title: m6A modification in cisplatin-resistant cells

city: Fuzhou

first: Jiahui

last: Chu

state: Fujian

address: 156 west erhuan north road

institute: PLA 900th Hospital

summary: We report the application of specific antibodies and high-throughput sequencing technologies (methylated RNA immunoprecipitation sequencing, MeRIP-seq) for high-throughput profiling of m6A modifications in NSCLC cisplatin resistant cells. We generated maps of m6A modified transcripts in A549 and A549/DDP cells. We find that the m6A level was significantly increased in A549/DDP cells compared to the A549 cells. We show that there was a close correlation between the m6A modification and cisplatin resistance.

overall_design: Examination of m6A modifications in 2 cell types


title: Transcriptomic analysis reveals the mechanism of sulfasalazine-induced liver injury in mice

status: Public on Nov 04 2022

city: Zhengzhou

first: Yucheng

last: Li

address: Jinshui East 156

country: China

institute: Henan University of Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: Liver injury is one of the main toxic effect of sulfasalazine (SASP). However, the toxicological mechanism of SASP-induced liver injury remains unclear. In the present study, the liver injury was induced by orally treatment with SASP for 4 weeks in mice. The hepatic mRNA profiles were detected by RNA sequencing and the differentially expressed genes (DEGs) were analyzed by bioinformatics methods. The elevated serum levels of alanine aminotransferase (ALT), alkaline phosphatase (ALP) and total bilirubin (TBIL), combined with the hepatic histopathological features verified that liver injury was successfully caused by SASP. Transcriptomic results showed that 187 genes (fold change > 1.5 and P < 0.05) were differentially expressed, of which 106 genes were up-regulated and 81 genes were down-regulated in SASP-treated group. Moreover, the further analysis showed that these 187 differentially expressed genes (DEGs) were enriched in 123 GO terms, which mainly including oxidation-reduction process, oxidoreductase activity and epoxygenase P450 pathway. KEGG pathway analysis showed 30 pathways including chemical carcinogenesis, retinol metabolism, arachidonic acid metabolism, linoleic acid metabolism and glutathione metabolism. Among these 187 DEGs, the top 22 hub genes were screened from network of protein-protein interaction (PPI) and verified by qRT-PCR. The results showed that the mRNA levels of hepatic drug-metabolizing enzymes, including cyp2b50, cyp2c50, cyp2c39, cyp2c38, cyp2c29, cyp2c54, cyp2c55, cyp2a5, gsta1, gsta2, gstt2, gstm2 and ephx1, were significantly up-regulated in SASP-treated group. Moreover, the expression of egfr, which has the highest score in PPI degree, were significantly down-regulated in SASP-treated group. The present study suggested that the toxicological mechanisms of SASP-induced liver injury might be related to multi-biological processes and pathways. Our results would be helpful for better understanding the hepatotoxic mechanism of SASP. However, the precise mechanism still needs further research.

overall_design: Hepatic transcriptome profiles of sulfasalazine (1000 mg/kg) and control mice were generated by RNA sequencing, in triplicate, using Illumina Hiseq 4000.

first: Jiduo

last: Shen


title: Studies on a hydrocephalus-causing mutation on Trim71

city: Rochester

first: Wenqian

last: Hu

state: Minnesota

address: 200 First St SW, GU16-01A

department: Biochemistry and Molecular Biology

country: USA

institute: Mayo Clinic

summary: We studies on how a hydrocephalus-causing mutation (R783H) on Trim71 alters Trim71's substrate mRNA binding

overall_design: Transcriptome-wide Trim71 (R783H) target mRNAs were identified through CLIPseq in mouse embryonic stem cells)

first: W

first: Q

last: Liu

first: M

middle: K

last: Novak

first: R

middle: M

last: Pepin

first: X

last: Chen

first: S

last: Zhang


title: Genetic mapping reveals Pou2af2-dependent tuning of tuft cell differentiation and intestinal type 2 immunity

city: Seattle

first: Jakob

middle: Helmuth

last: von Moltke

state: Washington

address: 750 Republican Street

department: Immunology

institute: University of Washington

summary: Chemosensory epithelial tuft cells contribute to innate immunity at barrier surfaces, but their differentiation from epithelial progenitors is not well understood. Here we exploited differences between inbred mouse strains to identify an epithelium-intrinsic mechanism that regulates tuft cell differentiation and tunes innate type 2 immunity in the small intestine. Balb/cJ (Balb) mice had fewer intestinal tuft cells than C57BL/6J (B6) mice and failed to respond to the tuft cell ligand succinate. A majority of this differential succinate response was determined by a single genetic locus from 50-67Mb on chromosome 9 (Chr9). Congenic Balb mice carrying the B6 Chr9 locus had elevated baseline numbers of tuft cells and responded to succinate. The Chr9 locus includes Pou2af2, a transcriptional cofactor essential for tuft cell development. Epithelial crypts expressed a previously unannotated short isoform of Pou2af2 that uses a novel transcriptional start site and encodes a non-functional protein. Low tuft cell numbers and the resulting lack of succinate response in Balb mice was explained by a preferential expression of the short isoform. Physiologically, differential Pou2af2 isoform usage tuned innate type 2 immunity in the small intestine. Balb mice maintained responsiveness to helminth pathogens while ignoring commensal Tritrichomonas protists and reducing norovirus burdens.

overall_design: Tuft cells were sorted as CD45-, EPCAM+ CD25+ SigF+ live cells from the small intestine or unmanipulated C57BL/6J, Balb/cJ and congenic Strain 3 mice

first: Marija

middle: N

last: Nadjsombati


title: Gene expression profile at single-cell level of hematopoietic stem and progenitor cells (HSPCs) from individuals with chronic myelomonocytic leukemia (CMML)

city: Gainesville

first: Meghan

last: Ferrall-Fairbanks

state: FL

address: 1275 Center Drive

department: Biomedical Engineering

institute: University of Florida

summary: Myeloblast expansion is a hallmark of disease progression in leukemias and comprises of CD34+ hematopoeitic stem and progeneitor cells. We used single-cell RNA sequencing (scRNAseq) to analyze the transcriptional states of HSPCs in CMML.

overall_design: CD34+ HSPCs were isolated from bone marrow mononuclear cells from patients diagnosed with CMML and transcriptionally profiled using scRNAseq.

middle: C

first: Eric

last: Padron


title: Increased blood microRNA-320 expression associated with imminent and severe lung cancer

city: Trondheim

first: Pål

last: Sætrom

address: Erling Skjalgsons gate 1

department: Clinical and Molecular Medicine

country: Norway

institute: Norwegian University of Science and Technology, NTNU

type: Non-coding RNA profiling by high throughput sequencing

summary: Altered levels of microRNAs (miRNAs) in blood may contribute to identification of individuals with lung cancer (LC) but may also be early systemic signals of increased LC risk. We compared expression of 1663 miRNAs in blood collected during diagnostic workup for confirmed LC cases (n=128) to that in individuals with suspected but confirmed negative LC (n=62) and identified nine candidate miRNAs upregulated in LC cases. Higher expression of three candidates, miR-320b, 320c, and 320d, was associated with poor survival, independent of LC stage and subtype. To investigate pre-diagnostic profiles of the candidate miRNAs, we assessed their blood expression up to eight years prior to LC diagnosis in population-based cohorts compared to matched controls (n=360 cases, 375 controls). Expression of miR-320c and miR-320d was higher especially in cases sampled within two years prior to LC diagnosis. Thus, elevated levels of miR-320c and miR-320d may be early indications of severe LC.

overall_design:
MicroRNA expression profiles from small RNA sequencing of serum from lung cancer patients at diagnosis (n=128) and individuals with confirmed negative LC (n=62).
**Raw data not provided due to patient privacy concerns**

first: Therese

middle: H

last: Nøst

first: Anne

last: Skogholt

first: Ilona

last: Urbarova

first: Robin

last: Mjelle

first: Erna-Elise

last: Paulsen

first: Tom

last: Dønnem

first: Sigve

last: Andersen

first: Maria

last: Markaki

first: Oluf

middle: D

last: Røe

first: Mikael

last: Johansson

first: Mattias

first: Bjørn

last: Grønberg

first: Torkjel

last: Sandanger


title: Rebalancing TGFβ1/BMP Signals Preserves Effector and Memory Programs in Terminally Dysfunctional CD8+ T Cells

status: Public on Nov 03 2022

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

type: Methylation profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Serum microRNAs as biomarkers for the therapeutic response to trastuzumab/pertuzumab/taxane therapy in HER2-positive metastatic breast cancer

city: Kamakura

first: Ichikawa

last: Makiko

state: Kanagawa

country: Japan

institute: Toray Industries, Inc.

summary: Serum microRNAs profiles of HER2 positive advanced breast cancer patients and their treatment response after the trastuzumab/pertuzumab/taxane therapy

overall_design: Association between serum microRNA profiles and response to trastuzumab/pertuzumab/taxane therapy of 30 advanced breast cancer patients.

first: Asuka

last: Kawachi

first: Akihiko

last: Shimomura

first: Juntaro

last: Matsuzaki

first: Satoko

last: Takizawa

first: Yoshiaki

last: Aoki

first: Hiromi

last: Sakamoto

first: Kato

last: Ken

first: Shimizu

last: Chikako

first: Takahiro

last: Ochiya

first: Kenji

last: Tamura


title: Transcriptome Sequencing Analysis (RNA-Seq) of Bone Marrow Hematopoietic Stem Cells from Per2-mutant Mice

city: Sacramento

first: Clifford

middle: G.

last: Tepper

state: CA

address: 4645 2nd Avenue, Room 2300A

department: Biochemistry and Molecular Medicine

institute: UC Davis School of Medicine

summary: Circadian rhythm (CR) and environmental low-dose radiation (LDR) evident on Earth’s surface may have coordinated in the evolution of early life; disturbed CR and/or overexposure to radiation are linked with aging and many human diseases including cancer. Although CR affects tumor response and normal tissue radiosensitivity in cancer radiotherapy, it is unclear how CR proteins function in LDR induced radioprotection. Herein, we demonstrated that mice carrying a deficient Period2 gene (C57BL-Per2 def ), a core CR regulator, were highly sensitive to radiation. Compared to Per2 wt mice, the population of bone marrow hemopoietic stem cells (BMHSCs) was reduced and a cluster of genes responsible for DNA damage repair and mitochondrial metabolism was silenced in the Per2 def BMHSCs . Consistently, unlike Per2 wt human and mouse cells capable of inducible radioresistance by LDR, Per2 def cells failed to induce such adaptive protection. Furthermore, LDR enhanced PER2 protein level together with phosphorylated GSK3β (pGSK3β) in the Wnt/β-catenin signaling pathway. Interaction of PER2 with pGSK3β activated β -catenin that in turn transactivated Per2 and other prosurvival genes. These results provide new insights into how CR and LDR communicate in genotoxic stress response. The PER2/pGSK3β/β-catenin/Per2 pathway may serve as a therapeutic approach to reduce normal cell injury in cancer radiotherapy.

overall_design: A total of 2 samples were analyzed in this study. The study included 2 samples of mouse bone marrow hematopoietic stem cells (HMCs) obtained from wild-type (Per2wt) and Per2-deficient (Per2def). The bone marrow HMCs were enriched by cell sorting into culture medium, pelleted by centrifugation, and harvested,. Total RNA was isolated and then submitted for RNA-sequencing analysis.

first: Jian

middle: J

last: Li

first: Aris

middle: T

last: Alexandrou

first: Ming

last: Fan

middle: G


title: Targeting Integrated Stress Response by ISRIB combined with Imatinib attenuates STAT5 signaling and eradicates therapy-resistant Chronic Myeloid Leukemia cells

city: Warsaw

first: Katarzyna

last: Piwocka

address: Pasteur 3

country: Poland

institute: Nencki Institute of Experimental Biology

summary: Integrated Stress Response (ISR) facilitates cellular adaptation to a variable environmental conditions by reprogramming cellular response. Activation of ISR was reported in neurological disorders and solid tumours, but its function in hematological malignancies remains largely unknown. Previously we showed that ISR is activated in chronic myeloid leukemia (CML) CD34+ cells, and its activity correlates with disease progression and imatinib resistance. Here we demonstrate that inhibition of ISR by small molecule ISRIB, but not by PERK inhibitor GSK2656157, restores sensitivity to imatinib and eliminates CML-BP CD34+ resistant cells. We found that In PDX mouse model bearing CD34+ imatinib/dasatinib-resistant CML blasts with PTPN11 gain-of-function mutation, combination of imatinib and ISRIB decreases leukemia engraftment. Furthermore, genes related to SGK3, RAS/RAF/MAPK, JAK2 and IFN pathways were downregulated upon combined treatment. Remarkably, we confirmed that ISRIB and imatinib combination decreases STAT5 phosphorylation and inhibits expression of STAT5-target genes responsible for proliferation, viability and stress response. Thus, our data point to a substantial effect of imatinib and ISRIB combination, that results in transcriptomic deregulation and eradication of imatinib-resistant cells. Our findings suggest such drug combination might improve therapeutic outcome of TKI-resistant leukemia patients exhibiting constitutive STAT5 activation.

overall_design: Comparative polyA mRNA profiling (RNA-sequencing – stranded, single-end) of chronic myeloid leukemia (CML) cells from patient derived xenograft (PDX) model mice either untreated (control) or treated with a) Imatinib only, b) ISRIB only, and c) both Imatinib and ISRIB.

first: Wioleta

last: Dudka

first: Shamba

middle: S

last: Mondal


title: Rebalancing TGFβ1/BMP Signals Preserves Effector and Memory Programs in Terminally Dysfunctional CD8+ T Cells [Bisulfite-Seq]

first: Amy

last: Hite

summary: T cell dysfunctionality prevents clearance of chronic infections and cancer. Furthermore, epigenetic programming in dysfunctional CD8+ T cells limits durable responses to T cell-based immunotherapies, including immune checkpoint blockade (ICB). However, major gaps concern how upstream signals drive acquisition of dysfunctional epigenetic programs, and whether therapeutically targeting these signals can remodel terminally dysfunctional T cells to an ICB-responsive state. Here, we use an in vitro model of human T cell dysfunction and complementary in vivo mouse chronic virus infection and tumor models. We show that post-effector TGFβ1 signaling establishes terminal dysfunction in human CD8+ T cells through stable epigenetic changes. Importantly, we demonstrate that promoting BMP signaling while blocking TGFβ1 restored effector and memory programs in dysfunctional human CD8+ T cells, induced superior anti-tumor activity, and boosted ICB responses during mouse chronic virus infection. Thus, rebalancing TGFβ1/BMP-signals in dysfunctional CD8+ T cells provides an exciting new approach to enhance T cell immunotherapies.

overall_design: In vitro acute or chronic stimulation of cord-blood derived human CD8+ T cells

first: Hazem

middle: E

last: Ghoneim

first: Abbey

middle: A

last: Saadey

first: Amir

last: Yousif

last: Webb


title: Rebalancing TGFβ1/BMP Signals Preserves Effector and Memory Programs in Terminally Dysfunctional CD8+ T Cells [RNA-Seq]

overall_design: In vitro chronic TCR stimulation of cord-blood derived human CD8+ T cells


title: Tracking the progression of Alzheimer’s disease with peripheral blood-based biomarkers

city: Sherbrooke

first: Mariano

last: Avino

address: 3201 Jean Mignault

department: Biochemistry and Functional Genomics

country: Canada

institute: Sherbrooke University

summary:
We investigate the gene expression signature of peripheral blood monocytes during the progression of Alzheimer's disease.
We profiled gene expression in the mouse cortex using data obtained from RNA-seq of three individuals at 6-months old and three individuals at 24-months old.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the monocytes

first: Benoit

last: Laurent


title: An effective therapy by co-targeting c-Myc and Bcl-2 for resistant acute myeloid leukemia.

city: Hangzhou

first: ping

last: wang

address: 88th Jiefang Road

department: School of Medicine

institute: Zhejiang University

summary: We showed that genetically double-knockdown of c-Myc/Bcl-2 synergistically killed AML cells and inhibited the growth of AML cells in vivo. Mechanically, co-targeting c-Myc/Bcl-2 reciprocally abrogated over-proliferation and apoptosis resistance via synergistically impairing mitochondrial biogenesis.

overall_design: To extend these observations, we examined the effects of double-knockdown of c-Myc and Bcl-2 on mitochondria compared with single-knockdown of c-Myc or Bcl-2 in MOLM-13 AML cells. We performed an RNA-seq experiment to reveal global gene expression changes caused by the double-KD in MOLM-13. Indeed, the transcriptional landscape of the MOLM-13 cells changed significantly upon c-Myc and/or Bcl-2 knockdown.

first: Ping

last: Wang

first: Shuwen

last: Zheng

first: Rongzhen

last: Xu


title: RNAseq of 8505c cell line with HHEX knockdown

city: Shanghai

first: Zhongyun

address: 1665 Kongjiang Road

institute: Shanghai Jiao Tong University School of Medicine

summary: HHEX KD led to the differential expression of genes in pathway or cellular function related to cell proliferation and anti-apoptosis

overall_design: Differential expression analysis of WT and HHEX KD 8505c cells (three biological replicates per condition)

first: Weiwei

last: Cheng


title: Effect of 1,5-AG addition on gene expression in pre-B ALL cells.

city: jinan

first: huasu

last: zhu

address: No.107 wenhua west load

institute: Qilu hospital of shandong university

summary: In order to study the effect of 1,5-AG addition on the function of HAL-01 cell line. We then performed gene expression profiling analysis using data obtained from RNA-seq of HAL-01 cells after 24  hours.

overall_design: After 24 hours of 0.8mM 1,5-AG intervention, comparative gene expression profiling analysis of RNA-seq data for HAL-01 cells.

first: Huasu

last: Zhu

first: Huixian

last: Ma

last: Dong

first: Min

last: Wu


title: A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Summary: Pioneer transcription factors engage nucleosomal DNA in chromatin to initiate gene regulatory events that control cell fate 1 . To determine how different pioneer transcription factors initiate the formation of a locally accessible environment within silent, compacted chromatin and collaborate with an ATP-dependent chromatin remodeler, we generated nucleosome arrays in vitro with a central nucleosome that can be targeted by the hematopoietic ETS factor PU.1 and bZIP factors C/EBPα, and C/EBPβ. Each class of factor can expose target nucleosomes on linker histone-compacted arrays, but with different hypersensitivity patterns, as discerned by long-read sequencing. The DNA binding domain of PU.1 is sufficient for mononucleosome binding but requires an additional intrinsically disordered domain to bind and open compacted chromatin. The canonical mammalian SWI/SNF (BAF) complex, cBAF, was unable to act upon two forms of locally open chromatin, in the presence of linker histone, unless cBAF was enabled by the acidic- and glutamine-enriched transactivation domain of PU.1. However, cBAF complexes potentiate the nucleosome binding DBD of PU.1 to weakly open chromatin in the absence of the PU.1 unstructured domain. Together our findings provide a mechanism for how pioneer factors initially target chromatin structures to provide specificity for action by nucleosome remodelers that further open local domains.

overall_design: MNase-seq performed on Cx3cr1 nucleosome arrays in the presence or absence of several transcription factors (CEBPa, CEBPb, PU.1, as well as combinations CEBPa+PU.1 or CEBPb+PU.1). Control conditions include those arrays without transcription factors or nucleosomes (free DNA), without transcription factors but with nucleosomes and linker histone H1 (NoTF), and without transcription factors or linker histone but with nucleosomes (array). Each condition was sequenced with two replicates. Additional samples are provided to examine the role of chromatin remodeler cBAF: an additional free DNA, array, and NoTF control, and two conditions incubated with PU.1 in the presence or absence of BAF. All conditions were sequenced with two replicates.

first: Megan

last: Frederick

first: Kaylyn

last: Williamson

first: Meilin

middle: F

last: Garcia

first: Max

middle: B

last: Ferretti

first: Ryan

middle: L

last: McCarthy

first: Greg

first: Edgar

last: Monteiro

first: Naomi

last: Takenaka

first: Janice

last: Reynaga

first: Cigall

last: Kadoch

first: Kenneth

last: Zaret


title: Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia [ChIP-Seq]

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

summary: Mutations in over one hundred genes, belonging to diverse classes of epigenetic regulators, resulted in significant fitness advantage under nutrient starvation and acidic conditions, suggesting that disruption of epigenetic control, at multiple levels of the regulatory network, promotes broad resistance of cells to stressful environments. To uncover the molecular mechanisms of such phenomenon, and to understand how loss of epigenetic regulators gives advantage during stress, we plan to examine how the chromatin landscape changes in nutrient-deprived conditions.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone modifications H3K27me3, H3K27Ac, H3K4me3 and H3K4me1 in PDX MEXF 2090 cells.

first: Fabrizio

last: Simeoni

first: Marta

last: Milan

first: Stephanie

last: Strohbuecker

first: Phil

last: East

first: Robert

last: Goldstone


title: Decoding the Protein Composition of Whole Nucleosomes with Nuc-MS

city: San Francisco

first: Wei

last: Wu

address: 600 16th street

department: Department of Medicine

institute: University of California, San Franciso

summary:
Current proteomic approaches disassemble and digest nucleosome particles, blurring readouts of the ‘histone code’. To preserve nucleosome-level information, we developed Nuc-MS, which displays the landscape of histone variants and their post-translational modifications (PTMs) in a single mass spectrum. Combined with immunoprecipitation, Nuc-MS quantified nucleosome co-occupancy of histone H3.3 with variant H2A.Z (sixfold over bulk) and the co-occurrence of oncogenic H3.3K27M with euchromatic marks (for example, a >15-fold enrichment of dimethylated H3K79me2). Nuc-MS is highly concordant with chromatin immunoprecipitation-sequencing (ChIP-seq) and offers a new readout of nucleosome-level biology.
Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for histone variants H3.3, H2AZ as well as the histone modifications H3K79me2 and H4K16ac in HEK293T cells.

overall_design: Luis,F,Schachner

last: Iwanaszko

first: Marc

last: Morgan

first: Ali

last: Shilatifard

first: Neil

last: Kelleher


title: Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia [ATAC-Seq]

summary: Mutations in over one hundred genes, belonging to diverse classes of epigenetic regulators, resulted in significant fitness advantage under nutrient starvation and acidic conditions, suggesting that disruption of epigenetic control, at multiple levels of the regulatory network, promotes broad resistance of cells to stressful environments. To uncover the molecular mechanisms of such phenomenon, and to understand how loss of epigenetic regulators gives advantage during stress, we examined how chromatin accessibility changes in nutrient-deprived conditions using ATAC-seq. ATAC-seq analysis of melanoma cells expressing 4-7sgRNAs targeting members of the PRC2 complex (EED, EZH2, SUZ12), histone H1B (HIST1H1B), the chromatin remodeller SMARCD1 and a non-expressed control gene (TNP2), and grown in either unperturbed conditions (d0) or under glutamine deprivation (d2).

overall_design: Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) for TNP2, EED, EZH2, SUZ12, HIST1H1B and SMARCD1 KO cells


title: Biallelic loss-of-function mutations in MAD1 result in systemic inflammation, clonal selection of aneuploid cells and high tumor susceptibility

city: Barcelona

first: Agustín

middle: Sánchez

last: Belmonte

state: Barcelona

address: Nazaret 115 -117

department: Systems Oncology Program

country: Spain

institute: Vall d ́Hebron Institute of Oncology (VHIO)

summary: Aneuploidy is a frequent feature of tumor cells. Yet, germline mutations leading to chromosomal instability are less frequent and are typically found in patients with mosaic variegated aneuploidy (MVA). We describe here novel germline biallelic loss-of-function mutations in MAD1L1, a gene that encodes the Spindle Assembly Checkpoint (SAC) protein MAD1, in a 36-year-old female with microcephaly and developmental delay. The patient developed a constelation of benign and malignant neoplasias derived from the three embryonic layers, some of them such as pilomatrixoma, bone tumors enchondromas and multinodular goiter rarely described in MVA. Cytogenetic and single-cell DNA analysis of peripheral blood cells detected ~35% of aneuploid cells with a variety of random gains of chromosomes. Functional studies demonstrated deficient SAC responses in the absence of MAD1 in mutant lymphocytes. Transcriptomic studies of peripheral blood cells at the single cell level suggested inhibition of protein synthesis, and increased antigen presentation and cytokine signaling in aneuploid T-cells. These pathways were also deregulated in euploid cells from the patient suggesting an immflamation-like, systemic response to chromosomal instability. In addition, single cell RNA-seq analysis detected clonal expansions affecting chromosomes 12 and 18 in specific B-cell and T-cell populations without evidence of hematopoietic neoplasias. These data point to MAD1L1 as a new gene mutated in MVA, and suggest that clonal expansion of minor aneuploid cell populations can be detected in pro-tumoral stages using single-cell technologies.

overall_design: PBMCs with wild type and MAD1L1 gene mutations

first: Carolina

last: Villarroya

last: Sánchez

first: Marcos

last: Malumbres

first: Miguel

last: Urioste


title: Regional transcriptomics and mechanical properties of rat Achilles tendons

city: New York

first: HSS Genomics

last: Research Center

state: New York

address: 535 E 70th St

department: Research

institute: Hospital for Special Surgery

summary: The transcriptome of different tendons varies based on anatomical location and is likely influenced by the biomechanical loading environment. While differences in biologic and mechanical properties of whole tendons have been assessed, less is understood about differences within a tendon along its proximal-distal axis. Therefore, our objective was to determine the characteristics of and relationship between the transcriptomes and mechanical properties of a single tendon.

overall_design: Since Achilles tendon injuries are among the most frequent and debilitating tendon disorders, and rats are classically used as a small animal model to study tendon biology and injury, we selected Achilles tendons from two-month-old male Sprague-Dawley rats. We then used RNA sequencing (RNAseq) and biomechanical testing to evaluate three regions – proximal, middle, and distal – to develop a comprehensive understanding of the biologic and functional properties of tendons along their proximal-distal axis.

first: Nathaniel

middle: P

last: Disser

first: Alexander

last: Piacentini

first: Andrea

last: De Micheli

first: Martin

middle: M

last: Schonk

first: Vincent

last: Yao

first: David

last: Oliver

first: Scott

last: Rodeo


title: Conditional expression of oncogenic KrasG12D and HrasG12D alleles in mouse keratinocytes reveals a dose dependent requirement for tumor formation.

city: Bethesda

first: Thomas

middle: Joshua

last: Meyer

state: Maryland

address: 41 Center Drive, Building 41, Room B620

department: National Cancer Institute

institute: National Institutes of Health

summary: The discovery that activation of the Hras gene was the driver mutation for tumor development in mouse skin treated with 7,12-dimethylbenz(a)anthracene illuminated the link between environmental and molecular carcinogenesis. Subsequent studies revealed that activating mutations in the closely related Kras gene could also drive skin tumor development and progression under certain conditions.  To address a head to head comparison of downstream signaling produced by each activated oncogene primary keratinocytes were isolated from the LSL-HrasG12D and LSL -KrasG12D C57BL/6J mouse models that carry conditionally expressed mutant alleles when a Lox-STOP-Lox segment is excised by Cre recombinase adenovirus treatment. Keratinocytes expressing two mutant alleles of HrasG12D (HH), only one mutant allele of HrasG12D (H), one mutant allele of KrasG12D (K) or one mutant allele of each (HK) were  evaluated for differences in downstream signaling, gene expression and the ability to form squamous papillomas orthotopically in vivo.

overall_design: To further characterize what unique transcriptional changes could be attributed to tumorigenic versus non tumorigenic cultures, we subjected WT, H, K, HH, and HK keratinocyte cultures to RNA-seq analysis.

first: C

last: Cataisson

first: S

last: Yuspa


title: Comparing the gene signature of mouse primary keratinocytes expressing a  KrasG12D allele on mixed C57BL/6 :FVB/N background versus an F3 FVB/N backcross

summary: LSL-KrasG12D mice were backcrossed with FVB/N mice and primary keratinocytes were harvested were from F1 and F3 and transduced in vitro with a Cre adenovirus to express a single mutant Kras allele. When cultures were harvested and transplanted on athymic hosts large squamous papilloma formed within 3 weeks but only from F3 keratinocyte cultures

overall_design: To further characterize what unique transcriptional changes could be attributed to tumorigenic (F3 backcross) versus non tumorigenic (F1) cultures, we subjected F1+Cre and F3 + Cre KrasG12D keratinocyte cultures to RNA-seq analysis.


title: Duodenal inflammation in Common variable immunodeficiency has altered transcriptional response to viruses

city: Oslo

first: Mingyi

last: Yang

address: Sognsvannsveien 20

department: Department of Microbiology, Rikshospitalet

institute: Oslo University Hospital

summary: To elucidate the role of duodenal microenvironment in Common variable immunodeficiency pathogenesis (CVID), we sought to explore the transcriptome regulation in duodenal biopsies.

overall_design:
Total RNA was isolated from snap-frozen pieces of duodenal biopsies and  analyzed by RNA-seq in CVID, celiac disease and healthy controls.  Comparative gene expression profiling between healthy control and disease condition.
CVID_N = CVID with normal levels of  intraepithelial lymphocytes
CVID_IEL = CVID with increased levels of  intraepithelial lymphocytes
celiac = celiac disease
control = healthy control

first: Mari

last: Kaarbø

first: Johannes

middle: R

last: Hov

first: Kristian

last: Holm

first: Mirta

last: Mittelstedt Leal de Sousa

first: Magnhild

last: Macpherson

first: Henrik

last: Reims

first: Anne

last: Kran

first: D

last: Reikvam

first: Bente

last: Halvorsen

first: Pål

last: Aukrust

first: Knut

last: Lundin

first: Børre

last: Fevang

first: Magnar

last: Bjørås

first: Silje

last: Fjellgård Jørgensen


title: B cells after CD74 activation.

city: Rehovot

first: Idit

last: Shachar

address: 234 Herzl Street

country: Israel

institute: Weizmann Institute

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

overall_design: Refer to individual Series


title: Genome wide H3K4me2 detection after CD74 activation.

summary: CD74 (invariant chain), expressed on B cells, is directly involved in shaping the B cell repertoire by regulating their survival in health and disease. Binding of its ligand, macrophage migration inhibitory factor (MIF), induces a cascade that results in CD74 intramembrane proteolysis, and the release of the CD74 intracellular domain (CD74-ICD). CD74-ICD translocates to the nucleus where it induces activation of transcription. In the current study, we characterized the transcription factor activity of CD74-ICD. Following histone modifications we are able to characterize CD74's binding sites as regulatory areas.

overall_design: Examination of the histone modifications with or without CD74 cell surface mulecule activation.

first: Keren

last: David


title: Elucidate the role of CD74 in gene transcription regulation by analyzing the genes up or down regulated after 8 hours of activation in human naive B cells.

summary: CD74 (invariant chain), expressed on B cells, is directly involved in shaping the B cell repertoire by regulating their survival in health and disease. Binding of its ligand, macrophage migration inhibitory factor (MIF), induces a cascade that results in CD74 intramembrane proteolysis, and the release of the CD74 intracellular domain (CD74-ICD). CD74-ICD translocates to the nucleus where it induces activation of transcription. In the current study, we characterize the transcription regulator activities of CD74 by analysing its ability to alter gene expression in mRNA levels.

overall_design: Examination of the genes that are being up or down regulated after CD74 cell surface mulecule activation.


title: High accuracy classification of developmental toxicants by in vitro tests of human neuroepithelial and cardiomyoblast differentiation

city: Dortmund

first: Jan

middle: Georg

last: Hengstler

address: Ardeystraße 67

department: Toxikologie / Systemtoxikologie

country: Germany

institute: Leibniz-Institut für Arbeitsforschung an der TU Dortmund

summary: Stem cell-based tests for developmental toxicity are currently intensively studied. Here, we used a protocol that differentiates human induced pluripotent stem cells (hiPSCs) to neural ectodermal progenitor cells (UKN1) and exposed them to 23 teratogens and 16 non-teratogens at human relevant concentrations. Substance-induced, genome-wide expression profiles were analyzed by two procedures that classified the compounds either based on the number of significantly deregulated genes or on a classification technique with cross-validation. Both procedures demonstrated a high performance with accuracy, sensitivity and specificity of 0.90, 0.83 and 1.0, as well as 0.87, 0.92 and 0.80, respectively. Comparing the present findings with the UKN1 test to those from our recently published UKK2 test that instead recapitulates cardiomyogenic differentiation showed a high congruence in compound classification. This may be explained by the fact that the same pathways, such as PI3K-Akt, P53, TGF-beta, MAPK, EGFR and Hippo were overrepresented among the differentially expressed genes for both tests. However, for some teratogens discrepant results were obtained, such as atorvastatin and thalidomide. In conclusion, UKN1 identifies teratogens with high sensitivity and specificity, and combined interpretation analysis with other tests that differentiate hiPSCs into otherdifferent cell types may further improve the results in the future.

overall_design: Human iPSCs were differentiated for 6 days according to a neuroepithelial protocol (UKN1) and incubated with compounds at the same time. RNA was isolated from these cells and a whole transcritpome analysis was performed with Affymetrix HG-U133 Plus 2.0 arrays. Compound-induced gene expression changes were determined with statistical models.

first: Florian

last: Seidel

first: Anna

last: Cherianidou

first: Franziska

last: Kappenberg

first: Miriam

last: Marta

first: Nadine

last: Dreser

first: Jonathan

last: Blum

first: Tanja

last: Waldmann

first: Nils

last: Blüthgen

last: Meisig

first: Katrin

last: Madjar

first: Margit

last: Henry

first: Tamara

last: Rotshteyn

first: Rosemarie

last: Marchan

first: Karolina

last: Edlund

first: Marcel

last: Leist

first: Jörg

last: Rahnenführer

first: Agapios

last: Sachinidis


title: Different expression of lincRNAs between wild type and oxaliplatin resistant HepG2 cell line

city: Shijiazhuang

first: Luyuan Ma

middle: Luyuan

last: Ma

address: No.68, Xiangjiang Road

institute: the Third Hospital of Hebei Medical University

summary: We found that there were 2109 differentially expressed lincRNAs between oxaliplatin resistant and wild type HCC cells, of which 1109 were up-regulated lincRNAs and 1000 were down-regulated lincRNAs.

overall_design: According to the construction method of drug-resistant HepG2 cells, we screened oxaliplatin resistant cells, detected the expression of lincRNA in drug-resistant cell lines and wild-type cell lines, and analyzed the up-regulated and down-regulated lincRNAs after summarizing the differentially expressed lincRNAs.

first: Luyuan


title: Investigation of target molecule alterations by a cDNA microarray in CU27-treated HCC cells

city: Beijing

first: Jun-Nian

last: Zhou

address: 27# Taiping Road

institute: Institute of Health Service and Transfusion Medicine

summary: BACKGROUND & AIMS: Growing lines of evidence suggests that a subpopulation of cancer cells with self-renewal and tumor-initiating capacity, termed as cancer stem cells (CSCs) or tumor initiation cells (TICs), play pivotal roles in tumor relapse and tumor distant organ metastasis. Therefore, to prevent and treat metastasis based on targeting essential molecules regulating CSCs emerges a promising strategy. Here we describe CU-27, a novel organic selenium compound, significantly diminishes hepatocarcinoma cancer cell (HCC) stemness and inhibits cacner cell metastasis in vitro and in vivo. METHODS: we performed a functional screen to identify compounds with anti-CSC and metastasis effects, In vitro CSC models, tumorspheres, drug resistance and the flow cytometry analysis of CSC markers together were used. In vivo CSC models, limiting dilution and metastatic mouse model were used. We compared mRNA expression profiles of the CU27-treated and control cells with mRNA microarray. The key biological target of CU27 was analyzed by Ingenuity pathway analysis (IPA). The surface plasmon resonance (SPR), chromatin immunoprecipition (ChIP) assays and the dual luciferase reporter assays were used to explore mechanisms of CU27. RESULTS: A novel selenium-containing small molecule-CU-27, was demonstrated to significantly inhibit CSCs self-renewal and function as a metastasis suppressor of HCC cells in vitro and in vivo. Through differentially expressed gene screening with cDNA microarray and IPA analysis, c-MYC, which is mostly recognized to play very important roles in tumor initiation and maintenance in many kinds of tumors, was identified as the major biological target of CU-27. CU-27 was found to significantly suppress c-MYC transcription function and downregulate expression levels of its target genes, thereby inhibit CSC self-renewal and distant metastasis of HCC cells. Ectopic expression of c-MYC rescues the inhibition effects of CU-27 on HCC cells. More important, CU-27 was further demonstrated to interact directly with the bHLH domain of c-MYC protein and decrease its occupancy of the promoter region of target genes, which, in turn, downregulates c-MYC target gene expressions. CONCLUSIONS: CU-27 which can inhibit HCC CSCs and distant metastasis through suppressing c-MYC transcriptional function. Our study provides a vital strategy for targeting CSC and metastasis by inhibiting c-MYC function with novel selenium-containing small molecules.

overall_design: The profiles of differentially expressed mRNAs were analyzed in Hep3b cells and Huh7.5.1 cells treated with 10 μM CU27 (48 hours) or DMSO as controls.

first: Biao

last: Zhang

first: Hai-Yang

last: Wang

first: Wen

last: Yue

first: Xue-Tao

last: Pei


title: Single-cell transcriptome of wet AMD patient-derived   endothelial cells in angiogenic sprouting

status: Public on Nov 02 2022

city: Singapore

first: Christine

last: Cheung

address: 59 Nanyang Drive

country: Singapore

institute: Nanyang Technological University

summary: Age-related macular degeneration (AMD) is a global leading cause of visual impairment in older populations. ‘Wet’ AMD, the most common subtype of this disease, occurs when pathological angiogenesis infiltrates the subretinal space (choroidal neovascularization), causing hemorrhage and retinal damage. Gold standard anti-vascular endothelial growth factor (VEGF) treatment is an effective therapy, but the long-term prevention of visual decline has not been as successful. This warrants the need to elucidate potential VEGF-independent pathways. We generated blood out-growth endothelial cells (BOECs) from wet AMD and normal control subjects, then induced angiogenic sprouting of BOECs using a fibrin gel bead assay. To deconvolute endothelial heterogeneity, we performed single-cell transcriptomic analysis on the sprouting BOECs, revealing a spectrum of cell states. Our wet AMD BOECs share common pathways with choroidal neovascularization such as extracellular matrix remodeling that promoted proangiogenic phenotype, and our ‘activated’ BOEC subpopulation demonstrated proinflammatory hallmarks, resembling the tip-like cells in vivo. We uncovered new molecular insights that pathological angiogenesis in wet AMD BOECs could also be driven by interleukin signaling and amino acid metabolism. A web-based visualization of the sprouting BOEC single-cell transcriptome (https://christinecheunglab.shinyapps.io/human_wet_AMD_sprouting/) has been created to facilitate further discovery research.

overall_design: BOECs were generated from blood buffy coat of 2 wet AMD and 1 normal subjects, allowed to sprout in a fibrin gel sprouting assay, and analyzed using scRNAseq.

first: Natalie

last: Yeo


title: Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia [Exome-seq]

first: Paola

last: Scaffidi

summary:
Aim: assess the contribution of de-novo clonal mutations to the observed adaptive behaviours to nutrient starvation in PDX derived melanoma and lung cancer cells.
Methods: Identical replicates from both cancer models were plated in 96 wells plates and grown in starvation (RPMI media lacking L-glutamine). After prolonged exposure to starvation, extensive phenotypic variability was observed. We selected populations that managed to adapt (t20 samples, strong but also moderate phenotypes) and performed exome-seq. Comparison of their mutational landscape with the initial parental populations (t=0) will uncover possible candidates that drive the adaptation of these populations.
Results: Absence of any selected clonal mutation within individual resistant populations or recurrent subclonal mutations across replicates
Conclusions: The stochastic adaptive behaviours observed upon starvation in PDX MeA5a and L1C5c derived lines does not seem to be confered through selection of clonal genetic events.

overall_design: Exome-seq in 10 populations (5x Melanoma, 5x NSCLC). Comparison with the mutational landscape of the parental populations before nutrient starvation (DAY O samples)

first: Ioannis

last: Loukas

first: Phil

last: East


title: Effect of AMP-CpG on lymph node immune response in mouse

city: Boston

first: Martin

last: Steinbuck

state: Massachusetts

address: 451D Street, Ste 501

institute: Elicio Therapeutics

summary: Despite the success of currently authorized vaccines for the reduction of severe COVID-19 disease risk, rapidly emerging viral variants continue to drive pandemic waves of infection, resulting in numerous global public health challenges. Progress will depend on future advances in prophylactic vaccine activity, including advancement of candidates capable of generating more potent induction of cross-reactive T cells and durable cross-reactive antibody responses. Here we evaluated an Amphiphile (AMP) adjuvant, AMP-CpG, admixed with SARS-CoV-2 Spike receptor binding domain (RBD) immunogen, as a lymph node-targeted protein subunit vaccine (ELI-005) in mice and non-human primates (NHPs). AMP-mediated targeting of CpG DNA to draining lymph nodes resulted in comprehensive local immune activation characterized by extensive transcriptional reprogramming, inflammatory proteomic milieu, and activation of innate immune cells as key orchestrators of antigen-directed adaptive immunity. Prime-boost immunization with AMP-CpG in mice induced potent and durable T cell responses in multiple anatomical sites critical for prophylactic efficacy and prevention of severe disease. Long-lived memory responses were rapidly expanded upon re-exposure to antigen. In parallel, RBD-specific antibodies were long-lived, and exhibited cross-reactive recognition of variant RBD. AMP-CpG-adjuvanted prime-boost immunization in NHPs was safe and well tolerated, while promoting multi-cytokine-producing circulating T cell responses cross-reactive across variants of concern (VOC). Expansion of RBD-specific germinal center (GC) B cells in lymph nodes correlated to rapid seroconversion with variant-specific neutralizing antibody responses exceeding those measured in convalescent human plasma. These results demonstrate the promise of lymph-node adjuvant-targeting to coordinate innate immunity and generate robust adaptive responses critical for vaccine efficacy.

overall_design: 3 groups of mice were injected with the following vaccines: mock control (SARS-CoV2-RBD without adjuvant), CpG (SARS-CoV2-RBD with CpG), AMP-CpG (SARS-CoV2-RBD with AMP-CpG). 4 time points (2h, 6h, 24h, 72h) with 2 mice per time point.

first: Peter

middle: C

last: DeMuth

first: Lochana

last: Seenappa

first: Erica

last: Palmer


title: Effect of AMP-CpG on lymph node immune response in rhesus macaque

overall_design: 1 group of three NHP (non-human primates) was injected with AMP-CpG vaccine (SARS-CoV2-RBD with AMP-CpG). Their immune responses within the draining inguinal lymph nodes at 24h post immunization were compared to baseline responses prior to immunization.

first: Lisa

middle: K

last: McNeil


title: Renal medullary carcinomas (RMC) habor a distinct methylation phenotype

city: Augsburg

first: Victoria

last: Fincke

state: Bayern

address: Stenglinstraße 2

department: pediatric oncology

institute: University hospital Augsburg

summary: Renal medullary carcinomas (RMC) are rare aggressive tumors of the kidneys, characterized by a -mostly- biallelic loss of SMARCB1. Characteristically, these tumors arise in patients with sickle cell trait or other hemoglobinopathies. Recent molecular and landscaping characterization efforts have unraveled oncogenic pathways that drive tumorigenesis. Among these, gene sets that characterize replicative stress and the innate immune response are upregulated in RMCs. Despite comprehensive genetic and transcriptomic characterizations, commonalities or differences to other SMARCB1 deficient entities so far have not been investigated. We analyzed the methylome of four novel primary RMC and compared it to other, SMARCB1 deficient entities such as rhabdoid tumors (RT) and epithelioid sarcomas using 850K methylation arrays.  In accordance with previous gene expression data, we find that RMCs separate from other SMARCB1 deficient entities such as extra-and intracranial rhabdoid tumors, pointing to a potentially different cell of origin and a role of additional mutations or genetic aberrations that may drive tumorigenesis and thus alter the methylome when compared to rhabdoid tumors.   In a focused analysis of genes that are important for nephrogenesis, we detected particularly genes that govern early nephrogenesis such as FOXI to be hypomethylated and expressed at high levels in RMC. Overall, our analyses underscore the fact that RMCs represent a separate entity with limited similarities to rhabdoid tumors warranting specific treatment, tailored to the aggressiveness of the disease.

overall_design: The DNA methylation of 4 RMC samples was analyzed.

first: Pascal

middle: D

last: Johann

first: Piyush

last: Joshi

first: Mateja

last: Krulik

first: Ying-Bei

last: Chen


title: Siponimod modulates the reaction of microglial cells to pro-inflammatory stimulation

city: Düsseldorf

first: Joel

last: Gruchot

address: Moorenstraße 5

department: Neurology

institute: Heinrich-Heine-University

summary: Siponimod (Mayzent®), a sphingosine 1-phosphate receptor (S1PR) modulator which prevents lymphocyte egress from lymphoid tissues, is approved for the treatment of relapsing-remitting- and active secondary progressive multiple sclerosis. It can cross the blood-brain-barrier (BBB) and selectively binds to S1PR1 and S1PR5 expressed by several cell populations of the central nervous system (CNS) including microglia. To investigate wether Siponimod modulates the genetic signature of inflammed microglia, we performed a transcriptome analyses of primary rat microglial cells stimulated with LPS and With or Without Siponimod.

overall_design: Transcriptome analysis of primary rat microglial cells stimulated with LPS and with or without Siponimod (3 replicates each).

first: Patrick

last: Küry


title: Effect of AMP-CpG on lymph node immune response in mouse and rhesus macaque

sample_organism:
Macaca mulatta
Mus musculus

platform_organism:
Macaca mulatta
Mus musculus


title: Next Generation Sequencing Facilitates Quantitative Analysis of METTL3 overexpression in THP-1 cells [RNA-seq]

city: Jinan

first: Chunyan

last: Ji

address: Wenhua West Road

institute: Qilu Hospital

summary: The goals of this study are to compare the downstream m6A modification changes and transcriptional changes in AML cells with or without METTL3 overexpression.mRNA profiles of METTL3-ovexpressing THP-1 cells and of its negative control cells were generated by RNA-seq and m6A-seq, in triplicate, using Illumina Hiseq 2000

overall_design: METTL3-ovexpressing THP-1 cells and  its negative control cells were collected, and the RNA extracted from samples with three biological replicates was subjected to m6A and RNA sequencing. For data analysis, the THP-1 cells were used as reference sample to investigate the role of m6A in AML chemotherapy resistance.

first: Mingying

last: Li

first: Tao

last: Sun

first: Yuan

last: Xia


title: Meta-analysis of Epigenome Wide Association Studies of Major Depressive Disorder

city: Titusville

first: Qingqin

state: NJ

address: 1125 Trenton-Harbourton Road

institute: Janssen R&D, LLC

summary: EPIC array data were generated from 2 MDD case control cohorts. EWAS was performed in each cohort, followed by meta-analysis between the 2 cohort. Cohort 1: A total of 191 blood samples from 112 patients with MDD was collected up till the interim analysis (wave 1 samples) from an observational clinical study OBSERVEMDD0001 (ClinicalTrials.gov Identifier: NCT02489305) compared to 32 healthy controls; Cohort 2: The MDD cases (N = 359) were drawn from the Molecular Biomarkers of Antidepressant Response study compared to 68 healthy controls.

overall_design: Whole blood samples were collected, and DNA was extracted for methylation profiling. DNA methylation was measured using Infinium® MethylationEPIC BeadChip (Illumina, Inc., San Diego, CA, USA) at 850 000 CpG sites throughout the genome. Genomic DNA samples were bisulfite-converted using the EZ-DNA Methylation Kits (Zymo Research, Irvine, CA, USA) and subsequently analyzed using the Illumina Infinium® HD methylation protocol on the HiScanTM system (Illumina, Inc, San Diego, CA, USA).


title: Integration of genomic and clinical data to predict endometrioid endometrial cancer recurrence

city: Iowa City

first: Jesus

last: Gonzalez Bosquet

state: IA

address: 200 Hawkins Dr

institute: University of Iowa

summary: Endometrial cancer (EC) incidence and mortality continues to rise. Molecular profiling of EC promises improvement of risk assessment and treatment selection. Though, we still lack robust and accurate models to predict those at risk of failing treatment. The objective of this pilot study is to create models with clinical and genomic data that will discriminate patients with EC at risk of disease recurrence. We performed a pilot, retrospective, case-control study evaluating patients with EC, endometrioid type: 7 with recurrence of disease (cases), and 54 without (controls). RNA was extracted from frozen specimens and sequenced (RNAseq). Genomic features from RNAseq included transcriptome expression, genomic, and structural variation. Feature selection for variable reduction was performed with univariate ANOVA with cross-validation. Selected variables, informative for EC recurrence, were introduced in multivariate lasso regression models. Validation of models was performed in machine learning platforms (ML) and independent datasets (TCGA).  The best performing prediction models (out of >170) contained the same lncRNA features (AUC of 0.9, and 95% CI: 0.75, 1.0). Models were validated with excellent performance in ML platforms and good performance in an independent dataset. Prediction models of EC recurrence containing lncRNA features have better performance than models with clinical data alone

overall_design: We performed a retrospective, single institution case-control study in which we included 61 patients with EEC from 1991 to 2010 available in our biobank with pre-operative and intra-operative clinical data.

last: Gonzalez-Bosquet

first: Eric

last: Devor


title: Spatial transcriptomics of triple negative breast cancer

city: Los Angeles

first: John

last: Carpten

address: 1450 Biggy St

institute: University of Southern California

summary: Triple negative breast cancer (TNBC) is an aggressive and clinically challenging subtype of breast cancer. TNBC disporportionately affects African-American (AA) women, but the biological basis of this disparity is not understood. To gain a better understanding of TNBC, particularly in AA patients, we applied spatial transcriptomics to thoroughly characterize gene expression and tissue architecture in TNBC. Our cohort consisted of 22 patients, 15 of whom were AA, and 7 who were Caucasian. We obtained 2 sections from each patient's tumor (except for patient 19) for a total of 43 samples.

overall_design: 28 tissue sections representing 14 primary TNBC tumors were subject to spatial transcriptomics using the 10x Genomics Visium platform, followed by high throughput sequencing. Raw data not submitted due to patient privacy concerns.

first: Rania

last: Bassiouni

first: Michael

last: Idowu

first: David

last: Craig


title: Pro-inflammatory cytokines promote selective transcription of circular RNAs in human pancreatic β cells

city: Herlev

first: Joachim

last: Størling

address: Borgmester Ib Juuls Vej 83,

country: Denmark

institute: Steno Diabetes Center Copenhagen

summary:
Circular RNAs (circRNAs) have recently been implicated in impaired β-cell function in diabetes. Using microarray-based profiling of circRNAs in human EndoC-βH1 cells treated with pro-inflammatory cytokines (interleuklin-1β + interferon-γ), this study aimed at investigating the expression and possible regulatory roles of circRNAs in human β cells.
We identified ~5,000 β-cell expressed circRNAs of which 84 were differentially expressed (DE) after cytokine exposure. Pathway analysis of the host genes of the DE circRNAs revealed enrichment for cytokine signaling pathways, indicative of selective transcription of circRNAs from inflammatory genes in response to cytokines. Multiple binding sites for β-cell enriched microRNAs and RNA-binding proteins were observed for the highly upregulated circRNAs, supporting their function as ‘sponges’ or ‘decoys’. We also present evidence for circRNA sequence conservation in multiple species, presence of cytokine-induced regulatory elements and putative protein-coding potential for the DE circRNAs. The study highlights the complex regulatory potential of selectively transcribed circRNAs, which may play a crucial role during immune-mediated β-cell destruction in type 1 diabetes.

overall_design: Human EndoC-βH1 cells were left untreated or exposed to proinflammatory cytokines (IL-1β+IFN-γ) for 24h and 48h (n=3, in each condition). Total RNA from 12 samples (four groups) was extracted and  profiled for circRNAs.

first: Simranjeet

last: Kaur

first: Flemming

last: Pociot


title: Transcriptomic-Metabolomic Profiling in Mouse Lung Tissues Reveals Sex- and Strain-Based Differences

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: Altered Transcriptomic Profiles in Sex, Strain, ATG-treatment and Hyperoxia Exposure

overall_design: There has been a heighted interest in understanding the influences of sex and strain on variety of diseases states. We assessed the metabolomics profiles of male and female C57B6/J as well as male and female C3H/HeN. We pretreated each of these mice groups with 25mg/kg of Aurothioglucose (ATG) prior to being exposed to either 100% filtered air, or >95% oxygen for 96 hours. These studies begin to address the underlying altered metabolomic signaling that is influenced by sex and/or strain.

first: Joyln

last: Fernendez

first: Katelyn

last: Dunigan Russell

first: Lynette

last: Rogers

first: Trent

last: Tipple


title: Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia [scRNA-seq]

city: London

first: Paola

last: Scaffidi

address: 1 Midland Road

institute: Francis Crick Institute

summary: Identification of gene expression changes at the single-cell level induced by glutamine deprivation in melanoma cells lacking various epigenetic regulators

overall_design:
scRNA-seq analysis of melanoma cells expressing 4-7sgRNAs targeting members of the PRC2 complex (EED, EZH2, SUZ12), histone H1B (HIST1H1B), the chromatin remodeller SMARCD1 and a non-expressed control gene (TNP2), and grown in either unperturbed conditions (d0) or under glutamine deprivation (d1, d2, d12).
With the guild sequences (guides.csv) in combination with the sample pairings (indicated in column "characteristic: Gex-CRISPR"), the 10x library type information, the fastq files can be used to quantify the libraries using the cellranger count software from 10x Genomics.

first: Ioannis

last: Loukas

first: Paolo

last: Inglese

first: Phil

last: East


title: Campylobacter jejuni interactions with Acanthamoeba castellanii

city: LONDON

first: Fauzy

last: Nasher

address: Keppel Street,

institute: London School of Hygiene and Tropical Medicine

summary:
To investigate the interaction of intra-amoebal C. jejuni with the transient host A. castellanii.
We then performed gene expression profiling analysis using data obtained from RNA-seq of control and intra-amoebal C. jejuni.

sample_organism:
Campylobacter jejuni
Acanthamoeba castellanii

overall_design: Comparative gene expression profiling analysis of RNA-seq data for C. jejuni 11168H intra-amoebal vs. control.

first: Burhan

last: Lehri


title: Different gene sets are associated with azacitidine response in vitro and myelodysplastic syndrome patients

city: Badalona

first: Jeannine

last: Diesch

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

institute: Josep Carreras Leukaemia Research Institute

summary: Myelodysplastic syndromes (MDS) are a heterogeneous group of hematopoietic disorders and characterized by dysplasia, ineffective hematopoiesis and predisposition to secondary acute myeloid leukemia (sAML). Azacitidine (AZA) is the standard care for high-risk MDS patients not eligible for allogenic bone marrow transplantation. However, only half of the patients respond and all patients eventually relapse. Response predicting biomarkers and combinatorial drugs targets enhancing response and its duration are needed. Here, we have taken a dual approach. First, we have evaluated genes encoding chromatin regulators for their capacity to modulate AZA response. We were able to validate several genes, whose genetic inhibition affected the cellular AZA response, including four genes encoding components of ISWI chromatin remodelling complex pointing towards a specific function and co-vulnerability. Second, we have used a classical cohort analysis approach measuring the association of expression of a gene panel in bone marrow samples collected at diagnosis of 36 MDS patients. The gene panel included the identified AZA modulators, genes known to be involved in AZA metabolism and previously identified candidate modulators. In addition to confirming a number of previously made observations, we were able to identify several new associations, such as SMARCA5 as positive indicator for AZA response, or NSUN3 that correlated with increased overall survival. Taken together we have identified a number of genes associated with AZA response in vitro and in patients. These groups of genes are largely non-overlapping suggesting that different gene sets need to be exploited for the development of combinatorial drug targets and response-predicting biomarkers.

overall_design: SKK-1 cells were transduced with the Epi9 shRNA library, selected with puromycin and half of the cells treated with 0.075µM azacitidine every two days for two weeks. 21 days after initiation of the treatment the cells were harvested, the gDNA extracted and sequenced using a custom primer recognizing the shRNA guide strands

first: Marguerite-Marie

last: Le Pannérer

first: Raquel

last: Casquero

last: Maher

first: Olga

last: Garcia

first: Torsten

last: Haferlach

first: Johannes

last: Zuber

first: Andrea

last: Kündgen

first: Katharina

last: Götze

first: Marcus

last: Buschbeck


title: Monodelphis domestica induced pluripotent stem cells reveal metatherian pluripotency architecture

city: McAllen

first: Satish

last: Kumar

state: Texas

address: 5300 North L Street (MBMRF-2.219)

department: Division of Human Genetics & South Texas Diabetes and Obesity Institute, UTRGV School of Medicine

institute: University of Texas Rio Grande Valley

summary: Marsupials have been a powerful comparative model to understand mammalian biology. However, because of the unique characteristics of their embryology, marsupial pluripotency architecture remains to be fully understood, and nobody has succeeded in developing embryonic stem cells (ESCs) from any marsupial species. We have developed an integration-free induced pluripotent stem cell (iPSC) reprogramming method and established validated iPSC lines from two fully inbred strains of the gray short-tailed opossum (Monodelphis domestica). A comprehensive characterization of the M. domestica skin fibroblasts and their reprogrammed iPSCs was performed by genome-wide mRNA sequencing. The established monoiPSCs showed a significant (6,181 DE genes) but highly uniform (between clone r2 at 95% CI = 0.973 ± 0.007) resetting of the cellular transcriptome during reprogramming and were highly similar to eutherian ESCs and iPSCs in their overall transcriptomic and functional profiles. However, monoiPSCs showed unique regulatory architecture of the core pluripotency transcription factors and were more like epiblasts. Our results suggest POU5F1 and the splice variant specific expression of POU5F3 synergistically regulate the opossum pluripotency gene network. It is plausible that POU5F1, POU5F3 splice variant XM_016427856.1, and SOX2 form a self-regulatory network. NANOG expression, however, was specific to monoiPSCs and epiblasts, and displayed a distinct expression profile in embryonic cells. Furthermore, POU5F1 was highly expressed in trophectoderm cells, whereas all other pluripotency transcription factors were significantly downregulated, suggesting that the regulatory architecture of core pluripotency genes of marsupials may be distinct from that of eutherians.

overall_design: To better understand marsupial pluripotency architecture, a genome-wide comparative gene expression analysis of the M. domestica skin fibroblasts and their reprogrammed iPSCs was performed.

first: John

last: VandeBerg


title: Grain RNAseq of two hard red winter wheat cultivars with contrasting grain protein contents

city: College Station

first: Sakiko

last: Okumoto

state: TX

address: 370 OLSEN BLVD MS 2474

institute: TAMU

summary: TAM 111 and TAM 112 are two popular cultivars grown in the Southern US Great Plains with significantly different protein content. Thus, to investigate likely regulatory differences, transcriptome data were analyzed from developing grains at early- and mid-filling stages.

overall_design: Grains of two cultivars (TAM111 and TAM112) were harvested at early (5DAP) and mid (14DAP) stages of grain filling.

first: Ze

middle: T

last: Fang

first: Shuyu

last: Liu


title: Single-nuclei analysis reveals depot-specific transcriptional heterogeneity and depot-specific cell types in adipose tissue of dairy cows [snRNA-seq]

city: Lexington

first: Shavahn

last: Loux

state: KY

address: 1400 Nicholasville

department: Veterinary Science

institute: University of Kentucky

summary: The objective for this study was to elucidate differences in cellular diversity of VAT and SAT in dairy cows at the single-nuclei level.

overall_design: Visceral adipose tissue (VAT) was collected from greater omentum and subcutaneous adipose tissue (SAT) from the right flank of the same three lactating Holstein dairy cows.

first: Tainara

last: Michelotti

first: Brent

last: Kisby

first: Lauryn

middle: S

last: Flores

first: Alexandra

last: Tegeler

first: Mohamed

last: Fokar

first: Chiquito

last: Crasto

first: Clarissa

last: Strieder-Barboza


title: Single-nuclei analysis reveals depot-specific transcriptional heterogeneity and depot-specific cell types in adipose tissue of dairy cows [bulkRNA-seq]


title: Next Generation Sequencing Facilitates Quantitative Analysis of METTL3 overexpression in THP-1 cells [m6A-Seq]

first: Chunyan

last: Ji

first: Mingying

last: Li

first: Tao

last: Sun

first: Yuan

last: Xia


title: Single-nuclei analysis reveals depot-specific transcriptional heterogeneity and depot-specific cell types in adipose tissue of dairy cows

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

overall_design: Refer to individual Series


title: Translation and Natural Selection of long non-canonical RNA micropeptides

city: Seville

first: Juan

middle: Pablo

last: Couso

address: Carretera de Utrera, Km 1

institute: Centro Andaluz de Biologia del Desarrollo

summary:
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides but lacking canonical coding sequences. Apparently unable to produce peptides, lncRNA function seems to only involve RNA sequence and structure. Here, we exhaustively detect in-vivo translation of small open reading frames (small ORFs) within lncRNAs using Ribosomal profiling during Drosophila melanogaster embryogenesis. We show that around 30% of lncRNAs contain small ORFs engaged by ribosomes, leading to regulated translation of 100 to 300 micropeptides. We identify lncRNA features that favour translation, such as cistronicity, Kozak sequences, and conservation.
For this latter, we develop a bioinformatics pipeline to detect small ORF homologues, and we reveal evidence of natural selection favouring the conservation of micropeptide sequence and function across evolution. Our results expand the repertoire of lncRNA functions, and suggest that lncRNAs give rise to novel coding genes throughout evolution. Since most lncRNAs contain small ORFs with as yet unknown translation potential, we propose to rename them “long non-canonical RNAs”.

overall_design:
We  performed gene expression profiling analysis by additional sequencing of previously-obtained Ribo-Seq and RNA-Seq libraries (Embryo and S2 cells), see Patraquim et a. (2020).
Comparative gene expression profiling analysis of RNA-seq data for C3H10T1/2 cells and its KD derivatives (shKDM4D, shNFIB, and shMLL1).

first: Pedro

last: Patraquim

first: Emile

last: Magny

first: José

last: Pueyo

first: Ana

last: Platero


title: Next Generation Sequencing Facilitates Quantitative Analysis of METTL3 overexpression in THP-1 cells


title: Effect of zinc chelator TPEN on gene expression of retinal ganglion cells during optic nerve injury

city: Guangzhou

first: Jiahui

last: Tang

address: 7 Jinsui Road

institute: State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University

summary: Retinal ganglion cells (RGCs) convey the major output of information collected from the eye to the brain. RGCs are irreversibly lost when injured in degenerative diseases such as glaucoma; this failure can be partially reversed by eliminating the retinal mobile zinc (Zn2+) and leads to substantial axon regeneration. Here, we conducted an mRNA sequencing of flow cytometry-isolated RGCs 3 days after optic nerve injury (NC) with or without TPEN treatment. We identified differentially expressed genes using a cutoff of at least 1.5-fold change and FDR of at least 0.05. We focused on the intersecting genes that were upregulated after NC and recovered in TPEN (TPEN/NC; fold change < -1.5; P < 0.05), namely, TPEN target genes.

overall_design: Ctrl: RGCs isolated from normal intact retinas  NC: RGCs isolated from optic nerve crush retinas with PBS intraocular injection  TPEN: RGCs isolated from optic nerve crush retinas with zinc chelator (TPEN) intraocular injection

first: Zhe

last: Liu

first: Yiqing


title: RNA bisulfite sequencing of mRNAs from E16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h.

city: Blacksburg

first: Xiguang

last: Xu

state: VA

address: 1015 Life Science Circle

department: Department of Biomedical Sciences and Pathobiology

institute: Virginia Tech

summary: We performed RNA methylation profiling for E16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h.

overall_design: RNA bisulfite sequencing of mRNAs from E16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h, in biological duplicates.

first: Hehuang

last: Xie


title: Genes differentially expressed between pea accession P665 (resistant to Peyronellaea pinodes) and pea cv. Messire (susceptible to P. pinodes) after inoculation with P. pinodes

city: Cordoba

first: Sara

last: Fondevilla

state: Cordoba

address: Avda. Menéndez Pidal s/n

institute: Instituto de Agricultura Sostenible-CSIC

summary:
To investigate which are the genes providing resistance to P. pinodes in pea accession P665 we applied MACE-seq to P665 and the susceptible accession Messire inoculated and not inoculated plants.
We then performed gene expression profiling analysis using data obtained from MACE-seq at two times points.

overall_design: Comparative gene expression profiling analysis of MACE-seq data for P665 and Messire control and inoculated plants.

first: Nicolas

last: Krezdorn

first: Diego

last: Rubiales

first: Björn

last: Rotter

first: Peter

last: Winter


summary: We performed RNA-seq of E16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h.

overall_design: RNA-seq of E16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h, in biological duplicates.


title: Epigenome analysis of aorta from normal and Stanford-A aortic dissection patients

city: Beijing

first: Xiaohan Fan

address: 167 Beilishilu, Xicheng District

institute: Fuwai hospital

summary: Genome wide DNA methylation profiling of normal and ascending aorta tissue samples from normal and aortic dissection patients. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,512 CpGs in ascending aorta tissue samples. Samples included 4 normal donors and 4 patients with aortic dissection.

overall_design: Bisulphite converted DNA from the 8 samples were hybridised to the Illumina Infinium 450k Human Methylation Beadchip

first: Xiaohan

last: Fan

first: Xiaojian

last: Wang


title: RNA bisulfite sequencing and RNA-seq of 16.5 mouse cortical neurons depolarized with 55mM KCl for 0h, 2h and 6h


title: Differential expression genes between PC9 cells and osimertinib resistant PC9OR cells

city: Xian

first: Yubo

address: Yanta Road

department: Medicine

institute: Xian Jiaotong University

summary:
To investigate the possible resistant mechanism to osimertinib, PC9 cells and their derived osimertinib-resistant PC9OR cells were sequenced using illumina HiSeq.
We then performed gene expression profiling analysis using data obtained from RNA-seq of PC9 cells and their derived PC9OR cells.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for PC9 cells and its osimertinib resistant derivatives (PC9OR).

first: Mingwei

last: Chen


title: Transcriptome analysis of Shank3-heterozygous and -homozygous mice in different brain regions

city: Daejeon

first: Eunjoon

last: Kim

address: Kuseong-dong

department: Center for Synaptic Brain Dysfunctions/Department of Biological Sciences

country: South Korea

institute: IBS/KAIST

summary: Shank3 is an abundant excitatory postsynaptic scaffolding proteins implicated in various neurodevelopmental and psychiatric disorders, including ASD, Phelan-McDermid syndrome, intellectual disability, and schizophrenia. Shank3-mutant mice with a homozygous deletion of exons 14-16 (Shank3-HM mice) show ASD-like behavioral deficits and altered synaptic and neuronal functions, but little is known about how different ages, brain regions, and gene dosages contribute to transcriptomic phenotypes in these mice. Here, we performed RNA-Seq-based transcriptomic analyses of the prefrontal cortex, hippocampus, and striatum in adult Shank3 heterozygous- and homozygous-mutant mice. In addition, juvenile and adult Shank3 homozygous-mutant forebrain transcriptomes were compared. Juvenile and adult forebrain transcriptomes from Shank3 homozygous-mutant mice showed the patterns that are opposite and similar to those observed in ASD: reverse-ASD and ASD-like patterns, respectively. Here, the juvenile reverse-ASD pattern involved synaptic gene upregulations and ribosomal and mitochondrial downregulations, whereas the adult ASD-like pattern involved opposite changes. Gene set enrichment analyses (GSEA) of brain regional transcripts in adult Shank3-HT and Shank3-HM mice revealed that the cortical, hippocampal, and striatal transcripts show distinctly altered biological functions and ASD-related/risk gene expressions. The cortex and striatum display ASD-like patterns whereas the hippocampus displays reverse-ASD patterns. The cortical ASD-like pattern more strongly involves ASD-risk genes whereas the striatal ASD-like pattern more strongly involves astrocyte/microglia genes. Shank3-HT and Shank3-HM transcripts in a given brain region display largely similar patterns in biological functions and ASD-related/risk gene expressions, suggestive of small gene dosage effects. These results suggest that heterozygous and homozygous Shank3 deletions in mice lead to age, brain region, and gene dosage-differential transcriptomic changes.

overall_design: Transcriptome analysis of adult Shank3-heterozygous, -homozygous mice in prefrontal cortex, hippocampus, and striatum

first: Taesun

last: Yoo

first: Hyojin

last: Kang


title: Transcriptome analysis of Shank3-homozygous mutant and wild-type mice of different ages

overall_design: Transcriptome analysis of Shank3-homozygous mutant and wild-type mice at P25 and P60 age


title: Transcriptome analysis of Shank3-heterozygous and -homozygous mice in different ages and brain regions


title: EHF and CDX1 co-operate to drive extensive transcriptional reprogramming and chromatin remodelling in CRC cells

city: Clayton

first: Wei

last: Shi

state: VIC

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology

country: Australia

institute: Monash University


title: EHF and CDX1 co-operate to drive extensive transcriptional reprogramming and chromatin remodelling in CRC cells [RNA-seq]

summary: EHF and CDX1 co-operate to drive differentation of CRC cells. To identify the transcriptional changes induced by these transcription factors, EHF and CDX1 were stably re-expressed in poorly differentiated HCT116 CRC cells and RNA sequencing analysis performed.

overall_design: HCT116 CRC cells were stably transfected with empty-vector control, EHF, CDX1, or EHF plus CDX1 and RNA-Seq analysis performed on each cell line.

first: Ian

last: Luk

first: Yang

last: Liao

first: John

last: Mariadason


title: EHF and CDX1 co-operate to drive extensive transcriptional reprogramming and chromatin remodelling in CRC cells [ATAC-seq]

summary: EHF and CDX1 co-operate to drive differentation of CRC cells. To identify the change in chromatin remodelling induced by these transcription factors, EHF and CDX1 were stably re-expressed in poorly differentiated HCT116 CRC cells and ATAC-seq analysis performed.

overall_design: HCT116 CRC cells were stably transfected with empty-vector control, EHF, CDX1, or EHF plus CDX1 and ATAC-seq analysis performed on each cell line.


title: Global binding profiles of MYBL2 and FOXM1 in lung adenocarcinoma reveal that MYBL2 regulates FOXM1 to control cell-cycle genes including CENPA [ChIP-seq]

city: Los Angeles

first: Suhn

last: Rhie

address: 1450 Biggy Street NRT 3504

department: Biochemistry and Molecular Medicine

institute: University of Southern California

summary: MYBL2 is a transcription factor that has either pro-survival or anti-survival functions in a cell-type specific manner. Overexpression of MYBL2 is associated with worse survival of lung adenocarcinoma, but the mechanism by which it regulates transcription has not yet been elucidated. In this study, we found that MYBL2 mainly binds to the promoters of highly expressed genes in lung adenocarcinoma cells using ChIP-seq. Using knock-down and RNA-seq approach, we identified over a thousand of genes deregulated by MYBL2. By integrating ChIP-seq and RNA-seq data, we identified target genes of MYBL2. We revealed that FOXM1 is regulated by MYBL2 in lung adenocarcinoma cells, and FOXM1 binding sites are largely shared with MYBL2 binding sites. We treated lung adenocarcinoma cells with FDI-6, a known FOXM1 inhibitor and investigated the effect of FDI-6 in transcriptional regulation of MYBL2 and FOXM1. We found that CENPA is one of the key genes regulated by MYBL2 and FOXM1, and that it can be inhibited by FDI-6. Our signaling pathway analysis results revealed that MYBL2 and FOXM1 activate cell-cycle genes, suggesting that MYBL2 and FOXM1 act as oncogenic transcription factors in lung adenocarcinoma cells and FDI-6 could be a potential treatment of the disease.

overall_design: Chromatin immunoprecipitation sequencing (ChIP-seq) of MYBL2 and FOXM1 in A549 lung cancer cells

first: Yuri

last: Lee

first: Zexun

last: Wu

first: Seolyn

last: Yang

first: Shannon

last: Schreiner


title: Selective advantage of epigenetically disrupted cancer cells via phenotypic inertia

first: Paola

last: Scaffidi


title: Transcriptome analysis of Shank2-heterozygous and -homozygous mice in different brain regions

summary: Shank2 is an abundant excitatory postsynaptic scaffolding protein implicated in neurodevelopmental disorders, including autism spectrum disorders (ASD), intellectual disability, developmental delay, and schizophrenia. Shank2-mutant mice with a homozygous deletion of exons 6 and 7 (Shank2-HM mice) show ASD-like behavioral deficits and altered synaptic functions, although little is known about how different brain regions contribute to Shank2-mutant phenotypes. Here we attempted transcriptomic analyses of the prefrontal cortex, hippocampus, and striatum in adult Shank2-heterozygous/HT and Shank2-homozygous/HM mice. The mutant cortex, hippocampus, and striatum displayed distinct sets of differentially expressed genes associated with neuronal and synaptic functions in a gene dosage-differential manner. Gene set enrichment analyses of cortical Shank2-HT transcripts revealed increased synaptic gene expression and transcriptomic changes that are opposite to those observed in ASD (reverse-ASD), whereas cortical Shank2-HM transcripts displayed decreased synaptic gene expression and ASD-like transcriptomic patterns. The hippocampal Shank2-HT transcripts displayed minimally altered synaptic gene expression and mixed ASD-like and reverse-ASD patterns, whereas the Shank2-HM-hippocampus showed increased synaptic gene expression and reverse-ASD patterns. The striatal Shank2-HT/HM transcriptomes were largely similar to the hippocampal transcriptomes, although the main changes were observed in cell-type-specific genes, unlike the hippocampal changes mainly involving ASD-related/risk genes. These results indicate that heterozygous and homozygous Shank2 deletions in mice lead to brain region- and gene dosage-differential transcriptomic changes.

overall_design: Transcriptome analysis of Shank2-heterozygous and -homozygous mice in prefrontal cortex, hippocampus, and striatum

first: Ye-Eun


title: Global binding profiles of MYBL2 and FOXM1 in lung adenocarcinoma reveal that MYBL2 regulates FOXM1 to control cell-cycle genes including CENPA.


title: Role of OspC effectors in the IFN response

first: Andreas

last: Wack

institute: The Francis Crick Institute

summary: Interferons (IFNs) are vital weapons in the arsenal of immune mediators produced in response to infection. We showed that Shigella sonnei blocks signaling and interferon-stimulated genes (ISGs) downstream of all families of IFN via secreted effectors of the OspC family. Notably, Ospc1 and OspC3 strongly block the IFN response. This project aims at investigating the cellular signaling pathways that are impacted by OspC1 and OspC3 with or without IFN stimulation and at clarifying whether observed changes in ISGs expression are general or specific to some ISGs.

overall_design: 293T cells expressing either empty GFP, OspC1 or OspC3 were treated or not with IFN beta overnight. Samples are provided as biological triplicates (experiments performed on different days), resulting in 3 vectors x 2 IFN treatments x triplicates =18 samples.

first: Noemie

last: Alphonse

first: Charlotte

last: Odendall


title: Global binding profiles of MYBL2 and FOXM1 in lung adenocarcinoma reveal that MYBL2 regulates FOXM1 to control cell-cycle genes including CENPA [RNA-seq]

overall_design: Comparative gene expression profilling analysis of RNA-seq data for A549 cells with its knockdown treatment (siMYBL2, siFOXM1, siBoth, FDI6)


title: Gene expression profiling of LLC-OVA tumors treated with gemcitabine, OVA and Imiquimod combinations in C57BL/6J mice

city: Pamplona

first: Pablo

last: Sarobe

address: Avda. Pio XII, 55

institute: CIMA

summary: To identify factors associated with the superior antitumor activity of the vaccine + gemcitabine combination, we collected tumors after a single treatment cycle and we performed an RNAseq study.

overall_design: Comparison of different tumor treatment groups: Untreated (UT) (n=2), vaccinated (VAC) (n=3), gemcitabine (GEM) treated (n=3) and combination of vaccine + gemcitabine (VG) treated mice (n=3).

first: Diana

last: Llopiz

first: David

last: Repáraz


title: A novel gene expression signatures associated with the response to concomitant chemo-radiation therapy in patients with esophageal squamous cell carcinoma

city: Taoyuan City

first: Hsuan

last: Liu

address: No.259, Wenhua 1st Rd., Guishan Dist.

country: Taiwan

institute: Chang Gung University

summary: In this study, esophageal squamous cell carcinoma (ESCC) patients’ endoscopic biopsy tumor tissues obtained before their concomitant chemo-radiation therapy (CCRT) were used to analyze the transcriptomes by using the RNA-sequencing approach. According to retrospective study of patients’ responses to CCRT, the treatment-naive specimen can be divided into two groups (16 good CCRT response and 12 poor CCRT response). This systematic profiling uncovered a gene set that is differentially expressed between the two patient groups.

overall_design: ESCC mRNA profiles of 16 good CCRT responders and 12 poor CCRT responders

first: Yi-Ching

last: Wang

first: Wei-Lun

last: Chang

first: Bertrand

last: Tan


title: Diurnal and nocturnal transcriptional profiling of hippocampal microglia from adult male mice

city: Berlin

first: Andranik

last: Ivanov

address: Chariteplatz 1

department: Core Unit Bioinformatics

institute: Berlin Institute of Health

summary: Microglia cells are the innate immune cells of the brain. They are increasingly studied for their role in virtually all pathological events in the central nervous system. However, no study has thus far looked at whether microglia cells undergo wake and sleep state-dependent changes in transcriptional and translational profile. Rodents are nocturnal animals, and most studies are investigating microglia cells during the rodent's sleep phase, hence during the day, for translational purposes. The aim of this study was to compare the microglial transcriptional, translational and functional profile between the wake and sleep phase. Our results provide evidence that the innate immune cells of the brain do undergo a transcriptional and translational adaptation to the wake or sleep state.

overall_design: diurnal and nocturnal transcriptional profiling of hippocampal microglia from adult male mice.

first: Daniele

last: Mattei

first: Dieter

last: Beule

first: Urs

last: Meyer


title: Gene expression profiling dendritic cells (DC) producing IL-10

summary: To identify factors associated with the immunosuppressor activity of IL-10+ DC, these cells were obtained from VertX mice immunized with OVA+imiquimod and compared with IL-10- DCs from the same mice and from VertX mice, either untreated or vaccinated with OVA+poly(I:C).

overall_design: DC IL-10+ were obtained from pooled spleens (n=20 per sample) from OVA+imiquimod immunized mice, whereas DC IL-10- were obtained from naive (n=3-4), OVA+imiquimod (n=20), and OVA+poly(I:C) (n=3-5) immunized mice.


title: Circular RNAs to predict clinical outcome after cardiac arrest

city: Luxembourg

first: Yvan

last: Devaux

address: 120 route d'Arlon

country: Luxembourg

institute: LIH

summary:
Background: Cardiac arrest (CA) represents the third leading cause of death worldwide. Among survivors, severe neurological sequelae are frequent but difficult to predict. Novel prognostic biomarkers would offer clinicians the possibility to deliver personalized healthcare. The potential of small circulating noncoding RNAs (microRNAs) to predict neurological outcome and survival after CA has been reported.
Objective: This study aims to identify circulating circular RNAs (circRNAs) associated with clinical outcome after CA.
Methods and Results: Methods and Results: Whole blood samples obtained 48h after return of spontaneous circulation from 23 sex-matched survivors and 23 deceased cardiac arrest (CA) patients were enrolled in this study. Whole transcriptome RNA sequencing identified candidate RNAs associated with neurological outcome and survival.
Conclusion: We have identified candidate RNAs associated with clinical outcome after CA whose predictive value remains to be confirmed in large populations.

overall_design: Whole blood circRNA profiles from 23 cardiac arrest patients with good neurological outcome (CPC1) and 23 patients with bad neurological outcome (CPC5)

first: Francesca

last: Stefanizzi

first: Lu

last: Zhang


title: Adrenal stress hormone regulation of hepatic homeostatic function after an acute ozone exposure

city: Research Triangle Park

first: Thomas

last: Jackson

state: NC

address: 109 TW Alexander Dr

department: CPHEA

institute: United States Environmental Protection Agency

summary: Ozone-induced lung injury/inflammation and pulmonary/hypothalamus gene expression are diminished in adrenalectomized (ADREX) rats. Acute ozone exposure induces metabolic alterations concomitant with increases in epinephrine and corticosterone. We hypothesized that adrenal hormones are responsible for observed hepatic ozone effects, and in ADREX rats, these changes would be diminished. Five-seven days after sham or ADREX surgeries, male Wistar-Kyoto rats were exposed to air or 0.8-ppm ozone for 4-hrs. Serum samples were analyzed for metabolites and liver for transcriptional changes immediately post-exposure. Ozone increased circulating triglycerides, cholesterol, free fatty acids, and leptin in sham but not ADREX rats. Ozone-induced inhibition of glucose-mediated insulin release was reversed in ADREX rats. Unlike diminution of hypothalamus and lung mRNA expression changes, ADREX in air-exposed rats (ADREX-air/sham-air) caused differential expression of ~1000 genes in liver. Likewise, ~1000 genes were differentially expressed in ozone-exposed ADREX rats (ADREX-ozone/ADREX-air). Ozone-induced hepatic changes in sham rats reflected enrichment for pathways involving metabolic processes, including acetyl-CoA biosynthesis, TCA cycle, and sirtuins. Upstream predictor analysis identified significant similarity to glucocorticoids and pathways involving CREBBP. These changes were absent in ADREX rats exposed to ozone. However, ozone caused unique changes in ADREX liver mRNA reflecting activation of synaptogenesis, neurovascular coupling, neuroinflammation, and insulin signaling with inhibition of senescence pathways. In these rats, upstream predictor analysis identified numerous microRNAs involved under glucocorticoid insufficiency. These data demonstrate the critical role of adrenal stress hormones in ozone-induced hepatic homeostasis and the need for further research elucidating their role in propagating environmentally driven diseases.

overall_design: Examination of hepatic transcriptome (RNA-seq) from sham and adrenalectomized rats exposed to either air or 0.8-ppm ozone for 4 hours

middle: W

first: Andres

last: Henriquez

first: Samantha

middle: J

last: Snow

first: Mette

last: Schladweiler

first: Anna

middle: A

last: Fisher

first: Devin

middle: I

last: Alewel

first: John

last: House

first: Urmila

last: Kodavanti


title: Gene expression-based dissection of inter-histotype, in-tra-histotype and intra-tumor heterogeneity in pediatric tumors

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: We aimed at assessing the extent of gene expression inter/intra-histotype heterogeneity and ITH in four different pediatric cancer histotypes, analysing multiple samples of each single tumor mass.

overall_design: Based on the availability of clinical, radiological and pathological information, as well as of multiple formalin-fixed, paraffin embedded (FFPE) viable tumor tissue blocksfrom spatially distinct areas of the primary tumor mass, possibly with different morphologies, 5 hepatoblastomas (HB), 5 neuroblastomas (NB), 5 rhabdomyosarcomas (RMS), and 5 Wilms tumors (WT) were selected. Gene expression profiling was performed and Principal Component Analysis (PCA), single sample Hallmark Gene Set (HGS) analysis and Weighted gene co-expression network analysis (WGCNA) were performed


title: A novel interplay between triglycerides and acute promyelocytic leukemia mediated by the cooperation between PPARα and PML/RARα.

city: SHANGHAI

first: Peng

last: Jin

state: SHANGHAI

address: No.197 RUIJIN ER RD

country: China

institute: SHANGH RUIJIN HOSPITAL

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

overall_design: Refer to individual Series


title: Role of YAP/TAZ in KGN human granulosa cell line

city: Eiheiji

first: Tetsuya

last: Mizutani

state: Fukui

address: 4-1-1 Kenjojima

institute: Fukui Prefectural University

summary:
To identify the YAP/TAZ target genes in granulosa cells, DNA microarray experiments were performed in KGN cells where YAP/TAZ were knocked down.
The effect of the presence or absence of 8Br-cAMP, an intracellular second messenger of FSH, was also investigated in KGN cells.

overall_design: Observation of gene expression changes in KGN cells after treatmet with siRNAs targeting YAP/TAZ using microarray.


title: MPA induced alterations in endometrial stromal cell transcriptome profile

city: Shanghai

first: Xiaojun

last: Chen

address: No. 419, Fangxie Road

institute: Obstetrics and Gynecology Hospital of Fudan University

summary: Normal endometrial stromal cells (ESCs) increase the inhibitory effect of progestin on EC cell proliferation via paracrine signaling, but the mechanisms involved remain unclear.ESCs had different morphological features between progestin-sensitive and -insensitive EC tissues. The purpose of this study was to detect differential gene expression in endometrial stromal cells after MPA treatment and to screen for potential secretory factors.

overall_design: The NSC cells were digested and passaged routinely at logarithmic growth stage, and then inoculated in six-well plates at 1*105/well after adjusted cell concentration. After 24h of cell walling, the cells were observed to be 60%-70% confluent, and the phenol red-free medium was starved for 8h, then replaced with phenol red-free medium supplemented with 2% charcoal-stripped FBS, and treated with ethanol or 10μM MPA for 6h, and then Trizol method was used to extract RNA. RNA-Seq was performed by Genergy Bio-Technology (Shanghai, China).

first: Yali

last: Cheng


title: Brain region and sex specific transcriptome of peripubertal stress induced adult  male mice showing escalated aggression and adult female mice with no signs of aggression.

city: New Delhi

first: Arpita

last: Konar

address: Mathura Road

country: India

institute: CSIR-Institute of Genomics and Integrative Biology

summary:
Purpose: The goal of this study is to uncover the molecular basis of peripubertal stress induced aggressive behaviour and its sex differences focussing on brain region specific transcriptome  profiling (RNA-seq) and validation by quantitative reverse transcription polymerase chain reaction (qRT–PCR)
Methods: Hypothalamus (Hypo) and Prefrontal cortex (PFC) mRNA profiles of 90-day-old control adult male and female and PPS exposed escalated aggressive adult male (SEagg) mice and non aggressive adult female (SNagg)  were sequenced on Illumina HiSeq 2500, in 3 biological replicates.The FASTQ sequencing reads were adapter-trimmed along with a minimum length cut-off of 50 bases using Prinseq-lite. The reads were aligned to mouse genome assembly using TopHat (v.2.0.11) followed by reference-based assembly using Cufflinks (v.2.2.1). Then differentially expressing transcripts were identified using Cuffdiff (v.2.2.1). qRT–PCR validation was performed using  SYBR Green assays.
Results:Hypo of SEagg males showed 49 differentially expressed genes (DEGs) amongst which 28 were down-regulated, 20 were up-regulated and 1 was expressed in SEagg males but not in control males. PFC of SEagg males showed 87 DEGs amongst which 57 were downregulated, 28 were upregulated and 2 were only expressed in SEagg males but not control males. SNagg females showed 684 DEGs in Hypo and 152 DEGs in PFC when compared to their respective control samples.
Conclusions:  We provide the first prefrontal cortex and hypothalamus specific transcriptome profiles of peripubertal stress (PPS) exposed, Balb/c adult male mice exhibiting escalated aggression and Balb/c adult female mice showing no signs of aggression.

overall_design: Brain mRNA profiles of  peripubertal stress exposed adult male and female mice.

first: Aksheev

last: Bhambri

first: Beena

last: Pillai


title: RNA-seq of rat nucleus pulposus cells after stabilizing G-Quadruplexes

city: Guangzhou

first: Shunlun

state: Guangdong

address: 58 Zhongshan 2nd Road

department: Spine Surgery

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: We report the RNA-seq data for rat nucleus pulposus cells after stabilizing G-Quadruplexes (G4). We sequenced rat nucleus pulposus cells treated with PDS, Braco-19 and Phen-DC3 separately and untreated with these G4 stabilizers, which could stabilize G4 structure in cells.

overall_design: SD rat mRNA profiles of nucleus pulposus cells treated with PDS, Braco-19 and Phen-DC3 separately for 24h.There are 18 samples,including 3 groups treated with PDS, Brao-19 and Phen-DC3 separately and 3 groups of control, and each group includes three biological repeats.

first: Xiaolin

last: Wang

first: Zhuoyang

last: Zhao

first: Huichuan

last: Yu

first: Jianru