title: Hallmarks of glyco-genes expression and their glycosylation pathways in squamous and adenocarcinoma cervical cancer

status: Public on Oct 24 2020

city: Puebla

first: Patricia

last: Martinez-Morales

address: Centro de Investigación Biomédica de Oriente Instituto Mexicano del Seguro Social HGZ No. 5 Km 4.5 Carretera Federal Atlixco-Metepec 74360 Metepec, Puebla, México

institute: CONACYT-IMSS

summary: Dysregulation of glyco-gene expression in cancer can lead to aberrant glycans and glycoconjugates, which in turn can promote tumorigenesis. Cervical cancer display augmentation of aberrant sialylated glycans and increase of glyco-genes, which encoded enzymes participate in the sialylation pathways. Besides sialiltranferases, other glyco-genes, analyzed individually are reported as altered in cervical cancer. Here we show a comprehensive analysis of glyco-gene expression in cervical cancer to obtain a wide scenery of global changes in glycosylation pathways. First, we compared glyco-gene expression between normal tissue and cervical cancer. Second, we analyzed the glycogene expression in subtypes of cc to obtain hallmarks of glyco-gene expression in each case. Our results indicate that in cervical cancer the GPI-anchored biosynthesis is increased in cc while the synthesis of chondroitin and dermatan sulfate are decreased. Moreover, data show that adenocarcinoma displayed a homogenous glyco-gene expression pattern, where chondroitin /dermatan sulfate and heparan sulfate glycogenes are decreased, while keratan sulfate genes are increased.   Dysregulation of glyco-gene expression in cancer can lead to aberrant glycans and glycoconjugates, which in turn can promote tumorigenesis. Cervical cancer display augmentation of aberrant sialylated glycans and increase of glyco-genes, which encoded enzymes participate in the sialylation pathways. Besides sialiltranferases, other glyco-genes, analyzed individually are reported as altered in cervical cancer. Here we show a comprehensive analysis of glyco-gene expression in cervical cancer to obtain a wide scenery of global changes in glycosylation pathways. First, we compared glyco-gene expression between normal tissue and cervical cancer. Second, we analyzed the glycogene expression in subtypes of cc to obtain hallmarks of glyco-gene expression in each case. Our results indicate that in cervical cancer the GPI-anchored biosynthesis is increased in cc while the synthesis of chondroitin and dermatan sulfate are decreased. Moreover, data show that adenocarcinoma displayed a homogenous glyco-gene expression pattern, where chondroitin /dermatan sulfate and heparan sulfate glycogenes are decreased, while keratan sulfate genes are increased.

overall_design: Two-condition experiment, normal cervix tissue and cervical cancer tissue. One replicate array. 10 µg of total pooled RNA from each case were used for cDNA synthesis incorporating dUTP-Alexa555 (for normal cervix) or dUTP-Alexa647 (for cervical cancer) employing the First-Strand cDNA labeling kit (Invitrogen). Incorporation of fluorophore was analyzed by using the absorbance at 555 nm for Alexa555 and 650 nm for Alexa647. Equal quantities of labeled cDNA were hybridized using hybridization solution UniHyb (TeleChem International INC). The arrays were incubated for 14 h at 42°C, and then washed tree times with 1X SCC, 0.05 % SDS at room temperature.

first: Veronica

last: Vallejo-Ruiz


title: Recapitulative hematopoietic development of human pluripotent stem cells in the absence of exogenous cytokines

status: Public on Oct 21 2020

city: Guangzhou

first: cuihua

last: wang

address: 190 Kaiyuan Avenue, Guangzhou Science Park, Luogang District, Guangzhou

country: China

institute: Guangzhou Institutes of Biomedicine and Health,Chinese Academy of Sciences

type: Expression profiling by high throughput sequencing

summary: We tested whether the sustained hematopoietic differentiation of hPSCs can be achieved in defined cell culture conditions without addition of hematopoietic cytokines. Here we show that the endogenous stimuli were sufficient to induce a robust generation of clonogenic hematopoietic progenitors, maturation of blood cells, emergence of the definitive cell lineages, and progenitors that were phenotypically identical to early human embryonic hematopoietic stem cells (HSCs). Our novel cytokine-free protocol is efficient, reproducible, and can be applied for hematopoietic differentiation of human induced pluripotent stem cells (hiPSCs) and embryonic stem cells (hESCs). The removal of cytokines from the differentiation led to detecting a vast developmental potential of the early human blood cells. We also found that the cytokine-free hematopoietic differentiation of hPSCs is associated with strong activation of hPSC-derived inflammatory cells. The spectrum of recapitulative features of the novel protocol makes the cytokine-free differentiation a preferred model for studying early human hematopoietic development

overall_design: Examination of gene expression during hematopoietic differentiation of human pluripotent stem cells

first: Cuihua

last: Wang

first: Igor

middle: M

last: Samokhvalov


title: Microbial exposure remodels and increases combat readiness of the naïve CD8 T cell compartment via type I interferons

status: Public on Oct 07 2020

city: Tucson

first: Janko

last: Nikolich-Zugich

state: AZ

address: 1656 E. Mabel St.

country: USA

institute: University of Arizona

summary: Studies in specific pathogen-free mice revealed that naïve T (Tn) cells require two homeostatic signals for long-term survival–the sub-threshold T cell receptor:self-peptide–MHC contact, and IL-7 stimulation. It is not known how microbial exposure impacts Tn homeostasis. We report that the presence of infections led to expansion of a novel subpopulation of long-lived, Ly6C+ Tn cells with rapid effector function. Monoinfection with West Nile virus transiently, and polymicrobial exposure persistently, enhanced Ly6C expression on CD5hi cells, the latter yielding a numerical Tn cell increase in the lymph nodes. Conversion and expansion of Ly6C+ Tn cells depended on IFN-I, that upregulated MHC class I expression and enhanced trophic TCR signaling in Tn cells. IFN-I-mediated signals extended lifespan, optimized homing to secondary and tertiary sites, and drove Ly6C+ Tn cells to higher “combat readiness” as judged by increased effector differentiation. Thereby, infection-driven IFN-I powerfully modulates Tn homeostasis and function.

overall_design: 2x10e5 CD8+CD62L+CD44loLy6C+ and Ly6C- naïve T cells were isolated from 4 SPF and 4 cohoused mice using a CD8a+ T cell isolation kit (Miltenyi Biotec) followed by FACS Aria III sorting (BD Biosciences).

first: Christopher

middle: P

last: Coplen

first: Mladen

last: Jergovic

first: Shu

last: Cheng


title: Transcriptomes of Major Proximal-Tubule Cell-Culture Models

status: Public on Oct 14 2020

city: Bethesda

first: Lihe

last: Chen

state: MD

address: 10 center drive MSC 1603, Building 10, Room 6N228

institute: NHLBI

summary:
Purpose:Cultured cell lines are widely used for research in the physiology, pathophysiology, toxicology and pharmacology of the renal proximal tubule. The lines that are most appropriate for a given use depend on the genes expressed.We have used modern RNA-sequencing techniques to identify the gene expression profile of 14 different cell lines plus primary cultures of mouse proximal tubule and compare them to transcriptomes of native kidney proximal tubules.
Methods: 14 different proximal tubule cell lines were grown on permeable supports under conditions specific for the respective lines. RNA-Seq followed standard procedures.
Results and conclusion: Transcripts expressed in cell lines showed variable match to transcripts selectively expressed in native proximal tubule. Opossum kidney (OK) cells displayed the highest percentage match (45%) with pig kidney cells (LLC-PK1) close behind (39%). Much lower percentage matches were seen for various human lines including HK-2 cells (26%) and lines from rodent kidneys (18-23%).An online resource (https://esbl.nhlbi.nih.gov/JBrowse/KCT/) has been created for interrogation of the data.No cell line closely matched the transcriptome of native proximal tubule cells. However, some of the lines tested are suitable for the study of particular metabolic and transport processes seen in the proximal tubule.

sample_organism:
Didelphis virginiana
Homo sapiens
Canis lupus familiaris
Sus scrofa
Mus musculus
Rattus norvegicus

overall_design: We provide a web-based resource that allows users to compare expression of specific transcripts across all cell lines and to download data for deeper analysis.

first: Syed

middle: J

last: Khundmiri

first: Eleanor

last: Lederer

first: Chin

middle: R

last: Yang

first: Mark

middle: A

last: Knepper


title: Histone H3.3 G34 mutations promote aberrant PRC2 activity and drive tumor progression

status: Public on Oct 12 2020

city: Madison

first: Peter

middle: W

last: Lewis

state: Wisconsin

address: 330 N Orchard Street

department: Department of Biomolecular Chemistry

institute: University of Wisconsin-Madison

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: scRNAseq of human iPSC-derived motor neurons from control and ALS patients.

city: Los Angeles

first: Michael

last: Workman

state: CA

address: 8700 Beverly Blvd., AHSP Suite 8405

institute: Cedars-Sinai Medical Center

summary: We compare single cell transcriptomic profiles of motor neurons differentiated in vitro from human induced pluripotent stem cells derived from control and ALS patients.

overall_design: Human induced pluripotent stem cell-derived motor neurons were differentiated in vitro over 18 days following a previously described protocol (Maury et al. Nat Biotechnol, 2015). Cells were processed for single cell sequencing following the manufacturer's guidelines for the 10X Genomics Chromium or Illumina/Bio-Rad ddSEQ platforms. A total of 25 samples were processed in 6 batches. Replicates of cell lines CS83iCTR-33n1, CS0179iCTR-n1, CS2XWCiALS-n1, CS29iALS-C9n1, CS52iALS-C9n6, CS25iCTR-18n2, and CS29iALS-C9n1.ISO were processed across multiple batches.

first: Clive

middle: N

last: Svendsen

first: Ritchie

last: Ho


title: The epithelial splicing regulator ESRP2 is epigenetically repressed by DNA hypermethylation in Wilms tumor and acts as a tumor suppressor

status: Public on Nov 02 2020

city: Bristol

first: Keith

middle: William

last: Brown

address: Biomedical Sciences Building, University Walk

department: School of Cellular and Molecular Medicine

country: United Kingdom

institute: University of Bristol

summary: Wilms tumor (WT), a childhood kidney cancer with embryonal origins, has been extensively characterised for genetic and epigenetic alterations, but a proportion of WTs still lack identifiable abnormalities.  To uncover DNA methylation changes critical for WT pathogenesis, we compared the epigenome of fetal kidney with two WT cell lines, using methyl-CpG immunoprecipitation.  We filtered our results to remove common cancer-associated epigenetic changes, and to enrich for genes involved in early kidney development.  This identified four candidate genes that were hypermethylated in WT cell lines compared to fetal kidney, of which ESRP2 (epithelial splicing regulatory protein 2), was the most promising gene for further study.  ESRP2 was commonly repressed by DNA methylation early in WT development (in nephrogenic rests) and could be reactivated by DNA methyltransferase inhibition in WT cell lines.  When ESRP2 was expressed in WT cell lines, it acted as an inhibitor of cellular proliferation in vitro and in vivo it suppressed tumor growth of orthotopic xenografts in nude mice.  RNA-seq of the ESRP2-expressing WT cell lines identified several novel splicing targets, in addition to well-characterised targets of ESRP2.  One of these targets, LEF1, is a component of the Wnt signalling pathway that is essential for kidney development and commonly disrupted in WT.  We propose a model in which the Wnt pathway can be disrupted in early kidney development to generate WT, either by genetic abnormalities such as WT1 mutations, or by epigenetic defects, such as ESRP2 methylation.

overall_design: To discover splicing  events induced by ESRP2 in Wilms tumor, we established a variant of the Wit49 Wilms tumor cell line that contained a doxycycline (DOX)-inducible ESRP2 expression construct (E200L).  In biological duplicates, we extracted RNA from E200L cells that were DOX-induced (ESRP2-expressing) or uninduced (non-expressing), and sequenced them, obtaining between 70 and 80 million paired-end reads per sample.  These reads were mapped onto the human genome and used in rMATS software to identify alternative splicing events.

first: Danny

last: Legge

first: Whei

last: Moriarty

first: David

last: Lee

first: Karim

middle: T

last: Malik

first: Sebastian

last: Oltean


title: The epithelial splicing regulator ESRP2 is epigenetically repressed by DNA hypermethylation in Wilms tumour and acts as a tumour suppressor

summary:
Wilms tumour (WT), a childhood kidney cancer with embryonal origins, has been extensively characterised for genetic and epigenetic alterations, but a proportion of WTs still lack identifiable abnormalities. To uncover DNA methylation changes critical for WT pathogenesis, we compared the epigenome of fetal kidney with two WT cell lines, using methyl-CpG immunoprecipitation. We filtered our results to remove common cancer-associated epigenetic changes, and to enrich for genes involved in early kidney development. This identified four candidate genes that were hypermethylated in WT cell lines compared to fetal kidney, of which ESRP2 (epithelial splicing regulatory protein 2), was the most promising gene for further study. ESRP2 was commonly repressed by DNA methylation early in WT development (in nephrogenic rests) and could be reactivated by DNA methyltransferase inhibition in WT cell lines. When ESRP2 was expressed in WT cell lines, it acted as an inhibitor of cellular proliferation in vitro and in vivo it suppressed tumour growth of orthotopic xenografts in nude mice. RNA-seq of the ESRP2-expressing WT cell lines identified several novel splicing targets, in addition to well-characterised targets of ESRP2. One of these targets, LEF1, is a component of the Wnt signalling pathway that is essential for kidney development and commonly disrupted in WT. We propose a model in which the Wnt pathway can be disrupted in early kidney development to generate WT, either by genetic abnormalities such as WT1 mutations, or by epigenetic defects, such as ESRP2 methylation.
The microarray data in this deposition identified ESRP2 as a commonly hypermethylated gene in Wilms tumour.

overall_design: Genome-wide DNA methylation was compared between fetal kidney (commercial; Biochain) and two Wilms tumour cell lines (17.94; Brown et al (2012) Cancer Genet 205:319-26 and Wit49; Alami et al (2003) Int J Cancer 107:365-74). The methylated fraction from each genomic DNA was purified by MCIP (see extract protocol) and co-hybridised with total genomic DNA onto a custom Nimblegen microarray. There was a single array used for each sample.

first: Marianna

last: Szemes


title: Genes with 5′ terminal oligopyrimidine tracts preferentially escape global suppression of translation by the SARS-CoV-2 NSP1 protein

status: Public on Oct 01 2020

city: Austin

first: Hakan

last: Ozadam

state: TX

address: Department of Molecular Biosciences Moffett Molecular Biology Building 2.122 2500 Speedway

department: Department of Molecular Biosciences

institute: University of Texas at Austin

summary: Viruses rely on the host translation machinery to synthesize their own proteins. Consequently, they have evolved varied mechanisms to co-opt host translation for their survival. SARS-CoV-2 relies on a non-structural protein, NSP1, for shutting down host translation. Despite this, it is currently unknown how viral proteins and host factors critical for viral replication can escape a global shutdown of host translation. Here, using a novel FACS-based assay called MeTAFlow, we report a dose-dependent reduction in both nascent protein synthesis and mRNA abundance in cells expressing NSP1. We perform RNA-Seq and matched ribosome profiling experiments to identify gene-specific changes both at the mRNA expression and translation level. We discover a functionally-coherent subset of human genes preferentially translated in the context of NSP1 expression. These genes include the translation machinery components, RNA binding proteins, and others important for viral pathogenicity. Importantly, we also uncover potential mechanisms of preferential translation through the presence of shared sites for specific RNA binding proteins and a remarkable enrichment for 5′ terminal oligo-pyrimidine tracts. Collectively, the present study suggests fine tuning of host gene expression and translation by NSP1 despite its global repressive effect on host protein synthesis.

overall_design:
Effects of NSP1 and NSP2 expression in translation and transcription in HEK293 cells.
Effects of NSP1 expression in translation and transcription in HEK293 cells.

first: Shilpa

last: Rao

first: Ian

last: Hoskins

first: Daniela

last: Garcia

first: Tori

last: Tonn

first: Elif

middle: S

last: Cenik

first: Can


title: Single-cell RNA sequencing samples from high-grade serous ovarian cancer (HGSOC)

status: Public on Oct 03 2020

city: Baltimore

first: Lukas

last: Weber

address: 615 N Wolfe St

department: Biostatistics

institute: Johns Hopkins University

summary: We measured gene expression in single-cell RNA sequencing samples from patients with high-grade serous ovarian cancer (HGSOC), for a study on improving HGSOC subtype definition by taking into account varying cell type proportions within tumors.

overall_design:
Gene expression was measured at single-cell level using single-cell RNA sequencing performed on HGSOC samples from separate, unrelated individuals. The initial dataset contains 3 samples (3 individuals).

**Raw data files will be submitted to dbGAP**

first: Ariel

last: Hippen

first: Kristofer

middle: C

last: Berrett

first: Jason

last: Gertz

first: Jennifer

last: Doherty

first: Casey

last: Greene

first: Stephanie

last: Hicks


title: RNA-Seq of E14 MGE, Prdm16 WT vs cKO

status: Public on Oct 22 2020

city: San Francisco

first: Corey

last: Harwell

address: 35 Medical Center way

department: Neurology

institute: University of California, San Francisco

summary: This study aimed to understand the role of the transcriptional regulator Prdm16 in the development of cortical interneurons in the mouse. Prdm16 was knocked out in cells derived from the medial ganglionic eminence (MGE) by using an Nkx2.1-Cre driver line in combination with a line carrying floxed Prdm16 alleles and with a Cre-dependent tdTomato reporter line (Ai14). The sequencing data compares the gene expression profiles of dissected MGEs at embryonic day 14 (E14), a stage when cortical interneurons are being generated from MGE progenitors.

overall_design: The MGEs of 3 pools of 3 embryos each were compared between control (labeled as "WT", containing Cre and Ai14 alleles) and mutant (labeled as "KO", homozygous for the floxed version of the Prdm16 allele) samples.

first: Miguel

last: Turrero Garcia


title: Chronic Colitis Impairs Cardiac Function by Suppressing Brain-Derived Neurotrophic Factor in the Adult Heart

status: Public on Oct 05 2020

city: Galveston

first: Qingjie

last: Li

state: Texas

address: 301 University Blvd

department: Internal Medicine

institute: University of Texas Medical Branch

summary: Inflammatory bowel disease (IBD) represents a spectrum of chronic inflammatory mediated conditions with known extraintestinal complications. The interplay between patients with heart failure (HF) and IBD has previously been noted, but the mechanisms driving these changes have not been well elucidated. We elucidated mechanisms in which chronic colitis can impair cardiac function via alteration of miRNA expression.

platform_organism:
Rattus norvegicus
synthetic construct

overall_design: To induce chronic colitis, dextran sodium sulfate (DSS, 3% in drinking water) was given to adult rats for 5 days followed by 9 days with normal drinking water for a total of 4 cycles over 8 weeks. Then transthoracic echocardiography (TTE) was performed and rats were euthanized for tissue collection. MiRNA profiling performed by LC sciences showed a total of 7 miRNAs significantly increased in DSS colitis and predicted targets of BDNF. RT-qPCR was performed to confirm DSS induced colitis augmented levels of miRNA in cardiac tissue.

first: Yanbo

last: Tang

first: Kevin

last: Kline

first: Ying

last: Xiao

first: Xiaoying

last: Zhong

first: Haifeng

last: Lian

first: Jun

last: Peng

first: Xiaowei

last: Liu

first: Don

last: Powell

first: Goudu


title: Targeted single-cell RNAseq of tonsil organoid cultures

status: Public on Sep 24 2020

city: Irvine

first: Lisa

last: Wagar

address: 843 Health Sciences Rd

institute: University of California Irvine

summary: Tonsil organoid cultures were prepared from one donor and stimulated with live-attenuated influenza vaccine (LAIV) or left unstimulated. Cells were harvested on the days described below, total T and B cells were sorted, and cells were sequenced using the BD Rhapsody platform with a targeted set of immune-related genes, BCR, and TCR repertoire analysis.

overall_design: Examination of T and B cells from influenza vaccine-stimulated and unstimulated organoid cultures.

middle: E


title: Gene Expression Signature of Microcalcification among Taiwanese Breast Cancer

city: New Taipei

first: Chih-Cheng

last: Chien

address: No 2, Ln 59, Jian-Cheng Rd, Sijhih Dist

country: Taiwan

institute: Sijhih Cathay General Hospital

summary:
Microcalcification is one of the most common radiological and pathological features of breast ductal carcinoma in situ (DCIS), and to a lesser extent, invasive ductal carcinoma. We evaluated transcriptional profiles associated with ectopic mammary mineralization.
We evaluated the transcriptional profiles associated with breast cancer microcalcification for Taiwanese breast cancer and a gene expression signature was derived.

overall_design: A total of 109 consecutive breast cancers were assayed with microarrays. The associations of differentially expressed genes with microcalcifications and relevant clinical features were evaluated.

first: Hsin-Tien

last: Tsai

first: Ching-Shui

last: Huang

first: Chao-Chiang

last: Tu

first: Chih-Yi

first: Chi-Jung

first: Yuan-Soon

last: Ho

first: Shih-Hsin

first: Ling-Ming

last: Tseng

first: Chi-Cheng


title: Effects of Dyrk1a and Kcnj6 normalization on the hippocampal transcriptome in the Dp(16)1/Yey mouse model of Down syndrome

first: Xiaoling

last: Jiang

state: Guangdong

address: 9 Jinsui Road, Tianhe District

department: Department of Genetics and Endocrinology

institute: Guangzhou Women and Children's Medical Center

summary: Down syndrome (DS), the most common human chromosomal disorder, is caused by trisomy 21. Recent studies show that the trisomic genes Dyrk1a and Kcnj6 play critical causative roles in DS cognitive deficits. Interestingly, an unexpected lack of improvement of hippocampal-dependent learning and memory deficits was observed when both Dyrk1a and Kcnj6 were normalized to diploidy in the DS mouse model, Dp(16)1/Yey (Dp16). In this study, we explored the molecular mechanisms underlying this phenomenon by using whole genome-wide hippocampal transcriptome analysis. In total, 142, 142, and 112 genes were found significantly differentially expressed in the Dp16, Dp16/Dyrk1aKO (Dyrk1a normalized) and Dp16;Dyrk1aKO/Kcnj6KO (Both Dyrk1a and Kcnj6 normalized) hippocampus, respectively, compared with the WT hippocampus. The majority of the common significantly differentially expressed genes (DEGs) were trisomic genes. Dyrk1a and Kcnj6 normalization mainly altered the expression of diploid genes. Normalizing Dyrk1a in the Dp16 hippocampus caused an overall downregulation of genes, whereas further Kcnj6 normalization caused an overall upregulation of genes. Both further rescuing effects and neutralizing effects were observed in Kcnj6 and Dyrk1a double-normalized mice compared with mice with Dyrk1a normalization alone.

overall_design: Four genetic groups:WT, Dp16, Dp16/D-KO and Dp16;D-KO/K-KO with 5-7 samples each group were analyzed

first: Zhaowei

last: Cai

first: Zhilan

first: Kangdi

last: Zhang

first: Sichi

first: Huazhen

first: Xiaoning

last: Zheng

first: Yani

first: Zhizi

last: Zhou

first: Chunhua

last: Zeng


title: A novel, alternatively activated neutrophil subset promotes CNS neuron survival and axon regeneration in vivo

status: Public on Sep 08 2020

city: Ann Arbor

first: Rajasree

last: Menon

state: Michigan

address: 4544E, MSRB2, Catherine Street, University of Michigan

department: Department of Computational  Medicine and Bioinformatics

institute: University of Michigan

summary: Transected axons typically fail to regenerate in the central nervous system, resulting in chronic neurological disability in individuals with traumatic brain or spinal cord injury, multiple sclerosis, and stroke, as well as glaucoma and ischemic reperfusion injury of the eye. Although neuroinflammation is often depicted as detrimental, there is growing evidence that alternatively activated, reparative  leukocyte subsets and their products can be deployed to improve neurological outcomes. In the current study we identify a unique granulocyte subset, with characteristics of an immature neutrophil, that has    neuroprotective properties and drives CNS axon regeneration in vivo, in part via secretion of a cocktail  of growth factors. This pro-regenerative neutrophil promotes repair in the optic nerve and spinal cord, demonstrating its relevance across CNS compartments and neuronal populations. Our findings could ultimately lead to the development of novel immunotherapies that reverse CNS damage and restore lost  neurological function across a spectrum of diseases.

overall_design: 10x Genomics single cell sequencjavascript:validateForm()ing on Ly6G +ve neutrophils isolated from the vitreos of mice subjected to  i.o zymosan injection and aCXCR2/NRS antisera treatment.

first: Benjamin

last: Segal

first: Andrew

last: Sas


title: Expression data from prostate tissues from mouse models of prostate cancer fed a high-fat diet.

status: Public on Sep 25 2020

city: Osaka

first: Makoto

last: Matsushita

address: 2-2 Yamadaoka, Suita

department: Urology

country: Japan

institute: Osaka University Graduate School of Medicine

summary: To examine the effects of antibiotics on gene expression in the prostate of a mouse model of prostate cancer fed a high-fat diet, we extracted RNA from the prostates of high-fat diet fed mice with or without antibiotics treatment, and compared their gene expressions with the two groups using microarrays.

overall_design: Prostate tissues from 3 high-fat diet fed prostate cancer model mice without antibiotics treatment and 5 high-fat diet fed prostate cancer model mice with antibiotics treatment at 22 weeks of age were analyzed for microarray

first: Kentaro

last: Jingushi


title: Gene expression profiles of CD105pos and CD105neg cancer-associated fibroblasts (CAFs) from KPC mice

status: Public on Aug 28 2020

city: MANCHESTER

first: Alexander

last: Kononov

address: Oglesby Building, 555 Wilmslow Rd,

institute: Cancer Research UK Manchester Institute

summary: CD105pos and CD105neg CAFs were isolated from KPC pancreatic ductal adenocarcinoma tumours and gene expression profiles measured

overall_design: Single live LINnegPDPNposCD90posCD105pos and CD105neg CAFs were FACS isolated from n=6 different KPC pancreatic ductal adenocarcinoma tumours, RNA isolated and gene expresion measured by next gen sequencing using standard methods

first: Colin

last: Hutton

first: Claus

last: Jorgensen


title: Transcriptome Alterations in Myotonic Dystrophy Frontal Cortex

status: Public on Sep 04 2020

city: Gainesville

first: Eric

last: Wang

state: Florida

address: 2033 Mowry Road

department: Molecular Genetics and Microbiology

institute: University of Florida

summary: Myotonic dystrophy is caused by expanded CTG/CCTG microsatellite repeats, leading to multi-systemic symptoms in skeletal muscle, heart, gastrointestinal, endocrine, and central nervous systems (CNS), among others. For many patients, CNS issues can be as or more debilitating than muscle symptoms; they include hypersomnolence, executive dysfunction, white matter atrophy, and neurofibrillary tangles. Although transcriptomes from DM1 skeletal muscle have provided useful insights into pathomechanisms and biomarkers, similarly extensive studies have not yet been performed in the CNS. To elucidate underlying causes of CNS dysfunction in patients, we have generated and analyzed RNA-seq transcriptomes from the frontal cortex of 21 DM1 patients, 4 DM2 patients, and 8 unaffected controls. One hundred and thirty high confidence splicing changes were identified, many occurring exclusively in the CNS and not in the periphery. Mis-spliced exons were found in neurotransmitter receptors, ion channels, and synaptic scaffolds, and we identified an alternative exon in GRIP1 that modulates association with kinesins. Splicing changes exhibited a gradient of severity correlating with CTG repeat length, as measured by optical mapping of individual DNA molecules. All individuals studied, including those with modest splicing defects, showed a subset of alleles with repeats longer than 1000 CTGs. Analyses of gene expression changes showed up-regulation of genes transcribed in microglia and endothelial cells, suggesting neuroinflammation, and down-regulation of genes transcribed in neurons. Gene expression changes for RNAs encoding proteins detectable in CSF were also found to correlate with mis-splicing, with implications for CNS biomarkers of disease severity. These findings provide a framework for future mechanistic and therapeutic studies of CNS issues in DM.

overall_design: We used Illumina RNA-sequencing across a cohort of frozen post-mortem autopsy tissue across 33 individuals to do comparative analysis.

first: Brittney

last: Otero

first: Kiril

last: Poukalov

first: Ryan

last: Hildebrandt

first: Charles

last: Thornton

first: Kenji

last: Jinnai

first: Harutoshi

last: Fujimara

first: Takashi

last: Kimura

first: Katharine

last: Hagerman

first: Jacinda

middle: B

last: Sampson

first: John

last: Day


title: Hypoxia Regulates Overall mRNA Homeostasis by Inducing Met1-linked Linear Ubiquitination of AGO2 in Cancer Cells

status: Public on Sep 26 2020

city: Shanghai

first: Jianxiu

last: Yu

address: Room 202, Building 7, 280 South Chongqing Road

department: Department of Biochemistry and Molecular Cell Biology

institute: Shanghai Jiao Tong University school of medicine

type: Non-coding RNA profiling by high throughput sequencing

summary: Hypoxia is the most prominent feature in human solid tumors and induces activation of hypoxia-inducible factors and their downstream genes to promote cancer progression. However, whether and how hypoxia regulates overall mRNA homeostasis is unclear. Here we show that hypoxia inhibits global-mRNA decay in cancer cells. Mechanistically, hypoxia induces the interaction of AGO2 with HOIL-1L/HOIP, two crucial components of a linear ubiquitin chain assembly complex, which co-localizes with miRNA-induced silencing complex and in turn catalyzes AGO2 occurring Met1-linked linear ubiquitination (M1-Ubi). A series of biochemical experiments reveal that M1-Ubi of AGO2 restrains miRNA-mediated gene silencing. Moreover, combination analyses of the AGO2-associated mRNA transcriptome by RIP-Seq and the mRNA transcriptome by RNA-Seq confirm that AGO2 M1-Ubi interferes miRNA-targeted mRNA recruiting to AGO2, and thereby facilitates accumulation of global mRNAs. By this mechanism, short-term hypoxia may protect overall mRNAs and enhances stress tolerance, whereas long-term hypoxia in tumor cells results in serious changing the entire gene expression profile, which is a driving force in the dynamic process of cell malignant evolution.

overall_design: mRNA assocatied with AGO2 profiles, mRNA expression profiles and miRNA expression profiles in HeLa stable cell lines.

first: Hailong

last: Zhang


title: Phase separation of Epstein-Barr virus EBNA2 reorganizes chromatin topology for epigenetic regulation

status: Public on Sep 22 2020

city: Guangzhou

first: Hao

last: bingtao

address: ShataiNan Road, Baiyun District, Guangzhou, Guangdong Province

institute: Southern Medical University

summary: Epstein-Barr virus nuclear antigen 2 (EBNA2) is a transactivator of viral and cellular gene expression, which plays a critical role in the Epstein-Barr virus-associated diseases. It was reported that EBNA2 regulates gene expression by manipulating epigenetics, but the details are unclear. Recent studies showed that liquid-liquid phase separation plays an essential role in epigenetic and transcriptional regulation. Through the recently developed ATAC-see technology, we observed that EBNA2 reorganized chromatin topology to form accessible chromatin domains (ACDs) of the host genome by phase separation. The N-terminal region of EBNA2, which is necessary for phase separation, is sufficient to induce ACDs. The C-terminal domain of EBNA2 promotes the acetylation of accessible chromatin regions by recruiting histone acetylase p300 to ACDs. According to these observations, we proposed a model of EBNA2 reorganizing chromatin topology for its acetylation through phase separation to explain the mechanism of EBNA2 hijacking the host genome by controlling its epigenetics. Our findings help to understand the molecular mechanism of the EBV-associated diseases and develop therapeutics for these diseases.

overall_design: Examination of 2 different histone modifications in Human  nasopharyngeal carcinoma cells.

first: Yiting

last: Yang

first: Xidong

last: Ye

first: Ranran

last: Dai

first: Zhaoqiang

last: Li


title: Gene expression profiles of in vitro CD105pos and CD105neg pancreatic fibroblasts (PaFs) after stimulation with various recombinant proteins

first: Alexander

last: Kononov

summary: CD105pos and CD105neg PaFs were isolated from B6 murine pancreas, subjected to in vitro stimulation for 6h and gene expression profiles measured

overall_design: In vitro growing CD105pos and CD105neg PaFs were treated with recombinant proteins for 6 h, RNA isolated and gene expresion measured by next gen sequencing using standard methods

first: Colin

last: hutton

first: Alex

first: Claus

last: Jorgensen


title: transcriptomic data of soleus WT and Lmnap.H222P/H222P pre- and post-symptomatic mice

status: Public on Sep 01 2020

city: Paris

first: Nicolas

last: Vignier

address: 105 bld de l'Hopital

country: France

institute: INSERM

summary:
The present research is devoted to the identification of gene(s) severely affected by LMNA mutations, leading to striated muscle laminopathies and more specifically the skeletal phenotype of Emery-Freifuss Muscular Dystrophy.
For this purpose, we developed a large-scale gene expression approach on soleus skeletal tissues from wild type  Lmna H222P homozygous Knock-In mouse mode at pre and post stages of the disease .

overall_design: Soleus muscle from WT and Lmna p.H222P homozygous mice were harvested at 80 and 200 days for RNA extraction and hybridization on Affymetrix microarrays.

first: Vignier

last: Nicolas

first: Muchir

last: Antoine


title: RNA-sequencing analysis of tumor-infiltrating B cells

status: Public on Jul 20 2020

city: Houston

first: William

last: Hudson

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Tumour-infiltrating lymphocytes are a major predictor for overall survival and response to immunotherapy for several malignancies. However, while tumour-infiltrating CD8 T cells have been extensively studied, little is known about the role of the humoral immune system within the tumour microenvironment (TME). Here we show that plasma cells are present in the TME and actively secrete human papillomavirus (HPV)-specific IgG antibodies in HPV-positive head and neck squamous cell carcinoma patients. Compared to circulating memory B cells, plasma cells in the TME were enriched for HPV-reactivity with little bystander recruitment of influenza-specific cells. HPV-specific plasma cells in the TME correlated with the antibody titres in peripheral blood and produced antibodies with a high degree of somatic hypermutation directed against HPV E2, E6 and E7 antigens. A striking proportion of HPV-specific antibodies produced in situ were directed against E2, which might thus be a promising target for immunotherapies in HPV-associated cancers. Overall, we show that antigen-specific activated and germinal centre B cells as well as plasma cells can be found in the TME, with plasma cells producing antibodies specific for tumour-associated antigens in situ. These findings provide a better understanding of humoral immune responses in human cancer and suggest that tumour-infiltrating B cells could be harnessed for the development of novel therapeutic agents.

overall_design: Antibody secreting cells (ASCs), activated B cells, and germinal center (GC) B cells were sorted from tumors and metastatic lymph nodes of HPV+ HNSCC patients.

first: Andreas

last: Wieland


title: Expression data from ectopic expression of ACAT1 in Nasopharyngeal carcinoma (NPC) cell lines

status: Public on Jul 28 2020

city: Nanning

first: Bo

state: Guangxi

address: No. 22 Shuangyong road

department: Radiation oncology

institute: Guangxi Medical University

summary:
Compare with normal nasopharyngeal epithelial cells, we found ACAT1 was decreased in NPC cells, we found that ACAT1 inhibited proliferation, colony formation, migration and invasion in NPC cells.  We used microarrays to identify differential genes regulated by ACAT1 in NPC cell lines.
We used microarrays to identify differential genes regulated by ACAT1 in NPC cell lines.

overall_design: A NPC cell line were included in the microarray analysis. the NPC cell line 5-8F was stably transfected with control vector and ACAT1 expression plasmid.

first: Yunliang

last: Lu

first: Xiaoying

last: Zhou

first: Zhe


title: Autophagy Promotes Growth of High Tumor Mutational Burden Tumors by Inhibiting a T Cell Immune Response [RNA-seq]

status: Public on Jul 27 2020

city: New Brunswick

first: SAURABH

middle: V

last: LADDHA

state: NEW JERSEY

address: 195 Little Albany Street

department: Center for Systems and Computational Biology

institute: Rutgers Cancer Institute of New Jersey

summary: Autophagy degrades and recycles intracellular components to sustain metabolism and survival during starvation. Tumor cells upregulate and require autophagy to support their metabolism and enhance their proliferation and malignancy, and host autophagy also promotes tumor growth by providing essential tumor nutrients such as arginine in the circulation or alanine in the local tumor microenvironment. In addition to its metabolic role, autophagy regulates immune cell homeostasis and function, and suppresses inflammation, which may also play a role in cancer. Although host autophagy does not promote a T cell anti-tumor immune response in tumors with low tumor mutational burden (TMB), whether this was the case in tumors with high TMB was not known. Here we show that in contrast to low TMB tumors, host-specific deletion of the essential autophagy gene Atg7 induces a pro-inflammatory cytokine response and limits the growth of high TMB tumors, which is rescued by T-cell depletion. Expression of immune-related genes is increased in tumors from Atg7Δ/Δ hosts in a T-cell dependent manner. Tumors from Atg7Δ/Δ hosts also have decreased T regulatory cells (Tregs), and depletion of Tregs phenocopies the reduced tumor growth observed in Atg7Δ/Δ hosts. Moreover, loss of Stimulator of interferon genes (Sting) or IFNg restores growth of high TMB tumors on Atg7Δ/Δ hosts. Finally, similar to whole-body loss of autophagy, specific loss of autophagy in the liver is sufficient to limit tumor growth. Thus, autophagy, especially in the liver, promotes tumor immune tolerance by limiting STING, T cells, and IFNg, which enables tumor growth. We have designated this: Hepatic Autophagy Immune Tolerance (HAIT). Autophagy thereby promotes tumor growth through both metabolic and immune mechanisms depending on mutational load, and autophagy inhibition is an effective means to promote an anti-tumor T-cell response in high TMB tumors.

overall_design:
Resected mouse tumors from Atg7+/+ and Atg7∆/∆ hosts were placed in complete media supplemented with 10% FBS and kept on ice. Dissociation of the tumor tissue was carried out using a commercially-available mouse tumor dissociation kit and the Miltenyi GentleMACS dissocation system (Miltenyi Biotec, Cologne, Germany). Isolated cells were filtered through a 40mm mesh strainer and PBMC’s were isolated by density-dependent centrifugation. Cells were washed complete media (10% FBS), then counted and assessed for viability using a Countess II cell counter (Invitrogen). Cells were then suspended to 1x10^6 per ml in complete media (10% FBS) for single cell emulsion preparation. scRNA-seq libraries were prepared according to 10X Genomics specifications (10X Genomics, Pleasanton, CA). Independent cell suspensions were loaded for droplet-encapsulation by the Chromium Controller (10X Genomics). Single-cell cDNA synthesis, amplification, and sequencing libraries were generated using the Single cell 5’ Reagent Kit following the manufacturer’s instructions. The libraries were shipped on dry ice to Novogene (Sacramento, CA), and sequenced in a single lane of an Illumina NovaSeq 6000 (Settings: Read1: 26, i7: 8, Read2: 91, for 200M bp paired-end reads per sample).
mRNA profiling of 8 mouse tumors (4 with Atg7+/+ genotype and 4 with Atg7∆/∆ genotype) using 10x Chromium Novaseq 6000 instruments.

first: Saurabh

last: Laddha

first: Chang

last: Chan

first: Laura

last: Poillet-Perez

first: Eileen

last: White


title: Low-dose decitabine modulates T cell homeostasis and restores immune tolerance in immune thrombocytopenia

status: Public on Jul 21 2020

city: Jinan

first: Ming

last: Hou

state: Shandong

address: 107 West Wenhua Road

department: Department of Hematology

institute: Qilu Hospital, Cheeloo College of Medicine, Shandong University

summary: Immune thrombocytopenia (ITP) is an acquired autoimmune disease triggered by abnormal T cell immunity, especially the impairment of regulatory T (Treg) cells and helper T (Th) cell subsets. Decitabine, a hypomethylating agent promoting cell differentiation at low dose, has been demonstrated the function of increasing the number of mature polyploidy megakaryocytes in ITP as well as Treg cells in allogeneic transplantation. Recently, our clinical study proved that decitabine was effective and safe in the management of adult ITP patients, and nearly half showed sustained responses. However, whether low-dose decitabine has the potential in restoring immune tolerance in ITP is unknown. In our in vitro studies, we identified that low-dose decitabine could promote the generation and differentiation and enhance the immunosuppressive function of Treg cells. Furthermore, low-dose decitabine alleviated thrombocytopenia and regained the balance of Treg/Th cell subsets in active murine models of ITP. For patients who received low-dose decitabine therapy and showed responses, the quantity and function of Treg cells were substantially improved, whereas Th1 and Th17 cells were depressed compared with the pretreatment levels. Finally, immunophenotyping and next-generation RNA sequencing analysis showed that low-dose decitabine restored T cell homeostasis and decreased the level of proinflammatory cytokines along with the downregulation of STAT3 and Akt in refractory ITP patients. Therefore, our data reveal the immunomodulatory effect of decitabine and provide unique insights into the sustained response achieved by decitabine in the management of ITP patients.

overall_design: PBMCs mRNA samples of 4 responders and 3 non-responders of low-dose decitabine

first: Panpan

last: Han

first: Yu

first: Hai


title: In vivo analysis of camptothecin effect in primary DRG neuron after sciatic nerve injury

status: Public on Jul 24 2020

city: Los Angeles

first: Riki

last: Kawaguchi

address: 760 Westwood Plaza, Room 37-420

department: Department of Neurology and Department of Psychiatry

institute: University of California Los Angeles

summary: Analysis of gene expression in injured primary DRG with or without camptothecin (CPT) treatment after sciatic nerve crushing may help us identify critical molecular pathways related to axon regeneration. We performed RNA-sequencing of (i) Naive primary DRG tissues without injury, (ii) Primary DRG  tissues with vehicle treatment different time-points (18, 24, 36 hours) after sciatic nerve injury, and (iii) Primary DRG tissues with camptothecin treatment different time-points (18, 24, 36 hours) after sciatic nerve injury.

overall_design: 12 weeks-old wild-type C57/BL6 mice underwent sciatic nerve crush (SNC). Thirty minutes after crush, 2 mg/kg of camptothecin was administered to injured mice by intraperitoneal injection. DRG tissues were harvested at 18, 24, and 36 hours after nerve injury either from camptothecin injected group or vehicle-injected group (n=4 at each time point).

first: Yung-Chih

last: Cheng

first: Clifford

last: Woolf

first: Giovanni

last: Coppola


title: Genome-wide maps of RNA polymerase II in WT and ssu72 mutant cells [8WG16_S2_Y1_ChIPseq]

status: Public on Jun 30 2020

city: Oxford

first: Dong-hyuk

last: Heo

address: South Parks Road

department: Department of Biochemistry

institute: University of Oxford

summary:
Deletion of ssu72 gene leads to a transcription elongation defect and the increase in the level of Ser5 and Ser7 phosphorylation in CTD of Rpb1
Phosphorylation of the RNA polymerase II C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that histone deacetylase complex activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of the antisense transcription when the C-terminal domain phosphorylation is dysregulated due to the loss of Ssu72 phosphatase.  Interestingly, while single hos2/set3 mutants have little effect, loss of hos2 or set3 in addition to ssu72? leads to synergistic increase in antisense transcription globally and correlates with increases genomic instability and formation of deleterious R-loop structures across these regions. We propose that Ssu72 is essential to suppress initiation of cryptic transcription in the 3?end of the RNA polymerase II transcribed regions. In the absence of Ssu72, antisense transcription is supressed by the Hos2/Set3 dependent surveillance mechanism to maintain genome stability.

overall_design: Rpb1, Ser2-P CTD, and Tyr1-P CTD ChIP-seq in WT and ssu72Δ

first: Krzysztof

last: Kuś

first: Tea

last: Kecman

first: Sue

last: Tan-Wong

first: Nikolay

last: Zenkin

first: Nick

last: Proudfoot

first: Lidia

last: Vasiljeva


title: A method for spatially resolved tissue transcriptomics applied to the mouse and lizard P. vitticeps brains

status: Public on Aug 02 2020

city: Stockholm

first: Sten

last: Linnarsson

address: Scheeles väg 1

department: Medical Biochemistry and Biophysics

country: Sweden

institute: Karolinska Institutet

summary: We have developed an imaging-free framework to localize nucleic acids within a tissue by combining  a compressed sensing tissue-sampling strategy based on multi-angle-sectioning and an associated image reconstruction algorithm.  Initially, the tissue is cut into consecutive thin slices. Subsequently these are further sliced along an orthogonal plane at predefined orientations resulting in tissue strips that are subject to RNA sequencing. We implemented this framework to transform a single-cell RNA sequencing protocol into an imaging-free spatial transcriptomics technique. The method was validated by profiling the transcriptome of the Murine brain, and used to spatially profile the brain transcriptome of the Australian Central bearded dragon, Pogona vitticeps.

sample_organism:
Mus musculus
Pogona vitticeps

platform_organism:
Mus musculus
Pogona vitticeps

overall_design:
One Mus musculus and one Pogona vitticeps brain in thin coronal sections, cut into stripes at several alternating angles

Please note that the 'GSE152989_new_suppl_files.tar.gz' contains the expression data formatted in ".cef" format. The "cef" is a tab delimited file format described at: https://github.com/linnarsson-lab/ceftools

first: Halima

middle: H

last: Schede

first: Gioele

last: LaManno


title: Investigation Of Genes Associated With Atherosclerosis In Patients With Systemic Lupus Erythematosus

status: Public on Jul 22 2020

city: Edirne

first: Mehmet

middle: Ali

last: Balci

address: Balkan campus

department: Rheumatology

country: Turkey

institute: Trakya University

summary: Systemic lupus erythematosus (SLE) is a chronic, autoimmune disease affecting multiple heterogeneous organs and systems. SLE is associated with increased risk of atherosclerosis and increased cardiovascular complications. In this study, we specifically aimed to identify patients with SLE who are genetically at risk for developing atherosclerosis. Sureprint G3 Human Gene Expression 8x60K Microarray kit (Agilent technologies, Santa Clara, CA, USA) was used in our study. Genes showing differences in expression between the groups were identified by using GeneSpring GX 10.0 program. A total of 155 genes showing expression level difference were detected between SLE patients and healthy controls. In molecular network analysis.

overall_design: 38 patients with systemic lupus erythematosus (36 females, 2 males) and 32 healthy controls (32 females) were included in the study. Sureprint G3 Human Gene Expression 8x60K Microarray kit (Agilent technologies, Santa Clara, CA, USA) was used in our study.

last: BALCI


title: Transcriptional control of CALMODULIN by CAMTA regulates neural excitablity [ChIP-seq]

status: Public on Sep 15 2020

city: Klosterneuburg

first: Thanh

middle: TK

last: Vuong-Brender

address: Am Campus 1

country: Austria

institute: Institute of Science and Technology Austria

summary: We identified the binding site of the transcription factor CAMT-1/CAMTA in C. elegans by ChIP-seq and examined the changes of binding sites in egl-19(lf) and egl-19(gf) mutants

overall_design: CAMT-1 is tagged endogenously with GFP using CRISPR, we then crossed this line with egl-19(lf) and egl-19(gf) mutants, CAMT-1 non-tagged strain (N2) was taken as control

first: Sean

last: Flynn

first: Mario

last: de Bono


title: Genome-wide maps of RNA polymerase II in WT and ssu72 mutant cells [S5_S7_ChIPseq]

summary:
Deletion of ssu72 gene leads to a transcription elongation defect and the increase in the level of Ser5 and Ser7 phosphorylation in carboxy-terminal domain (CTD)  of Rpb1
Phosphorylation of the RNA polymerase II C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that histone deacetylase complex activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of the antisense transcription when the C-terminal domain phosphorylation is dysregulated due to the loss of Ssu72 phosphatase.  Interestingly, while single hos2/set3 mutants have little effect, loss of hos2 or set3 in addition to ssu72? leads to synergistic increase in antisense transcription globally and correlates with increases genomic instability and formation of deleterious R-loop structures across these regions. We propose that Ssu72 is essential to suppress initiation of cryptic transcription in the 3?end of the RNA polymerase II transcribed regions. In the absence of Ssu72, antisense transcription is supressed by the Hos2/Set3 dependent surveillance mechanism to maintain genome stability.

overall_design: Ser5-P CTD, and Ser7-P CTD ChIP-seq in WT and ssu72Δ

middle: M


title: Autophagy Promotes Growth of High Tumor Mutational Burden Tumors by Inhibiting a T Cell Immune Response [Exome-seq]

status: Public on Aug 03 2020

first: SAURABH

last: LADDHA

summary:
Autophagy degrades and recycles intracellular components to sustain metabolism and survival during starvation. Tumor cells upregulate and require autophagy to support their metabolism and enhance their proliferation and malignancy, and host autophagy also promotes tumor growth by providing essential tumor nutrients such as arginine in the circulation or alanine in the local tumor microenvironment. In addition to its metabolic role, autophagy regulates immune cell homeostasis and function, and suppresses inflammation, which may also play a role in cancer. Although host autophagy does not promote a T cell anti-tumor immune response in tumors with low tumor mutational burden (TMB), whether this was the case in tumors with high TMB was not known. Here we show that in contrast to low TMB tumors, host-specific deletion of the essential autophagy gene Atg7 induces a pro-inflammatory cytokine response and limits the growth of high TMB tumors, which is rescued by T-cell depletion. Expression of immune-related genes is increased in tumors from Atg7Δ/Δ hosts in a T-cell dependent manner. Tumors from Atg7Δ/Δ hosts also have decreased T regulatory cells (Tregs), and depletion of Tregs phenocopies the reduced tumor growth observed in Atg7Δ/Δ hosts. Moreover, loss of Stimulator of interferon genes (Sting) or IFNg restores growth of high TMB tumors on Atg7Δ/Δ hosts. Finally, similar to whole-body loss of autophagy, specific loss of autophagy in the liver is sufficient to limit tumor growth. Thus, autophagy, especially in the liver, promotes tumor immune tolerance by limiting STING, T cells, and IFNg, which enables tumor growth. We have designated this: Hepatic Autophagy Immune Tolerance (HAIT). Autophagy thereby promotes tumor growth through both metabolic and immune mechanisms depending on mutational load, and autophagy inhibition is an effective means to promote an anti-tumor T-cell response in high TMB tumors.
Genomic DNA Profiling using Agilent SureSelect Mouse All Exon kit and sequencing using Illumina NextSeq550

overall_design:
DNA was extracted from MB49, YUMM 1.1 and UV YUMM 1.1-9 cell lines using the QIAsymphony DSP DNA midi kit (937255, Qiagen). Mouse whole exome libraries were constructed using Agilent SureSelect Mouse All Exon kit according to the manufacturer’s protocol. The resulting sequencing libraries were analyzed using Agilent D1000 screentape and quantified using KAPA qPCR. Libraries were then normalized and pooled into one pool. The library pool was then clustered and sequenced on the Illumina NextSeq550 instrument using 2x151bp paired end reads to a mean death of 80X, following the manufacturer’s protocols
4 samples

first: Saurabh

last: Laddha

first: Chang

last: Chan

first: Laura

last: Poillet-Perez

first: Eileen

last: White


title: Comprehensive molecular features of polycystic ovary syndrome revealed by transcriptome analysis of oocytes and cumulus cells

status: Public on Sep 08 2020

city: Tianjin

first: Jie

last: Li

address: Wei Jin Road Nankai District No. 94

department: Department of Cell Biology and Genetics

institute: Nankai University

summary: We aimed to elucidate the molecular features and identify causative factors for PCOS through an integrated, transcriptomic analysis of oocytes and cumulus granulosa cells (GCs) from the same patients with PCOS

overall_design: We obtained matched oocytes and GCs from three PCOS patients and compared them with age-matched, women without PCOS, and performed RNA sequencing analysis to explore the transcriptional characteristics of their oocytes and GCs

first: J

first: H

last: Chen

first: M

last: Gou

first: C

last: Tian

last: Wang

first: D

middle: L

last: Keefe

first: X

last: Bai

first: L

last: Liu


title: Blocking of the CD80/86 axis as a therapeutic approach to prevent progression to more severe forms of COVID-19

status: Public on Jul 01 2020

city: Barcelona

first: Antonio

last: Julià

state: Barcelona

address: c/ Baldiri Reixac nº15

department: Rheumatology Research Group

country: Spain

institute: Vall d'Hebron Hospital Research Institute

summary: In its more severe forms, COVID-19 progresses towards an excessive immune response, leading to the systemic overexpression of proinflammatory cytokines like IL6, mostly from the infected lungs. This cytokine storm can cause multiple organ damage and death. Consequently, there is a pressing need to identify therapies to treat and prevent severe symptoms during COVID-19. Based on previous clinical evidence, we hypothesized that inhibiting T cell co-stimulation by blocking CD80/86 could be an effective therapeutic strategy against progression to severe proinflammatory states. To support this hypothesis, we performed an analysis integrating blood transcriptional data we generated from rheumatoid arthritis patients treated with abatacept -a CD80/86 costimulation inhibitor- with the pathological features associated with COVID-19, particularly in its more severe forms. We have found that many of the biological processes that have been consistently associated with COVID-19 pathology are reversed by CD80/86 co-stimulation inhibition, including the downregulation of IL6 production. Also, analysis of previous transcriptional data from blood of SARS-CoVinfected patients showed that the response to abatacept has a very high level of antagonism to that elicited by COVID-19. Finally, analyzing a recent single cell RNA-seq dataset from bronchoalveolar lavage fluid cells from COVID-19 patients, we found a significant correlation along the main elements of the C80/86 axis: CD86+/80+ antigen presenting cells, activated CD4+ T cells and IL6 production. Our in-silico study provides additional support to the hypothesis that blocking of the CD80/CD86 signaling axis may be protective of the excessive proinflammatory state associated with COVID-19 in the lungs.

overall_design: Whole RNAseq Blood Samples of patients treated with abatacept at week 0 and week 12.

first: Irene

last: Bonafonte

last: Gómez


title: RNA-seq analysis in ssu72 mutant cells [WT_ssu72]

first: Dong-hyuk

last: Heo

summary:
We report accumulation of cryptic antisense transcripts in ssu72 mutant cells. A histone deacetylase (Hos2) is not required to repress the cryptic transcription in SSU72+ strain  however in ssu72 mutant cells, Hos2 has an important role in suppression of the cryptic transcription
Phosphorylation of the RNA polymerase II C-terminal domain on heptad Y1S2P3T4S5P6S7 coordinates key events during transcription and when its deregulation leads to defects in transcription and RNA processing. Here we report that histone deacetylase complex activity of the fission yeast Hos2/Set3 complex plays an important role in suppressing cryptic initiation of the antisense transcription when the C-terminal domain phosphorylation is dysregulated due to the loss of Ssu72 phosphatase.  Interestingly, while single hos2/set3 mutants have little effect, loss of hos2 or set3 in addition to ssu72? leads to synergistic increase in antisense transcription globally and correlates with increases genomic instability and formation of deleterious R-loop structures across these regions. We propose that Ssu72 is essential to suppress initiation of cryptic transcription in the 3?end of the RNA polymerase II transcribed regions. In the absence of Ssu72, antisense transcription is supressed by the Hos2/Set3 dependent surveillance mechanism to maintain genome stability.

overall_design: RNA-seq in WT, ssu72Δ

first: Krzysztof

last: Kuś

first: Tea

last: Kecman

first: Sue

last: Tan-Wong

first: Nikolay

last: Zenkin

first: Nick

middle: J

last: Proudfoot

first: Lidia

last: Vasiljeva


title: scRNAseq of activated cells of the B cell lineage in the tumor microenvironment

first: William

last: Hudson

summary: The goals of this study were to gain a better understanding of the heterogeneity and transcriptional profile of activated cells of the B cell lineage in the tumor microenvironment.

overall_design: Activated cells of the B cell lineage (live CD3/14/16-CD19+IgD-CD71+) from primary tumors and metastatic lymph nodes of 3 HPV+ HNSCC patients and, as comparison, from PBMC of a healthy individual 7 days post seasonal Influenza vaccination were FACS-purified. Single-cell suspensions of FACS-purified cells were loaded onto the 10X Genomics Chromium Controller. Library construction was performed using the Chromium Single Cell 5’ Library Construction Kit followed by sequencing on a HiSeq3000 or NovaSeq6000.

first: Andreas

last: Wieland

first: Rafi

last: Ahmed


title: Cancer-specific CTCF binding facilitates oncogenic transcriptional dysregulation

status: Public on Aug 19 2020

city: Charlottesville

first: Zhenjia

last: Wang

state: VIRGINIA

address: 1300 Jefferson Park Avenue

department: Center for Public Health Genomics

institute: University of Virginia

type: Methylation profiling by high throughput sequencing

summary: The three-dimensional genome organization is critical for gene regulation and can malfunction in diseases like cancer. As a key regulator of genome organization, CCCTC-binding factor (CTCF) has been characterized as a DNA-binding protein with important functions in maintaining the topological structure of chromatin and inducing DNA looping. Among the prolific binding sites in the genome, several events with altered CTCF occupancy have been reported as associated with effects in physiology or disease. However, hitherto there is no comprehensive survey of genome-wide CTCF binding patterns across different human cancers. To dissect functions of CTCF binding, we systematically analyze over 700 CTCF ChIP-seq profiles across human tissues and cancers and identify cancer-specific CTCF binding patterns in six cancer types. We show that cancer-specific lost and gained CTCF binding events are associated with altered chromatin interactions, partially with DNA methylation changes, and rarely with sequence mutations. While lost bindings primarily occur near gene promoters, most gained CTCF binding events exhibit enhancer activities and are induced by oncogenic transcription factors. We validate these findings in T-cell acute lymphoblastic leukemia cell lines and patient samples and show that oncogenic NOTCH1 induces specific CTCF binding and they cooperatively activate expression of target genes, indicating transcriptional condensation phenomena. Our results substantiate CTCF binding alteration as a functional epigenomic signature of cancer.

overall_design: We collected a total of 793 CTCF ChIP-seq datasets, including 787 public datasets and 6 datasets we generated. 771 CTCF ChIP-seq datasets with peaks more than 2,000 were used in this study. We identified specific CTCF binding patterns in six distinct cancer types, including T-cell acute lymphoblastic leukemia (T-ALL), acute myeloid leukemia (AML), breast cancer (BRCA), colorectal cancer (CRC), lung cancer (LUAD) and prostate cancer (PRAD). We characterized a series of genomic and epigenomic features of cancer-specific CTCF binding events using multi-omics profiling techniques including WGS, TF and histone modification ChIP-seq, RNA-seq, ATAC-seq, bisulfite sequencing, and in situ Hi-C.

first: Celestia

last: Fang

first: Panagiotis

last: Ntziachristos

first: Chongzhi

last: Zang


title: RNA-seq analysis in ssu72 and hos2 mutant cells

overall_design: RNA-seq in WT, ssu72Δ, hos2Δ, and hos2Δssu72Δ


title: Autophagy Promotes Growth of High Tumor Mutational Burden Tumors by Inhibiting a T Cell Immune Response

first: SAURABH

last: LADDHA

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

overall_design: Refer to individual Series


title: Circular RNA circGNAQ acts as the sponge of miR-146a-5p to delay endothelial cell senescence and atherosclerosis progression

status: Public on Jun 18 2020

city: Dongguan

first: weipeng

last: Wu

address: Xin Cheng Avenue 1#, Songshan Lake

institute: Guangdong Medical University

summary: Endothelial cell senescence is one of the most important causes of vascular dysfunction and atherosclerosis. Circular RNAs (circRNAs) are endogenous RNA molecules with covalently closed-loop structures, which have been reported to be abnormally expressed in many human diseases. However, the potential role of circRNAs in endothelial cell senescence remains unknown. Here, we compared the expression patterns of circRNAs in young and senescent human endothelial cells using RNA sequencing. Among the differentially expressed endothelial cell senescence-associated circRNAs, we identified circGNAQ, generated by circularization of exons 4 and 5 of the GNAQ gene, as a circRNA showing markedly reduced levels in senescent endothelial cells. CircGNAQ silencing in young endothelial cells triggered senescence, as determined by a rise in senescence-associated β-galactosidase activity, reduced cell proliferation, and suppressed angiogenesis; circGNAQ overexpression showed the opposite effects. Mechanistic studies revealed that circGNAQ acted as an endogenous miR-146a-5p sponge to sequester and inhibit miR-146a-5p activity, leading to increased PLK2 expression. In vivo studies showed that circGNAQ overexpression delayed endothelial cell senescence and atherosclerosis progression in ApoE-/- mice. These results revealed an important role for circGNAQ in cellular senescence and provide novel insight into the role of circRNAs in atherosclerosis progression.

overall_design: circRNA sequencing on ribosomal RNA-depleted total RNA from young and senescent endothelial cells (HUVECs and HCAECs)

first: Xing-dong

last: Xiong

first: Meng-yun

last: Cai

first: Wei-peng

first: Meng-yuan

last: Zhou


title: RNA-seq for the tissues of Pcgf6 knockout mice and wild type mice

status: Public on Jun 16 2020

city: Nanjing

first: Mengjie

last: Liu

address: No. 12, Xuefu Road, Pukou District

institute: Nanjing university

summary: Polycomb group (PcG) proteins are essential for maintenance of lineage fidelity by coordinating developmental gene expression programs. Polycomb group protein Pcgf6 has been previously reported to repress lineage-specific genes, especially germ cell-related genes in mouse embryonic stem cells (ESCs) via the non- canonical Polycomb repressive complex PRC1. 6. However, the potential mechanism of this repressive activity remains largely unknown. Here, we demonstrated that Pcgf6 played an essential role in embryonic development as indicated by the partially penetrant embryonic lethality in homozygous mice. Additionally, we found that surviving Pcgf6-deficient mice exhibited compromised fertility. Using the Pcgf6 mutant mice, we revealed that ablation of Pcgf6 in somatic tissues also led to robust derepression of such germ cell-related genes. We provided evidence that these genes were direct targets of Pcgf6 in ESCs and endogenous Pcgf6 colocalized with G9a/Glp and Hdac1/2 on the promoters of these germ cell-related genes and that binding of these proteins to target genes correlated with methylation of H3K9 and the status of histone acetylation. Moreover, the recruitment of G9a/Glp and Hdac1/2 to target promoters was dependent on the binding of Pcgf6. Therefore, our study demonstrated a critical role for Pcgf6 in safeguarding lineage decisions and in protecting germ cell-related genes against aberrant expression.

overall_design: mRNA profiles of the liver, brain, and testis of 8-week old Pcgf6 knockout and wildtype mice were generated by deep sequencing，in triplicate, using Illumina Hiseq 4000. The raw data had already submitted to SRA. The BioProject accession is PRJNA597260.

first: Jinzhong

last: Qin


title: Intervertebral disc degeneration, a loose definition for a more complex pathology? Insights from aging inbred mouse strains

status: Public on Jun 08 2020

city: Philadelphia

first: Emanuel

middle: José

last: Novais

state: PA

address: 1025 Walnut St., Suite 511 College Bldg.

department: Department of Orthopaedic Surgery

institute: Thomas Jefferson

summary:
Intervertebral disc degeneration is an important contributor to chronic low back pain. While a wide spectrum of clinically relevant degenerative disc phenotypes have been observed during aging, their molecular underpinning have not been established.
We used microarrays to explore the transcriptomics of differentially expressed genes during aging (6M to 23M) in two strains: C57BL/6 and LG/J.

overall_design: NP tissue was dissected from caudal discs of 6M and 23M BL6 mice (n=7), LG/J (n=5/6)  RNA extraction and hybridization on Affymetrix microarrays. 6- and 23-month time point were choosen to explore the trancsriptome signature of young and old mice's nucleus pulposus, respectively.

first: Sankar

last: Addya


title: Aborigines of Taiwan and their genetic relationship to East Asian and Pacific populations

status: Public on Jun 10 2020

city: Tartu

first: Tuuli

last: Reisberg

address: Riia 23

country: Estonia

institute: University of Tartu

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array


title: Gene expression data from Brazilian SPAH study

city: São Paulo

first: Levi

middle: Higino

last: Jales Neto

state: SP

address: Dr Arnaldo 455

country: Brazil

institute: FMUSP

summary:
This study is part of previous epidemiologic project, including a population-based survey (Sao Paulo Ageing & Health study (SPAH Study). The data from this study was collected between 2015 to 2016 and involved elderly women (ages ≥65 yeas) living in the Butanta district, Sao Paulo. The purpose of the study was identification of association between transcriptome and the osteo metabolism diseases phenotype, like osteoporosis, vertebral fracture and coronary calcification.
Peripheral blood cells suffer alterations in the gene expression pattern in response to perturbations caused by calcium metabolism diseases.   The purpose of this study is to identify possible molecular markers associated with osteoporosis, vertebral fractures and coronary calcification in elderly women from community from Brazilian SPAH study. Vertebral fractures were the most common clinical manifestation of osteoporosis and coronary calcifications were associated with high morbimortality.

overall_design: Fasting blood samples were withdrawn from community elderly women with osteo metabolism diseases. RNA was extracted from peripheral total blood, and hybridized into Affymetrix microarrays.

first: L

first: Z

last: Wicik

first: G

last: Torres

last: Takayama

first: V

middle: F

last: Caparbo

first: N

last: Lopes

first: M

last: Silva

last: Steban

first: A

last: Pereira

first: R

last: R Pereira


title: Neutrophils expressing lysyl oxidase-like 4 protein are present in colorectal cancer liver metastases resistant to anti-angiogenic therapy

status: Public on May 27 2020

city: Seongnam-si

first: Je-Gun

last: Joung

address: 335, Pangyo-ro, Bundang-gu

country: South Korea

institute: CHA University

summary: Colorectal cancer liver metastases (CRCLM) that present with a replacement histopathological growth pattern (HGP) are resistant to neoadjuvant anti-angiogenic therapy. Surrogate biomarkers are not available to preoperatively identifypatients with these tumors. Here we identify differentially expressed genes between CRCLM with a replacement HGP and those with a desmoplastic HGP using RNA sequencing.We demonstrate that LOXL4 is transcriptionally upregulated in replacement HGP CRCLM compared with desmoplastic HGP CRCLM and the adjacent normal liver. Interestingly, lysyl oxidase-like 4 (LOXL4) protein was expressed by neutrophils present in the tumor microenvironment in replacement HGP CRCLM. We further demonstrate that LOXL4 expression is higher in circulating neutrophils of cancer patients compared with healthy control patients and its expression can be induced by stimulation with lipopolysaccharide and TNF-alpha. Our study is the first to show the expression of LOXL4 in neutrophils and reveals the potential for LOXL4-expressing neutrophils to support the replacement HGP phenotype and to serve as a surrogate biomarker for this subtype of CRCLM.

overall_design: Examination of RNA samples of Colorectal cancer liver metastases (CRCLM)

first: Anthoula

last: Lazaris


title: Variation in gene expression between two Sorghum bicolor lines differing in innate immunity response

status: Public on Jun 06 2020

city: Columbia

first: Gary

last: Stacey

state: Missouri

address: 1201 Rollins st.

department: Divisions of Plant Science and Biochemistry

institute: University of Missouri

summary: Comparative RNA-seq analysis of MAMP triggered gene expression in two sorghum bicolor lines, BTx623 and SC155-14E, revealed a clear transcriptional response to elicitation with the microbe associated molecular pattern (MAMPs) flagellin (flg22) or chitin elicitation.

overall_design: Leaf discs of the second youngest leaves of fifteen-day old Sorghum bicolor lines, BTx623 and SC155-14E, were treated with flagellin (flg22) or chitin for 1 hour. The samples [2 genotypes (BTx623 and SC155-14E), 3 treatments (mock, flg22 or chitin), 3 biological replicates] were collected and the RNAs  were extracted. Non-strand-specific RNA-seq libraries were multiplexed and sequenced using Illumina HiSeq 2000 (Illumina, Sandiego, CA).

first: Yaya

last: Cui

first: Dongqin

last: Chen

first: Yuexu

last: Jiang

first: Dong

last: Xu

first: Peter

last: Balint-Kurti


title: Single cell RNA-seq analysis on human endometrium across the natural menstrual cycle

status: Public on Jun 29 2020

city: Stanford

first: Wanxin

last: Wang

address: James H Clark Center, 318 Campus Drive, room E300

institute: Stanford Univeristy

summary: To unbiasedly and systematically characterize endometrial transformation across the human menstrual cycle in preparation for embryo implantation,  we analyzed the transcriptomic transformation of human endometrium at single cell resolution, dissecting multidimensional cellular heterogeneity of the tissue across the entire natural menstrual cycle.

overall_design:
We collected single cell transcriptome profile of endometrium biopsies sampled from 19 healthy and fertile females, at 4-27 days of their menstrual cycle.

[10x dataset] - collected to validate main findings drawn from the original C1 dataset of this study.  In this dataset, we collected additional data from 10 endometrial biopsies using the 10x Chromium system. Importantly, we collected both C1 and 10x data for two biopsies, one from mid-secretory phase and the other early-secretory. They served as anchors for a direct comparison between the two datasets, and were referred as ?anchor biopsies? in the manuscript of this study. Biopsies in the 10x dataset were obtained following the same protocol used for the C1 dataset, as described in the manuscript.

first: Alina

last: Isakova

first: Felipe

last: Vilella

first: Pilar

last: Alama

first: Inmaculada

last: Moreno

first: Wenying

last: Pan

first: Carlos

last: Simon

first: Stephen

middle: R

last: Quake


title: Combining multi-omics and drug perutbation profiles to identify novel treatments that improve disease phenotypes in spinal muscular atrophy [RNA-seq]

status: Public on May 14 2020

city: Cardiff

first: Viola

last: Volpato

address: Maindy Rd

department: UK DRI

institute: Cardiff University

summary: We used an in-depth and parallel approach combining proteomics, transcriptomics and the drug pertubational dataset Connectivity Map (CMap)  to identify differentially expressed (DE) transcripts and proteins in skeletal muscle of the severe Taiwanese Smn-/-;SMN2 SMA mice that could potentially be restored by known and available pharmacological compounds. This strategy uncovered several potential therapeutic candidates, including harmine, which was further evaluated in cell and animal models, showing an ability to restore molecular networks and improve several disease phenotypes, including SMN expression and lifespan.

overall_design: Examination of harmine treatment effect by comparison of three untreated SMA mice, three treated SMA mice, three untreated control mice and three treated control mice.

first: Katharina

last: Meijboom

first: Jimena

last: Monzón-Sandoval

first: Joseph

last: Hoolachan

first: Suzan

last: Hammond

first: Frank

last: Abendroth

first: Olivier

last: Gerrit de Jong

first: Gareth

last: Hazell

first: Nina

last: Ahlskog

first: Matthew

last: Wood

first: Caleb

last: Webber

first: Melissa

last: Bowerman


title: Fused in sarcoma regulates DNA replication timing and progression

status: Public on May 13 2020

city: Madison

first: WEIYAN

last: JIA

state: WI

address: 1111 Highland Ave., 3068 WIMR

department: Department of Human Oncology

institute: University of Wisconsin- Madison

summary: Fused in sarcoma (FUS) encodes a low complexity RNA-binding protein with diverse roles in transcriptional activation and RNA processing.  While oncogenic fusions of FUS and transcription factor DNA-binding domains are associated with soft tissue sarcomas, dominant mutations in FUS cause amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). FUS has also been implicated in DNA double-strand break repair (DSBR) and genome maintenance. However, the underlying mechanisms are unknown. Here we employed quantitative proteomics, transcriptomics, and DNA copy number analysis (Sort-Seq), in conjunction with FUS-/- cells to ascertain roles of FUS in genome protection. FUS-/- cells exhibited alterations in the recruitment and retention of DSBR factors BRCA1 and 53BP1 but were not overtly sensitive to genotoxins. By contrast, FUS-deficient cells had reduced proliferative potential that correlated with reduced replication fork speed, diminished loading of pre-replication complexes, and attenuated expression of S-phase associated genes. FUS interacted with lagging strand DNA synthesis factors and other replisome components, but did not translocate with active replication forks. Using a Sort-Seq workflow, we show that FUS contributes to genome-wide control of DNA replication timing and is essential for the early replication of transcriptionally active DNA. These findings illuminate new roles for FUS in DNA replication initiation and timing that may contribute to genome instability and functional defects in cells harboring disease-associated FUS fusions.

overall_design: FUS+/+, FUS-/-,  FUS-/-:FUS cells (U-2 OS background)were collected 2 days later after spliting to new dishes. Total RNA was extracted for non-stranded cDNA library building and sequencing at PE150 with NovoSeq 6000

first: Weiyan

last: Jia

first: Randal

last: Tibbetts


title: Expression profiles of skeletal muscle from Taiwanese Smn-/-;SMN2 spinal muscular atrophy mouse model treated with Pip6a-PMO

address: Maindy Road

institute: UK Dementia Research Institute at Cardiff University

summary: Spinal muscular atrophy (SMA) is a neuromuscular disorder caused by loss of survival motor neuron (SMN) protein. While SMN restoration therapies are beneficial, they are not a cure. We aimed to identify novel treatments to alleviate muscle pathology combining transcriptomics, proteomics and perturbational datasets. This revealed potential drug candidates for repurposing in SMA. One of the candidates, harmine, was further investigated in cell and animal models, improving multiple disease phenotypes, including SMN expression and lifespan. Our work highlights the potential of multiple and parallel data driven approaches for the development of novel treatments for use in combination with SMN restoration therapies.

overall_design: 18 total samples were analyzed. Smn-/-;SMN2 mice received a facial intravenous injection at postnatal day (P) 0 and P2 of Pip6a-scrambled or Pip6a-PMO (10 μg/g). The tibialis anterior was harvested from P2 untreated Smn-/-;SMN2 and WT mice, P7 untreated, Pip6a-scrambled-treated and Pip6a-PMO-treated Smn-/-;SMN2 mice and P7 untreated WT mice (3 biological replicates

middle: G

last: de Jong


title: Combining multi-omics and drug perutbation profiles to identify novel treatments that improve disease phenotypes in spinal muscular atrophy


title: Cytosolic aggregation of mitochondrial proteins enhances degeneration of cellular homeostasis

status: Public on May 01 2020

city: Poznan

first: Barbara

last: Uszczyńska-Ratajczak

address: Noskowskiego 12/14

country: Poland

institute: Institute of Bioorganic Chemistry, Polish Academy of Sciences

summary: Analysis of global expression changes in the Saccharomyces cerevisiae transcriptomes triggered by mutations in pam16 genes and overexpression of Rip1 protein, respectively.

overall_design: Investigating effects of the pam16 mutation and Rip1 overexpression on Saccharomyces cerevisiae transcriptomes, respectively.

first: Karen

last: Stroobants

last: Uszczynska-Ratajczak

first: Rishika

last: Kundra

first: Urszula

last: Nowicka

first: Piotr

last: Chroscicki

first: Agnieszka

last: Chacinska

first: Michele

last: Vendruscolo


title: Genetic interaction mapping for fatty acid synthesis uncovers LUR1/C12orf49 as novel regulator of SREBP activity

status: Public on Apr 30 2020

city: Toronto

first: Jason

last: Moffat

state: ON

address: 686 Bay Street, Room 13.9705

department: Molecular Genetics

country: Canada

institute: University of Toronto


title: Chromatin profiling of the relationship between EWS/FLI, LSD1, and H3K27 acetylation

status: Public on May 12 2020

city: Columbus

first: Emily

middle: Rose

last: Theisen

state: OH

address: 700 Childrens Drive

department: Center For Childhood Cancer and Blood Diseases

institute: Nationwide Children's Hospital

summary: The purpose of this study was to define the genome-wide functional relationship between LSD1 and EWS/FLI in Ewing sarcoma cells. We found EWS/FLI and LSD1 co-localize throughout the genome and that EWS/FLI induces a large change in the genomic distribution of LSD1.

overall_design: A673 cells were assayed with either wildtype ("A673"), depleted ("EFKD"), or depleted and ectopically rescued (714 or "wtEF") levels of EWS/FLI. For knockdown of shRNAs were retrovirally delivered targeting either EWS/FLI ("EFKD") or luciferase as a negative control ("A673") and cells were selected in 2 µg/mL puromycin. For rescue cDNAs were retrovirally transduced and cells were selected in puro with 100 µg/mL hygromycin B.  For CUT&Tag two independent replicates were performed for each sample including LSD1 and H3K27ac, with a non-specific Rb IgG control. Samples were submitted for 150-bp paired end sequencing. Bigwigs for H3K27ac and relevant non-specific control, and all CUT&Tag samples are spike-in normalized representations of the aligned reads.

first: Stephen

last: L Lessnick


title: Cell-intrinsic differences between human tracheal epithelial cells from children and adults [laser-captured fresh epithelial cells]

status: Public on Apr 20 2020

city: London

first: Adam

last: Pennycuick

address: 5 University Street

department: UCL Respiratory

institute: University College London

summary: The airway epithelium is a key protective barrier whose integrity is preserved by the self-renewal and differentiation of basal progenitor cells. Epithelial cells are central to the pathogenesis of multiple chronic lung diseases for which age is a principle risk factor. Children are also less susceptible to SARS-CoV-2 infection, suffer less severe symptoms than adults and have a lower rate of mortality. Few studies have addressed differences between airway epithelial cells in children and adults. Here, we perform bulk RNA sequencing studies in laser-captured whole epithelium, FACS-sorted basal cells and cultured basal cells, as well as in vitro cell proliferation experiments, to address the intrinsic molecular differences between paediatric and adult airway basal cells. We find that, while the cellular composition of the paediatric and adult tracheal epithelium is broadly similar, in cell culture, paediatric airway epithelial cells displayed higher colony forming ability, better in vitro growth and outcompeted adult cells in competitive proliferation assays. Although recurring differences between airway epithelial gene expression were seen between samples from children and adults, RNA sequencing showed broad conservation of transcriptional programmes. Genes associated with SARS-CoV-2 infection were not differentially expressed between children and adults, although individuals showed some variability in their expression of viral infection-associated genes. Our results chart important cell intrinsic differences in transcriptional profile and regenerative capacity between tracheal epithelial cells of children and adults.

overall_design:
Comparison of airway RNAseq data between adults and children. Three related datasets are presented: fresh airway epithelial cells, fresh sorted basal cells and cultured basal cells. This dataset contains laser-captured fresh epithelial cells.

***Please note that the raw data files have been lost and thus are not included in the records.

first: Elizabeth

last: Maughan


title: Cell-intrinsic differences between human tracheal epithelial cells from children and adults


title: Rif1 functions in a tissue-specific manner to control replication timing through its PP1-binding motif

status: Public on Apr 13 2020

city: Nashville

first: Jared

last: Nordman

state: Tennessee

address: 465 21st Ave South MRB III 4268

institute: Vanderbilt University

summary: Replication initiation in eukaryotic cells occurs asynchronously throughout S phase, yielding early and late replicating regions of the genome, a process known as replication timing (RT). RT changes during development to ensure accurate genome duplication and maintain genome stability. To understand the relative contributions that cell lineage, cell cycle, and replication initiation regulators have on RT, we utilized the powerful developmental systems available in Drosophila melanogaster. We generated and compared RT profiles from mitotic cells of different tissues and from mitotic and endocycling cells of the same tissue. Our results demonstrate that cell lineage has the largest effect on RT, whereas switching from a mitotic to an endoreplicative cell cycle has little to no effect on RT. Additionally, we demonstrate that the RT differences we observed in all cases are largely independent of transcriptional differences. We also employed a genetic approach in these same cell types to understand the relative contribution the eukaryotic RT control factor, Rif1, has on RT control. Our results demonstrate that Rif1 can function in a tissue-specific manner to control RT. Importantly, the Protein Phosphatase 1 (PP1) binding motif of Rif1 is essential for Rif1 to regulate RT. Together, our data support a model in which the RT program is primarily driven by cell lineage and is further refined by Rif1/PP1 to ultimately generate tissue-specific RT programs.

overall_design: Replication timing profiles prepared in female 3rd instar larval wing disc and adult ovarian follicle cell of Drosophila melanogaster by Illumina sequencing. Transcriptome analysis by rRNA-depleted mRNA sequencing in female 3rd instar larval wing disc and ovarian follicle cell of Drosophila melanogaster.

first: Robin

last: Armstrong

first: Souradip

last: Das

first: Christina

middle: A

last: Hill

first: Robert

last: Duronio

middle: T


title: Estrogen receptor alpha mutations in breast cancer cells cause gene expression changes through constant activity and through secondary effects [ATAC-seq]

status: Public on Apr 08 2020

city: Salt Lake City

last: Gertz

state: UT

address: 1950 Cir of Hope Dr

institute: University of Utah

summary: While breast cancer patients with tumors that express estrogen receptor α (ER) generally respond well to hormone therapies that block ER’s actions, a significant number relapse. Approximately 30% of these recurrences harbor activating mutations in ER’s ligand binding domain. ER mutations have been shown to confer ligand-independent function to ER; however, much is still unclear regarding the effect of mutant ER beyond its estrogen independence. To investigate mutant ER’s molecular effects, we developed multiple isogenic ER mutant cell lines for the two most common ER ligand binding domain mutations, Y537S and D538G. We found that these mutations induce differential expression of thousands of genes, the majority of which are specific to one or the other mutation and are not observed upon estrogen treatment of wildtype cells. The mutant-specific genes show consistent differential expression across ER mutant lines developed in other laboratories. The observed gene expression changes cannot be explained by constitutive ER activity alone, as wildtype cells with long term estrogen exposure only exhibit some of these transcriptional changes, suggesting that mutant ER causes novel regulatory effects that are not simply due to constant activity. While ER mutations have minor effects on ER genomic binding, with the exception of ligand independence, we observed substantial differences in chromatin accessibility due to ER mutations. Mutant ER is bound to approximately a quarter of mutant-enriched accessible regions that are enriched for other DNA binding factors including FOXA1, CTCF, and OCT1. Our findings indicate that mutant ER causes several consistent effects on gene expression both indirectly and through constant activity.

overall_design: ATAC-seq of ESR1 mutant and wildtype T-47D breast cancer cell lines.

first: Spencer

last: Arnesen


title: Ssu72 is essential to suppress initiation of cryptic transcription in the 3' end of the RNA polymerase II transcribed regions.

status: Public on Jun 30 2020

city: Oxford

first: Dong-hyuk

last: Heo

address: South Parks Road

institute: University of Oxford


title: Estrogen receptor alpha mutations in breast cancer cells cause gene expression changes through constant activity and through secondary effects [RNA-seq]

overall_design: RNA-seq of ESR1 mutant and wildtype MCF-7 and T-47D breast cancer cell lines.


title: Estrogen receptor alpha mutations in breast cancer cells cause gene expression changes through constant activity and through secondary effects [ChIP-seq]

overall_design: ChIP-seq of ESR1 mutant and wildtype MCF-7 and T-47D breast cancer cell lines.


title: Estrogen receptor alpha mutations in breast cancer cells cause gene expression changes through constant activity and through secondary effects

overall_design: Refer to individual Series


title: p53-induced apoptosis is specified by a translation program regulated by PCBP2 and DHX30.

status: Public on Mar 30 2020

city: Trento

first: Erik

last: Dassi

state: TN

address: Via Sommarive, 9

department: CIBIO

country: Italy

institute: University of Trento

summary: Activation of p53 by the small molecule Nutlin can result in a combination of cell cycle arrest and apoptosis. The relative strength of these events is difficult to predict, leaving uncertainty as to the therapeutic benefits of Nutlin. Here, we report a new translation control mechanism shaping p53-dependent apoptosis. We performed polysomal profiling in the cell lines SJSA1 and HCT116, of which only the first undergoes robust cell death in response to p53 activation by Nutlin. We establish Nutlin-induced apoptosis in SJSA1 cells to be associated with a set of translationally enhanced mRNAs carrying a newly identified 3’UTR motif which we labeled CG-motif. We identified PCBP2 and DHX30 as interactor proteins of the CG-motif that are more abundant in HCT116 cells compared to SJSA1. The binding of DHX30 to the CG-motif detected in HCT116 cells was shown to be dependent on PCBP2. Interestingly, DHX30 depletion enhances polysome association of CG-motif mRNAs in HCT116 cells, shifting their outcome towards apoptosis. In U2OS, an osteosarcoma-derived cell line that unlike SJSA1 undergoes persistent cell cycle arrest in response to Nutlin, DHX30 is highly expressed and its depletion enhances the expression of CG-motif mRNAs.

overall_design: 4 biological samples per condition are used. A total of 24 samples were used: 12 polysomal DMSO (scramble, DHX30 silencing and PCBP2 silencing) and 12 polysomal Nutlin (scramble, DHX30 silencing and PCBP2 silencing).

first: Sara

last: Zaccara

first: Dario

last: Rizzotto

first: Alberto

last: Inga


title: Single nucleus RNA-seq of cardiomyocytes from neonatal mouse hearts after injury

status: Public on Mar 18 2020

city: New York

first: Zhaoning

last: Wang

state: New York

address: 701 West 168th Street Hammer 14 - 1410

department: Genetics and Development

institute: Columbia University

summary: The adult mammalian heart is incapable of regeneration following injury. In contrast, the neonatal mouse heart can efficiently regenerate during the first week of life. The molecular mechanisms that mediate the regenerative response and its blockade in later life are not understood. Here, by single-nucleus RNA sequencing, we map the dynamic transcriptional landscape of five distinct cardiomyocyte populations in healthy, injured and regenerating mouse hearts. We identify immature cardiomyocytes that enter the cell-cycle following injury and disappear as the heart loses the ability to regenerate. These proliferative neonatal cardiomyocytes display a unique transcriptional program dependent on NFYa and NFE2L1 transcription factors, which exert proliferative and protective functions, respectively. Cardiac overexpression of these two factors conferred protection against ischemic injury in mature mouse hearts that were otherwise non-regenerative. These findings advance our understanding of the cellular basis of neonatal heart regeneration and reveal a transcriptional landscape for heart repair following injury.

overall_design: We performed myocardial infarction (MI) or sham surgeries to mouse hearts at postnatal day 1 or day 8. At 1d and 3d post P1 and P8 surgery, ventricle samples below the surgery plane were collected for single nucleus RNA-Seq.

first: Miao

last: Cui

first: Wei

last: Tan

first: Eric

middle: N

last: Olson


title: Manuscript title: C/EBPα is methylated by PRMT1 to regulate Cyclin D1 gene transcription in human breast cancer

status: Public on Apr 05 2020

city: Beijing

first: Liming

last: Liu

address: dongdan Si Tiao

institute: Chinese Academy of Medical Sciences & Peking Union Medical College

summary: C/EBPα is an essential transcription factor involved in regulating the expression or function of certain cell-cycle regulators. However, little is known about the role of methylation in regulating the antiproliferation activity of C/EBPα. Here, we report that knockdown of protein arginine methyltransferases 1 (PRMT1) leads to cellular growth arrest accompanied by a decrease in Cyclin D1 gene expression in breast cancer cells. Furthermore, we reveal that C/EBPα is methylated by PRMT1 at three arginine residues (R35, R156, and R165), which impairs the interaction of C/EBPα with HDAC3 and modulates the transcription activity of C/EBPα and Cyclin D1 gene expression. PRMT1 is upregulated in human breast cancer, and elevated PRMT1 is correlated with cancer malignancy. Most importantly, a specific inhibitor of PRMT1 significantly impedes the growth of cancer cells from triple-negative breast cancer patients. Our data demonstrate that high expression of PRMT1 promotes the expression of Cyclin D1 through methylation of C/EBPα to interfere with the repressive function of HDAC3, which leads to rapid growth of tumor cells during the pathogenesis of breast cancer. This evidence that PRMT1 mediates C/EBPα methylation sheds light on a novel therapeutic pathway for breast cancer.

overall_design: mRNA profiles of sh1, sh2 and shGFP cells, sh1 and sh2 cells were obtained by infecting MDA-MB-231 cell using lentivirus expressing shPRMT1, while the control sample shGFP cell was generated by  infecting MDA-MB-231 cell with lentivirus expressing shGFP. Independent biology triplicate for each sample was performed.

first: Li-ming

first: Ye

last: Zhang


title: Genome-wide transcriptional analysis in intestinal biopsies from Crohn's disease (CD) patients.

status: Public on Jun 08 2020

city: Barcelona

first: Adrià

last: Aterido

address: c/ Baldiri Reixac nº15

institute: Vall d'Hebron Hospital Research Institute

summary: Differential gene expression analysis between CD patients and controls to identify the transcriptional signature that defines the inflamed intestinal mucosa in CD.

overall_design: Intestinal biopsy samples were obtained from CD patients and healthy controls. RNA was subsequently extracted from each sample. Gene expression intensities were measured using GE Healthcare/Amersham Biosciences CodeLink Human Whole Genome Bioarray. After performing the gene expression quality control analysis, we characterized the transcriptional profile of the inflamed intestinal mucosa in CD.

first: Manyé

last: Josep


title: CELL CONTRACTILITY AND AN ACTIN GRADIENT DRIVE POLAR ALIGNMENT OF FIBROBLASTS IN CONSTRAINED GEOMETRIES

status: Public on Apr 07 2020

city: Amherst

first: Tianfa

last: Xie

state: Massachusetts

address: 240 Thatcher Way

department: Mechanical and Industrial Engineering

institute: University of Massachusetts Amherst

summary: When REF 2c cells were placed on circular micro-contact printed patterns, the boundary cells radially aligned over a period of 48 h. Video tracking of specific boundary and inner cells showed that this phenomenon was not caused by cells migrating towards or away from the periphery. Cell contractility, intercellular junctions, and cell-cell adhesion are required for radial alignment.

overall_design: Examination the gene expression differences between 2 different REF subclones.

first: Sarah

last: St. Pierre

first: Yubing

last: Sun


title: Dynamic transcriptional responses to injury of regenerative and non-regenerative cardiomyocytes revealed by single-nucleus RNA sequencing

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

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus