrictive anti metastatic influence that act intrinsically and non-cell automomously. We identify VSIG1 as critical mediator of this influence.

overall_design: Exome

first: Carolina

last: Bernal

first: Marianna

last: Silvano

first: Yann

last: Tapponnier

first: Santosh

last: Anand

first: Cecilia

last: Angulo

first: Ariel

last: Ruiz i Altaba


title: The expression landscape of hepatocarcinogeneis in a rat model

city: Shanghai

first: Shengli

address: 650 Xinsongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: Hepatocellular carcinoma (HCC) initiation is characterized by the sequential stepwise accumulation of molecular alterations. However, the earliest events during the dynamic temporal trend of hepatocarcinogenesis are still unknown. Using a diethylnitrosamine (DEN)-induced rat HCC model, we report a comprehensive transcriptomic landscape of liver tissues at the stages of hepatitis, cirrhosis, and HCC.

overall_design: To profile the expression landscape in rat HCC model, we performed microarray expression profiling on 9 liver tissues and 3 HCC tissue, including 3 from normal mock group, 3 from liver hepatitis group (LH), 3 from liver cirrhosis group (LC), and 3 from HCC group.


title: Haldane’s rule in the placenta: sex-biased misregulation of the Kcnq1 imprinting cluster in hybrid mice

city: Riverside

first: Polly

last: Campbell

address: 3401 Watkins Drive

department: Evolution, Ecology, and Organismal Biology

institute: University of California Riverside

summary: Hybrid phenotypes that contribute to postzygotic reproductive isolation often exhibit pronounced asymmetry, both between reciprocal crosses and between the sexes in accordance with Haldane's rule. Inviability in mammalian hybrids is associated with parent-of-origin placental growth abnormalities for which misregulation of imprinted genes is the leading candidate mechanism. However, direct evidence for the involvement of imprinted genes in hybrid growth dysplasia is limited. We used transcriptome and reduced representation bisulfite sequencing to conduct the first genome-scale assessment of the contribution of imprinted genes to parent-of-origin placental growth dysplasia in the cross between the house mouse (Mus musculus domesticus) and the Algerian mouse (Mus spretus). Imprinted genes with transgressive expression and methylation were concentrated in the Kcnq1 cluster, which contains causal genes for prenatal growth abnormalities in mice and humans. Hypermethylation of the cluster’s imprinting control region, and consequent misexpression of the genes Phlda2 and Ascl2, is a strong candidate mechanism for transgressive placental undergrowth. Transgressive placental and gene regulatory phenotypes, including expression and methylation in the Kcnq1 cluster, were more extreme in hybrid males. While consistent with Haldane’s rule, male-biased defects are unexpected in rodent placenta because the X-chromosome is effectively hemizygous in both sexes. In search of an explanation we found evidence of leaky imprinted (paternal) X-chromosome inactivation in hybrid female placenta, an epigenetic disturbance that may buffer females from the effects of X-linked incompatibilities to which males are fully exposed. Sex differences in chromatin structure on the X and sex-biased maternal effects are non-mutually exclusive alternative explanations for adherence to Haldane’s rule in hybrid placenta. The results of this study contribute to understanding the genetic basis of hybrid inviability in mammals, and the role of imprinted genes in speciation.

sample_organism:
Mus musculus domesticus
Mus spretus
Mus musculus domesticus x Mus spretus

overall_design: Analysis of 29 samples of placental DNA at e17.5 of the same pregnancies (3 groups, 4-5 biological replicates per sex, per group)

first: Lena

last: Arévalo


title: Tumor cell endogenous HIF-1alpha activity induces aberrant angiogenesis and interacts with TRAF6 pathway required for colorectal cancer development

city: Zurich

first: Lubor

last: Borsig

address: Winterthurerstrasse 190

department: Physiology

institute: University of Zurich

summary: Hypoxia and inflammation are key factors for colorectal cancer tumorigenesis. The colonic epithelium belongs to the tissues with the lowest partial pressure of oxygen in the body, and chronic inflammation is associated with an increased chance to develop colon cancer. How the colonic epithelium responds to hypoxia and inflammation during tumorigenesis remains to be elucidated. Here we show, that murine colon adenocarcinoma cells with attenuated response to hypoxia, due to a knock-down (KD) of HIF-1alpha produce smaller and less hypoxic tumors in an orthotopic mouse model when compared to tumors induced with control cells. HIF-1alpha-KD tumors showed more functional perfused vasculature associated with increased levels of vessel-stabilizing factors and reduced levels of pro-angiogenic factors, including extracellular matrix protein Cyr61/CCN1. Intratumoral injection of Cyr61 in HIF-1alpha-KD tumors revealed an in increased vessel permeability and tumor hypoxia. Further bioinformatics analysis identified a possible interaction between HIF-1alpha and TRAF6, an upstream effector of the NF-kappaB pathway that was confirmed by co-immunoprecipitation in MC-38 and CT26 colon adenocarcinoma cells. Down-regulation of TRAF6 resulted in virtual abrogation of orthotopic tumor growth. Subcutaneous TRAF6-KD tumors were smaller and contained reduced vessel size and differently polarized macrophages. These data demonstrate that the tumor cell response to increased hypoxia in the colon leads to promotion of non-functional angiogenesis, regulated by both hypoxia and TRAF6 pathways.

overall_design: The study objective was to compare the transcriptomes of murine colon adenocarcinoma cells, MC-38 cells with attenuated hypoxia response, knock-down of HIF-1alpha (HIF-1alpha-KD) versus control (Mock) cells, which were isolated (sorted) from an orthotopic tumor grown in cecum wall of a mouse. Downregulation of HIF-1alpha expression resulted in smaller tumors, characterized by reduced tumor hypoxia and increased functional (perfused) vasculature when compared to control (Mock) tumors. To identify factors leading to this phenotype, we performed deep RNAseq (Illumina HiSeq 4000) and searched for genes that are either up-regulated or down-regulated in sorted HIF-1alpha-KD MC-38 cells versus Mock-control cells). All samples were analyzed in triplicates (HIF-KD sorted 1-3, Mock-sorted 1-3).

first: Jesus

last: Glaus Garzon