title: Mesenchymal tumor cells drive adaptive resistance of Trp53-/- breast tumor cells to inactivated mutant Kras

city: Stanford

first: Michael

middle: F.

last: Clarke

state: CA

address: 265 Campus Dr

department: Institute for Stem Cell Biology and Regenerative Medicine

institute: Stanford University

summary: As precision medicine increases the response rate of treatment, tumors frequently bypass inhibition and reoccur. In order for treatment to be effective long term, the mechanisms enabling treatment adaptation need to be understood. Here, we report a mouse model that, in the absence of p53 and the presence of oncogenic KrasG12D, develops breast tumors. Upon inactivation of KrasG12D, tumors initially regress and enter remission. Subsequently, the majority of tumors adapt to the withdrawal of KrasG12D expression and return. KrasG12D-independent tumor cells show a strong mesenchymal profile with active MAPK/ERK signaling. Both KrasG12D-dependent and KrasG12D-independent tumors display a high level of genomic instability, and KrasG12D-independent tumors harbor numerous amplified genes that can activate the MAPK/ERK signaling pathway. Our study identifies both epithelial–mesenchymal transition (EMT) and active MAPK/ERK signaling in tumors that adapt to oncogenic KrasG12D withdrawal in a novel Trp53-/- breast cancer mouse model. To achieve long-lasting responses in the clinic to RAS-fueled cancer, treatment will need to focus in parallel on obstructing tumors from adapting to oncogene inhibition.

overall_design: Two Trp53-/- KrasG12D-dependent primary tumors with each three matched Trp53-/- KrasG12D-independent tumors

first: Linda

last: van Weele


title: Synergy of chemotherapy and macrophage depletion leads to T cell memory activation and durable triple negative breast cancer regression

status: Public on Apr 04 2022

city: Houston

first: Swarnima

last: Singh

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

country: USA

institute: Baylor College of Medicine

type: Expression profiling by high throughput sequencing

summary: Immunosuppressive elements within the tumor microenvironment such as Tumor Associated Macrophages (TAMs) can present a barrier to successful anti-tumor responses by cytolytic T cells. We employed preclinical syngeneic p53 null mouse models of TNBC to develop a treatment regimen that harnessed the immunostimulatory effects of low-dose chemotherapy coupled with the pharmacologic inhibition of TAMs. Combination therapy was used to successfully treat several highly aggressive, claudin-low murine mammary tumors and lung metastasis. Long-term responders developed tertiary lymphoid structures co-infiltrated by T and B cells at the treatment site. Mechanistically, CD86+ antigen-experienced T cells exhibited polyclonal expansion and resulted in exceptional responses upon tumor rechallenge. Combination treatment also eliminated lung metastases. High dimensional transcriptomic data for CD45+ immune cells lead to the identification of an aberrant developmental trajectory for TAMs that were resistant to treatment. This study illustrates the complexity of tumor infiltrating myeloid cells and highlights the importance of personalized immuno-genomics to inform therapeutic regimens

overall_design: Examining CD45+ immune cells in murine mammary tumors before and after immunotherapy treatment

first: Nigel

last: Lee


title: Transcriptomic analysis of hepatic genes in pair-fed and ethanol-fed wild type and Sirt6 liver-specific knockout mice

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Drive, MS1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: RNA-seq was performed on mRNA samples purified from the livers of wild type (WT) and Sirt6 liver-specific knockout (KO) mice.

overall_design: Two genotypes (WT and KO) and two feeding conditions (pair-fed and ethanol-fed) were designed for this study. There were a total of four groups and each group had three liver mRNA samples isolated from individual mice.

first: Xiwen

last: Xiong

middle: C


title: Tumor tissues  vs normal  tissues  from 21 cases  ESCA

status: Public on Apr 03 2022

city: Zhengzhou

first: Haiyang

last: Du

state: Henan

address: 156 Jinshui East Road, Zhengzhou, Henan, China

country: China

institute: Henan University of Chinese Medicine

summary: Transcriptional profiling of  tumor tissues and normal  tissues from ESCA.

overall_design: Tumor tissues  vs normal  tissues. Biological replicates: 21.

first: Fuchun

last: Si

first: Gao

first: Jiqing


title: Transcriptome dysregulation in hepatoblastomas: the pivotal role of noncoding RNAs and detection of altered lipid metabolism

city: Sao Paulo

first: Ana

middle: Cristina

last: Victorino Krepischi

address: Rua do Matao 277

department: Genética e Biologia Evolutiva

country: Brazil

institute: Universidade de São Paulo

summary: We report the application of the RNA sequencing technology for profiling gene expression alterations in hepatoblastomas. Comparing 14 hepatoblastomas to a group of control liver samples, a set of 1492 differentially expressed genes (DEGs) was detected, both coding and non-coding. We describe the enrichment of specific biological processes related to up- and downregulated genes, and the disruption of metabolic pathways including lipids, amines, and nicotinamides. Finally, we disclose a robust ncRNA transcriptome perturbation, highlighting a new epigenetic player in the control of gene expression in hepatoblastomas.

overall_design: Comparative analysis of RNA sequencing data from 14 hepatoblastomas and 05 normal liver samples.


title: Spatial Environment Affects HNF4A Mutation-Specific Proteome Signatures and Cellular Morphology in hiPSC-Derived β-Like Cells

city: Bergen

first: Helge

last: Ræder

address: Dept of Pediatrics, Haukeland University Hospital

department: Department of Clinical Science

country: Norway

institute: University if Bergen

summary: Studies of monogenic diabetes are particularly useful as we can gain insight into the molecular events of pancreatic β-cell failure. Maturity-onset diabetes of the young 1 (MODY1) is a monogenic diabetes form, caused by a mutation in the HNF4A gene. Human induced pluripotent stem cells (hiPSC) provide an excellent tool for disease modelling by subsequent directed differentiation toward desired pancreatic islet cells, but cellular phenotypes in terminally differentiated cells are notoriously difficult to detect. Re-creating a spatial (3D) environment may facilitate phenotype detection. In this study, we studied MODY1 using hiPSC-derived pancreatic β-like patient and isogenic control cell lines in two different 3D contexts. Using size-adjusted cell aggregates and alginate capsules we showed that the 3D context was critical to facilitate the detection of mutation-specific phenotypes. In 3D cell aggregates we identified irregular cell clusters and lower levels of structural proteins by proteome analysis, whereas in 3D alginate capsules we identified altered levels of glycolytic proteins in the glucose sensing apparatus by proteome analysis. Our study provides novel knowledge on normal and abnormal function of HNF4A paving the way for translational studies of new drug targets that can be used in precision diabetes medicine of MODY.

overall_design: Examination of the transcription profile effects by HNF4A mutation in hiPSC-derived β-Like cells

first: Manuel

last: Carrasco

first: Chencheng

last: Wang

first: Anne

middle: M

last: Søviknes

first: Yngvild

last: Bjørlykke

first: Shadab

last: Abadpour

first: Joao

middle: A

last: Paulo

first: Erling

last: Tjora

first: Pål

last: Njølstad

first: Jonas

last: Ghabayen

first: Ingrid

last: Nermoen

first: Valeriya

last: Lyssenko

first: Simona

last: Chera

first: Luiza

last: Ghila

first: Marc

last: Vaudel

first: Hanne

last: Scholz


title: Interaction between CO2 levels and nitrogen nutrition in Pinus pinaster

city: Malaga

first: Rafael

last: Cañas

address: Facultad de Ciencias, Campus de Teatinos

department: Biología Molecular y Bioquímica

country: Spain

institute: Universidad de Málaga

summary: The main objective of the present work is the transcriptomic analysis of the interaction between nitrogen nutrition and CO2 levels in maritime pine. For this purpose, seedlings were fertilized with nitrate or ammonium and grown in two different CO2 levels: normal (400 ppm) and high (720ppm).

overall_design: Pine seedlings were subdivided into four groups. The treatments were maintained one month. Two groups were irrigated with 40 mL of 8 mM NH4Cl once a week, the two remaining groups were supplied with 40 mL of 8 mM KNO3 once a week. Of the groups irrigated with each solution, one was maintained at 400 ppm CO2 and the other at 720 ppm CO2. Pools of 12 seedlings were harvested per each biological replicate. The three main organs (needles, stem and roots) were isolated and immediately frozen in liquid nitrogen. Total RNA was extracted for the 36 samples, which were sequenced on an Illumina NovaSeq 6000 as paired-end reads of 150 bp length.

first: José

last: Urbano-Gámez

last: Valderrama-Martín

first: Jesús

middle: D

last: López-Arredondo

first: Juan

last: Serrano

first: Francisco

last: Ortigosa

first: Cristina

last: Fernández-Muñoz

first: Marina

last: González-Bazán

middle: R

last: Cantón


title: Liver Transposase-Accessible Chromatin signal changes related to fat content in pigs

city: Balice

first: Kacper

last: Zukowski

address: Krakowska 1 Street

country: Poland

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The present work emplyed pigs as an animal model for recognition of molecular processes associated with fat deposition. The Transposase-Accessible Chromatin signal changes dependent on fat content were showed at the liver levels. In the experiment Złotnicka White pigs were used that were not under selection pressure, because they are included in to National Preservation Program.

overall_design: The Transposase-Accessible Chromatin signal changes related to fat deposition in pigs experiment was supported by the statutory activity of National Research Institute of Animal Production no. 01-18-05-21 and BIOSTRATEG2/297267/14/NCBR/2016

first: Piórkowska

last: Katarzyna

first: Żukowski

last: Kacper

first: Katarzyna

last: Ropka-Molik

first: Mirosław

last: Tyra


title: Identification of genes involved in RAS oncogenic activity in human colorectal cancer cell line HCT116

city: London

first: Philip

last: East

state: London

address: 1 Midland Road, London

department: Bioinformatics

country: United Kingdom

institute: The Francis Crick Institute

summary: The study aimed to identify genes essential for the maintenance of the transformed phenotype of the colorectal cancer cell line HCT116, which is dependent on the continued expression of the activated KRAS oncogene (KRASG13D). We generated HCT116 cell lines stably expressing an inducible shRNA-expressing retroviral vector targeting KRAS (Ngo et al., Nature, 2006). In cells engineered to express the bacterial tetracycline repressor, the shRNA is expressed specifically upon doxycycline addition. With this system, we showed that inducible down-regulation of KRAS is triggering cell death in the HCT116 cells, suggesting oncogene addiction in this cell line. In this study, we compared the gene expression profile of HCT116 cells where KRAS has been downregulated for different lengths of time, aiming at identifying RAS-target genes. We also compared the gene expression profile of the parental HCT116 cell line with two derived isogenic cell lines, Hke3 and Hkh-2, where the activated KRAS gene has been deleted by homologous recombination.

overall_design: HCT116 cell line stably expressing inducible shRAS vectors (Ngo et al., Nature, 2006) were treated with 25 ng/ml docycycline or vehicle control for 3 days or 6 days. Hke3, Hkh-2 and parental HCT116 were cultured in basal condition. All conditions were done in triplicate.

first: Michela

last: Marani

first: David

last: Hancock

first: Julian

last: Downward


title: leptin b and its regeneration enhancer illustrate regenerative features of zebrafish hearts

city: Madison

first: Kwangdeok

last: Shin

state: WI

address: 4451 WISCONSIN INSTITUTE FOR MEDICAL RESEARCH II

institute: University of Wisconsin - Madison

summary: We obtained uninjured and injured hearts transcritome profiles of wild-type and LEN deletion mutant zebrafish. Note that LEN is the leptin b-linked regenreation enhancer located about 6kb upstream of leptin b gene.

overall_design: uninjured and 3 days post-amputation (dpa) heart profiles of adult wild-type and LEN mutant zebrafish.

first: Junsu

last: Kang


title: Bronchoalveolar lavage alveolar macrophage subset transcriptomes in WT and NOX2-knockout mice

city: St Louis

first: Mary

last: Dinauer

state: Missouri

address: 660 South Euclid Ave

department: Pathology & Immunology

institute: Washington University In St Louis

summary: The leukocyte NADPH oxidase 2 (NOX2) plays a key role in pathogen killing and immunoregulation. Genetic defects in NOX2 result in chronic granulomatous disease (CGD), associated with microbial infections and inflammatory disorders, often involving the lung. Alveolar macrophages (AM) are the predominant immune cell in the airways at steady state, and limiting their activation is important given constant exposure to inhaled materials, yet the importance of NOX2 in this process is not well-understood. Here, we show a previously undescribed role for NOX2 in maintaining lung homeostasis by suppressing AM activation, as studied using CGD mice or mice with selective loss of NOX2 primarily in macrophages. AM lacking NOX2 have increased cytokine responses to TLR2 and TLR4 stimulation ex vivo. Moreover, between 4 and 12 weeks of age, mice with global NOX2 deletion developed an activated CD11bhigh subset of AM with epigenetic and transcriptional profiles reflecting immune activation compared to WT AM. The presence of CD11bhigh AM in CGD mice correlated with increased numbers of alveolar neutrophils and proinflammatory cytokines at steady state as well as increased lung inflammation following insults. Moreover, deletion of NOX2 primarily in macrophages was sufficient for mice to develop an activated CD11bhigh AM subset and accompanying pro-inflammatory sequela.  Additionally, we showed that the altered resident macrophage transcriptional profile in the absence of NOX2 is tissue-specific as these changes were not seen in resident peritoneal macrophages. Thus, these data demonstrate that absence of NOX2 in alveolar macrophages leads to their pro-inflammatory remodeling and dysregulates alveolar homeostasis.

overall_design: BAL alveolar macrophages were studied from 4 week and 12 week old control and CybbKO mice. For each replicate, BAL AM from various groups of mice were sorted into RPMI+20%FBS on the basis of CD45+Ly6G-SiglecF+CD11c+ markers and CD11b expression (CD11b+or CD11b). To achieve a sufficient number of AM cells (~50,000) per each replicate sample, 2 to 3 mice from same group were pooled. Cells were centrifuged followed by resuspension in RLT-plus RNA Lysis buffer (Qiagen). RNA isolation was done using RNAeasy micro-plus columns (Qiagen). 3 independent replicates from each group were analyzed. RNA seq libraries were generated with Clontech SMARTer kits and sequencing were performed on a HiSeq3000 sequencer.

first: Sourav

last: Bhattacharya

first: Wei

last: Yang

first: Jeffrey

last: Magee


title: Inhibition of Histone H3-H4 Chaperone Pathways Rescues Dysfunctional Oncohistone H2B

city: Beijing

first: Ruixue

last: Zhao

state: Beijing

address: Qinghua yuan street

department: School of life sciences

institute: Tsinghua University

summary: Oncohistone mutations are crucial drivers for tumorigenesis, but how a living organism responds to and governs the loss-of-function oncohistone remains unclear. Here, we generated a histone H2B triple knockout (3KO) strain in Caenorhabditis elegans, which decreased the embryonic H2B level, disrupted cell divisions, and caused animal sterility. Our genetic screens identified mutations defective in a histone H3-H4 chaperone UNC-85 as suppressors that recovered H2B 3KO fertility. We found that unc-85 mutations reduced chromatin H3-H4 levels and that inhibiting other H3-H4 chaperones or H3-H4 histones also rescued H2B 3KO sterility. The oncohistone H2BE76K mutation disrupts the H2B-H4 interface and causes nucleosome instability, and we showed that blocking H3-H4 chaperones restored cell division defects in C. elegans or human cells carrying H2BE76K. Thus, our results indicate that reducing chromatin H3-H4 rescues H2B loss and suggest that inhibiting H3-H4 chaperones may be a therapeutic strategy to treat cancers resulting from loss-of-function H2B oncohistone.

overall_design: Examination of  histone H3 by Chromatin immunoprecipitation with reference exogenous genome (ChIP-Rx) in wild-type (WT) and H2B TKO;unc-85(cas1100) C.elegans. ChIP-Rx was generated by deep sequencing, in duplicate, using Illumina NovaSeq 6000.

first: Ruxu

last: Geng

first: Zhiwen

last: Zhu

first: Xuguang

last: Jiang

last: Li

first: Guangshuo

last: Ou


title: Analysis of resident peritoneal macrophage's transcriptome in WT and CGD mice

summary: The leukocyte NADPH oxidase 2 (NOX2) plays a key role in pathogen killing and immunoregulation.  Genetic defects in NOX2 result in chronic granulomatous disease (CGD), associated with microbial infections and inflammatory disorders, often involving the lung. Alveolar macrophages (AM) are the predominant immune cell in the airways at steady state, and limiting their activation is important given constant exposure to inhaled materials, yet the importance of NOX2 in this process is not well-understood.  Here, we show a previously undescribed role for NOX2 in maintaining lung homeostasis by suppressing AM activation, as studied using CGD mice or mice with selective loss of NOX2 primarily in macrophages.  AM lacking NOX2 have increased cytokine responses to TLR2 and TLR4 stimulation ex vivo.  Moreover, between 4 and 12 weeks of age, mice with global NOX2 deletion developed an activated CD11bhigh subset of AM with epigenetic and transcriptional profiles reflecting immune activation compared to WT AM. The presence of CD11bhigh AM in CGD mice correlated with increased numbers of alveolar neutrophils and proinflammatory cytokines at steady state as well as increased lung inflammation following insults.  Moreover, deletion of NOX2 primarily in macrophages was sufficient for mice to develop an activated CD11bhigh AM subset and accompanying pro-inflammatory sequela.   Additionally, we showed that the altered resident macrophage transcriptional profile in the absence of NOX2 is tissue-specific as these changes were not seen in resident peritoneal macrophages.  Thus, these data demonstrate that absence of NOX2 in alveolar macrophages leads to their pro-inflammatory remodeling and dysregulates alveolar homeostasis.

overall_design: Resident Peritoneal macrophages from WT and CGD mice were sorted into RPMI 1640 with 20% of FBS

first: Bhattacharya

last: Sourav

first: Yang

last: Wei

first: Bagaitkar

last: Juhi

first: Dinauer

last: Mary C


title: The leukocyte NADPH oxidase 2 (NOX2) plays a key role in pathogen killing and immunoregulation

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

overall_design: Refer to individual Series


title: Genome-wide epigenome mapping in alveolar macrophages (CD45+ Siclec F+ CD11c+) from WT (4wks and 12 wks)  and CGD (4wks and 12 wks) mice

overall_design: Alveolar macrophage subsets were isolated  from WT and CGD mice at the stated ages for ATAC seq.

first: Yanan


title: IL-15 Enhances HIV-1 infection by Promoting Differentiation and Survival of CCR5+CD4+ T cells

city: St. Louis

first: Yuhao

state: MO

address: 425 S. Euclid Ave, BJCIH 7403

department: Department of Medicine

institute: Washington University School of Medicine

summary: HIV-1 usually utilize CCR5 as the co-receptor and rarely switches to CXCR4-tropic until late stage of infection. CCR5+CD4+ T cells are the major virus-producing cells in patients as well as SIV-infected non-human primates. The differentiation of CCR5+CD4+ T cells is associated with the availability of IL-15, which increases during acute HIV-1 infection. Here, we report that CCR5 is expressed by CD4+ T cells exhibiting effector or effector memory phenotype with high expression levels of the IL-2/IL-15 receptor common beta and gamma chains. IL-15 but not IL-7 improves the survival of CCR5+CD4+ T cells, drives their expansion, and facilitates HIV-1 infection in vitro and in humanized mice. Our study suggests that IL-15 plays confounding roles in HIV-1 infection, and future studies on the IL-15-based boosting of anti-HIV-1 immunity should carefully exam the potential effects on the expansion of HIV-1 reservoirs in CCR5+CD4+ T cells.

overall_design: Human primary CD4+ T cells were purified by negative selection with MojoSort™ Human CD4 T Cell Isolation Kit (Biolegend) or EasySep™ Human CD4+ T Cell Isolation Kit (Stem Cell Technology).  Purified CD4+ T cells (106 cells/mL) were cultured in RPMI 1640 medium supplemented with 10% FCS, penicillin (100 unit/mL) and streptomycin (100 µg/mL). To generate activated cells, CD4+ T cells were stimulated with plate-bound anti-CD3 and anti-CD28 antibodies at 1μg/mL (BioLegend) for 3 days in the presence of 20 ng/mL IL-2. Stimulated CD4+ T cells were cultured with 20 ng/mL IL-7 or IL-15. Fresh medium was provided every 3 days to keep the cell densities at 1-2*106 cells/mL.  Activated blood CD4+ T cells were cultured with the presence of IL-15 for 6 days. CCR5+ and CCR5- CD4+ T cells were sorted followed by bulk RNA-Seq experiments.

first: Hongbo

last: Gao

first: Kolin

last: Clark

first: Liang

last: Shan


title: Imortalized mouse preadipocyte response to Il13 pre-treatment

city: Boston

first: Yae-Huei

last: Liou

state: MA

address: 665 Huntington Ave.

department: MET

institute: Harvard School of Public health

summary: RNA-seq analysis of Il13 pre-treated imortalized mouse pre-adipocyte.

overall_design: Differential expression of mRNA from Il13 pre-treated imortalized mouse preadipocyte, 4 samples from each groups was analyzed.

first: Chih-Hao

last: Lee


title: Cytotoxic Innate Lymphoid Cells Sense Cancer Cell-Expressed Interleukin-15 to Suppress Human and Murine Malignancies

status: Public on Apr 02 2022

city: New York

first: Christina

last: Leslie

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: Malignancy can be suppressed by the immune system. However, the classes of immunosurveillance responses and their mode of tumor sensing remain incompletely understood. Here, we show that while clear cell renal cell carcinoma (ccRCC) was infiltrated by exhaustion-phenotype CD8+ T cells which negatively correlated with patient prognosis, chromophobe RCC had abundant infiltration of granzyme A-expressing intraepithelial type 1 innate lymphoid cells (ILC1s) that positively associated with patient survival. Interleukin-15 (IL-15) promoted ILC1 granzyme A expression and cytotoxicity, and IL-15 expression in chRCC tumor tissue positively tracked with the ILC1 response. An ILC1 gene signature also predicted survival of a subset of breast cancer patients in association with IL-15 expression. Notably, ILC1s directly interacted with cancer cells, and IL-15 produced by cancer cells supported the expansion and anti-tumor function of ILC1s in a murine breast cancer model. Thus, ILC1 sensing of cancer cell IL-15 defines an immunosurveillance mechanism of epithelial malignancies.

overall_design: We conducted single cell RNA-sequencing of a single patient with advanced stage kidney cancer and chromophobe subtype.  We analyzed CD45+ cells with a focus on innate lymphoid cells, conventional NK cells, and CD8+ Exhausted cells.  These data were used to develop a gene signature of ILCs and CD8 Exhausted cells, and to inform validation experiments in larger cohorts of RCC patients.

first: Chirag

last: Krishna

middle: S

first: Ming

middle: O

first: Emily

last: Kansler


title: small RNA shorter than 15 nt in commercial dairy cow's milk

city: Montréal

first: Abderrahim

last: Benmoussa

state: Québec

address: 240 Murray Street

department: Nutrition

country: Canada

institute: Université de Montréal

type: Non-coding RNA profiling by high throughput sequencing

summary: We enlarged the usual 15-30 nt sequencing frame to 8-30 nt and discovered the existence in milk of 12-13 nt rRNA-derived small extracellular RNAs (exRNAs) previously reported in other datasets as doRNAs. We repeated the process on fractions of milk obtained by ultracentrifugation and found a specific enrichment of these unusually short rRNA between different milk fractions.

overall_design: We isolated total RNA from milk and milk fractions

first: Benmoussa

last: Abderrahim

first: Zeinab

last: Husseini

first: Jeffrey

last: HO

first: Patrick

last: Provost


title: Microarray transcriptomic profiling of Arabidopsis root stem cells within the BRL3 expression domain treated with Brassinolide (BL) [microarray]

city: Cerdanyola

first: Fidel

last: Lozano-Elena

state: Barcelona

address: Edifici CRAG - Campus UAB

department: Molecular Genetics

institute: Center for Research in Agricultural Genomics (CRAG)

summary: Brassinosteroids (BRs) are steroid hormones involved in multiple processes of plant growth and development, and the adaptation to the environment. Some of the processes regulated by BRs are meristem activity and stem cell divisions. At the core of the root stem cell niche, it is placed the quiescent center (QC), that act as a cell reservoir. QC cells only trigger their divisions when need to replenish the stem cells, for example, after a DNA damage. BR signaling is in charge of triggering these QC divisions, but the exact mechanisms of how this process is regulated is still unknown. Here, we use an interdisciplinary approach, using Arabidopsis thaliana as a model system, including molecular genetics, physiology and bioinformatics to decipher the role of BR receptors upon DNA damage regulating the QC divisions. The results uncover novel roles for the BR-receptor kinase BRL3 (BRI1-like 3) receptor in DNA damage response (DDR) in plants, by modulating the DNA repair and the cell-cycle progression. We identified candidate tissue-specific transcriptional regulator, specifically expressed in the QC cells, the RNR2A (RIBONUCLEOTIDE REDUCTASE 2A), in charge of maintaining dNTPs (deoxynucleotide triphosphates) supply during DNA synthesis that is modulated by BRL3 downstream signaling events. Considering the importance of plant stem cells and their tissues for biomass accumulation and constantly exposed to adverse environmental stresses that can cause DNA damage or cell-cycle arrest in the RAM, here we stablished the mechanism linking root meristematic activity to the DDR through the cell-specific steroid receptor kinase BRL3.

overall_design: One factor experimental design (BL-treated vs. Control). Primary root tips of 6-day-old transgenic Arabidopsis seedlings expressing the reporter pBRL3:nlsYFP were treated with 10 nM of BL for 2h (in liquid media). Then the roots were submitted to protoplasting and the cells expressing YFP (BRL3 expression domain) selected using Fluorescence- Activated Cell Sorting (FACS). mRNA from selected cells in BL-treated or control conditions was extracted, converted to cDNA and hybridized to Affymetrix ATH1 GeneChip.

first: Ainoa

last: Planas-Riverola

first: Mary

middle: P

last: Gonzalez-Garcia

first: Ana

middle: I

last: Caño-Delgado


title: Transcriptomic profiling of Arabidopsis primary root tips of brl3 mutant exposed to DNA damaging agent zeocin [RNA-seq]

overall_design: A two factor experimental design (Genotype and treatment). Primary root tips of 6-day-old Arabidopsis seedlings of Col-0 (WT) and brl3 mutant (SALK_006024C), in control conditions and treated with 2h 10µm zeocin. Three biological replicates per genotype and condition. A total of 12 samples, whose libraries were sequenced twice.


title: Changes in exosomal miRNA from macrophage under silica exposure

city: Changsha

first: Zhiyuan

last: Niu

state: Hunan

address: 172 Tongzipo Road

department: School of Basic Medical Science

institute: Central south university

summary: In this study, we isolated the exosomes derived from macrophage treated with or withnot silica for 48h, and  identified a subset of differentially expressed miRNAs enriched in the exosomes compared with blank control

overall_design:
Small RNA-Seq data of RNA extracted from exosomes from macrophage treated with silica or not, each group has 3 independent repetition.

Submitter states that raw data files are lost.

first: Wang

last: Lei

first: Niu

last: Zhiyuan

first: Hu

last: Yongbin


title: Human prostate cancer cells (VCaP and AIVCaP): siAR alone (single siRNA) vs. siAR plus OPRK1 (combo-siRNA)

city: Kyoto

first: Yuki

last: Makino

address: 54 Shogoinkawahara-cho, Sakyo-ku

department: Urology

country: Japan

institute: Kyoto University Graduate School of Medicine

summary:
Through comparative genomics using PDX models of androgen-dependent (AD) and castration-resistant (CR) tumors, we identify opioid receptor kappa 1 (OPRK1) as being associated with castration-resistance. Loss of OPRK1 function delays castration-resistance and inhibits castration-resistant growth of prostate cancer cells in culture and in vivo, suggesting OPRK1 as a therapeutic target.
To gain insight with regard to biological function of OPRK1 under androgen-depleted condition, we set up two distinct comparisons using VCaP and AIVCaP cells.  AIVCaP is an androgen-independent subline of VCaP which we established. VCaP or AIVCaP were treated with siRNA for AR plus siRNA for OPRK1 (combo-siRNA) or siRNA for AR alone (single siRNA) (n = 4 each), and then expression profile gained from microarray analysis of the respective cell line treated with combo-siRNA was compared with that of cells treated with single siRNA.

overall_design:
Two cell lines, two-condition experiment: VCaP/AIVCaP treated with siAR alone (single siRNA) vs. siAR plus siOPRK1 (combo-siRNA). Biological replicates: 4 control (single siRNA) replicates, 4 combo-siRNA replicates.
*** For VCaP samples, the original raw files have been lost. ***

first: Takashi

last: Kobayashi


title: Genomic, Transcriptomic, and Metabolomic Profiles of iPSC-derived Dopaminergic Neurons from Clinically Discordant Brothers with Identical PRKN Deletions

city: Miami

first: Anthony

last: Griswold

state: FL

address: 1501 NW 10th Ave, BRB 318

institute: University of Miami

summary: We have previously reported on two brothers, PM and SM, that carry identical compound heterozygous PRKN mutations but show significantly different clinical Parkinson disease (PD) phenotypes. The occurrence of juvenile cases demonstrates that PD is not necessarily an age-associated disease; indeed, evidence is accumulating that there is a developmental component to PD pathogenesis. The divergence in the clinical presentations between PM and SM lead us to hypothesize that an additional genetic modifier(s) may influence the risk conferred by PRKN. To test our hypothesis, we differentiated human induced pluripotent stem cells (iPSCs) from SM and PM into mitotically active mesencephalic neural precursor cells (floor plate cells) and early postmitotic dopaminergic neurons, and performed whole exome sequencing, and transcriptomic  and metabolomics analysis. Our transcriptomic analysis revealed a significant down regulation of three known neurodevelopmentally relevant cell adhesion molecules in PM compared to SM cultures on days 11 and 25 of differentiation, CNTN4, CNTN6, and CHL1. In addition, several HLA genes, known to play a role in neurodevelopment, independent of their well-established function in immunity, were differentially regulated in developing dopamine neurons. EN2, a transcription factor crucial for mesencephalic dopamine neuron development, was also differentially regulated. We further report on a single nucleotide polymorphism in DBH, a gene encoding an enzyme involved in dopamine metabolism, as well as differential expression. Our metabolomics data reveal differential biosynthesis of tyrosine, the precursor for dopamine synthesis. Lastly, our whole exome sequencing revealed the homozygous deletion in SM of two glutathione S-transferases, GSTM1 and GSTT1, which encode enzymes involved in glutathione (GSH) metabolism. Moreover, our RNA sequencing analysis shows a lack of expression of these two enzymes in SM cells and our metabolomics analysis indicates differences in GSH homeostasis between SM and PM neurons. This finding builds on previous evidence of glutathione dysregulation being implicated in PD pathogenesis. Our data support our hypothesis that additional genetic differences at least partially underlie the differential clinical PD presentation between PM and SM.

overall_design: Trancriptomic data from iPSC-derived day 11 mesencephalic neural precursor cells and day 25 postmitotic dopaminergic neurons

first: Holly

middle: N

last: Cukier

first: Hyunjin

last: Kim

middle: J

first: Simona

middle: G

last: Codreanu

first: Lisa

last: Prince

first: Stacy

last: Sherrod

first: John

last: McLean

first: Derek

last: Dykxhoorn

first: Peter

last: Hedera

first: Aaron

middle: B

last: Bowman

first: M

last: Neely


title: Mechanism for Human Adipose Stem Cell-Derived Exosomes' Therapeutic Effect on Chronic Liver Fibrosis

city: Chengdu

first: zilong

last: zhang

state: Sichuan

address: Western Section 2, 1st Ring Rd

department: Hepatobiliary-Pancreatic Surgery Center, Cell Transplantation Cente

institute: Sichuan Academy of Medical Sciences & Sichuan Provincial People’s Hospital

summary: The goal of this study was to understand the effect of  human adipose stem cell and its derived exosomes on  mouse chronic liver fibrosis. After eight weeks of intraperitoneal injection of CCl4, we treated 200μl PBS, normal human adipose stem cell (1×106/200μl PBS), human adipose stem cell-derived exosomes(250μg/200μl PBS) once a week for 4 weeks. Then the livers were collected and isolated RNA for RNA-sequencing to explore alterations in mRNA expression between different treatments

overall_design: To screen and identify the candidate mRNAs and pathways by which hADMSCs-Exosomes play the antifibrotic role in CCL4-induced fibrosis, mRNA profiles were used to profile the simultaneously upregulated or downregulated mRNAs and pathways between different treatments.

first: Zilong

last: Zhang

first: Ying

last: Shi

first: Xiaolun

last: Huang


title: G Protein-coupled Receptor 91 (GPR91) Indicates Prognosis and Enhances Chemoresistance by Regulating DNA Damage Pathway and ERK Signaling Pathways in Neuroblastoma

city: Shanghai

first: Kai

last: Chen

address: NO.1665, Kongjiang Road

institute: Xinhua hospital

summary: This study first reveals that GPR91 is a potential oncogene in neuroblastoma, which is significantly correlated with poor prognosis and significantly represses  the sensitivity to chemotherapeutic drugs including doxorubicin and cisplatin of NB cells. It is regulated by GPR91 though the DNA damage pathway and the ERK signaling pathway.

overall_design: GPR91 knockout was performed in neuroblastoma cell line SK-N-BE(2)

first: Wang

last: Yi

first: Cai

last: Yuanxia

first: Chen

last: Kai


title: Specification of fetal liver endothelial progenitors to functional zonated adult sinusoids requires c-Maf induction [development stage]

first: Franco

last: Izzo

state: NY

address: 1470 Madison Avenue

department: Oncological Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: Endothelial cell heterogeneity shapes the unique attributes of organ-specific blood vessels; however, how intra-organ vascular cell diversity is established remains unsolved. Liver vascular network is patterned by sinusoidal and hepatocyte co-zonation, however how intra-liver vessels acquire their hierarchical specialized functions is unknown. Here, we resolve the heterogeneity of hepatic vascular cells during development through functional and single-cell RNA sequencing. We show that acquisition of sinusoidal endothelial cell identity is initiated during early development and is completed postnatally, originating from a pool of undifferentiated vascular progenitors at E12. Notably, we identify the peri-natal induction of the transcription factor c-Maf as a critical switch for sinusoidal identity determination. Endothelium-restricted deletion of c-Maf disrupts liver sinusoidal development, aberrantly expands postnatal liver hematopoiesis, promotes excessive postnatal sinusoidal proliferation, and aggravates liver pro-fibrotic sensitivity to chemical insult. Notably, c-Maf overexpression in generic differentiated endothelial cells switches on a liver sinusoidal transcriptional zonation program that maintains hepatocyte function. Therefore, c-Maf represents an inducible intra-organotypic and niche-responsive molecular determinant of sinusoidal cell identity and lays the foundation for designing strategies to initiate vasculature-driven liver repair.

overall_design: Single cell RNA sequencing of liver endothelial cells along developmental time points E12, E14, E16, E18, P2, P8, P15 and P30.

first: Jesus

last: Gomez Salinero

first: Shahin

last: Rafii


title: Effect of vitrification temperature and cryoprotectant concentrations on the mRNA transcriptome of bovine immature oocytes

city: LuoYang

first: Fan

state: HeNan

address: No. 263 Kaiyuan Road, Luolong District

institute: HeNan university of science and technolgy

summary: The present study mainly aimed to investigate the effect of vitrification temperature (VT) and cryoprotective agent concentrations (CPAs) on the mRNA transcriptome of bovine immature oocytes (BIOs). Cumulus oocyte complexes (COCs) were randomly divided into the following five groups: fresh oocytes (control), oocytes vitrified in liquid helium (LHe; -269℃) with 5.6 M CPAs (LHe 5.6 M), oocytes vitrified in LHe with 6.6 M CPAs (LHe 6.6 M), oocytes vitrified in liquid nitrogen (LN; -196℃) with 5.6 M CPAs (LN 5.6 M), and oocytes vitrified in LN with 6.6 M CPAs (LN 6.6 M). mRNA transcriptomes of each sample were analyzed by Smart-seq4, and the diﬀerentially expressed genes (DGEs) were detected by edgeR (p≤0.05; fold-change≥2). Compared with the control group, 505 DGEs were detected with 342 up-regulated and 163 down-regulated genes in LHe 5.6 M; 609 DGEs were detected with 493 up-regulated and 116 down-regulated gene in LHe 6.6 M; 218 DGEs were determined with 101 up-regulated and 117 down-regulated genes in LN 5.6 M; and 221 DGEs were detected with 104 up-regulated and 117 down-regulated genes in LN 6.6 M. LHe vitrification affected the mRNA transcriptome of vitrified BIOs mainly by up-regulating gene expression. Reduced CPAs (5.6 M) decreased the effect of vitrification on mRNA transcriptome when LHe vitrification was used. Among all the DGEs closely related to bovine immature oocytes, the genes possibly related to VT were ND2, MPV17L2, PIF1, LPIN1, IMP3, BRD1, DCTN3, DERA, ATP7B, NEK5, HVCN1 and MARK2. The gene that may be associated with CPAs is CC2D2A. Genes that may be affected by both VT and CPAs were PGK1, SLC7A3, FITM2, NPM3, ISCU, CWC15 and PSAP. DERA was up-regulated when reduced VT (-269 °C) was used, which may have contributed to the recovery and stress prevention of vitrified oocyte.

overall_design: Examination the effect of vitrification temperature and cryoprotectant concentrations on the mRNA transcriptome of bovine immature oocytes

first: Zhi-Yang

first: Meng-Dan

last: Cai

first: Xiao-Xia

last: Li

first: Ying-Hua

first: Lei

last: Ying

first: Xue-LI

last: Yu


title: Rpd3 regulates single-copy origins independently of the rDNA array by opposing origin stimulation by Fkh1 [ChIP-seq]

status: Public on Apr 01 2022

city: Los Angeles

first: Yiwei

last: He

state: CA

address: 1050 Childs Way RRI 203

department: Molecular Biology

institute: University of Southern California

summary: The replication of eukaryotic genomes is highly regulated to ensure faithful transmission of all genetic information through cell divisions. In addition to stringent control of origin initiation by cell cycle controls and DNA damage checkpoints, spatial and temporal control of origins serves to stage and balance replication of different genomic regions, with potential implications for development and genome stability. Replication of highly repetitive sequences creates stressful competition between genomic regions for sufficient replication resources. Here, we examined histone deacetylases Rpd3 and Sir2 in balancing replication between unique sequences and the multi-copy ribosomal DNA gene cluster(s), which has emerged as an evolutionarily conserved node of genomic instability.  We elucidate Rpd3's mechanism of origin regulation, which is distinct and independent of Sir2.

overall_design: exp4: sample 25-30

first: Jared

last: Peace

first: Oscar

last: Aparicio


title: Gene expression profile of hematopoietic stem cells from mutCALR transgenice mice

city: Vienna

first: Christoph

last: Bock

address: Lazarettgasse 14

country: Austria

institute: CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences

summary: Transcriptome data of HSCs (Hematopoietic stem cells - LSKs) sorted from the bone marrow of vavCRE (wildtype) and CALRdel52 fl/fl; vavCre (mutCALR homozygous) mice

overall_design: 200 cells/sample sorted into lysis buffer of a 96 well plate and full length mRNA-sequencing (SMART-seq) was performed. Reads from the same mouse were pooled together. Three mice/genotype were used for the experiment.

first: Robert

last: Kralovics


title: Chromosome remodelling by SMC/Condensin in B. subtilis is regulated by Soj/ParA during growth and sporulation

city: Lausanne

first: Anna

last: Anchimiuk

state: Vaud

address: UNIL-Sorge District

department: Department of Fundamental Microbiology

country: Switzerland

institute: University of Lausanne

summary: SMC complexes, loaded at ParB-parS sites, are key mediators of chromosome organization in bacteria. ParA/Soj proteins interact with ParB/Spo0J in a pathway involving ATP-dependent dimerization and DNA binding, leading to chromosome segregation and SMC loading. In Bacillus subtilis, ParA/Soj also regulates DNA replication initiation, and along with ParB/Spo0J is involved in cell cycle changes during endospore formation. The first morphological stage in sporulation is the formation of an elongated chromosome structure called an axial filament. We now show that a major redistribution of SMC complexes drives axial filament formation, in a process regulated by ParA/Soj. Unexpectedly, this regulation is dependent on monomeric forms of ParA/Soj that cannot bind DNA or hydrolyse ATP. These results reveal a new role for ParA/Soj proteins in the regulation of SMC dynamics in bacteria, and yet further complexity in the web of interactions involving chromosome replication, segregation, and organization, controlled by ParAB and SMC.

overall_design: ChIP-seq against ScpB of Bacillus subtilis cells during sporulation

first: David

last: Roberts

first: Stephan

last: Gruber

first: Jeff

last: Errington


title: RNA sequence for mammary gland of ICR mice at pregnant day 17 with supplementation of methionine (Met) alone or with methionyl-methionine (Met-Met) dipeptide.

city: Hangzhou

first: Qiong

last: Chen

state: Zhejiang

address: Yuhangtang Road 866

department: animal science

institute: Zhejiang University

summary: Using RNA-seq to explore the mechanisms underlysing the effects of methionyl-methionine dipeptide (Met-Met) or free methionine (Met) supplementation in Met-restricted mice during pregnancy on mammogenesis and lactation.

overall_design:
In the Met group, pregnant mice were fed a methionine-deficient diet with i.p. injection of 35% methionine contained in the control diet. The Met-Met group was treated as the Met group, except that 25% of injected methionine was replaced with methionyl-methionine dipeptide.

Please note that raw data was also analyzed for the long-noncoding RNAs (Annotated_lncRNA_FPKM.xls, Novel_lncRNA_FPKM.xls).

first: Hongyun

last: Liu


title: Primary hepatocyte transcriptional response to Pink1 over-expression by adenovirus

first: Yae-Huei

last: Liou

summary: RNA-seq analysis of Ad-LacZ, Ad-Pink1 infected primary hepatocyte.

overall_design: Differential expression of mRNA from Ad-LacZ, Pink1 infected primary hepatocyte. 4 samples from each groups was analyzed.

first: Chih-Hao

last: Lee


title: IL-17A-producing gdT cells promote muscle regeneration in a microbiota-dependent manner

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Subsequent to acute injury, skeletal muscle undergoes a stereotypic regenerative process that re-establishes homeostasis. Various types of innate and adaptive immunocytes exert positive or negative influences at specific stages along the course of muscle regeneration. We describe an unanticipated role for gdT cells in promoting healthy tissue recovery after injection of cardiotoxin into murine hindlimb muscle. Within a few days of injury, IL-17A-producing gdT cells displaying primarily Vg6+ antigen receptors accumulated at the wound site. Punctual ablation experiments showed that these cells boosted early inflammatory events, notably recruitment of neutrophils; fostered the proliferation of muscle stem and progenitor cells; and thereby promoted tissue regeneration. Supplementation of mice harboring low numbers of IL-17A+ gdT cells with recombinant IL-17A largely reversed their inflammatory and reparative defects. Unexpectedly, the accumulation and influences of gdT cells in this experimental context were microbiota-dependent, unveiling an orthogonal perspective on the treatment of skeletal muscle pathologies such as catastrophic wounds, wasting, muscular dystrophies and myositides.

overall_design: For sorted Vg6+ gdT cells, cells isolated from the colon and from injured skeletal muscle and these groups were analyzed relative to one another. For analysis of trizol lysed skeletal muscle, a time-course of wild-type control and gdT cell-depleted samples was collected. Analysis was between the gdT cell depleted sample relative to the respective wild-type controls at each time-point, additionally we examined how modules of genes changed over the time-course (and how this differed between genotypes). For analysis of the impact of IL-17 on muscle regeneration, we analysed samples from rIL-17 treated mice against PBS treated controls at a specific time-point (7 days after injury). For sorted muscle satellite cells, samples isolated from gdT cell depleted mice were compared against those isolated from wild-type controls mice. All cell types or treatment conditions are represented by 2-3 independent bioloigcal replicates

first: Alexander

last: Mann

first: Bola

last: Hanna

first: Christophe

last: Benoist

first: Diane

last: Mathis


title: Expression data from plasma exosomal microRNA of rats with remote ischemic conditioning and normal controls

city: Jinan

first: Xinhui

last: Fan

state: Shandong Province

address: 107 Wenhuaxi Road

institute: Qilu Hospital of Shandong University

summary:
Remote ischemic conditioning (RIC) is a safely therapeutic strategy for a variety of ischemic diseases, with efficiency comparable to the classic in-situ ischemic methods. Recent evidence has shown that RIC could alter the content of circulating exosomes. microRNAs involves in numerous functionally different biological and physiological processes. The aim of this study is to identify the differentially expressed exosomal microRNAs in rat plasma with RIC and to further explore the functions in ischemic heart diseases.
Five RIC rats and 5 control rats were enrolled in this study. We used microarray analysis to identify miRNA expression in their plasma exosomes.

overall_design: A total of 5 rats with RIC and 5 healthy controls participated in the study. Wistar rats were subjected to four cycles of remote ischemia, and each cycle consisted of 5-minute ischemia and 5-minute reperfusion. We collected venous blood (10 ml) from each participant using an EDTA-anticoagulated tube. Exosomes were isolated via differential centrifugation.

first: Yuguo


title: Real-time quantitative PCR analysis of human visceral adipose tissue and whole blood

city: Durban

first: Christen

last: Erasmus

state: KwaZulu-Natal

address: 719 Umbilo Road, Durban

department: Medical Biochemistry

country: South Africa

institute: University of KwaZulu-Natal

summary: Adipose tissue and whole blood samples were collected from human pregnant females.

overall_design: qPCR gene expression profiling for ADIPOQ, LEP, LEPR, and FTO. GAPDH served as the endogenous control to normalize mRNA expression.

first: C


title: Phospholipid Metabolites of the Gut Microbiota Promote Hypoxia-induced Intestinal Injury via CD1d-dependent gd T Cells

first: Yuyu

last: Li

address: Xiaoying

summary: Phospholipid metabolites PE and PC are presented by intestinal epithelial CD1d to induce the proliferation of IL-17A-producing γδ T cells, which aggravates intestinal injury.

overall_design: The 5' ends of the primers were tagged with specific barcods per sample and sequencing universal primers.PCR amplification was performed in a total volume of 25 μL reaction mixture containing 25 ng of template DNA, 12.5 μL PCR Premix, 2.5 μL of each primer, and PCR-grade water to adjust the volume. The PCR conditions to amplify the prokaryotic 16S fragments consisted of an initial denaturation at 98 ℃ for 30 seconds; 32cycles of denaturation at 98 ℃ for 10 seconds, annealing at 54℃ for 30 seconds, and extension at 72 ℃ for 45 seconds; and then final extension at 72 ℃ for 10 minutes. The PCR products were confirmed with 2% agarose gel electrophoresis. Throughout the DNA extraction process, ultrapure water, instead of a sample solution, was used to exclude the possibility of false-positive PCR results as a negative control. The PCR products were purifyied by AMPure XT beads (Beckman Coulter Genomics, Danvers, MA, USA) and quantified by Qubit( Invitrogen, USA). The amplicon pools were prepared for sequencing and the size and quantity of the amplicon library were assessed on Agilent 2100 Bioanalyzer (Agilent, USA) and with the Library Quantification Kit for Illumina (Kapa Biosciences, Woburn, MA, USA), respectively. The libraries were sequenced on NovaSeq PE250 platform.

first: Lanjuan

first: Hongyan

last: Diao


title: RNA-lncRNA sequencing for human nevus sebaceous（NS) and normal scalp tissues

city: NANJING

first: Xianhong

last: Yang

address: 12 JIANGWANGMIAO ROAD

department: dermatopathology

institute: Hospital of Skin Diseases, Chinese Academy of Medical Sciences and Peking Union Medical College

summary: To identify NS- associated mRNA and lncRNA profiles and predict their potential roles in the development of the folliculo-sebaceous-apocrine unit and adnexal tumorigenesis.RNA-seq was used to identify NS-associated genes and lncRNAs.

overall_design: four paired nevus sebaceous and normal skin tissues were obtained from different subjects' scalp.mRNA and lncRNA profiles were examed and evaluated.

first: Yiqun

last: Jiang

first: Jianfang

last: Sun

first: Rui

last: Qiao


title: Pegvisomant-treated mouse prostate epithelium renal grafts

city: Madison

first: Paul

last: Marker

state: WI

address: 600 Highland Avenue

institute: University of Wisconsin Madison

summary: PTEN-CaP2 mouse prostate cancer cells were grafted under the kidney capsule of immunocompromised mice. After three weeks, mice were treated with 100 mg/kg pegvisomant (provided by Pfizer) or PBS vehicle 3X weekly for three weeks. Grafts were harvested three days after final treatment, flash frozen, and total RNA was extracted for sequencing.

overall_design: 6 samples. Three biological replicates each of vehicle- and drug-treated

first: Chris

last: Unterberger

first: Sean

last: McIlwain

first: Philippos

last: Tsourkas


title: A Developmentally Prometastatic Niche in Neonatal Liver to Hepatoblastoma mediated by Cxcl1/Cxcr2 Axis

city: Memphis

first: Liqin

last: Zhu

state: TN

address: 262 Danny Thomas Pl

department: Department of Pharmacy and Pharmaceutical Sciences

institute: St. Jude Children’s Research Hospital

summary: We find that various HB cell lines including HepG2 cells are consistently and considerably more tumorigenic and metastatic in the P5Tx model than in the P60Tx models. Sc-RNAseq of the P5Tx and P60Tx HepG2 models reveals that the P5Tx tumor is more hypoxic and has more activated hepatic stellate cells (aHSCs) in the tumor-surrounding liver which express significantly higher levels of Cxcl1 than those from the P60Tx model. We find these differences are developmentally present in the normal P5 and P60 liver. We show that Cxcl1/Cxcr2 axis mediates HB cell migration and is critical to HB cell survival under hypoxia. Treating HepG2 P60Tx model with recombinant CXCL1 protein induces multifocal intrahepatic and pulmonary metastasis and CXCR2 knockout in HepG2 cells abolishes their metastatic potential in the P5Tx model. Lastly, we show that in metastatic HB patient tumors there is a similar larger population of aHSCs in the tumor-surrounding liver than the localized tumors, and tumor hypoxia is significantly associated with HB patient prognosis.

overall_design: Investigation of influence of CXCR2 knock-out or hypoxia on gene expression pattern in HepG2 or HB214 PDX Hepatoblastoma cells.

first: Li


title: Small RNA profiling of differentiated and de-differentiated vascular smooth muscle cell

city: Pittsburgh

first: Delphine

last: Gomez

state: PA

address: 200 Lothrop St

department: Department of Medicine, Division of Cardiology

institute: University of Pittsburgh

summary: We report the application of small RNA sequencing for high-throughput profiling of small RNA under 75 bp in vascular smooth muscle cell. By a reading depth of 30M and single stranded sequencing, we generated the small RNA signature on differentiated and de-differentiated vascular smooth muscle cell induced by PDGF-BB and H3K4me2 editing. We found that PDGF-BB and H3K4me2 editing induced de-differentiation modulated miRNA profile significantly, which was demonstrated at least in part responsible for modulated vascular smooth muscle cell phenotype.

overall_design: Profiling of differentiated and PDGF-BB and H3K4me2 edited de-differentiated vascular smooth muscle cell

first: Mingyuan

last: Du

first: Cristina

last: Espinosa

first: Mingjun

last: Liu

first: Sidney

last: Mahan

first: Adam

last: Handen

first: Stephen

middle: Y

last: Chan


title: Long-Term Hyperandrogenemia and/or Western-Style Diet Treatment Impairs Rhesus Macaque Preimplantation Embryo Development

city: Portland

first: Brett

last: Davis

state: Oregon

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

summary: Long-term WSD consumption reduces the capacity of fertilized oocytes to develop into blastocysts and that the addition of T further impacts gene expression and embryogenesis.

overall_design: Pre-pubertal female rhesus macaques received either a standard control (C) diet, testosterone (T) implants that increased circulating T to PCOS levels, an obesogenic Western-style diet (WSD), or both (T+WSD). After 5-6 years of treatment, the females underwent metabolic assessments and controlled ovarian stimulations to induce development of multiple follicles. Both follicular fluid (FF) and oocytes were collected, with FF being analyzed for steroids and cytokines and oocytes undergoing in vitro fertilization (IVF).

first: Sweta

last: Ravisankar

first: Melinda

last: Murphy

first: Nash

last: Redmayne-Titley

first: Fangzhou

last: Luo

first: Diana

last: Takahashi

first: Jon

last: Hennebold

first: Shawn

middle: L

last: Chavez


title: RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history

city: Cologne

first: Achim

last: Tresch

state: North Rhine-Westphalia

address: Paul-Schallueck-Str. 10

department: Institute of Medical Statistics and Computational Biology

country: Germany

institute: University of Cologne

summary: Our work sheds light on the metabolism of RNA transcripts derived from genomic Alu repeats. Since it is unclear whether Alu elements are transcribed mainly by RNA polymerase II or III, we conducted a transcription shutoff experiment and metabolic RNA labeling. We find that Alu transcripts are as stable as mRNAs and originate in part from RNA polymerase II. Furthermore, we use the de Bruijn graph of all Alu sequences to discover sequence features that match transcription factor binding motifs.

overall_design: Differential expression analysis with DESeq2 of various RNA types (Alu transcripts, canonical transcripts, tRNA, mtRNA) under RNA polymerase II inhibition by alpha-amanitin using paired-end TT-seq. Alpha-amanitin and water control with two replicates each, labeled and total fraction.

first: Till

last: Baar

first: Sebastian

last: Dümcke

first: Saskia

last: Gressel

first: Björn

last: Schwalb

first: Alexander

last: Dilthey

first: Patrick

last: Cramer


title: Digital Spatial Profiling Reveals Functional Shift of Enterochromaffin Cell in Patients with Ulcerative Colitis

first: Dongping

last: Lyu

address: No. 44, Wenhuaxi Road

institute: Shandong University

summary: As a major component of the enteroendocrine system, enterochromaffin (EC) cells play a key role in ulcerative colitis (UC). However, the scarcity of EC cells has limited the investigation of their function. In this study, we applied digital spatial profiling to acquire transcriptomic data for EC cells and other epithelial cells from colonoscopic biopsy samples from 8 UC patients and 7 healthy controls. Differential expression analysis, gene set enrichment analysis, and weighted gene co-expression network analysis were performed to identify differentially expressed genes and pathways and co-expression networks. Results were validated using an online dataset obtained by single-cell RNA sequencing, along with immunofluorescence staining and qRT-PCR. In healthy participants, 10 genes were significantly enriched in EC cells, functionally concentrated in protein and bioamine synthesis. A co-expression network containing 17 hub genes, including TPH1, CHGA, and GCLC, was identified in EC cells. In UC patients, EC cells gained increased capacity for protein synthesis, along with novel immunological functions such as antigen processing and presentation, whereas chemical sensation was down-regulated. The specific expression of CHGB and RGS2 in EC cells was confirmed by immunofluorescence staining. Our results illuminate the transcriptional signatures of EC cells in the human colon. EC cells’ newly observed functional shift from sensation to secretion and immunity indicate their pivotal role in UC.

overall_design: Colonoscopic biopsies from 12 UC patients and 11 healthy subjects underwent digital spatial profiling (DSP) to acquire the transcriptomic profile of EC cell and epithelium.

first: Guanjun

last: Kou

first: Shiyang

last: Li

first: Lixiang

first: Bing

first: Ruchen

last: Zhou

first: Xiaoxiao

last: Yang

first: Wenyu

last: Tian

first: Yanqing

first: Xiuli

last: Zuo


title: Methionine starvation caused reprogrammed metabolism in Streptococcus pneumoniae

city: Beijing

first: Jing-Ren

last: Zhang

state: Beijing

address: Room 312, Renhuan Building, Tsinghua University

department: School of Medicine

institute: Tsinghua University

summary: In our study, deletion of methionine synthesis gene metE (SPD_0510) impaired the growth of Streptococcus  pneumoniae strain D39 significantly when bacteria were cultured in chemically defined medium with a low concentration of methionine. Bacteria undergo methionine starvation in this condition. We  aimed to know how S. pneumoniae responses to methionine starvation, particularly at the transcriptional level. RNA-seq results show that 804 genes (41.2 % of whole genome)  were differentially expressed under methionine starvation. Among them, 258 genes (32.1 %) are related to cell metabolism, with 75 genes involved in sugar and carbon metabolism, 88 genes for synthesis of metabolic products and 95 genes for uptake of amino acids and sugars. Combined with other experiments data, this showed the reprogrammed metabolism in S. pneumoniae under methionine starvation.

overall_design: Transcriptome comparison of D39 WT and metEmutant in CDM with 1 µg/ml methionine. It was done by deep sequencing, using an Illumina instrument with 150 nt paired-end reads.

first: Chengwang


title: High-throughput sequencing of in vitro fecal fermentation samples

first: zuorui

last: xie

address: Zhejiang Gongshang University

institute: ZFM

summary: We report the use of high-throughput sequencing technology to detect the microbial composition and abundance of human feces after in vitro co-fermentation with citrus peel flavonoid extracts. The genomic DNA was obtained by the QIAamp PowerFecal DNA Kit. Then, the DNA samples were sent to Biomarker Bio-Tech (Beijing, China) for V3-V4 region of the 16S rDNA gene high-throughput sequencing with an Illumina MiSeq platform. DNA samples were sequenced using primers 338F (forward primer sequence ACTCCTACGGGAGGCAGCAG)-806R (reverse primer sequence GGACTACHVGGGTWTCTAAT). A total of 8,816,250 pairs of Reads were obtained from the 112 samples sequenced, and 8,721,112 Clean Reads were generated from the double-ended Reads after quality control and splicing. The sequencing analyses were carried out using the SILVA database as a reference for the assignation of operational taxonomic units (OTUs) with 97% of identity.

overall_design:
The genomic DNA was obtained by the QIAamp PowerFecal DNA Kit. Then, the DNA samples were sent to Biomarker Bio-Tech (Beijing, China) for V3-V4 region of the 16S rDNA gene high-throughput sequencing with an Illumina MiSeq platform. DNA samples were sequenced using primers 338F (forward primer sequence ACTCCTACGGGAGGCAGCAG)-806R (reverse primer sequence GGACTACHVGGGTWTCTAAT). A total of 8,816,250 pairs of Reads were obtained from the 112 samples sequenced, and 8,721,112 Clean Reads were generated from the double-ended Reads after quality control and splicing. The sequencing analyses were carried out using the SILVA database as a reference for the assignation of operational taxonomic units (OTUs) with 97% of identity.
Examination of 16 different microbial composition and abundance differences in fecal fermentation samples.

first: Qing

last: Gu

first: Ping

first: Qingqing

first: Xia

last: Meng


title: Transcriptome-wide N6-methyladenine methylation in granulosa cells of women with decreased ovarian reserve

city: Wuhan

first: Chang

last: Liu

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: The results revealed the transcriptional significance of m6A modifications and provide potential therapeutic targets to promote fertility reservation for aging women.

overall_design: Granulosa cells from three older women and three younger women were collected and used for RNA sequeicing.

first: Liu

last: Chang

first: Linshuang

first: Bo

first: Lan

last: Wang


title: RNA-seq analysis of wild-type and blmp-1(s71) young adult mutant

city: Taipei

first: Yi-Chun

last: Wu

address: No. 1 Sec. 4 Roosevelt Road

department: Institute of Molecular and Cellular Biology

country: Taiwan

institute: National Taiwan University

summary: We performed RNA-seq analysis of wild-type and blmp-1(s71) mutant at the young adult stage, to identify genes regulated by BLMP-1.

overall_design: Three WT and three blmp-1(s71) mutant biological replicates were analyzed.

first: Yun-Zhe

first: Isheng

last: Tsai

first: Min

last: Lu


title: Probiotic consortia improve anti-viral immunity to SARS-CoV-2 in Ferrets [RNA-seq]

first: Bryan

last: Zabel

state: wi

address: 3329 Agriculture Dr

department: GEM

institute: International Flavors & Fragrances Inc

summary:
Probiotics have been suggested as one solution to counter detrimental health effects by SARS-CoV-2, however, data so far is scarce.  We tested the effect of two probiotic consortia, OL-1 and OL-2, against SARS-CoV2 in ferrets and assessed their effect on cytokine production and transcriptome in a human monocyte- derived macrophage (Mf) and dendritic cell (DC) model.
The results showed that the consortia significantly reduced the viral load, modulated immune response, and regulated viral receptor expression in ferrets compared to placebo. In human Mf and DC model, OL-1 and OL-2 induced cytokine production and genes and related to SARS-CoV-2 anti-viral immunity.
The study results indicate that probiotic stimulation of the ferret immune system leads to improved anti-viral immunity against SARS-COV-2 and that critical genes and cytokines for anti-SARS-CoV-2 immunity are stimulated in human immune cells in vitro. The effect of the consortia against SARS-CoV-2 warrants further investigations in human clinical trials.

overall_design: Human isolated dentritic cells and macrophages (40 samples) exposed to probiotic bacteria and measure expression differences using biospyder probe based kit.

first: Markus

last: Lehtinen

first: Sanna

last: Makela

first: Sinikka

last: Latvala


title: Probiotic consortia improve anti-viral immunity to SARS-CoV-2 in Ferrets [RT-PCR]

overall_design: Two trials of ferrets eaching testing for specific genes of interest in lung and duodenum tissues. Each plate contains a positive control (prepared from stimulated ferret PBMC cells) in duplicate wells, an NTC in duplicate wells and all test samples in duplicate wells. Study 1 took samples at D0 (pre-infection) day 5 and 21. Study 2 took samples at Day 5 and day 10. 5 Ferrets for each group tested.

first: Derek

last: Nedveck

first: Ritesh

last: Kumar


title: Single-cell Sequencing Analysis of Head and Neck Squamous Cell Carcinoma

city: Tianjin

first: xuan

last: zhou

address: West huanhu road

institute: Tianjin Medical University Cancer Institute and Hospital

summary: To investigate the mechanism of cetuximab resistance in head and neck squamous cell carcinoma (HNSCC), we performed single-cell RNA sequencing  analysis  in biopsy from two HNSCC patients before and after cetuximab treatment.

overall_design: Fresh HNSCC tissues were dissociated with the Gentle MACS Dissociator (Miltenyi Biotec) according to the manufacturer’s instructions. Next, single cells were counted using automated cell counter and adjusted to the concentration of 1000 cells/μL and we retained single-cell transcriptomes for 13,903 cells after initial quality controls. Cellular suspensions were loaded on a 10X Genomics GemCode Single-cell instrument that generates single-cell Gel Bead-In-EMlusion (GEMs). Cells were lysed, and the RNAs were reverse-transcribed into cDNAs. Libraries were generated from the cDNAs with Chromium Next GEM Single Cell 3’ Reagent Kits v3.1. Finally, the cDNA libraries were sequenced using the nova 6000 Sequencing System (Illumina).

first: Xuan

last: Zhou


title: Probiotic consortia improve anti-viral immunity to SARS-CoV-2 in Ferrets

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

sample_organism:
Homo sapiens
Mustela putorius furo

platform_organism:
Homo sapiens
Mustela putorius furo

overall_design: Refer to individual Series


title: Whole-genome mapping of ETV6-RUNX1 in pre-B lymphoblast models

city: Rennes

first: Gilles

last: Salbert

address: 263 Av. Gal. Leclerc

department: IGDR UMR6290

country: France

institute: University Rennes 1

summary: Genome binding/occupancy profiling of ETS Variant Transcription Factor 6- Runt Related Transcription Factor 1 fusion protein (ETV6-RUNX1) in REH cells by high throughput sequencing. ETV6-RUNX1 is expressed in pediatric t(12;21) ETV6-RUNX1 B cell precursor acute lymphoblastic leukemia.

overall_design: ETV6-RUNX1 genome-wide distribution is determined using ChIP-seq. Cells used in this study are pre-B lymphoblast REH cells. ChIP samples and libraries were done by Sérandour A.A and Debaize L. High-throughput sequencing was conducted on a Genome HiSeq1500/2500. The input, REH RUNX1 Chip-Seq and histone marks are deposited in GEO GSE117684.

first: Marie

last: Troadec

first: Lydie

last: Debaize


title: Cryptococcus neoformans wild type and sir2delta

city: Buffalo

first: Tao

last: Liu

address: Elm and Carlton St

department: Biostatistics and Bioinformatics

institute: Roswell Park Comprehensive Cancer Institute

summary: Wild type strain H99 compared to independent sir2 deletion mutants grown to mid-log (0.6 OD600) in rich medium (YPD) shaking at 250rpm in baffled flasks.

overall_design: Libraries were constructed from two biological replicates of wild type (Control), as well as two biological replicates of two independent sir2 delta clones.

first: John

last: Panepinto

first: Laura

last: Rusche

first: Jeffrey

last: Toussaint

first: Jan

last: Kaur

first: Amanda

last: Bloom


title: CircRNA_051778 in Exosomes as A Potential Biomarker for Distinguishing Lung Adenocarcinoma-Associated Malignant Pleural Effusion from Tuberculous Pleural Effusion

city: Chengdu

first: Yanyun

last: Wang

address: No. 20 Ren Min Nan Lu

institute: West China Second University Hospital, Sichuan University

overall_design: We profiled the exosomal circRNA in lung adenocarcinoma-associated malignant (LA-MPE) and tuberculous (TPE) pleural effusion samples by circRNA microarray to determine the potential functions and diagnostic value of the differential expressed circRNAs (DECs). The expression of DECs were verified by droplet digital PCR. In addition, we constructed a putative circRNA-miRNA-mRNA network, and performed Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses to predict the function of the DECs.


title: Temporal and functional determinants of intra-hepatic vascular homeostatic specialization [human liver + HUVEC]

city: NEW YORK

first: Jesus

middle: Maria

last: Gomez Salinero

address: 1300 York Avenue

institute: Weill Cornell Medicine

summary:
RNAseq1: Single cell analysis of human liver CD31+ CD45- cells

RNAseq2: Comparison of human umbilical vein endothelial cells from Control and MAF knockout conditions.

overall_design:
RNAseq1: Single cell RNAseq analysis of purified by fluorescent activated cell sorting of CD31+ CD45- cells from human livers

RNAseq2: RNA sequencing of WT and MAF KO human umilical vein endothelial cells.

first: Sean

last: Houghton

first: Franco

last: Izzo

first: Shahin

last: Rafii


title: CDK7 inhibition interdicts deregulated transcription and cell cycle control in multiple myeloma [Sensitive_MM_Cell_Lines_RNA-seq]

city: Houston

first: Charles

middle: Yang

last: Lin

state: TX

address: 1 Baylor Plaza

department: Molecular and Human Genetics

institute: Baylor College of Medicine

summary:
Cyclin dependent kinases (CDKs) are high value therapeutical targets owing to their important roles in regulating transcription and the cell cycle — two pathways commonly altered in cancer and especially in multiple myeloma (MM). Among CDKs, CDK7 uniquely bridges cell cycle and transcriptional control by activating other cell cycle CDKs and forming the general transcription factor TFIIH. Utilizing a recently developed highly selective covalent inhibitor of CDK7, we demonstrate that CDK7 inhibition elicits a strong therapeutic response in MM blocking proliferation in vitro and driving tumor regression and prolonged survival in vivo. CDK7 inhibition counteracts molecular hallmarks of deregulated cell cycle control at the G1/S checkpoint. Additionally, we show CDK7 inhibition selectively downregulates oncogenic E2F and cell cycle gene expression programs. Combination treatment with JQ1 which target oncogenic enhancer driven gene expression programs proved highly synergistic. These results support CDK7 as an attractive and therapeutically actionable molecular vulnerability in MM.
Cell count normalized RNA-seq in Sensitive MM cell lines (H929 and MM1S; 24 total samples; 3 technical replicates) upon treatment with the selective covalent CDK7 inhibitor YKL-5-124
Mariateresa,Fulciniti
Nikhil,Munshi

overall_design: Charles,Y,Lin

first: Yao

last: Yao

first: Woojun

last: Park


title: CDK7 inhibition interdicts deregulated transcription and cell cycle control in multiple myeloma [Resistant_MM_Cell_Lines_6Hr_RNA-seq]

summary:
Cyclin dependent kinases (CDKs) are high value therapeutical targets owing to their important roles in regulating transcription and the cell cycle — two pathways commonly altered in cancer and especially in multiple myeloma (MM). Among CDKs, CDK7 uniquely bridges cell cycle and transcriptional control by activating other cell cycle CDKs and forming the general transcription factor TFIIH. Utilizing a recently developed highly selective covalent inhibitor of CDK7, we demonstrate that CDK7 inhibition elicits a strong therapeutic response in MM blocking proliferation in vitro and driving tumor regression and prolonged survival in vivo. CDK7 inhibition counteracts molecular hallmarks of deregulated cell cycle control at the G1/S checkpoint. Additionally, we show CDK7 inhibition selectively downregulates oncogenic E2F and cell cycle gene expression programs. Combination treatment with JQ1 which target oncogenic enhancer driven gene expression programs proved highly synergistic. These results support CDK7 as an attractive and therapeutically actionable molecular vulnerability in MM.
Cell count normalized RNA-seq in Resistant MM cell lines (XG1 and AMO1; 18 total samples; 3 technical replicates) upon treatment with the selective covalent CDK7 inhibitor YKL-5-124
Mariateresa,Fulciniti
Nikhil,Munshi


title: Transcriptomic changes associated with CCN2/CTGF deficiency in the mouse embryonic retina

city: Brooklyn

first: Brahim

last: Chaqour

address: 450 Clarkson Avenue

department: Cell Biology

institute: SUNY Downstate Medical Center

summary: The cellular communication network (CCN) 2, also known as CTGF, is a secreted matricellular protein with regulatory functions in vasoproliferative and fibrotic diseases. Although CCN2 functions extend to developmental processes, the impact of CCN2/CTGF expression, or lack thereof, during retinogenesis is unknown. Herein, we used bulk RNA-sequencing to determine the transcriptomic changes associated with global deletion of CCN2 in E18.5 mouse retinas. we show that CCN2 signals act on intrinsic signal transduction pathway genes and induce genetic reprogramming of retinal progenitor cells  endowing these cells with neurogenic and gliogenic potentials.

overall_design: Retinal mRNA profiles of E18.5 wild-type (WTCCE) (obtained from mice with CCN2flox/flox genotype) and CCN2-deficient (KoCCE) mouse retinas (obtained from mice with CCN2flox/flox- CMV-Cre genotype) were generated by deep sequencing, in triplicate( WTCCE1, WTCCE2, WTCCE3 and KoCCE1, KoCCE3, KoCCE4)). Total RNA from each sample was enriched by oligo (dT) magnetic beads  to remove rRNA. RNA-seq libraries were prepared using KAPA Stranded RNA-Seq Library Prep Kit (Illumina). The completed libraries were qualified with Agilent 2100 Bioanalyzer and quantified by absolute quantification qPCR method. To sequence the libraries on the Illumina HiSeq 4000 instrument, the barcoded libraries were mixed, denatured to single stranded DNA in NaOH, captured on Illumina flow cell, amplified in situ, and subsequently sequenced for 150 cycles for both ends on Illumina HiSeq instrument.  Image analysis and base calling were performed using Solexa pipeline v1.8 (Off-Line Base Caller software, v1.8). Sequence quality was examined using the FastQC software. The trimmed reads (trimmed 5’, 3’-adaptor bases using cutadapt) were aligned to reference genome using Hisat2 software. The transcript abundance for each sample was estimated with StringTie, and the FPKM value for gene and transcript level was calculated with R package Ballgown. The differentially expressed genes and transcripts were filtered using R package Ballgown. The novel genes and transcripts were predicted from assembled results by comparing to  the reference annotation using StringTie and Ballgown, then use CPAT to assess the coding potential of  those sequences.

first: Golam

last: Mohiuddin

first: Sohyun

last: Moon


title: Knockdown of Ino80 complex subunits Actr5, Ies6, and Ino80 in RD cells

city: Wakayama

first: Tsuyoshi

last: Morita

address: Mikazura 580

department: Department of Biology

institute: Wakayama Medical University

summary: INO80 complex is an ATPase-dependent chormatin remodeling complex, which regulates various DNA metabolic processes such as DNA replication and repair. Additionally, INO80 complex also contributes to the regulation of gene expression in sterss response and development. In order to investigate the function of INO80 complex in rhabdomyosarcoma, we examined the knockdown of subunits of INO80 complex Actr5, Ies6, and Ino80 in human rhabdomyosarcoma RD cells. As a result, it was found that INO80 complex is involved in the sarcomagenicity and the disregulation of myogenic properties of rhabdomyosarcoma cells.

overall_design: Subunits of INO80 complex Actr5, Ies6, and Ino80 were knocked down in RD cells, respectively.

first: Ken'ichiro

last: Hayashi


title: Investigating the altered brain metastatic transcriptome in breast cancer

city: Dublin

first: Leonie

last: Young

state: Dublin

address: York House, York Street,, Dublin 2

country: Ireland

institute: Royal College of Surgeons in Ireland

summary: Brain metastatic disease occurs in 10-30% of metastatic breast cancer cases. The incidence of brain metastases is increasing with median overall survival < 2 years for patients. In order to better characterize oncogenic pathway activity pertinent to breast cancer brain metastasis, exome capture RNA sequencing was carried out on patient matched primary breast with brain metastatic tumor samples for 45 cases of breast cancer brain metastasis (N= 90 samples). Here, exome capture RNA sequencing data is deposited as sequencing batch corrected log2 transformed trimmed M of means (TMM) normalized counts per million (CPM) (log2(TMM-CPM +1) gene expression values (n=16,714 protein coding genes; N=90 tumor samples).

overall_design:
Exome capture RNA sequencing was carried out on patient matched primary breast with brain metastatic tumor samples for 45 cases of breast cancer brain metastasis (N= 90 samples). Raw sequencing data are not publicly available for this series due to patient privacy concerns.
>>> The raw data have been deposited at dbGaP for controlled access under accession ID: phsXXXXXX (T.B.C). <<<

first: Adrian

middle: V

last: Lee

first: Steffi

last: Oesttereich

first: Fergus

last: Couch


title: Sulfiredoxin promotes cancer cell invasion through regulation of the miR143-Fascin axis

city: Lexington

first: Qiou

last: Wei

state: KY

address: 324 HSRB, 1095 VA Drive

institute: University of Kentucky College of Medicine

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

summary: including datasets of DNA microarrays and miRNA arrays from HCT116 control and HCT-ShSrx cells

platform_organism:
Homo sapiens
synthetic construct

overall_design: Compare gene expression profiling and miRNA profiling between control and ShSrx cells


title: CDK7 inhibition interdicts deregulated transcription and cell cycle control in multiple myeloma [Resistant_MM_Cell_Lines_24Hr_RNA-seq]


title: Integrated omics profiling reveals FOXA1 and Ku70/Ku80 as the direct target of ivermectin for prostate carcinogenic inhibition

city: Guangzhou

first: Shidong

last: Lv

address: Guangzhou Ave. North No. 1838

department: Urology

institute: Nanfang Hospital, Southern Medical University

summary: Here, we show that ivermectin suppress prostate cancer progression by inhibiting AR signaling pathway and attenuate cellular DNA damage repair capacity. We applied an integrated omics profiling including RNA-seq and Thermal proteome, that found pioneer factor Forkhead Box Protein A1 (FOXA1) and Non-homologous End Joining (NHEJ) repair executer Ku70/Ku80 was the direct target of Ivermectin in prostate cancer. Ivermectin binds to these two proteins and block their biological function, which results in blockade of AR signaling transcription and deficiency of DNA double-strand breaks (DSBs) repair system, and thereby leads to G0/G1 arrest and trigger synthetic lethality Our findings demonstrate both the effect and target of Ivermectin in prostate cancer comprehensively and systemically, indicating that use of Ivermectin may constitute a new therapeutic approach for prostate cancer.

overall_design: C4-2 and 22RV1 cells were treated with 8 or 12 μM ivermectin for 48 hours and the transcription profiling was analyzed by RNA-seq

first: Zeyu

last: Wu

first: Zhou

last: Wang

first: Qiang


title: FOXC1 induces cisplatin resistance through enhancer activation [ChIP-seq]

city: Alhambra

first: Yi-Tsung

last: Lu

address: 516 SAN PASQUAL DR

institute: University of Southern California

summary: We previously reported that an aggressive subpopulation of highly tumorigenic, drug-resistant bladder cancer cells can arise from the bulk tumor cells without mutational events and that this phenotypic plasticity is driven at least in part by epigenetic mechanisms. In the current work, we analyzed the chromatin accessibility of enhancers to identify transcription factors that contribute to this transition to a drug-resistant state. Comparing the drug resistant side population (SP) cells and the less drug resistant non-side population (NSP) cells in bladder cancer cells, we identified differential accessible enhancers and differentially expressed genes. Transcription factor motif analysis showed that FOX family motif was enriched in accessible enhancers near SP-overexpressed genes. Among FOX family transcription factors, FOXC1 was the only overexpressed transcription factor, and it was also the most significantly overexpressed gene in SP cells. FOXC1 ChIP-seq confirmed that FOXC1 binding sites are more accessible in SP cells and showed a significantly more FOXC1 binding near the overexpressed genes in SP cells. When the FOXC1 is knocked out, bladder cancer cells exhibit decreased cisplatin resistance and less percentage of SP cells. This change in cisplatin resistance is partially related to the FOXC1-driven expression of ABCB1 gene. In summary, our observations suggest that differential expression and enhancer binding of FOXC1 promotes the previously observed, mutation-independent shift towards cisplatin resistance in bladder cancer.

overall_design: mRNA profile of side-population and non-side population of J82 human bladder cancer cells; mRNA profile of FOXC1 knock-out and vector control J82 cells; FOXC1 ChIP-seq of FOXC1


title: FOXC1 induces cisplatin resistance through enhancer activation [RNA-seq_FOXC1_KO]


title: FOXC1 induces cisplatin resistance through enhancer activation


title: FOXC1 induces cisplatin resistance through enhancer activation [RNA-Seq_SPNSP]


title: Primary hepatocyte transcriptional response to Mfn2 over-expression by adenovirus

city: Boston

first: Yae-Huei

last: Liou

state: MA

address: 665 Huntington Ave.

department: MET

institute: Harvard School of Public health

summary: RNA-seq analysis of Ad-LacZ, Ad-Mfn2 infected primary hepatocyte.

overall_design: Differential expression of mRNA from Ad-LacZ, Ad-Mfn2infected primary hepatocyte. 4 samples from each groups was analyzed.

first: Chih-Hao


title: Molecular classification of histological origin of NSCLC

city: Jinan

first: Qing

last: Sun

address: JINGSHI Road 16766

institute: The First Affiliated Hospital of Shandong First Medical University

summary:
Lung cancer is one of the most common malignant tumors in the world. The latest edition of WHO classifies lung cancer on the basis of histological morphology and molecular typing, which is a relatively complete pathological classification of lung cancer at present. However, in clinical practice, it is difficult to make accurate subtype classification of NSCLC only by using morphological structure and immunohistochemical characteristics, and the degree of coincidence with gene mutation and clinicopathological parameters is poor, which has limited guiding effect on clinical diagnosis and treatment.
In this study, we proposed Molecular Pathological Classification Model of NSCLC Tissue Origin.

overall_design: On the basis of WHO morphological classification, 98 NSCLC samples were labeled by immunohistochemical P63/Napsin A and TTF-1/CK7 double staining, and were divided into the following five groups according to tissue origin: A) Bronchoalveolar carcinoma; B) Alveolar epithelial carcinoma; C) Bronchial epithelial carcinoma; D) secretory adenocarcinoma; E) Mucinous adenocarcinoma.


title: Expression data from knockdown of EIF3C in TE-1 cells

city: xi'an

first: zhengyang

last: lu

state: shannxi

address: xi'an shannxi

institute: the first affiliated hospital of xi'an jiaotong university

summary:
Eukaryotic initiation factor 3c,one of the important subunits of eIF3 that is the largest mammalian scaffolding initiation factor.
We used microarray analysis to identify the genes that are regulated by EIF3C in TE-1 cells.

overall_design: EIF3C expression was stably knocked-down in TE-1 cells. RNA from this clone and parental (control) cells were purified for microarray analysis.


title: Single nuclei transcriptomic profiling of human astrocytes and oligodendrocytes in Alzheimer’s disease II

city: New York

first: Shane

middle: A.

last: Liddelow

state: NY

address: 435 E. 30th Street

department: Neuroscience Institute

institute: NYU Langone Medical Center

summary: Single nuclei RNA sequencing (snRNA-seq) dataset characterizing nuclei from a putative astrocyte enrichment method: SOX9-positive sorting.

overall_design: As a pilot to test this putative astrocyte enrichment method, nuclei were isolated from human post-mortem prefrontal cortex from 5 donors (NS patients = 3, AD patients = 2). Sorted SOX9-positive and SOX-negative were prepared for snRNA-seq using Single Cell 3’ Gene Expression kit v3 (10x Chromium). Generated snRNA-seq libraries were sequenced using an Illumina NovaSeq 6000.

first: Jessica

last: Sadick


title: Single nuclei transcriptomic profiling of human astrocytes and oligodendrocytes in Alzheimer’s disease I

summary: Single nuclei RNA sequencing (snRNA-seq) dataset characterizing astrocytes and oligodendrocytes isolated from human postmortem APOE e2/3 Alzheimer's disease (AD) and aged-matched non-symptomatic (NS) brains.

overall_design: Nuclei were isolated from human post-mortem prefrontal cortex from 16 donors (NS patients = 6, AD patients = 10; all donors were validated as having an APOE e2/3 haplotype). In order to improve astrocyte capture for snRNA-seq, we optimized a platform to enrich for astrocytes by labeling and sorting nuclei based on LIM/Homeobox protein (LHX2)-positive/NeuN-negative staining. Nuclei were then prepared for snRNA-seq using Single Cell 3’ Gene Expression kit v3 (10x Chromium). Generated snRNA-seq libraries were sequenced using an Illumina NovaSeq 6000.

middle: A


title: FOXA1 ChIP-seq analysis of genome-edited T47D ESR1 mutant cell models

first: Zheqi

last: Li

state: Massachusetts

address: 450 Brookline Avenue, Smith Building SM1006

institute: Dana-Farber Cancer Institute

summary: This study is designed to comprehensively characterize the FOXA1 cistromes of Y537S and D538G mutated ER versus WT ER in breast cancer cells.

overall_design: Genome-edited T47D cells were hromone derpvied (with one group of WT cells treated with 1nM E2 for 45 min). Chromatin DNA was then extracted from each sample. The immunoprecipitation was performed using FOXA1 (abcam, ab23738)  antibodies. Pooled DNA samples from individual clones were sent to sequencing with Illumina NextSeq Platform. ChIP-seq reads were aligned to either hg19 genome assembly using Bowtie 2.0, and peaks were called using MACS2.0 with q value below 0.05. DiffBind was used to perform principle component analysis, identify differentially expressed binding sites and analyze intersection ratios with other data sets. Genomic feature distribution were called using ChIPseeker.

last: Oesterreich


title: Single-cell RNA-seq profiles of murine sarcoma tumors with vehicle and digoxin treatments

city: Xi'an

first: Zhengtao

last: Xiao

state: Shaanxi

address: No.76,Western Yanta Road

department: Department of Biochemistry and Molecular Biology

institute: Xi’an Jiaotong University

summary: Digoxin, a cardiac glycoside widely used in humans, acts through disruption to central carbon metabolism via on target inhibition of the Na+/K+ ATPase.  Acute Digoxin treatment remodels the tumor microenvironment, leading to cell-type specific transcriptional reprogramming of metabolic processes.

overall_design: We treated murine allograft sarcoma model with vehicle or 2 mg/kg digoxin (using two mice per group) every 24 hours and collected tumors after the fourth dose.

first: Sydney

middle: M

last: Sanderson

first: Emily

last: Hocke

first: Simon

last: Gregory

first: Jason

middle: W

last: Locasale


title: ADRB3 overexpression in rat

city: Nantes

first: Marja

last: Steenman

address: 8 quai Moncousu

institute: L'institut du thorax

summary: Effect of endothelial overexpression of ADBR3 in rats on the cardiac transcriptome

overall_design: RNA was isolated from left ventricle of rats overexpressing ADBR3 (n=5) and of WT rats (n=4) and hybridized to microarrays .


title: Temporal and functional determinants of intra-hepatic vascular homeostatic specialization

first: Jesus

last: Gomez Salinero

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: ChIP-seq of HOXC10 in gastric cancer cell

city: Hangzhou

first: jiamin

last: he

address: Qingchun East Road

institute: Sir runrun Shaw hospital

summary: HOXC10 is a member of the HOX family and participates in the regulation of malignant biological behaviors such as growth, migration, and invasion of tumor cells by binding to target genes. ChIP-seq is a powerful tool for studying the interaction between proteins and DNA in the study. Therefore, we use the ChIP-seq method to explore the potential regulatory genes and nucleic acids of HOXC10 in gastric cancer cells.

overall_design: MKN45 cells were seeded in 15 cm plate with density of 70-80% supplemented with 10% FBS and incubated at 37℃ for 24h, and then transfected with GV141-HOXC10-Flag or GV141 empty vector using Fugene HD(Roche).Approximately 5*10^7 cells were used for each CHIP-seq assay according to the manufacturer’s instructions(Merk, Germany)

first: Jiamin

last: He

first: Shuejie

last: Chen


title: Gene expression of invasive lobular carcinoma tumor epithelium and tumor stroma isolated by laser-capture microdissection

city: Edinburgh

first: Andrew

middle: H

last: Sims

address: Carrington Crescent

department: Institute of Genetics and Molecular Medicine

institute: University of Edinburgh

summary: We used laser-capture microdissection (LCM) to separate tumor epithelium (TE) from stroma (TS) in 23 ILC samples. Gene expression analysis was used to identify genes that are enriched in the stroma of ILC, but not IDC or normal breast.

overall_design: Gene expression data was generated for a total of 22 TE and 18 TS samples, including 17 pairs of TE and TS samples from the same patients.

first: Laura

last: Gómez-Cuadrado

first: Valerie

last: Brunton

first: Morag

last: Park


title: Human Dental Pulp Cell exosomes vs Human iPS Cell exosomes

city: Gifu City

first: Ken-ichi

last: Tezuka

state: Gifu

address: 1-1 Yanagido

department: Gifu University Graduate School of Medicine

summary: Small vesicles, known as exosomes, are secreted from various cell types. Exosomes secreted by mesenchymal stem cells have therapeutic effects against a variety of diseases, and may be able to partially replace stem cell therapies. Previously, we established  and characterized human leukocyte antigen (HLA) haplotype homo (HHH) dental pulp cell (DPC) lines from human wisdom teeth. In this report, we purified the exosomes secreted from HHH-DPCs and evaluated their therapeutic potential in a periodontitis model. The exosomes purified from HHH-DPCs showed homogeneous and spherical membrane structures, and showed low but significant expression of HLA class I molecules. The exosomes further promoted proliferation and migration in DPCs. A comparison of miRNAs revealed that the HHH-DPC exosomes contained higher levels of multiple Let-7 family miRNAs compared to HHH-induced pluripotent stem cell (iPSC)-derived exosomes. Finally, the HHH-DPC exosomes showed preventive effects in a mouse model of periodontitis induced by lipopolysaccharides (LPS). In summary, HHH-DPC exosomes expressed HLA molecules which may induce an immune response in HLA-mismatched transplantations. However, they successfully stimulated the proliferation and migration of cells and showed suppressive effects on LPS-induced periodontitis. Therefore, HHH-DPC exosomes show great potential for applications in periodontal treatments.

overall_design: To identify genes expressed in exosomes, comprehensive gene expression analysis was performed using exosomes from DP74, DP94 and DP263 and exosomes from iPS74, iPS94 and iPS263.

first: K

first: Y

last: Shimizu

first: T

last: Kawaguchi


title: Transcriptional phenotype in a novel ataxin-3 knock-in mouse model for spinocerebellar ataxia type 3

city: Saarbrücken

first: Julia

last: Schulze-Hentrich

address: Campus, Building A2.4

department: Genetics and Epigenetics

institute: Saarland University

summary: Spinocerebellar ataxia type 3 is the most common autosomal dominant inherited ataxia worldwide and caused by a CAG repeat expansion in the Ataxin-3 gene resulting in a polyQ expansion in the corresponding protein. The disease is characterized by neuropathological (aggregate formation, cell loss), phenotypical (gait instability, body weight reduction) and transcriptional changes. So far there is no mouse model available representing all the different aspects of the disease, but a representative model is highly needed to gain a better understanding of the disease pathomechanism. Here we characterized a novel Ataxin-3 knock-in mouse model, expressing an expansion of 304 CAG/CAAs either heterozygous or homozygous in the murine Ataxin-3 locus using biochemical, behavioral and transcriptomic approaches. Further, we correlated the transcriptional changes of the knock-in mice to those found in human SCA3 patients, to prove the comparability of our model. The novel Ataxin-3 knock-in mouse is characterized by the expression of polyQ-expanded Ataxin-3 in the murine protein, leading to massive aggregate formation, especially in brain regions known to be vulnerable in SCA3 patients, and impairment of Purkinje cells. Caused by these neuropathological changes, the mice demonstrated phenotypically reduction in body weight accompanied by gait and balance instability. Transcriptomic analysis of cerebellar tissue revealed downregulation of differentially expressed genes enriched in myelinating oligodendrocytes. Comparing these transcriptional changes with those found in cerebellar tissue of SCA3 patients, we discovered an overlap of differentially expressed genes pointing towards disturbances in the myelin sheaths and myelinating oligodendrocytes.

overall_design: gene expression of cerebellar samples was analyzed in samples of 2 and 12 month old mice. For each time point 5 wild-type and 5 knock-in mice, carrying the CAG expansion in the ataxin-3 locus were analyzed

first: Jeannette

last: Hübener-Schmid