title: RNASeq of TET2-mutant human neutrophils

first: Hector

last: Huerga Encabo

address: The Francis Crick Institute, 1 Midland Rd

institute: The Francis Crick Institute

summary: Somatic mutations acquired by hematopoietic stem cells (HSCs) are commonly found over the course of a lifespan. Some of these clones will outgrow through a process known as clonal hematopoiesis (CH) and produce mutated immune cell progeny, which will shape host immunity. Individuals with CH are asymptomatic but have increased risk of developing leukemia, cardiovascular and pulmonary inflammatory diseases, and severe infections. Despite the key role that neutrophils play in the development of such diseases, little is known about how these prevalent somatic mutations affect neutrophil functionality. In this work, we describe how mutations in TET2, one of the most common mutated genes in individuals with CH, affect human neutrophil biology.

overall_design: Using CRISPR-mediated genetic engineering of human HSCs and transplantation in immunodeficient mice, we have sorted and analyzed the transcriptome of TET2 mutant (TET2Mut) neutrophils from 4 biological replicates.

last: Encabo

first: Robert

last: Goldstone

first: Miriam

last: Sopena

first: Dominique

last: Bonnet


title: Comparison of gene expression similarity between mouse extrahepatic bile duct and pancreatic duct epithelia and organoids prepared from these epithelia.

status: Public on Jun 06 2023

city: Harbin

first: Miao

last: Liu

address: College of Life Sciences, Northeast Forestry University, No. 26, Hexing Road, Xiangfang District,

country: China

institute: Northeast Forestry University

type: Expression profiling by high throughput sequencing

summary: By RNA sequencing we found that extrahepatic bile duct organoids and pancreatic duct organoids have similar gene expression signatures compared with duct epithelia.

overall_design: mRNA profiles of extrahepatic bile duct epithelia, pancreatic duct epithelia, three extrahepatic bile duct organoids and three pancreatic duct organoids. There is no control sample.

first: Wen

last: Yu

first: Chun-bo

last: Teng


title: SARS-CoV-2 nsp13 restricts episomal DNA transcription without affecting chromosomal DNA

city: Wuhan

first: Aixin

last: Li

state: Hubei Province

address: No.299, Bayi Road, Wuchang District, Wuhan City, Hubei Province

department: School of Basic Medical Sciences

institute: Wuhan University

summary: Non-structural protein 13 (nsp13), the helicase of SARS-CoV-2, has been shown to possess multiple functions that are essential for viral replication and is considered an attractive target for the development of novel antiviral drugs. We were initially interested in the interplay between nsp13 and interferon signaling, and found that nsp13 inhibited reporter signal of IFN-β promoter assay. Surprisingly, the ectopic expression of different components of the RIG-I/MDA5 pathway, which were used to stimulate IFN-β promoter, was also mitigated by nsp13. However, endogenous expression of these genes was not affected by nsp13. Interestingly, nsp13 restricted expression of foreign genes originated from plasmid transfection, but failed to inhibit them after chromosome integration. These data together with results from run-off transcription assay and RNA sequencing suggested a specific inhibition of episomal but not chromosomal gene transcription by nsp13. By using different truncated and mutant forms of nsp13, we demonstrated that its NTPase and helicase activities contributed to episomal DNA transcriptional inhibition, And this restriction required direct interaction with episomal DNA. Further, we developed a high-throughput nsp13 drug screening method based on the correlation between the helicase activity and nsp13 inhibition on episomal DNA. This method evaluates the inhibitory effect of compounds on nsp13 by detecting the expression of reporter plasmids after co-transfection with nsp13 plasmids, which is economical and convenient compared with conventional methods. In conclusion, we found that nsp13 can specifically inhibit episomal DNA transcription and developed a high-throughput drug screening method targeting nsp13 to facilitate the development of new antiviral drugs.

overall_design: HEK293T cells were co-transfected with pEF1α-Luc and pHA-NSP13 or empty vector for 24 h, chromosomal gene expression was determined by RNA-seq. This experiment to detect the effect of SARS-CoV-2 NSP13 on chromosomal gene expression.

first: Yuchen

last: Xia


title: Group-specific cellular metabolism in Medulloblastoma

city: Münster

first: Carolin

last: Walter

address: Domagkstraße 9

department: Medical Faculty of the WWU Münster

country: Germany

summary:
Background
Cancer metabolism influences multiple aspects of tumorigenesis and causes diversity across malignancies. Although comprehensive research has extended our knowledge of molecular subgroups in medulloblastoma (MB), discrete analysis of metabolic heterogeneity is currently lacking. This study seeks to improve our understanding of metabolic phenotypes in MB and their impact on patients’ outcomes.

Methods
Data from four independent MB cohorts encompassing 1,288 patients were analysed. We explored metabolic characteristics of 902 patients (ICGC and MAGIC cohorts) on bulk RNA level. Moreover, data from 491 patients (ICGC cohort) were searched for DNA alterations in genes regulating cell metabolism. To determine the role of intratumoral metabolic differences, we examined single-cell RNA-sequencing (scRNA-seq) data from 34 additional patients. Findings on metabolic heterogeneity were correlated to clinical data.

Results
Established MB groups exhibit substantial differences in metabolic gene expression. By employing unsupervised analyses, we identified three clusters of group 3 and 4 samples with distinct metabolic features in ICGC and MAGIC cohorts. Analysis of scRNA-seq data confirmed our results of intertumoral heterogeneity underlying the according differences in metabolic gene expression. On DNA level, we discovered clear associations between altered regulatory genes involved in MB development and lipid metabolism. Additionally, we determined the prognostic value of metabolic gene expression in MB and showed that expression of genes involved in metabolism of inositol phosphates and nucleotides correlates with patient survival.

Conclusion
Our research underlines the biological and clinical relevance of metabolic alterations in MB. Thus, distinct metabolic signatures presented here might be the first step towards future metabolism-targeted therapeutic options.

overall_design: This study provides a comprehensive analysis of metabolic heterogeneity in MB on genomic and transcriptomic levels using published bulk RNA and nDNA data of ICGC and MAGIC cohorts. We performed scRNA seq analyses of six human G3/G4 MB samples (G3 n=2; G4 n=4) to determine intratumoral metabolic heterogeneity across these groups. Additional scRNA-seq samples were retrieved from a previously published cohort.

first: Viktoria

middle: L

last: Funke

last: Melcher

first: Lanying

last: Wei

first: Sarah

last: Sandmann

first: Marc

last: Hotfilder

first: Julian

last: Varghese

first: Natalie

last: Jäger

first: Marcel

last: Kool

first: David

middle: T

last: Jones

first: Stefan

middle: M

last: Pfister

first: Till

last: Milde

first: Martin

last: Mynarek

last: Rutkowski

first: Jochen

last: Seggewiß

first: Daniela

last: Jeising

first: Flavia

middle: W

last: de Faria

first: Thorsten

last: Marquardt

first: Thomas

middle: K

last: Albert

first: Ulrich

last: Schüller

first: Kornelius

last: Kerl


title: The Hedgehog gene expression program regulates lipid metabolism in basal cell carcinoma and medulloblastoma

city: San Francisco

first: Vikas

last: Daggubati

state: CA

department: Radiation Oncology

country: USA

institute: University of California, San Francisco

summary: Misactivation of the Hedgehog (Hh) pathway can cause cancers such as medulloblastomas, the most common malignant brain tumor in children, and basal cell carcinomas, the most common cancer in the United States. Hedgehog signals are transmitted through primary cilia, where Hedgehog ligands bind to Patched1 and activate Smoothened through interactions with cilia-associated sterol lipids. The gene expression programs driving cellular responses to ciliary Hh signals are incompletely understood. Thus, to define Hh target genes, we performed RNA sequencing of cells after treatment with Hh ligands (Shh, Dhh, Ihh), cilia-associated lipids (7b,27-dihydroxycholesterol, 24(S),25-epoxycholesterol), or synthetic lipids or small molecules that activate Smoothened (20(S)-hydroxycholesterol, SAG). Treatment with Hh pathway agonists identified a core gene expression program comprised of 155 genes driving lipid synthesis, metabolism, signaling, adhesion, or angiogenesis. These datasets were integrated with RNA sequencing of Hh-human medulloblastomas (n=?), a Math1-Cre SmoM2 mouse genetic model of Hh-associated medulloblastoma (n=?), and human basal cell carcinomas (n=10) to ascertain how malignant Hh signaling differs from canonical Hh signaling. We discover a conserved response to ciliary Hh signals in human or mouse medulloblastomas, including known target genes such as Gli1 or Ptch1, and novel target genes such as Hsd11b1 or Retnla. Importantly, mechanistic studies reveal Hsd11b1 to be a putative negative regulator of Hh signaling that is dysregulated in malignancies. We further demonstrate Retnla to be a positive regulator of Hh signaling that drives expression of Hsd11b2, a druggable dependency underlying Hedgehog-associated medulloblastoma. Orthotopic implantation of neuroepithelial stem cells that overexpress either Hsd11b1 and Retnla demonstrate that tumors derived Hsd11ß1 overexpression are more primitive and less aggressive whereas Retnla overexpression forms tumors that are more differentiated and behave more aggressively. In sum, we illuminate the first comprehensive transcriptome of Hh signaling and highlight the intricate interplay between Hh signaling and lipid metabolism that Hh-dependent malignancies dysregulate to drive tumor progression.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Hedgehog signaling defined in vitro in NIH3T3 wildtype and Smoothened knockout cells. Treated with 2 oxysterol lipids, 2 artifical Hedgehog agonists, and 3 endogenous Hedgehog ligands, and 3 vehicle controls. Bulk RNA-sequencing performed therafter. This gene expression program was then compared to that of 9 human basal cell carcinomas and 9 normal skin samples. Lastly, Retnla and Hsd11b1 biology, which was discovered in this paper, was compared through orthotopic tumors seeded from neuroepithelial stem cells that either overexpress Hsd11b1 or Retnla.

first: Akshara

last: Vykunta

first: Abrar

last: Choudhury

first: Zulekha

last: Qadeer

first: Olivier

last: Saulnier

first: Naomi

last: Zakimi

last: Arron

first: Michael

middle: D

last: Paul

first: Natalia

last: Jura

first: Libin

last: Xu

first: Jeremy

middle: F

last: Reiter

first: William

middle: A

last: Weiss

last: Taylor

middle: R

last: Raleigh


title: Interrogating the diurnal transcriptome of the muscle autonomous clock in vivo

status: Public on Jun 05 2023

city: irvine

first: Siwei

last: Chen

address: 66304 Verano Road South

department: Computer Science

institute: University of California, Irvine

summary: In this study, we used RNA sequencing to interrogate which aspects of circadian gene expression in skeletal muscle are autonomous or require clocks in other tissues

overall_design: WT, KO and skeletal muscle Bmal1 reconstituted mice ( see Koronowski et al Cell 2019 and Greco et al Science Advances 2021 for general model description) were used to collect tissues at 6 time points over the diurnal cycle - 12 hr light: 12 hr dark conditions and ad libitum feeding of normal chow; tissues harvested at ZT0, 4, 8, 12, 16, 20

first: Jacob

middle: G

last: Smith

first: Kevin

middle: B

last: Koronowski

first: Tomoki

last: Sato

first: Ekaterina

last: Deyneka

first: Muntaha

last: Samad

first: Pierre

last: Baldi

first: Selma

last: Masri

first: Paolo

last: Sasone-Corsi


title: The transcription factor Bcl6 represses active Notch signalling in fetal thymocytes

city: London

first: Tessa

last: Crompton

address: 30 Guilford Street

department: Immunobiology

country: United Kingdom

institute: UCL

summary: We used Affymetrix microarrays to understand the genome wide differences between DMSO and Bcl6 inhibitor (79-6) anti-CD3 treated Rag1-/- E17.5 thymocytes (n=2) .

overall_design: Thy1.2+ cells were sorted from anti-CD3 stimulated Rag1-/- FTOCs after 40 hours with treatment with 50uM 79-6 or DMSO alone, compared to fresh E17.5 thymi unstimulated time zero controls (n=2). RNA extracted from these sorted cells was used to perform microarrays.

first: Anisha

last: Solanki

first: Hemant

last: Sahni


title: Global genetic profiling of a pediatric series of T-cell lymphoblastic lymphoma

city: Barcelona

first: Joan

middle: Enric

last: Ramiz-Zaldivar

address: Rosselló, 153

department: Molecular Pathology Laboratory

country: Spain

institute: IDIBAPS

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

overall_design: Refer to individual Series


title: Bulk RNA sequencing from  sorted thymic populations and tumors from control Cdc20(+/D)  and aneuploid Cdc20(D/AAA)mice

city: Cambridge

first: Dunaduan

last: Ma

state: Ma

address: 77 Massachusetts Ave

department: Koch Institute

institute: MIT

summary:
Purpose: The goals of this study are to compare the transcriptome profile of specific thymic populations in control Cdc20(+/D)  and Cdc20(D/AAA)mice after the induction of chromosome missegregation as well the profile of tumors generated in those mice.
Methods:  Total RNA was isolated from primary cells or tumors, using the RNeasy Plus Mini Kit (Qiagen) and sequenced on an Illumina HiSeq2000. At least 5000 cells were sorted  directly  in lysis buffer for specifc T cell progenitor populations in the thymus while at least 5 million cells have used for RNA isolation form thymic lymphomas. Unless otherwise indicated samples from tumors were isolated without sorting specific polulations.

overall_design: bulk RNA-seq of tumor and non-tumor thymus of control Cdc20(+/D)  and Cdc20(D/AAA) mice.

first: Marianna

last: Trakala

first: Angelika

last: Amon


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [ORC1_RIPseq]

city: Pamplona

first: Maite

last: Huarte

state: Navarra

address: c/ Avd Pio XII, 55

institute: Centro de Investigación Médica Aplicada

summary: By investigating the RNA binding activity of human ORC1, we show that it interacts with RNAs transcribed at active origins, which is linked to ORC1 dynamic association to the chromatin and optimal origin firing in S phase.

overall_design: ORC1 native RIP-seq from nuclei of untreated HCT116 cells.

first: Aina

last: Mas

first: Enrique

last: Goñi

first: Igor

last: Ruiz de los Mozoa


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [SNSseq_ASO]

overall_design: Short Nascent Strand purification and sequencing from control or anti-GAA knocked down HCT116 cells, in duplicate

first: María

last: Gómez

first: Aida

last: Arcas


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [ORC1_iCLIP]

overall_design: ORC1 3XFlag iCLIP from nuclei of untreated HCT116 cells.

first: Lorea

last: Blázquez


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [SNSseq_WT_MUT]

overall_design: Short Nascent Strant purification and sequencing from untreated HCT116 cells (stably expressing WT and MUT-ORC1), in duplicate


title: The diapause-like colorectal cancer cells induced by SMC4 attenuation are characterized by low proliferation and chemotherapy insensitivity [RNA-seq]

city: hefei

first: sun

last: xuedan

address: daoxiangcun

institute: ustc

summary: Comparative gene expression profiling analysis of RNA-seq data for HCT116 cells and its shSMC4.

first: xuedan

last: sun

first: lifang

last: he

first: mian

last: wu

first: lianxin

last: liu


title: Interaction of muscle and liver circadian clocks on the transcriptome

first: Siwei

last: Chen

summary: In this study, we used RNA sequencing to interrogate how muscle and liver autonomous clocks influence the circadian transcriptome across these two organs.

overall_design: WT and liver+muscle Bmal1 reconstituted mice ( see Koronowski et al Cell 2019 and Greco et al Science Advances 2021 for general model description) were used to collect tissues at 6 time points over the diurnal cycle - 12 hr light: 12 hr dark conditions and ad libitum feeding of normal chow; tissues harvested at ZT0, 4, 8, 12, 16, 20

first: Jacob

last: Smith

first: Kevin

last: Koronowski

first: Tomoki

last: Sato

first: Ekaterina

last: Deyneka

first: Pierre

last: Baldi

first: Selma

last: Masri

first: Paolo

last: Sasone-Corsi


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [AntiGAA_RNAseq]

first: Maite

last: Huarte

overall_design: RNA-Seq of HCT116 cells treated with control or anti-GAA antisense oligonucleotides.

first: Aina

last: Mas

first: Enrique

last: Goñi


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [CDC45_ChIP-seq]

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: CDC45 ChIP DNA purification and sequencing from untreated HCT116 cells (stably expressing WT or MUT-ORC1) in duplicate


title: The transcriptome analysis of Peri-infarct areas of infarction for sham, PT, and Pushen treatment

city: Nanjing

first: Yuan

last: Zhang

address: No. 87 Dingjiaqiao

institute: School of Medicine, Southeast University,

summary: We investigated the functional recovery of  in ischemic stroke by Photothrombotic stroke (PT) model.   RNA-Seq of the peri-infarct cortex at 28 day after PT to clarify the potential mechanisms of pushen capsule against ischemic stroke.   Pushen (drug approval number: Z20040074;  batch number: 20082403;  Suzhong pharma) was dissolved in the vehicle of ultrapure water, and it was administered by oral gavage at 24 hours after surgery continuously for 28 days.  Mice in the Sham and Vehicle group were administered with a vehicle of ultrapure water equal to the Pushen group.  By applying the cutoﬀs of P <0.05 and |log2 (fold change)|>1, 2369 differentially expressed genes (DEGs) were identified between sham vs PT, and  231 differentially expressed genes (DEGs) were identified between PT vs Pushen.

overall_design: Peri-infarct areas of infarction from the three groups were respectively collected in TRIzol reagent at 28 days after PT. Each group contained three replicates.


title: Adipose METTL14-elicited N6-methyladenosine promotes obesity, insulin resistance, and NAFLD by suppressing β adrenergic signaling and lipolysis

status: Public on Jun 04 2023

city: Ann Arbor

first: Liangyou

last: Rui

state: Michigan

address: 2800 plymouth road

department: Molecular and Integrative Physiology

institute: University of Michigan

summary: Obesity is associated with impaired β-adrenergic receptor (Adrb1-3) signaling and lipolysis, leading to aberrant white adipose tissue (WAT) growth. WAT research has been centered on transcriptional and posttranslational regulations, but posttranscriptional regulation and mRNA modifications are poorly understood. Here, we unveil a METTL14/N6-methyladenosine (m6A) paradigm guiding β-adrenergic signaling and lipolysis. METTL14 complex installs m6A on RNA, regulating mRNA fate and translation. We found that feeding and insulin increased adipose Mettl14 and m6A levels. Adipose Mettl14 and m6A were upregulated in high fat diet (HFD)-induced obesity. Ablation of adipose Mettl14 decreased Adrb2, Adrb3, Atgl (encoding lipase), and Cig-58 (Atgl activator) transcript m6A contents while increasing their translation and protein levels, thereby enhancing adipose β-adrenergic signaling and lipolysis. Consequently, adipocyte-specific Mettl14 knockout mice were resistant to HFD-induced obesity, insulin resistance, glucose intolerance, and NAFLD. These results unravel a METTL14/m6A-based epitranscriptomic mechanism governing β-adrenergic signaling, lipolysis, and adipose growth in health and disease.

overall_design: We aimed to identify Mettl14 target transcripts. Mettl14Δfat and Mettl14f/f male mice were fed an HFD for 20 weeks to increase adipose Mettl14 expression in Mettl14f/f but not Mettl14Δfat mice, and eWAT was isolated for RNA-Seq analysis. We used DEseq2 algorithms to detect the DEGs.

first: Qianqian

last: Kang

first: Xiaorong

last: Zhu

first: Decheng

last: Ren

first: Alexander

last: Ky

first: Ormond

last: MacDougald

first: Robert

last: O’Rourke


title: Responder vs non-responder in vivo tumours in response to poly(I:C) loaded hydrogel (WEHI-164)

city: Nedlands

first: Rachael

last: Zemek

state: WA

address: 15 hospital Ave

department: Cancer Centre

country: Australia

institute: Telethon Kids Institute

summary: WEHI-164  tumour samples taken after 75% debulking surgery, followed by treatment with poly(I:C) loaded hydrogel.

overall_design: Responders (complete regression) and non-responders (no delay in tumour growth)


title: Responder vs non-responder in vivo tumours in response to poly(I:C) loaded hydrogel (CT26)

summary: CT26  tumour samples taken by 90% debulking surgery, followed by treatment with poly(I:C) loaded hydrogel.


title: Estrogen Receptor β Activation Inhibits Colitis by Promoting the NLRP6-Mediated Autophagy

first: Wentao

last: Fan

address: Tongwei road 6

institute: Nanjing Agricultural University

summary: Estrogen receptor β (ERβ) and NOD-, LRR- and pyrin domain-containing 6 (NLRP6) are highly expressed in intestinal tissues and reduce intestinal inflammation, but their underlying mechanisms are unclear. We found that ERβ and NLRP6 levels were reduced in patients with inflammatory bowel disease (IBD), and that deletion of ERβ or NLRP6 was exacerbated colitis in mouse models. We discovered that ERβ exerted its anti-inflammatory activity by inducing NLRP6-mediated autophagy. Specifically, ERβ directly regulated NLRP6 gene expression and NLRP6 inflammasome activation through genomic and non-genomic effects. NLRP6 directly interacted with multiple autophagy-related proteins (including ULK1, BECN1, ATG5-ATG12-ATG16L1 complex, p62, and PHB2). Autophagy stimulation suppresses the inflammatory response by eliminating excess ERβ, NLRP6, ASC, Casp-1, IL-1β, TNF-α and damaged mitochondria. These findings indicate that ERβ-NLRP6-autophagy forms a negative feedback loop to maintain intestinal epithelial cell homeostasis and facilitate tissue repair.

overall_design: Colon mRNA profiles of 21-day old wild type (WT) and Esr2-/- mice were generated by deep sequencing, in triplicate, using Illumina GAIIx.

first: Suquan

last: Song


title: Transcriptome Alterations Associated with Age-Related Decline in Physical Function

city: Greenville

first: Ted

middle: G.

last: Graber

state: NC

address: 600 Moye BLVD., Mail Route 668

department: Physical Therapy

institute: East Carolina University

summary: One inevitable consequence of the effect of age on our bodies is the graduated deterioration of physical function and exercise capacity, driven, in part by the adverse effect of age on muscle tissue. Our primary purpose was to determine the relationship between patterns of gene expression in skeletal muscle and loss of physical function. We hypothesized that some genes that change expression with age would correlate with functional decline, or conversely with preservation of function. Male C57Bl/6 mice were randomly selected from large cohorts [RNA isolated from: adults (6-7 months old, n=9), older (24-25 months old, n=9), and elderly (28+ months of age, n=9)} that were tested for physical ability using a comprehensive functional assessment battery [CFAB, a composite scoring system: comprised of the rotarod (overall motor function), grip strength (fore-limb strength), inverted cling (4-limb strength/endurance), voluntary wheel running (activity rate/volitional exercise), and treadmill tests (endurance)]. We extracted RNA from the tibialis anterior muscles, ran RNAseq to examine the transcriptome using an Illumina NextSeq 550, comparing adults (n=7) to older (n=7) and elderly mice (n=9). Age resulted in gene expression differences of 1.5 log2 fold change or greater (p<0.01) in 46 genes in the older mice and in 252 genes in the elderly (both compared to adults). Current ongoing work is examining the physiological relevance of these genes to age-related loss of physical function. We are in the process of using linear regression to determine which of the genes with age-related changes in expression are associated (R>0.5 and p<0.05) with functional status as measured by CFAB.

overall_design: Next Generation Sequencing of adult mice (6 months old, n=7) versus older mice (24 month old, n=8) and samples from the same adult mouse  (n=7) with elderly mice (28+ months old, n=7). All three groups were extensively tested for physical function and exercise capacity, which declined with age.

first: Rosario

last: Maroto

first: Jill

last: Thompson

first: Steven

last: Widen

first: Blake

last: Rasmussen


title: Global genetic profiling of a pediatric series of T-cell lymphoblastic lymphoma [Cytoscan]

first: Joan

last: Ramiz-Zaldivar

type: Genome binding/occupancy profiling by SNP array

summary: T-cell lymphoblastic lymphoma T-LBL is a rare aggressive neoplasm of precursor T cells whose pathogenesis is not fully elucidated and it is closely related to acute lymphoblastic leukemia (T-ALL), the most common subtype of cancer in children, although recent studies suggest biological differences between the two entities.

overall_design: The aim of this study was to characterize the genetic and molecular heterogeneity of these tumors. A large series of 32 tumors were characterized using an integrated approach, including targeted gene sequencing and copy-number arrays.

first: Julia

last: Salmeron-Villalobos

first: Idoia

last: Martin-Guerrero

first: Itziar

last: Salaverria


title: Comparison of transcriptome signature of NCC-like scNS/PCs with bona fide NCCs and MSCs

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

state: Tokyo

address: 35 Shinanomachi

department: Department of Physiology

country: Japan

institute: Keio University School of Medicine

summary: We performed transcriptome analysis to examine whether the NCC-like scNS/PCs have similar global expression patterns with NCCs  and MSCs.

overall_design: RNA-seq analysis on hiPSC-NS/PCs, hiPSC-NCCs, MSCs, and Whole bone marrow (WBM)


title: Profiling of a series of triple positive (CD10+BCL6+MUM1+) diffuse large B-cell lymphoma cases

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

summary: Gene expression profiling (GEP) divides DLBCL according to the cell of origin into GCB, ABC and unclassifiable, exhibiting different mutational profiles.  The Hans algorithm, a surrogate of GEP, classifies cases expressing CD10, BCL6 and MUM1 as GCB but it is not clear whether all these cases correspond to GCB-type. Accordingly, LBCL with IRF4 rearrangement  usually expresses GCB phenotype (CD10+, BCL6+) together with strong MUM1/IRF4.

overall_design: The aim of this study was to characterize the molecular heterogeneity of DLBCL triple positive (CD10+ BCL6+MUM1+) in adults. CN alterations were examined in 9 out of 13 cases with available material and IRF4 rearrangement and/or IRF4 mutations using OncoScan platform

first: Natalia

last: Castrejon-de-Anta

first: Leonie

last: Frauenfeld

first: Olga

last: Balagué

first: Leticia

last: Quintanilla-Martinez


title: Single Cell Transcriptomic Analysis of hiPSC-lt-NES cells

summary: We performed single-cell RNA-seq of human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells)  using Quartz-seq methods to characterize cellular heterogeneity .

overall_design: Single cell RNA sequencing of 173  hiPSC-lt-NES cells.


title: Transcriptome analysis of hiPSC derived lt-NES cells

summary: To identify cell-populations within human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells) which retain capacities to generate undesired grafts, we performed gene expression microarray analysis.

overall_design: 4 hiPSC derived lt-NES cells were analyzed by microarray


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [ORC1_FLAG_RIPseq]

first: Maite

last: Huarte

overall_design: ORC1-FLAG native RIP-seq from nuclei of transfected HCT116 cells.

first: Aina

last: Mas

first: Enrique

last: Goñi


title: The SWI/SNF subunit Dpf2 licenses Nrf2-dependent gene expression to enforce multilineage control of inflammation

city: Miami

first: Gloria

last: Mas Martin

state: Florida

address: 1501 NW 10th Avenue

institute: University of Miami

overall_design: Refer to individual Series


title: Global genetic profiling of a pediatric series of T-cell lymphoblastic lymphoma [Oncoscan]

last: Salmerón Villalobos


title: The second Validation set of the 95GC in 2013.

status: Public on Jun 03 2023

city: Suita

first: Yoshiaki

last: Sota

state: Osaka

address: Yamadaoka 2-15

department: Breast and Endocrine Surgery

institute: Osaka University

summary: The aim of this study was to validate the efficacy of 95(GC) and compare it with that of 21(GC) (Oncotype DX) as well as to evaluate the combination of 95(GC) and 21(GC). DNA microarray data (gene expression) of ER-positive and node-negative breast cancer patients (n = 459) treated with adjuvant hormone therapy alone were classified with 95(GC) and 21(GC) (Recurrence Online at http://www.recurrenceonline.com/ ). 95(GC) classified the 459 patients into low-risk (n = 285; 10 year relapse-free survival: 88.8 %) and high-risk groups (n = 174; 70.6 %) (P = 5.5e-10), and 21(GC) into low-risk group (n = 286; 89.3 %), intermediate-risk (n = 81; 75.7 %), and high-risk (n = 92; 64.7 %) groups (P = 2.9e-10). The combination of 95(GC) and 21(GC) classified them into low-risk (n = 324; 88.9 %) and high-risk (n = 135; 65.0 %) groups (P = 5.9e-14).  This DATA set: J02 is 56 of the above 459 cases from Japan who were assayed after the J01 DATA set.    *Note: This old data has been updated multiple times by others.  Then, there are some differences from the original 2013 paper and unclear points still remain.  Therefore, do not use it for formal analysis aimed at public insurance coverage etc. This is for research purposes only. Please cite this paper when writing a new paper.  PMID: 23884597  DOI: 10.1007/s10549-013-2640-9

overall_design: RNA was extracted from 56 fresh frozen tumor samples obtained from radical breast cancer surgery and hybridized on Affymetrix microarrays.

first: Ryo

last: Tsunashima

first: Yasuto

last: Naoi


title: Tumorigenic iPSC-NS/PCs with mesenchymal properties

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


title: ORC1 binds to cis-transcribed RNAs for efficient activation of human origins [SNSseq]

overall_design: Short Nascent Strand purification and sequencing from untreated HCT116 cells in triplicate.

first: María

last: Gómez

first: Aida

last: Arcas


title: Transcriptomic and methylomic analyses of liver tissue in nonalcoholic steatohepatitis

city: shanghai

first: Fei

last: Mao

state: State...

address: Fudan university

institute: Fudan University


title: SMARCA3 is a histone H3K23 ubiquitin ligase that regulates H3K9me3 in colorectal cancer

city: New York

first: Aarthi

last: Ramakrishnan

state: New York

address: 1425 Madison Avenue

department: Neuroscience

institute: Icahn School of Medicine at Mount Sinai

summary: Histone ubiquitination is an important post-translational modification (PTM) that mediates diverse chromatin functions1-3. However, our understanding of the enzymes that regulate histone ubiquitination, along with their relationships to human disease, remains limited. Here, we identify the tumor suppressor SMARCA3 as a histone H3K23 E3 ubiquitin ligase that functions through a distinct mechanism from its characterized role in post-replication repair. We show that cellular depletion of SMARCA3 results in reduced H3K9me3 levels and altered genomic distribution, leading to cancer-associated rewiring of cellular transcriptional programs . Using both cell lines and patient-derived organoids, we demonstrate that colorectal cancer tumors driven by downregulation of SMARCA3 display similar decreases in H3K9me3, as well as alterations in the expression of cancer-promoting genes. Taken together, our data indicate critical roles for SMARCA3 in maintaining chromatin integrity, and provide a mechanism through which its normal tumor-suppression function may precipitate colorectal cancer when perturbed.

overall_design: ChIP-seq analysis of H3K9me3 in both wild type vs. SMARCA3 knockout 293T cells

first: Jakob

last: Hebert

first: Ryan

last: Bastle

first: Richard

first: Li

last: Shen

first: Ian

last: Maze

first: Yael

last: David


title: Transcriptomic and methylomic analyses of liver tissue in nonalcoholic steatohepatitis  [Bisulfite-Seq]

type: Methylation profiling by high throughput sequencing

summary: Recent studies have shown that DNA methylation is strongly associated with many important biological processes. However, the relationship between DNA methylation and NASH remains poorly understood.In the present study, through WGBS and RNA transcriptome sequencing in high-fructose-high-cholesterol diet for 28 weeks NASH mice, we found that enrichment of DNA methylation dependent DEGs mainly enriched in steroid metabolic process, steroid hormone biosynthesis were significantly down-regulated in NASH group, while those DEGs enriched in negative regulation of cytokine production were significantly up-regulated in NASH group. We identified 992 overlapping and differentially expressed genes (DEGs) that changed at both the mRNA expression level and DNA methylation. Among them, 332 genes displayed DNA methylation dependent changes of mRNA expression, indicating that DNA methylation tend to be positively correlated with NASH development. Taken together, our results demonstrate that DNA methylation may play an important role in the development of NASH.

overall_design: Male C57BL/6J mice aged 8 weeks were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China). A high-fat-high-cholesterol high-fructose diet  was purchased from Research Diets (D09100310, Research Diets Inc, New Brunswick, USA). After a 28-weeks intervention period in which mice were fed either a normal diet (ND) or HFHC, mice were anesthetized with 10% chloral hydrate.

first: Hanqi

last: Bi

first: Yan

last: Lu

first: Yuping

last: Song


title: Identification and characterization analysis of the different  genes in primary mouse microglia response to ACT-PARP14 using RNA-seq.

first: Ying

last: Tang

address: Dingjiaqiao 87

institute: southeast university

summary: Poly(ADP-ribose) polymerases (PARPs) modify target proteins with ADP-ribose by using nicotinamide adenine dinucleotide as a substrate, and contribute to various signaling pathways. PARP14 is the largest member of PARP superfamily. Whole RNA-sequencing analysis was performed and analyzed by Lc. Biotech Co., Ltd. (Hangzhou, China). Primary mouse microglia from the Con + ACT-Con group, Con + ACT-PARP14 group, OGD + ACT-Con group, and OGD + ACT-Con group were collected in TRIzol. Total RNAs were extracted from Trizol. UMI technology was used to label each sequence fragment with sequence tags, which minimized the interference of duplication caused by PCR amplification on the quantitative accuracy of the transcriptome. RNA sequencing reads were aligned to the mouse genome (GRCh37/hg19) using the software Hisat2 (2.0.4). Transcript abundance was evaluated by calculating fragments per kilo base of exon per million fragments mapped (FPKM).

overall_design: Examination of different genens in ACT-PARP14-treated or ACT-Con-treated primary mouse microglia by RNA-seq. All data were obtained from 2 independent experiments.

first: Honghong

last: Yao


title: Epigenetic regulation of SARS-Cov-2 spike protein modulates cellular viability and nascent RNA transcription in neuronal cells

city: Luzhou

first: Zheng

last: Bao

state: Sichuan

address: No. 25, Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

summary:
To investigate the effect of SARS-CoV-2 spike RBD on the transcription of nascent RNA in nerve cells, we treated SH-SY5Y cells with RBD and extracted nascent RNA for RNA-seq.
We then performed gene expression profiling analysis using data obtained from RNA-seq of SH-SY5Y cells at two time points.

overall_design: Comparative analysis of gene expression profiles of RNA-seq data from SH-SY5Y cells treated with RBD at different time and its control group.

first: Xi

last: Kong

first: Jinyue

last: Zhang


title: Gene expression profiling of Fah-deficient mouse livers upon short-term nitisinone discontinuation

city: Brussels

first: Joery

last: De Kock

address: Laarbeeklaan 103

department: In Vitro Toxicology and Dermato-Cosmetology

country: Belgium

institute: Vrije Universiteit Brussel (VUB)

summary:
Hereditary tyrosinemia type 1 (HT1) is a severe genetic disorder that affects the liver due to a defective fumarylacetoacetate hydrolase (Fah) enzyme in hepatocytes. The drug nitisinone (NTBC) has offered a life-saving treatment for HT1 patients by inhibiting the upstream enzyme 4-hydroxyphenylpyruvate dioxygenase (HPD).
We used microarray analyses to define the impact of short-term (ie. seven days) NTBC therapy discontinuation on the gene expression profile of liver tissue of Fah-deficient mice. Consequently, we investigated the modulation of canonical pathways related to oxidative stress, glutathione metabolism and liver regeneration.

overall_design: FAH5981SB mice (C57Bl/6J background) bears a single point mutation (G>A loss) in the final nucleotide of exon 8 within the Fah gene, ultimately leading to formation of truncated, unstable and degraded Fah protein and served thereby as experimental model for HT1. Fah deficient mice were either continuously treated with 8 mg/l NTBC through their drinking water or deprived from NTBC therapy for seven consecutive days. Withdrawal samples were collected seven days after NTBC discontinuation.

first: Haaike

last: Colemonts-Vroninks

first: Paul

last: Claes

first: Anja

last: Heymans

first: Geert

last: Martens

first: Tamara

last: Vanhaecke


title: Ribosomal RNA 2’-O-methylation dynamics during development and differentiation impact cell fate decisions

city: Copenhagen N

first: Sophia

middle: Julia

last: Häfner

address: Ole Maaløes Vej 5

department: Biotechnology Research and Innovation Centre (BRIC)

country: Denmark

institute: University of Copenhagen

summary: Ribosomes, essential for the interpretation of genetic information, are not identical machineries without any control over the translation process. We and others have unveiled the natural diversity of ribosomes and how this impacts their function. One source of ribosome heterogeneity is the 2'-O-methylation (2'-O-me) of ribosomal RNA (rRNA). Here, we show that the rRNA 2'-O-me profile dynamically changes during mouse brain development and the directed differentiation of human embryonic stem cells (hESCs). Moreover, we demonstrate that the removal of one specific 2'-O-me, at position 28S:U3904, prompts hESCs to become early neural progenitor cells and favours hindbrain differentiation. Further analyses point towards an increased binding to FMRP and better translation of WNT pathway mRNAs by ribosomes devoid of 28S:U3904-me as the underlying mechanism for this identity shift.

overall_design: Embryonic mouse brain cortex at seven stages of differentiation, as well as hippocampus, cerebellum, and olfactory bulb at the neonate and adult stage, and hESCs at the pluripotency stage and subjected to directed differentiation into ecto-, endo-, and mesoderm were analysed as biological triplicates for their rRNA 2'-O-me profile using RiboMeth-seq.

middle: J

first: Anders

middle: H

last: Lund


title: Effect of nicotinamide mononucleotide on doxorubicin-induced cardiac injury in mice

city: London

first: Tianqing

last: Peng

state: Ontario

address: 800 Commissioners Road

country: Canada

institute: Western University

summary: Doxorubicin (DOX) is the cornerstone of chemotherapy regimens for many malignancies, but its clinical usage is limited by severe cardiotoxicity. Accumulating evidence suggest that nicotinamide adenine dinucleotide (NAD+) depletion contributes to DOX-induced cardiotoxicity, making NAD+ boosting an appealing strategy. Nicotinamide mononucleotide (NMN) is an NAD+ precursor that shows promising therapeutic effects in various diseases. To understand the impact of NMN on gene expression in myocardial tissue of DOX-exposed mice, a RNA-seq  assay was carried out.

overall_design: Male C57BL/6 mice aged 8 weeks were treated with a single dose of DOX (15 mg/kg, i.p., Pfizer). Sham mice received the same volume of sterile saline. NMN (500 mg/kg, i.p., ApexBio) or saline was given 30 min prior to DOX injection. After 5 days of DOX administration, mice were sacrificed with hearts harvested and subjected to RNA-seq analysis

first: Ting

last: Cao


title: miRNA expression in Twist overexpressing breast cancer cell line MCF-7

city: Baltimore

first: Venu

last: Raman

state: Maryland

address: 720 Rutland Ave, Traylor 338

department: Radiology

institute: Johns Hopkins University

summary: The breast cancer cell line MCF-7 was engineered to overexpress the Twist gene resulting in the MCF-7/Twist cell line. To study which miRNA are regulated by Twist, we employed whole genome microarray expression profiling and compared miRNA expression between MCF-7/Twist and MCF-7 cells.

overall_design: Two biological replicates of each cell line were analyzed for miRNA expression.

first: Farhad

last: Vesuna


title: Clearance of senescent macrophages ameliorates tumorigenesis in KRAS-driven lung cancer

status: Public on Jun 02 2023

first: Juan Pedro

last: Martinez-Barbera

address: 30 Guilford Street

department: Developmental Biology and Cancer

institute: Institute of Child Health, UCL

summary: Accumulation of senescent cells in the tumour microenvironment can drive tumourigenesis in a paracrine manner through the senescence-associated secretory phenotype (SASP). Using a new p16-FDR mouse line, we show that macrophages and endothelial cells are the predominant senescent cell types in murine KRAS-driven lung tumours. Single cell transcriptomics identify a population of tumour-associated macrophages, expressing a unique array of pro-tumourigenic SASP factors and surface proteins, that are also present in normal aged lungs. Genetic or senolytic ablation of senescent cells, and macrophage depletion, result in a significant reduction in tumour burden and increased mouse survival of KRAS-driven lung cancer models. Of translational relevance, we reveal the presence of macrophages with senescent features in human lung premalignant lesions, but not in adenocarcinomas. Together, our results have uncovered a population of senescent macrophages contributing to the initiation and progression of lung cancer, thus opening potential therapeutic avenues and cancer preventative strategies.

overall_design: Isolation of YFP-positive (tumour cells), mCherry-positive (p16INK4a-expressing cells) and YFP/mCherry-negative (remainder of the lung) cells from KrasG12D/+; p16FDR/+; Rosa26loxP-STOP-loxP-YFP mice induced to form lung tumours by intranasal AdCre administration. Cells isolated and subjected to bulk RNA-sequencing 8 weeks post tumour initiation.

first: Scott

last: Haston

first: Juan

first: Daniel

last: Munoz-Espin


title: Pan KRAS inhibitor selectively inactivates oncogenic signaling and tumor growth

first: Dongsung

last: Kim

state: NY

address: 1275 YORK AVE

department: HOPP

institute: Memorial Sloan Kettering Cancer Center

summary:
To investigate the effect of KRASi treatment on transcriptional output, we sequenced RNAs from 22 cell lines with different KRAS genotypes.
We then performed gene expression profiling analysis using data obtained from RNA-seq comparing untreated and 2hr treated samples.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for cells with different KRAS genotypes (WT, UAWT,G12C,G12D,G12V,G13D).

first: Piro

last: Lito


title: Genome-wide transcriptional, epigenetic, and topological changes occurring in human natural killer cells in response to HDAC inhibitor [HiChIP]

city: Seoul

first: Hyoung-Pyo

address: Yonsei-ro 50-1

department: Department of Tropical Medicine

country: South Korea

institute: Yonsei University College of Medicine

summary:
Purpose: The aim of this study is to examine the complex transcriptional network of NK cells in the context of 3D chromatin architecture.
Conclusions: HDAC inhibitor reshape transcriptional profile through long-range enhancer-promoter interactions in natural killer cells

overall_design: HiChIP profiles of untreated control and SAHA treated cells with biological replicates.

first: Eun-Chong

last: Lee

first: Woong-Jae

last: Jung


title: Genome-wide transcriptional, epigenetic, and topological changes occurring in human natural killer cells in response to HDAC inhibitor [in situ Hi-C]

overall_design: Hi-C profiles of untreated control and SAHA treated cells with biological replicates.

first: Kyungwoo


title: Genome-wide transcriptional, epigenetic, and topological changes occurring in human natural killer cells in response to HDAC inhibitor [ChIP-seq]

overall_design: ChIP-seq profiles of untreated control and SAHA treated cells with biological replicates.


title: Genome-wide transcriptional, epigenetic, and topological changes occurring in human natural killer cells in response to HDAC inhibitor


title: Genome-wide transcriptional, epigenetic, and topological changes occurring in human natural killer cells in response to HDAC inhibitor [RNA-seq]

overall_design: RNA profiles of untreated control and SAHA treated cells with biological replicates.


title: Identification of consensus molecular subtypes in muscle-invasive bladder cancer: A comparison of two sequencing methods and gene sets using FFPE specimens

city: Frankfurt

first: Florestan

middle: Johannes

last: Koll

address: Theodor-Stern-Kai 7

department: Department of Urology

institute: University Hospital Frankfurt, Goethe University

summary: To evaluate two methods for analysis of gene expression data from FFPE and to compare different gene-sets to call subtypes.

overall_design: Compare values and molecular subtypes identified with the consensusMIBC classifier

first: Claudia

last: Döring


title: Single-cell transcriptomics suggest distinct upstream drivers of IL-17A/F in hidradenitis versus psoriasis

city: Sacramento

first: JAEHWAN

last: KIM

address: 10535 Hospital Way

department: Dermatology

institute: University of California, Davis

summary: Background: Based on the mounting evidence that Type 17 T-cells (T17 cells) and increased IL-17 play a key role in driving hidradenitis suppurativa (HS) lesion development, biologics previously used in psoriasis that block signaling of IL-17A and/or IL-17F isoforms have been repurposed to treat HS.   Objective: Our aim was to characterize the transcriptome of HS T17 cells compared to the transcriptome of psoriasis T17 cells, and their ligand-receptor interactions with neighborhood immune cell subsets.   Methods: Single-cell data of 12,300 cutaneous immune cells from 8 de-roofing surgical HS skin samples that included dermal tunnels were compared with single-cell data of psoriasis skin (19,525 cells from 11 samples) and control skin (11,920 cells from 10 samples). All the single-cell data were generated by the identical protocol.  Results: HS T17 cells expressed lower levels of IL23R and higher levels of IL1R1 and IL17F compared to psoriasis T17 cells (p < 0.05). HS regulatory T-cells (Tregs) expressed higher levels of IL1R1 and IL17F compared to psoriasis Tregs (p < 0.05). Semimature dendritic cells (DCs) were the major immune cell subsets expressing IL1B in HS, and IL-1B ligand-receptor interactions between semimature DCs and T17 cells were increased in HS compared to psoriasis (p < 0.05). HS dermal tunnel keratinocytes (KCs) expressed inflammatory cytokines (IL17C, IL1A, IL1B, and IL6) different from HS epidermis KCs (IL36G) (p < 0.05). IL6, which synergizes with IL1B to maintain cytokine expression in T17 cells, was mainly expressed by fibroblasts in HS, which also expressed IL11+ inflammatory fibroblast genes (IL11, IL24, IL6, and POSTN) involved in paracrine IL-1/IL-6 loop.   Conclusion: The IL-1B-T17 cell cytokine axis is likely a dominant pathway in HS with HS T17 cells activated by IL-1B signaling, unlike psoriasis T17 cells which are activated by IL-23 signaling.    Clinical Implication: Biologics targeting IL-17 isoforms and IL-1B may be effective for HS but biologics targeting IL-23 may be less effective for HS.

overall_design: Emigrating cells from 28 samples of lesional & nonlesional human psoriasis skin and normal control skin were obtained via 6 mm punch skin biopsy and subjected to single-cell RNA sequencing analysis. Data include 11 psoriasis lesional skin samples before secukinumab treatment, 4 psoriasis lesional skin samples 12 weeks after secukinumab treatment, 1 psoriasis lesional skin sample 24 weeks after secukinumab treatment, 1 psoriasis lesional skin sample 48 weeks after secukinumab treatment, 1 psoriasis nonlesional skin sample before secukinumab treatment and 10 control skin samples from healthy volunteers. Data include 14 samples from GSE151177, which are generated under the identical experiment protocol by the identical investigators.

first: Jaehwan

first: James

last: Krueger


title: Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions [4C-seq]

city: Beijing

first: Xiong

last: Ji

address: Haidian District, Beijing Summer Palace Road No. 5

department: School of Life Sciences

institute: Peking University

summary: One bottleneck in understanding the principles of 3D chromatin structures is caused by the paucity of known regulators. Cohesin is essential for 3D chromatin organization, and its interacting partners are candidate regulators. Here, we performed proteomic profiling of the Cohesin in chromatin and identified transcription factors, RNA-binding proteins, and chromatin regulators associated with Cohesin. Acute protein degradation followed by time-series genomic binding quantitation and BAT Hi-C analysis were conducted, and the results showed that the transcription factor ZBTB21 contributes to Cohesin chromatin binding, 3D chromatin interactions and transcriptional repression. Strikingly, multiomic analyses revealed that the other four ZBTB factors interacted with Cohesin, and double degradation of ZBTB21 and ZBTB7B led to a further decrease in Cohesin chromatin occupancy. We propose that multiple ZBTB transcription factors orchestrate the chromatin binding of Cohesin to regulate chromatin interactions, and we provide a catalog of many additional proteins associated with Cohesin that warrant further investigation.

overall_design: We performed ChIP-Seq, ChIP-MS, RNA-Seq, ATAC-Seq and Hi-C to investigate the roles of ZBTB transcription factors in chromatin interactions.

first: Rui

last: Wang

first: Qiqin

last: Xu


title: Serial Immune Profiling During Intraperitoneal Chemotherapy Shows Changes in Loco-regional Immunity in Ovarian Cancer [III]

city: Pittsburgh

first: Anda

middle: M.

last: Vlad

state: PA

address: 204 Craft Avenue, B403

institute: Magee-Womens Research Institute

summary: The immune system is active in the tumor microenvironment (TME) of epithelial ovarian cancer (EOC) and carries both effector and suppressive functions. We profiled biomarker expression on serial biological specimens collected during intraperitoneal (IP) chemotherapy to better define treatment-induced tumor involution.

overall_design: Serial biological samples were collected at several time points during IP chemotherapy from a cohort of 9 EOC patients. An additional cohort of 8 patients was used for validation. RNA from IP fluid cells and tumor tissue was analyzed via NanoString. Tumors were further analyzed by immunohistochemistry (IHC) for cytotoxic T cells (CTLs) and B cells.

first: Vlad

last: Anda


title: Serial Immune Profiling During Intraperitoneal Chemotherapy Shows Changes in Loco-regional Immunity in Ovarian Cancer [II]


title: Genome-wide transcriptional, epigenetic, and topological changes occurring in human natural killer cells in response to HDAC inhibitor [ATAC-seq]

overall_design: ATAC-seq profiles of untreated control and SAHA treated cells with biological replicates.


title: Transcriptomic and methylomic analyses of liver tissue in nonalcoholic steatohepatitis [RNA-seq]

first: Fei

last: Mao

overall_design: Male C57BL/6J mice aged 8 weeks were purchased from the Shanghai Laboratory Animal Company (SLAC, Shanghai, China). A high-fat-high-cholesterol high-fructose diet  was purchased from Research Diets (D09100310, Research Diets Inc, New Brunswick, USA). After a 28-weeks intervention period in which mice were fed either a normal diet (ND) or HFHC, mice were anesthetized with 10% chloral hydrate.

first: Hanqi

last: Bi

first: Yan

last: Lu

first: Yuping

last: Song


title: Serial Immune Profiling During Intraperitoneal Chemotherapy Shows Changes in Loco-regional Immunity in Ovarian Cancer

overall_design: Refer to individual Series


title: Serial Immune Profiling During Intraperitoneal Chemotherapy Shows Changes in Loco-regional Immunity in Ovarian Cancer [I]


title: Cerebrospinal fluid transcripts may predict shunt surgery responses in normal pressure hydrocephalus

city: Providence

first: Zachary

last: Levin

state: RI

address: 185 Meeting Street

institute: Brown University

summary: Molecular biomarkers for neurodegenerative diseases are critical for advancing diagnosis and therapy. Normal pressure hydrocephalus (NPH) is a neurological disorder characterized by progressive neurodegeneration, gait impairment, urinary incontinence and cognitive decline. In contrast to most other neurodegenerative disorders, NPH symptoms can be improved by the placement of a ventricular shunt that drains excess CSF. A major challenge in NPH management is the identification of patients who benefit from shunt surgery. Here, we perform genome-wide RNA sequencing of extracellular vesicles in CSF of 42 NPH patients, and we identify genes and pathways whose expression levels correlate with gait, urinary or cognitive symptom improvement after shunt surgery. We describe a machine learning algorithm trained on these gene expression profiles to predict shunt surgery response with high accuracy. The transcriptomic signatures we identified may have important implications for improving NPH diagnosis and treatment and for understanding disease aetiology.

overall_design: Profiling of mRNA in extracellular vesicles isolated from ventricular cerebrospinal fluid in 42 patients diagnosed with normal pressure hydrocephalus

first: Owen

middle: P

last: Leary

first: Victor

last: Mora

first: Shawn

last: Kant

first: Sarah

last: Brown

first: Konstantina

last: Svokos

first: Umer

last: Akbar

first: Thomas

last: Serre

first: Petra

last: Klinge

first: Alexander

last: Fleischmann

first: Maria

last: Ruocco


title: Ago iCLIP of TLE patient resected hippocampus

city: Aarhus N

first: Morten

middle: T

last: Veno

state: DK

address: Aabogade 15

institute: Omiics ApS

type: Non-coding RNA profiling by high throughput sequencing

summary: Nine patients with temporal lobe epilepsy (TLE) underwent hippocampal resection. Six had hippocampal sclerosis, three did not show signs of hippocampal sclerosis. Resected hippocampi were used for Ago iCLIP to detect miRNA targeting in the resected tissue.

first: Jorgen

last: Kjems

first: Sebastian

last: Bauer

first: Felix

last: Rosenow


title: Transcriptome analysis of single cell-derived  hiPSC-lt-NES cell clones

city: Shinjuku-ku

first: Tsukasa

last: Sanosaka

address: 35 Shinanomachi

institute: Keio University School of Medicine

summary: To identify cell-populations within human iPSC-derived long-term self-renewing neural epithelial stem cells (hiPSC-lt-NES cells) which retain capacities to generate undesired grafts, we established single cell-derived hiPSC-lt-NES cell clones and performed gene expression microarray analysis.

overall_design: 90 hiPSC-lt-NES cell clones were analyzed by microarray.


title: Transcriptomic analysis of SEFA-6179 treatment in preterm piglets receiving parenteral nutrition

city: Boston

first: Scott

middle: C

last: Fligor

state: MA

address: 300 Longwood Ave

department: Surgery

institute: Boston Children's Hospital

summary: Preterm Yorkshire piglets were provided parenteral nutrition for 14 days, receiving treatment with SEFA-6179 or a medium chain triglyceride vehicle control. At the end of 14 days, MCT piglets developed cholestasis and histologic liver injury.

overall_design: RNA-Seq was performed on liver tissue obtained at sacrifice on day of life 15 from all treatment (SEFA-6179) and control animals (MCT).

first: Savas

last: Tsikis

first: Mark

last: Puder


title: Murine neonatal cardiac B cells promote cardiomyocyte proliferation and heart regeneration

city: Shanghai

first: Zhenzhen

last: Zhan

address: Jimo Road 150

department: Research Center for Translational Medicine

institute: Shanghai East Hospital, Tongji University School of Medicine,

summary: Since the proliferative capacity of cardiomyocytes is extremely limited in the adult mammalian hearts, the irreversible loss of cardiomyocytes following cardiac injury markedly reduces cardiac function, leading to cardiac remodeling and heart failure. However, the early neonatal mice have a strong ability in cardiomyocyte proliferation and cardiac regeneration after heart damage such as apical resection. Besides of cardiomyocytes, non-myocytes in heart tissue also play important roles in the regeneration process. Previous studies showed that cardiac macrophages, regulatory T cells and CD4+ T cells are all involved in regulating the myocardial regeneration process. However, the roles of other cardiac immune cells in cardiac regeneration remains to be elucidated.  B cells is a prominent immune cell in injured heart; here we discovered the indispensable function of cardiac B cells in improving cardiomyocyte proliferation and heart regeneration in neonatal mice.

overall_design: WT P1 and P7 mice were performed on apical resection (AR). At day 7 after AR, heart tissue were harvested and CD45+ cells were isolated from heart tisssue for single-cell RNA sequencing.

first: yong

last: tan

first: xingguang

last: liu

first: zhenzhen

last: zhan


title: Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions [ChAR-seq]

first: Xiong

last: Ji

overall_design: We performed ChIP-Seq, ChIP-MS, RNA-Seq, and Hi-C to investigate the roles of ZBTB transcription factors in 3D chromatin organization.

first: Rui

last: Wang

first: Qiqin

last: Xu


title: Next Generation Sequencing Analysis of control and siSRSF2 treated RKO cells Transcriptomes

city: Nanjing

first: Weizhen

last: Liu

state: Jiangsu

address: No.138,Xianlin Avenue,Qixia District

institute: Nanjing University Of Chinese Medicine

summary: We treated the RKO cells with siSRSF2 or control siRNA for 48 hours.Then, we extracted RNAs and performed next generation sequencing. By comparing sequencing data from control and siSRSF2 samples, we profiled the alternative splicing events and gene expression regulated by SRSF2 in CRC.

overall_design: RKO cells mRNA profiles of control and siSRSF2 were generated by deep sequencing, using HiSeq X(Illumina, San Diego, CA).

first: Linlin

last: Chen


title: Human pluripotent stem cell-derived cardiomyocyte maturation both in vivo and in vitro

city: Seattle

first: Charles

middle: E

last: Murry

address: 850 Republican Street

department: Pathology

institute: University of Washington

summary: We studied cardiomyocytes maturation through extended in vitro culture and also used the adult rat as a bioreactor,

sample_organism:
Homo sapiens
Rattus norvegicus

platform_organism:
Homo sapiens
Rattus norvegicus

overall_design: Human PSC-CMs were cultured for up to one year and also studied at different stages after transplantation into infarcted athymic hearts (1 day, 1 week, 4 weeks, and 3 months after transplantation)

first: Xiulan

last: Yang

first: Shin

last: Kadota

first: Paul

last: Fields


title: Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions [RNA-Seq]


title: Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions

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


title: Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions [Hi-C]


title: Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions [ChIP-Seq]

first: Kai

last: Tian


title: The pathology of ineffective erythropoiesis in Rpl11 haploinsufficienct mice

first: Raymond

last: Doty

department: Division of Hematology

summary: Single-cell analysis of early erythroid precursors in Rpl11 haploinsufficient mice reveals both heme-dependent and heme-independent pathologies.

overall_design: Single-cell transcriptome analysis of BFU-E through basophilic erythroblasts isolated from Rpl11 haploinsufficient mice.


title: Multi-omics atlas of combinatorial abiotic stress responses in wheat

city: Saskatoon

first: Sateesh

last: Kagale

state: SK

address: 110 Gymnasium Place

department: Aquatic and Crop Resource Development

institute: National Research Council Canada

summary: We present a transcriptomic atlas of abiotic stress tolerance in wheat. We employed a systems biology approach to study physiological, metabolomic and transcriptomic responses associated with heat, drought, salinity and their possible combinations. Our objectives were to (1) rank stress treatments based on the overall physiological and growth impacts, (2) identify the core sets of genes common to a particular stress type, (3) examine pathways that are uniquely expressed in the various stress combinations, (4) detect associations between phenotypic and transcriptomic responses, (5) suggest possible transcription factors for further characterization and use in improving wheat performance in multi-stress environments.

overall_design: Triticum aestivum cv. Stettler, a Canada Western Red Spring wheat variety, was selected for this study. To evaluate plant adjustments to sub-lethal stress and stress combinations, transcriptomic changes in flag leaves during grain filling were assessed. From spike initiation (Feekes scale stage 8) onwards, greenhouse potted Stettler plants were subjected to one of eight treatments: control (C), heat (H), drought (D), salinity (S), heat and drought (HD), salinity and heat (SH), salinity and drought (SD) and, lastly, a salinity, heat and drought (SHD) treatment. For transcriptome analysis, total RNA was extracted from flag leaf from at least four independent biological replicates per stress treatment, and was sequenced using Illumina platform, generating over a billion paired-end short reads. Filtered reads were aligned to the wheat reference genome (IWGSC v1.1) using STAR. Transcript abundance was estimated using the RSEM (v1.3.3) and the IWGSC v1.1 annotation, and transcripts per million (TPM) values were generated.

first: Raju

last: Soolanayakanahally


title: Multiomic analysis of Cohesin reveals that ZBTB transcription factors contribute to chromatin interactions [ATAC-Seq]

first: Hui


title: Extracellular vesicles shed by follicular lymphoma B cells promote polarization of the bone marrow stromal cell niche

city: RENNES

first: vonick

last: sibut

address: avenue du Prof Leon BERNARD

country: France

summary: We report specific signatures of up or down regulated genes form each of the stimuli comparing to the untreated situation. These signatures are semmed to be in link with the specific bone marrow or lymphnode niches organisaton observed during the pathological course of follicular lymphomas.

overall_design: Examination of differentially expressed genes between untreated BM-MSC or the same cells treated by TNF Alpha+Lymphotoxin Alpha Beta or by extracellular vesicles from lymphoma B cells lines.

first: Erwan

last: Dumontet

first: Karin

last: Tarte


title: Axon-enriched lincRNA ALAE is required for axon elongation via regulating local mRNA translation

city: Zhuhai

first: Bin

state: Zhuhai

address: Room 2007, Building 6, North HuanDao  Road 2515,

institute: Guangdong institute of intelligence and science technoloty

summary: Long intergenic noncoding RNAs (lincRNAs) are critical regulators involved in diverse biological processes. However, the roles and related mechanisms of lincRNAs in axon development are largely unknown. To seek the axon-enriched lincRNAs in DRG neurons, we performed high-throughput RNA-seq of cultured rat dorsal root ganglion (DRG) neurons at P0 to profile lincRNAs. Profiling of highly expressed lincRNAs in RNA-seq and their enrichment in the axon of DRG neurons. We report a previously unappreciated axon-enriched lincRNA regulating axon elongation, thus referred to as ALAE. ALAE functionally associates with KHSRP for preventing KHSRP binding on Gap43 mRNA, thereby maintaining GAP43 synthesis and facilitating axon elongation.

overall_design: RNA-seq of P0 dorsal ganglion root neurons

first: Manyi

last: Wei

first: Jiansong

last: Huang

first: Lan

last: Bao


title: Next Generation Sequencing Analysis of Wild Type and SRSF2-MKO Skeletal Muscle Transcriptomes

city: s

first: ruochen

last: guo

address: 320 Yueyang RD.

institute: Shanghai Institute of Nutrition and Health

summary: We report skeletal muscle developmental defects in SRSF2 MyoD-Cre mice, in which SRSF2 is ablated in skeletal muscle.

overall_design: The control and SRSF2 MyoD-Cre gene in hindlimbs mRNA profiles were generated by deep sequencing, using HiSeq 2500 instrument.

first: Ruochen

last: Guo

first: Ying

last: Feng


title: Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells [4C]

status: Public on Jun 01 2023

city: New York

first: Julian

last: Pulecio

department: Developmental Biology

summary: It remains unclear how ESCs rapidly establish enhancer regulatory elements to activate lineage-specific genes at the earliest differentiation stages. Previous studies suggest that some tissue-specific enhancers are pre-marked in ESCs with permissive features that support their competence to induce gene expression in response to the binding of lineage transcription factors (TFs). However, the absence of functional assays to identify chromatin regions with the competence to activate gene expression upon TF binding has impeded to better define any pre-marking features and their role on the transcriptional competence of the chromatin. To address this, we leveraged a CRISPR-activation(a) system to systematically interrogate the presence of chromatin regions able to induce the expression of 5 lineage-specific genes that are inactive in human ESCs (hESCs). Multiple CRISPRa screens discovered 42 regions, which we termed Competent Chromatin Regions (CCRs), that can induce the expression of the 5 lineage genes upon CRISPRa targeting. ChIP seq analyses showed that CCRs do not represent primed or active enhancers, since they are not enriched in H3K4me1 or H3K27ac histone modifications. Instead, CCRs exhibit a significant enrichment in POU sequence motifs, along with higher levels of binding by OCT4 and other pluripotent TFs. CCRs have an enriched presence of several repressive and activating chromatin-associated factors, including the DNA demethylation factors TET1 and QSER1 and various HDAC enzymes, which regulate their transcriptional competence. Although CCRs are exclusively found at the topologically associated domains shared with their related genes, we found they do not require an enrichment in pre-established chromatin contacts to exert their function. To assess the extent of our findings, we simulated the earliest stages of lineage differentiation by inducing the expression of the lineage TF FOXA2 in undifferentiated hESCs and we found it preferentially binds to the regions predicted as CCRs. Our results suggest that the factors enriched at CCRs facilitate the binding of lineage TFs and enable ESCs to promptly activate the expression of lineage genes. This study advances our understanding of pluripotency regulation in ESCs by identifying a novel type of regulatory regions that supports their developmental plasticity.

overall_design: 4C using as viewpoints the GATA6, EOMES, PDX1 and SOX17 loci in hESCs. Each 4C experiment had n=2 biological replicates.

first: Danwei

last: Huangfu

first: Wilfred

last: Wong

first: Dylan

last: Murphy

first: Jielin

last: Yan

first: Renhe

last: Luo


title: Effect of ISG20 expression (wild-type or M1 mutant) on total RNA expression.

city: Lyon

first: Andrea

last: CIMARELLI

address: 46 Allée d'Italie

institute: CIRI-ENS-L

summary: ISG20 is an interferon-induced 3'-to-5' RNA exonuclease that acts as a broad antiviral innate defense factor. At present, the features that expose RNA to the action of ISG20 remain unclear. However recent studies have pinpointed to RNA epitranscriptomic modifications as modulators that either expose or protect viral RNAs from ISG20, raising the question as to how cellular RNAs, on which these modifications are abundant, cope with ISG20. To obtain an unbiased perspective on this issue, we used RNAseq to pinpoint to the RNA elements that regulate the balance between susceptibility and resistance to ISG20.

overall_design: Cells (HEK293T) were co-transfected with a plasmid coding for GFP (serving as an ectopically expressed mRNA) and a plasmid coding for wild-type ISG-20 (ISG20_WT) or a mutant version (ISG20_M1) or a control plasmid (pcDNA3.1). We allowed cells to express these proteins for 24h before collecting total RNA and proceeding to high-throughput sequencing in order to asses the consequences of ISG20 expression on the cellular transcriptome.

first: Emiliano

last: Ricci

first: Antoine

last: Corbin

first: Marie

last: Cariou

first: Emmanuel

last: Labaronne

last: Cimarelli


title: Microbiota dysbiosis associated with type 2 diabetes-like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish [II]

city: Ottawa

first: Hyojin

last: Lee

address: 75 Laurier Ave E

department: Biology

institute: University of Ottawa

summary: Mixtures of chlorinated persistent organic pollutants (C-POPs-Mix) are chemically related risk factors for type 2 diabetes mellitus (T2DM); however, the effects of chronic exposure to C-POPs-Mix on microbial dysbiosis remain poorly understood. Herein, male and female zebrafish were exposed to C-POPs-Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02, 0.1, and 0.5 μg/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance, richness, and evenness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C-POPs-Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 μg/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis, Rhizobium tibeticum, Bifidobacterium catenulatum, B. adolescentis, and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation, which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM-related molecular pathways. Thus, microbial dysbiosis in T2DM-triggered zebrafish occurred as a result of chronic exposure to C-POPs-Mix, indicating strong host–microbiome interactions.

overall_design: Samples consisted of the control group and three treatment groups exposed to 0.02, 0.1, and 0.5 ug/L of C-POPs-Mix (containing five OCPs and Aroclor1254) for the mechanistic study to demonstrate the relationship between microbiota dysbiosis and type 2 diabetes in C-POPs-Mix exposed zebrafish. Six female livers were pooled for each group and used to perform RNA-seq on the Illumina HiSeq 2500 platform. For 16S rRNA-seq analysis, total genomic DNAs were individually extracted from five intestines in each group and sequenced by Illumina Miseq system.

first: Sojeong

last: Yoon

first: Youngja

last: Park

first: Jeong-Soo

first: Dong

last: Rhyu

first: Ki-Tae

last: Kim


title: Microbiota dysbiosis associated with type 2 diabetes-like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish


title: DNA methyltransferase 1 deficiency improves macrophage motility and wound healing by ameliorating cholesterol accumulation

city: Beijng

first: Chuanrong

last: Zhao

address: 38 Xue yuan Road, Peking University Health Science Center

department: School of Basic Medical Sciences

summary: Healing of the cutaneous wound requires macrophage recruitment at the sites of injury, where chemotactic migration of macrophages toward the wound is regulated by local inflammation. Recent studies suggest a positive contribution of DNA methyltransferase 1 (Dnmt1) to macrophage pro-informatory responses; however, its role in regulating macrophage motility remains unknown. In this study, myeloid-specific depletion of Dnmt1 in mice promoted cutaneous wound healing and de-suppressed the lipopolysaccharides (LPS)-inhibited macrophage motility. Dnmt1 inhibition in macrophages eliminated the LPS-stimulated changes in cellular mechanical properties in terms of elasticity and viscoelasticity. LPS increased the cellular accumulation of cholesterol in a Dnmt1-depedent manner; cholesterol content determined cellular stiffness and motility. Lipidomic analysis indicated that Dnmt1 inhibition altered the cellular lipid homeostasis, probably through down-regulating the expression of cluster of differentiation 36 CD36 (facilitating lipid influx) and up-regulating the expression of ATP-binding cassette transporter ABCA1 (mediating lipid efflux) and sterol O-acyltransferase 1 SOAT1 (also named ACAT1, catalyzing the esterification of cholesterol). Our study revealed a Dnmt1-dependent epigenetic mechanism in the control of macrophage mechanical properties and the related chemotactic motility, indicating Dnmt1 as both a marker of diseases and a potential target of therapeutic intervention for wound healing.

overall_design: We conducted RNA sequencing of peritoneal macrophages from DNMT1fl/fl and DNMT1KO mice to provide insight into the overall impact of Dnmt1 deficiency on gene expression.

first: Qianru

last: Yang

first: Jing

last: Zhou


title: Synaptic and transcriptomic features of fear matrix pyramidal neurons predict inefficient fear extinction

city: Rome

first: Daniela

last: Laricchiuta

state: Rome

address: Via del fosso di fiorano, 64

department: Preclinical neuroscience

country: Italy

institute: IRCCS Fondazione Santa Lucia

summary: Trauma-related disorders arise from inefficient fear extinction and have immeasurable social and economic costs. Here, we characterized mouse phenotypes that spontaneously show individual differences in adaptive or maladaptive fear extinction and, before the traumatic experience, we found that specific morphological, electrophysiological and transcriptomic patterns of fear matrix pyramidal neurons predispose to trauma-related disorders. Finally, by using an optogenetic approach we showed the possibility to rescue the inefficient fear extinction activating fear matrix infralimbic pyramidal neurons

overall_design: RNA extracted from amygdala pyramidal neurons of 9 B6.Cg-Tg(Thy1-YFP)HJrs/J (Thy1-YFP; Jackson Laboratories, Maine, USA) transgenic mice

first: Juliette

last: Gimenez

first: Giuseppe

last: Sciamanna

last: Termine

first: Carlo

last: Fabrizio

first: Silvia

last: Caioli

first: Luana

last: Saba

first: Marco

last: De Bardi

first: Francesca

last: Balsamo

first: Francesco

last: Della Valle

first: Anna

last: Panuccio

first: Noemi

last: Passarello

last: Mattioni

first: Elisa

last: Bisicchia

first: Cristina

last: Zona

first: Laura

last: Petrosini

first: Valerio

last: Orlando


title: Combined transcriptomics and proteomics analysis unveiled the impact of vitamin C in modulating specific mitochondrial protein abundance in the mouse liver.

city: Québec

first: Antoine

last: BODEIN

state: QC

address: 2705 bd Laurier

institute: Université Laval

summary: Vitamin C (ascorbate) is a crucial antioxidant and an essential cofactor of biosynthetic and regulatory enzymes. Unlike humans, mice can synthesize vitamin C thanks to the key enzyme gulonolactone oxidase (Gulo). In the present study, we used the Gulo-/- mouse model, which cannot synthesize their own ascorbate to determine the impact of this vitamin on both the transcriptomics and proteomics profiles in the liver. The study included Gulo-/- mouse groups treated with either sub-optimal or optimal vitamin C concentrations in drinking water. We found a distinctive difference in the mRNA and protein profiles as a function of sex between all the mouse groups. Despite this sexual dimorphism, Spearman correlation analyses were conducted to divulge which transcripts and proteins correlated with hepatic vitamin C concentrations in both females and males. Such analysis on transcriptomics data from females and males revealed changes in a wide array of biological processes involved in glucose, lipid, steroid, and glutathione metabolisms as well as in acute-phase response. Furthermore, although several proteins of the mitochondrial complex III significantly correlated with vitamin C concentrations, their corresponding transcripts did not correlate with vitamin C in both females and males. Thus, this side-by-side comparison between transcriptome and proteome supported the view that post-transcriptional processes play a major role in the regulation of cellular respiration in the liver upon vitamin C deficiency. Our findings suggest that transcriptome profiling alone provides an incomplete picture of molecular changes associated with vitamin C deficiency in the liver of mice and examination of changes in protein abundances is essential to unveil variations that are not transcriptionally regulated.

overall_design: RNA-seq analyses were performed on the liver of 4 months old mice. Groups of mice included: 3 Gulo-/- males and 3 Gulo-/- females treated with 0.4% vitamin C (weight/volume of L-ascorbate) in drinking water since weaning until the age of 4 months (3 MGL40 and 3 FGL40); Gulo-/- males and females treated with 0.05% vitamin C (weight/volume of L-ascorbate) in drinking water since weaning until the age of 4 months (3 MGL05 and 3 FGL05); Gulo-/- males and females treated with 0.01% vitamin C (weight/volume of L-ascorbate) in drinking water since weaning until the age of 4 months (3 MGL01 and 3 FGL01); a fourth cohort of Gulo-/- mice was treated with 0.4% ascorbate until the age of three months at which point ascorbate was then removed from drinking water for four weeks (3 MGL00) and 3 FGL00); a fifth cohort of Gulo-/- mice were treated with 0.4% ascorbate from weaning until the age of two months at which point ascorbate was removed from drinking water for one month. Then ascorbate was added back (0.4%) to drinking water until the mice reached the age of four months (3 MGLR40 and 3 FGLR40); finally, wild type control (Gulo+/+) mice were maintained in the same room with no ascorbate supplementation in drinking water and were used as our normal reference cohort (3 MWT00 and 3 FWT00).

first: Lucie

last: Aumailley

last: Bodein

first: Pauline

last: Adjibade

first: Mickael

last: Leclercq

first: Sylvie

last: Bourassa

first: Arnaud

last: Droit

first: Rachid

last: Mazroui

first: Michel

last: Lebel


title: Microbiota dysbiosis associated with type 2 diabetes-like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish [I]

first: Hyojin

last: Lee

first: Sojeong

last: Yoon

first: Youngja

last: Park

first: Jeong-Soo

first: Dong

last: Rhyu

first: Ki-Tae

last: Kim


title: Discovery of Competent Chromatin Regions in Human Embryonic Stem Cells [PRO-Seq]

first: Julian

last: Pulecio

institute: Memorial Sloan Kettering Cancer Center

overall_design: Precision Nuclear Run On PRO-seq in hESCs.

first: Danwei

last: Huangfu

first: Hyunwoo

last: Cho

first: Wenbo

last: Li


title: Single Cell RNA sequencing of the Monocytes from controls and pulmonary arterial hypertension (PAH) patients

city: Sunnyvale

first: Xin

last: Zhou

state: CA - California

address: 3165 Porter Drive

department: Department of Genetics

institute: Stanford University

summary: We report the application of single cell RNA sequencing on human Peripheral Blood Mononuclear cells. The 12 samples are sequenced as biological replications (6 control and 6 patients), and pooled at the analysis stage. The library was prepared using the Chromium Single Cell 3' v2 and v3 Reagent Kit, and sample processing was under bcl2fastq2/2.20.0 and cellranger/2.2.0. We report a decreased CD14 in classical monocytes among PAH patients, with greater potential of apoptosis for CD14+ monocytes population. This study provide a reference for studying the monocytes related abonormalties in PAH and other inflammatory diseases.

overall_design: Six control samples and six patient samples are barcoded for sequencing in the same flowcell on Illumina HiSeq-4000 platform. For each sample, 5000 alive cells are used as input.

first: Rebecca

middle: L

last: Harper

first: Michael

last: Snyder

first: Marlene

last: Rabinovitch


title: Ancient transcriptional regulators can easily evolve new pair-wise cooperativity

city: San Francisco

first: Kyle

last: Fowler

state: California

address: 600 16th Street

institute: University of California San Francisco

summary: We investigate how a protein-protein interaction between two ancient transcriptional regulators (a homeodomain and MADS box protein) was gained approximately 200 million years ago in a clade of ascomycete yeasts that includes Saccharomyces cerevisiae. We combine deep mutational scanning of Matα2 with a functional selection for cooperative gene expression and tested millions of possible alternative evolutionary solutions to this interaction interface. Pooled Matα2 mutants were deeply sequenced before and after selection for functional Matα2-Mcm1 interaction. The changes in frequency of each variant allowed us to determine their relative fitness.

overall_design: Targeted short-read sequencing of pooled Matα2 mutants, including from the starting library, following growth in rich media, and following growth in canavanine to select for functional Matα2-Mcm1 interactions.

first: Fredrick

last: Leon

first: Alexander

middle: D

last: Johnson


title: Immunoregulatory potential of erythroid nucleated cells induced from CD34+ progenitors from bone marrow

city: Novosibirsk

first: Roman

middle: Yurievich

last: Perik-Zavodskii

state: Novosibirsk region

address: Yadrincevskaya 14

country: Russia

institute: "Research Institute of Fundamental and Clinical Immunology" (RIFCI)

summary: In this work, we compared the expression profiles of cytokine genes between in vitro grown  and adult bone marrow CECs.

overall_design: We profiled total RNA from the CD71+ erythroid cells (CECs) from in vitro grown from CD34+ cells or bone marrow on NanoString Sprint Platform using Immunology V2 panel.


title: Effect of TRIB1 knockdown on gene expression in MCF7 breast cancer cells

city: Dunedin

first: Anita

last: Dunbier

address: 710 Cumberland Street

department: Biochemistry

country: New Zealand

institute: University of Otago

overall_design: Diiferential gene expression analysis of siRNA and shRNA TRIB1 knockdown relative to there respective non-targeting controls (TRIB1 siRNA vs Non-Targeting siRNA and TRIB1 shRNA monoclone vs Non-Targeting shRNA monclone)

first: Hamish

last: McMillan


title: JANUS, a spliceosome-associated protein, promotes miRNA biogenesis in Arabidopsis

city: Lincoln

first: Chi

last: Zhang

state: NE

address: 1901 Vine Street

institute: University of Nebraska - Lincoln

summary: MicroRNAs (miRNAs) are important regulators of gene expression. Their levels are precisely controlled through modulating the activity of the microprocesser complex (MC). Here we report that JANUS, a homology of the conserved U2 snRNP assembly factor in yeast and human, is required for miRNA accumulation. JANUS associates with MC components Dicer-like 1 and SERRATE (SE) and directly binds the stem-loop of pri-miRNAs. In a hypomorphic janus mutant, the activity of DCL1, the numbers of MC, and the interaction of primary miRNA transcript (pri-miRNAs) with MC are reduced. These data suggest that JANUS promotes the assembly and activity of MC through its interaction with MC and/or pri-miRNAs. In addition, JANUS modulates the transcription of some pri-miRNAs as it binds the promoter of pri-miRNAs and promotes Pol II occupancy of at their promoters. Moreover, global splicing defects are detected in janus. Taken together, our study reveals a novel role of a conserved splicing factor in miRNA biogenesis.

overall_design: Comparative mRNA and miRNA expression profiling analysis for janus mutant and Col-0 wildtype.

first: Mu

first: Bin

last: Yu


title: Sugar utilization by microglia in Alzheimer's disease

city: Madison

first: Daniel

last: Shippy

address: 1111 Highland Avenue

institute: UW-Madison

summary: The goal of this study is to investigate the effect of different sugar sources on microglial metabolism.

overall_design: Murine N9 microglia were cultured in T75 flasks under control (standard physiological), high glucose (15 mM) and high fructose (15 mM) conditions for 18 hours. Microglia (250,000/well) were seeded in 24-well plates with the same media as in the T75 flasks and stimulated with LPS (1 µg/ml) for 6 hours. RNA was extracted and gene expression differences between the groups was determined using RNA-seq.

first: Kaitlyn

middle: M

last: Marino

first: Tyler

middle: K

last: Ulland


title: Synergistic effects of PARP inhibition and cholesterol biosynthesis modulation

city: Heidelberg

first: massimo

last: petretich

address: Meyerhofstrasse 1

institute: Cellzome

summary: Investigate the effects of PARP inhibition in different contexts.

overall_design: Investigate the effects of Olaparib and Niraparib treatment in T47D cells in presence/absence of PARP1 KO.

first: Anna

last: Rutkowska


title: Impact of Cry1 KO on single-cell genomic program during iPSC reprogramming

city: College Station

first: Shogo

last: Sato

state: Texas

address: 3258 TAMU, Biological Science Building West (BSBW) 309

institute: Texas A&M University

summary: We profiled genome-wide gene expression duirng iPSC reprogramming from Cry1 KO and the wild-type MEFs at the single cell resolution

overall_design: Primary MEFs derived from Cry1 KO and the WT mice were transfected with Yamanaka 4F and cultured in ESC medium. Both before and after the treatment with 2i, cells underwent the FACS sorting followed by scRNA-seq.

first: Juan

last: Izpisua Belmonte

first: Quy

last: Nguyen

first: Kai

last: Kessenbrock


title: RNAseq from Mfn1/2 knockout MEFs with adipogenic differentiation

city: Cambridge

first: David

middle: B

last: Savage

address: Addenbrooke's Hospital

department: Institute of Metabolic Science

institute: University of Cambridge

summary: Objective: A biallelic missense mutation in mitofusin 2 (MFN2) causes multiple symmetric lipomatosis and partial lipodystrophy, implicating disruption of mitochondrial fusion or interaction with other organelles in adipocyte differentiation, growth and/or survival. In this study, we aimed to document the impact of loss of mitofusin 1 (Mfn1) or 2 (Mfn2) on adipogenesis in cultured cells. Methods: We characterised adipocyte differentiation of wildtype (WT), Mfn1-/- and Mfn2-/- mouse embryonic fibroblasts (MEFs) and 3T3-L1 preadipocytes in which Mfn1 or 2 levels were reduced using siRNA. Results: Mfn1-/- MEFs displayed striking fragmentation of the mitochondrial network, with surprisingly enhanced propensity to differentiate into adipocytes, as assessed by lipid accumulation, expression of adipocyte markers (Plin1, Fabp4, Glut4, Adipoq), and insulin-stimulated glucose uptake. RNA sequencing revealed a corresponding pro-adipogenic transcriptional profile including Pparg upregulation. Mfn2-/- MEFs also had a disrupted mitochondrial morphology, but in contrast to Mfn1-/- MEFs they showed reduced expression of adipocyte markers. Mfn1 and Mfn2 siRNA mediated knockdown studies in 3T3-L1 adipocytes generally replicated these findings. Conclusions: Loss of Mfn1 but not Mfn2 in cultured pre-adipocyte models is pro-adipogenic. This suggests distinct, non-redundant roles for the two mitofusin orthologues in adipocyte differentiation.

overall_design: Mouse embyronic fibroblasts (MEFs) underwent adipogenic differentiation from day -2 to day +8. Cells used: wild-type, Mfn1-/-, Mfn2-/-. WT (n=6), Mfn1-/- (n=3), and Mfn2-/- (n=3) cells obtained at day -2 and day +8 of differentiation. Mfn1-/- cell also obtained at  day zero (0) and day +3 of differentiation (n=3).

first: Jake

last: Mann


title: Expression profile of iPS cells from NEDAMSS patients as well as sibling controls

city: Tochigi

first: Ken-ichi

last: INOUE

address: 880 Kitakobayashi, Mibu-machi, Shimotsuga-gun

institute: Dokkyo Medical University

summary:
NEDAMSS (neurodevelopmental disorder with regression, abnormal movements, loss of speech, and seizures, MIM: 618088) is a recently discovered neurological disorder.
We developed iPS cells from peripheral blood mononuclear cells of two NEDAMSS patients and performed microarray.

overall_design: Total RNA was isolated from growing iPS cells and the expression profiles were analyzed.

last: Inoue

first: Ryoichi

last: Sohma

first: Shinobu

last: Yamauchi

first: Kazumi

last: Akimoto

first: Sachiko

last: Suzuki

first: Yoshiaki

last: Ito

first: Keiko

last: Imamura

first: Haruhisa


title: Comparision of transcriptomes between murine WT type 1 conventional DCs to XCR1-deficient type 1 conventional DCs

city: Seoul

first: Yeon Duk

last: Woo

address: 103 Daehak-ro, Jongno-gu

department: Department of Biomedical Sciences

institute: Seoul National University, College of Medicine

summary: We sought to compare the overall transcriptomic differences between TLR stimulated WT and XCR1-deficient type 1 conventional DCs. In addition, we also wanted to investigate functional role of XCR1 signaling in WT type 1 conventional DCs by treating recombinant murine XCL1, a ligand of XCR1 to these cells as well

overall_design: Total 4 samples are analyzed (WT LPS treated, WT LPS & rXCL1 treated, XCR1 KO LPS treated, XCR1 KO LPS & rXCL1 treated)

first: Yeon


title: A multicenter study of poor prognosis chromosome 1q gain and/or 6q loss in posterior fossa A ependymoma shows increased prevalence from 20% at diagnosis to 60% at first recurrence.

city: Aurora

first: Andrew

last: Donson

state: CO

department: Pediatrics

institute: CU Anschutz Medical Campus

summary: Ependymoma (EPN) posterior fossa group A (PFA) has the highest rate of recurrence and the worst prognosis of all EPN types. At relapse, it is typically incurable even with re-resection and re-irradiation. The biology of recurrent PFA EPN remains largely unknown, which hinders clinical advances. In this large longitudinal multicenter study, we examined matched samples of primary and recurrent disease from PFA EPN patients (n=95) to investigate the biology of recurrence. DNA methylomic data was used to measure copy number variants (CNVs), revealing progressive large scale chromosome gains and losses in successive recurrences. These CNV changes were dominated by chromosome 1q gain and/or 6q loss (1q+/6q-), both previously identified as high-risk factors in PFA EPN, which were present in ~20% at presentation but increased to ~60% at 1st recurrence. These CNV changes were correlated with hypomethylation of heterochromatin associated DNA at presentation. Evolution of chromosomal aberrations was further explored using CNV analysis of single-nuclei RNAseq on approximately 46,000 PFA EPN cells from 6 matched pairs of primary and 1st relapse tumors that harbored CNV changes at recurrence. No evidence of rare subclones in primary tumors was observed, suggesting that chromosomal rearrangement events occur after initial presentation. Cellular and molecular characteristics associated with CNVs were examined by single-nuclei RNAseq, bulk transcriptomic analysis and immunohistochemistry, revealing that 1q+/6q- PFA have a significantly higher mitotic index, increased proportions of proliferative epithelial progenitors and decreased differentiated neoplastic subpopulations. Multivariate survival analyses showed that cases with 1q gain or 6q loss at 1st recurrence were significantly more likely to recur than cases with no 1q or 6q change. The high prevalence of 1q+/6q- at recurrence and the associated shortened survival, suggest that both these abnormalities should be routinely tested for, and used for trial stratification.

overall_design: single cell RNA-seq of childhood posterior fossa subgroup A ependymoma

first: Kent

middle: A

last: Riemondy


title: Gene expression signatures of mammalian longevity across species

city: Boston

first: Alexander

last: Tyshkovskiy

state: Massachusetts

address: 77 Avenue Louis Pasteur

institute: Brigham & Women's Hospital, Harvard Medical School

summary: Lifespan varies both within and across species, but the general principles of its control are not understood. To identify transcriptomic signatures of mammalian longevity, we sequenced multiple organs of young adult mammals corresponding to 8 different species, including Canadian beaver, long-tailed macaque, greater tube-nosed bat, baboon, white-footed mouse, sugar glider, Siberian chipmunk and American black bear. We aggregated this dataset with publicly available pan-mammalian data and performed multi-tissue gene expression analyses across 41 mammalian species. This allowed us to identifiy signatures of species longevity and assess their relationship with biomarkers of aging and lifespan-extending interventions. This dataset complements RNAseq profiles of tissues from 23 mammalian species stored at GSE43013.

sample_organism:
Macaca fascicularis
Papio anubis
Ursus americanus
Peromyscus leucopus
Petaurus breviceps
Castor canadensis
Tamias sibiricus
Murina leucogaster

overall_design: RNA-seq gene expression profiling of 48 liver, kidney, brain and cerebellum samples from 8 mammalian species.

first: Siming

last: Ma

first: Vadim

middle: N

last: Gladyshev


title: Distinct longevity mechanisms across and within species and their association with aging

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

sample_organism:
Macaca fascicularis
Papio anubis
Ursus americanus
Peromyscus leucopus
Mus musculus
Petaurus breviceps
Castor canadensis
Tamias sibiricus
Murina leucogaster

overall_design: Refer to individual Series


title: Epigenetic methylation chip analysis of childhood ependymoma PFA subgroup patient samples [Infinium 450K Methylation Beadchip]

summary: DNA methylation analysis was perfomed using Infinium 450K Methylation BeadChip platform on 140 PFA ependymoma patient samples. Resulting .idat files were then uploaded to the molecularneuropathology.org classifier to obtain molecular subgroup and copy number variance. Idat files were batch normalized and background corrected using default settings of the R package ChAMP to obtain GpG methylation beta values for analysis of differentially methylated GpG regions.

overall_design: Bisulphite converted DNA from the 140 samples were hybridised to the Illumina Infinium 450K Methylation Beadchip

first: Timothy

last: Ritzmann

first: Kristian

last: Pajtler

first: Martin

last: Sill


title: RNA sequencing of mouse liver and kidney after 1-month treatment with predicted longevity compounds

summary: This dataset consists of liver and kidney gene expression profiles of young UM-HET3 mice subjected to the following compounds for 1 month: AS-703026 (liver and kidney), enzastaurin (liver and kidney), GDC-0941 (liver and kidney), ascorbyl-palmitate (kidney), AZD8055 (kidney) and KU0063794 (kidney). Corresponding age-, sex- and strain-matched littermate controls for kidney are also presented. This dataset complements liver RNAseq profiles of control UM-HET3 mice and mice subjected to ascorbyl-palmitate, AZD8055 and KU0063794 (collected and sequenced at the same time) stored at GSE131868.

overall_design: 3-month old UM-HET3 male mice from University of Michigan Medical School were subjected to GDC-0941 (50 ppm), enzastaurin (75 ppm), AS-703026 (30 ppm), KU0063794 (10 ppm), AZD8055 (20 ppm) and ascorbyl-palmitate (6.3 ppm) for 1 month. Their littermate controls of the same age and sex were also used for the analysis. 4 biological replicates were used for the each compound, and 6 biological replicates were used for the control group. In all cases, interventions continued until the animals were sacrificed.


title: RNAseq analysis of childhood posterior fossa subgroup A ependymoma

summary: Posterior fossa subgroup A (PFA) ependymoma is a brain tumor of childhood with a high rate of recurrence. Here we have performed RNAseq on a longitudinal cohort of patient samples obtained at presentation and at recurrence(s), in order to identify the biological correlates of treatment failure and tumor evolution.

overall_design: We performed RNAseq on a longitudinal cohort of patient samples obtained at presentation and at recurrence(s) in order to identify differentially expressed genes between tumors grouped according to chromosomal copy number variants. Differentially expressed genes were analysed using gene ontology enrichment and deconvolution to estimate neoplastic subpopulation heterogeneity.