title: A Tale of Two Molds: Comparative Penicillium spp. transcriptomics reveals conserved pathways, processes, and loci associated with ungerminated conidia and blue mold decay

status: Public on Jul 31 2022

city: Beltsville

first: Wayne

last: Jurick II

state: MD

address: 10300 Baltimore Ave

department: Food Quality Lab

institute: USDA-ARS

summary: A transcriptomic approach was implemented using two Penicillium species to identify genes related to fungal aggressiveness in apple fruit and loci contained in ungerminated conidia. Total RNA was isolated from ungerminated conidia and decayed apple fruit infected with P. expansum R19 (aggressive) or P. polonicum RS1 (weak). There were 2,442 differentially expressed genes (DEGs) between the R19 and RS1 in apple and comparisons within species between apple and conidia revealed 4,404 DEGs for R19, and 2935 for RS1, respectively. Gene ontology (GO) revealed differential regulation in fungal transport and metabolism genes expressed during decay, suggesting a flux in nutrient acquisition and detoxification strategies. In R19, the oxidoreductase GO category comprised 20% of all groups differentially expressed in decayed apple verses ungerminated conidia in addition to those involved in hydrogen peroxide metabolism. Ungerminated conidia from both species showed higher expression of genes encoding the glyoxylate shunt and beta-oxidation, specifying the earliest metabolic requirements for germination

sample_organism:
Penicillium expansum
Penicillium polonicum

overall_design: Four replicate samples of highly agressive Penicillium expansum R19 from the decayed margin of apple fruit, four replicate samples of R19 ungerminated conidia, four replicate samples from weakly virulent P. polonicum RS1 from apple tissue, and four replicate samples of RS1 ungerminated conidia all were used to extract RNA for RNA-Seq to compare transcriptomes of the two blue mold pathogens before infecting apple and during apple infection. Transcripts were quality filtered and assembled before finding log2 fold change expression differences between the four sample types. Data was visualized for interpretation via heat maps of virulence genes of interest, volcano plots of all genes, and venn diagrams of differentially regulated genes. Gene ontology and Kegg mapping were used to group genes based on molecular function and pathway shifts between the pathways shifts between pathogen type and pre or post infection status. Both strains were also evaluated for germination timing (14 hours postinoculation and 24 hpi - 3 technical replicates/trial, two trials), radial growth on PDA media (3, 5, and 7 days postinoculation - 3 technical replicates/trial, two replicate trials), and lesion size on infected apples (10 apples/inoculum/trial, two trials) over time to demonstrate differences between growth and pathogenicity of the strains.

first: Holly

last: Bartholomew

first: Franz

middle: J

last: Lichtner

first: Michael

last: Bradshaw

first: Verneta

last: Gaskins

first: Jorge

last: Fonseca

first: Joan

last: Bennett


title: MafB binding in P7 intestinal epithelium

status: Public on Jul 30 2022

city: Durham

first: Anne (Maggie)

middle: M

last: Bara

state: NC

address: 307 Research Dr.

department: Cell Biology and Dermatology

country: USA

institute: Duke University

summary: To investigate the genetic loci bound by MafB in the intestinal epithelium, we used CUT&RUN.

first: Maggie

first: Tongyu

last: Sun

first: Jianhong

last: Ou

first: Yarui

last: Diao

first: Terry

last: Lechler


title: Modulation of protease expression by PITX transcription factors regulates protein quality control during aging

status: Public on Aug 15 2022

city: Memphis

first: David

last: Finkelstein

state: TN

address: 332 N. Lauderdale St.

department: Computational Biology

institute: St Jude Children's Research Hospital

type: Expression profiling by high throughput sequencing

summary: Protein quality control is important for healthy aging and is dysregulated in several age-related diseases. The autophagy-lysosome and ubiquitin-proteasome systems are key for proteostasis but it remains largely unknown whether other proteolytic systems maintain protein quality control during aging. Here, we find that the expression of proteolytic enzymes (proteases/peptidases) distinct from the autophagy-lysosome and ubiquitin-proteasome systems declines during skeletal muscle aging in Drosophila. Age-dependent downregulation of proteases undermines proteostasis, as demonstrated by the increase in detergent-insoluble poly-ubiquitinated proteins and pathogenic huntingtin-polyQ in response to protease RNAi. Transcriptomic analysis identifies Ptx1, homologous to human PITX1/2/3, as a transcriptional regulator of proteases. Specifically, RNAi for Ptx1 increases the expression of age-downregulated proteases and improves protein quality. Moreover, muscle-specific expression of Ptx1 RNAi extends lifespan. These findings indicate that protein quality control is ensured during aging by autophagy/proteasome-independent proteases that degrade misfolded and aggregation-prone proteins and by their transcriptional modulator Ptx1.

overall_design: Here 3 Drosophila melanogaster RNA seq samples treated with Pitx RNAi are compred to control samples from GSE149799:  GSM4512833  FD_GFP_1TH  GSM4512834  FD_GFP_2TH  GSM4512835  FD_GFP_3TH  GSM4512836  FD_white_1TH  GSM4512837  FD_white_2TH  GSM4512838  FD_white_3TH

first: Jianqin

last: Jiao

first: Michelle

last: Curley

first: Flavia

middle: G

last: Zuanazzi

first: Maricela

last: Robles-Murguia

first: Abbas

last: Shirinifard

first: Beisi

last: Xu

first: Yiping

last: Fan

first: Fabio

last: Demontis


title: poly-PR expression invokes massive changes in cellular transcriptome and leads to upregulation of RQC genes at transcriptional level

status: Public on Aug 01 2022

city: Parkville

first: Viacheslav

last: Kriachkov

state: VIC

address: 30 Flemington Road

department: Department of Biochemistry and Pharmacology

country: Australia

institute: University of Melbourne

summary: Hexanucleotide expansion mutations in C9ORF72 are a cause of familial amyotrophic lateral sclerosis. We previously reported that long arginine-rich dipeptide repeats (DPR), mimicking abnormal proteins expressed from the hexanucleotide expansion, caused translation stalling when expressed in cell culture models. Whether this stalling provides a mechanism of pathogenicity remains to be determined. Here we explored the molecular features of the stalling and examined whether known regulatory mechanisms of ribosome quality control (RQC) are involved in efforts to sense and resolve the stalls. The most well-known RQC mechanisms come largely from studies of mRNA lacking stop codons, whereby ribosomes become stalled at the poly-adenylate sequence in the 3`UTR.  Here we find that arginine-containing DPRs lead to stalling in a length dependent manner, with lengths longer than 40 repeats to invoke strong stalling. Mutational screening of 40×Gly-Xxx DPRs finds that stalling is most pronounced where Xxx are positively charged amino acids. Through a  genome-wide CRISPR screen we find that genes that regulate poly-adenylate readthrough respond differently to the readthrough of arginine-rich DPRs. Indeed, we find evidence that DPR-mediated stalling has no natural regulatory responses even though the stalls may be sensed, as evidenced by an upregulation of RQC gene expression. These findings therefore implicate Arg-rich DPR-mediated stalled ribosomes as posing a particular danger to cellular health and viability. This dataset contains the RNA-sequencing data used to support the conclusions from this study.

overall_design: To determine whether poly-adenylate-mediated stalling induces similar gene expression responses as poly-PR mediated stalling, we performed transcriptome analysis. We created three stable HEK293T cell lines expressing GFP-P2A-ChFP (negative control), GFP-P2A-poly-adenylate and GFP-P2A-102×PR under a Tet-inducible promoter. HEK293K cell lines harbouring the constructs under the Tet-on expression system were induced for expression by adding 500 ng/μl doxycycline to the cells for 48 h prior to analysis. RNA-seq analysis was performed for both uninduced cells and cells with 48-h induced expression. Triplicate samples were prepared. Count tables were generated in Galaxy.org using HISAT2 algorithm, and the list of differentially expressed genes were generated with DESeq2 package in R.

first: Luc

last: Furic

first: Danny

last: Hatters


title: Moringa isothiocyanate-1 inhibits inflammation via NF-κB pathway in skeletal muscle cells

status: Public on Jul 28 2022

city: Piscataway

first: Sohaib

last: Hassan

state: NJ

address: 145 Bevier Road

department: Department of Genetics and Human Genetics Institute of New Jersey

institute: Rutgers University

summary: This study aims to investigate the effect of Moringa isothiocyanate-1 (MIC-1) derived from seeds of Moringa oleifera Lam in lipopolysaccharide (LPS)-induced muscle inflammation models.  MIC-1 decreased nitric oxide production, and reduced the expression of pro-inflammatory markers, in C2C12 myoblasts. The daily oral treatment of MIC-1 (80 mg/kg) for three days significantly reduced the expression of pro-inflammatory markers (TNF-α, Ifn-α, IL-1β, IL-6) in gastrocnemius tissue of mice. Transcriptomic analysis provided insight into the inhibitory effects of MIC-1 on the LPS-induced inflammation, which suggests that MIC-1 acts via inflammation, and immunity pathways in myoblasts and skeletal muscle tissue. MIC-1 inhibited the nuclear accumulation of the nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB) in the LPS-treated murine, which supports that MIC-1 decreases inflammation and regulates immune responses at a gene expression level in LPS-induced inflammation murine model.

overall_design: Mouse data comprising RNA-Seq from 18 samples was obtained: 9 samples from the myoblast [3 saline control replicates, 3 LPS (1 μg/mL) treated replicates, 3 LPS+10uM MIC-1 treated replicates] and 9 samples from skeletal muscle tissues [3 saline control replicates, 3 LPS (10 mg/kg b.w., i.p.) treated replicates, 3 LPS+MIC-1 (80 mg/kg, b.w., p.o) treated replicates].

first: Badi

middle: S

last: Sailaja

first: Evan

last: Cohen

first: Michael

middle: P

last: Verzi


title: Articular chondrocyte  inflammation- and senescence- related gene expression is altered with mitochondrial inhibition and in non-physiologic culture conditions

status: Public on Aug 10 2022

city: Ithaca

middle: L

last: Delco

state: NY

address: 930 Campus Road C3-117 VMC

department: Clinical Sciences

institute: Cornell University College of Veterinary Medicine

summary: Avascular soft tissues of the skeletal system, including articular cartilage, have an extremely limited healing capacity, in part due to their low metabolic activity. No drugs are available that can prevent or slow the development of osteoarthritis (OA) after joint injury. Therefore, mesenchymal stromal cell (MSC)-based regenerative therapies are increasingly common in the treatment of OA, but questions regarding their clinical efficacy and mechanisms of action remain unanswered. Our group recently reported that mitochondrial dysfunction is one of the earliest responses of cartilage to injury, resulting in chondrocyte death, extracellular matrix degeneration, and ultimately OA. MSCs have been found to rescue injured cells and improve healing by donating healthy mitochondria in highly metabolic tissues, but mitochondrial transfer has not been investigated in cartilage. To investigate how gene expression changes in stressed chondrocytes, and therefore how they might elicit mitochondrial donation from MSCs, we developed a custom quantitative PCR panel of relevant genes involved in chondrocyte metabolism and OA. We cultured chondrocytes under conditions known induce chondrocyte mitochondrial dysfunction, including stimulation with rotenone/antimycin and non-physiologic culture conditions (hyperoxia and hyperglycemia). We found that expression of gap junction alpha 1 (GJA1), the gene that encodes the Cx43 protein, was increased in hyperoxia. The senescence associated markers, cyclin-dependent kinase inhibitor 2A (CDKN2A) and tissue inhibitor of metalloproteinases 1 (TIMP1), were also increased in hyperoxia. In addition, hyperoxia caused chondrocytes to increase the expression of the antioxidant enzyme, SOD2. This work provides insights into the chemical and environmental conditions that can alter gene expression in chondrocytes. Further, this provides supporting evidence to our hypothesis that stressed chondrocytes may trigger mitochondrial donation from MSCs may via direct or indirect signaling involving the inflammation- and senescence-related genes identified in the present study.

overall_design: Four replicates were performed (n=4). Within replicates, 8, 96-well custom PCR plates were used. The 8 plates represented the unique combinations of the 3 factors studied: stimulation (no stim or Rot/A), oxygen (physioxia or hyperoxia) and glucose (euglycemia or hyperglycemia) conditions. The control condition was chondrocytes that were non-stimulated and cultured at physioxia and euglycemia. The custom panel of genes included a manufactuer control (18sRNA), a no template control, and three housekeeping genes (GAPDH, RPL13A, RPL3).

first: Matthew

last: Thomas

first: Nikita

last: Srivistava

first: Megan

last: Fahey


title: Genomic testing in early localized prostate cancer may define subsets of African Americans with aggressive disease—a prospective study

status: Public on Jul 29 2022

city: Tampa

first: Kosj

last: Yamoah

state: Florida

address: 12902 Magnolia Drive

institute: Moffitt Cancer Center

summary: Gene expression study of the VANDAAM Phase II clinical trial

overall_design: Prospective analysis of 226 tumor transcriptomes from VANDAAM.

first: Awasthi

last: S.

first: Grass

last: D.

first: Torres-Roca

last: J.

first: Johnstone

last: P.

first: Pow-Sang

first: Dhillon

first: Park

first: Davicioni

last: E.

first: Fink

first: DeRenzis

last: A.

first: Creed

first: Poch

last: M.

first: Li

last: R.

first: Manley

last: B.

first: Fernadez

first: Naghavi

first: Gage

last: K.

first: LuYao

last: G.

first: Katoulakis

first: Burri

first: Leone

first: Ercole

first: Palmer

first: Vapiwala

last: N.

first: Deville

last: C.

first: Rebbeck

last: T.

first: Dicker

first: Kelly

last: W.

first: Yamoah


title: Comparison of adult stem cells of various human donors

status: Public on Aug 09 2022

city: Pohang

first: Hyeonji

last: Kim

address: 77 Cheongam-ro

country: South Korea

institute: Pohang University of Science and Technology

summary: We would like to check differences among stem cells derived from various donors. The purpose of this project is to investigate donor dependency for stem cell implantation.

overall_design: Comparative gene expression profiling analysis of mRNA-seq data for adult stem cells (derived from human turbinate).

first: Sung

middle: W

first: Dong-Woo

last: Cho

first: Jung-Min

last: Yon

first: Jinah

last: Jang


title: The presence of plasmids in L. lactis IL594 determines changes in host phenotype and expression of chromosomal genes

status: Public on Jul 27 2022

city: Warszawa

first: Marek

last: Skoneczny

email: kicia@ibb.waw.pl, mrksknc@gmail.com

address: Pawińskiego 5A

country: Poland

institute: Institute of Biochemistry and Biophysics PAS

summary: The L. lactis IL594 strain contains seven plasmids (pIL1 to pIL7) and is the parental strain of the plasmid-free L. lactis IL1403, one of the most studied lactic acid bacteria (LAB) strain. The genetic sequences of pIL1 to pIL7 plasmids have been recently described, however the knowledge of global changes in host phenotype and transcriptome remains poor. In presented study, global phenotypic analyses were combined with transcriptomic studies to evaluate a potential influence of plasmidic genes on overall gene expression in industrially important L. lactis strains. High-throughput screening of phenotypes differences revealed pronounced phenotypic differences in favor of IL594 during the metabolism of seven C-sources, including carbohydrates and β-glucosides. A plasmid-bearing strain presented increased resistance to unfavorable growth conditions, including the presence of heavy metal ions, antibiotics and antimicrobial compounds. Global comparative transcriptomic study of L. lactis strains revealed variation in the expression of over 370 of chromosomal genes caused by plasmids presence. The general trend presented upregulated energy metabolism and biosynthetic genes, differentially expressed regulators, prophages and cell resistance proteins. Our findings suggest that plasmids maintenance leads to significant perturbation in global gene regulation that provide changes in central metabolic pathways and adaptive properties of the IL594 cells.

overall_design: The comparison of transcriptomes of the parental Lactococcus lactis IL594 strain containing seven plasmids (pIL1 to pIL7) to the plasmid-free L. lactis IL1403 strain, both grown in the medium with either glucose or cellobiose or galactose as carbon sources and harvested at various growth phases: early exponential (E), mid-exponential (M), transition (T) and stationary (S). For each sample, two technical replicates with dye swapping were performed.

first: Katarzyna

last: Kosiorek

first: Anna

last: Koryszewska-Bagińska

first: Tamara

last: Aleksandrzak-Piekarczyk


title: MNase-seq of sir2 in Saccharomyces cerevisiae

city: Stockholm

first: Stefan

last: Åström

address: Svante Arrhenius väg 20B

country: Sweden

institute: Stockholm University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Telomere chromatin structure is pivotal for maintaining genome stability by regulating the binding of telomere-associated proteins and inhibition of a DNA damage response. In yeast, the silent information regulator (Sir) proteins bind to terminal telomeric repeats and to subtelomeric X-elements resulting in histone deacetylation and transcriptional silencing. Herein, we show that sir2 mutant strains display a very specific loss of a nucleosome residing in the X-element. Most yeast telomeres contain an X-element and the nucleosome occupancy defect in sir2 mutants is remarkably consistent between different telomeres.

overall_design: MNase-seq of WT and sir2 strains in 3 replicates

first: Stefanie

last: Bauer

first: Thomas

last: Grochalski

first: Agata

last: Smialowska


title: Small RNA-seq data of peripheral blood obtained from treatment-näive IBD patients and control individuals (small RNA-Seq I)

status: Public on Aug 16 2022

city: Kiel

first: Simonas

last: Juzenas

address: Am Botanischen Garten 11

department: Institute of Clinical Molecular Biology

country: Germany

institute: Christian-Albrechts-University of Kiel

type: Non-coding RNA profiling by high throughput sequencing

summary: Comperhensive analysis of blood transcriptomes obtained from treatment-näive IBD patients.

overall_design: Total RNA extracted from peripheral blood samples (n = 205) was used to generate small RNA libraries employing TruSeq Small RNA Sample Preparation Kit (Illumina) according to the manufacturer’s instructions.

first: Mauro

last: D'Amato

first: Jonas

last: Halfvarsson

first: Mårten

last: Lindqvist

first: Andre

last: Franke


title: Neonatal hyperoxia induces sex-dependent pulmonary cellular and transcriptomic changes in an experimental mouse model of bronchopulmonary dysplasia

city: Kansas City

first: Sheng

last: Xia

state: MO

address: 2401 Gillham Rd

department: Children's Mercy Research Institute

institute: Children's Mercy Kansas City

summary: To investigate sex-dependent molecular and cellular programming involved in hyperoxia, we surveyed the mouse lung using single cell RNA sequencing (scRNA-seq).

overall_design: WT C57BL/6 (Charles River) mice were used in the study. For hyperoxia, pups with dam were placed in cages in a hyperoxia chamber for 14 days from P1 to P14. We used 3 females and 3 males/experimental condition (room air and hyperoxia) for scRNA-seq.

first: Venkatesh

last: Sampath

first: Lisandra

middle: V

last: Ellis

first: Daniel

last: Louiselle

first: Elin

last: Grundberg

first: Konner

last: Winkley

first: Margaret

last: Gibson


title: Anti-inflammatory compounds from the mangrove endophytic fungus Amorosia sp. SCSIO 41026

status: Public on Aug 04 2022

city: Beijing

first: Zihui

last: Yu

address: 2 Yabao Road, Chaoyang District, Beijing

country: China

institute: Capital Institute of Pediatrics

summary: To further explore the mechanism of compound 13 in ameliorating LPS-induced inflammation, high-throughput sequencing of RNAs from RAW264.7 macrophages was conducted.

overall_design: RNA-seq was performed on LPS-induced inflammatory cell models to analyze specific signaling pathways in which the compound exerts anti-inflammatory activity

first: Xue

last: Ren

first: Chunmei

last: Chen


title: Intrauterine Botulinum Toxin A administration promotes thin endometrium regeneration in a manner dependent on regulatory effect of insulin-like growth factor-binding protein 3 on osteopontin proteolytic cleavage in mice

status: Public on Jul 15 2022

city: Sungnam

first: Danbi

last: Lee

address: sampyeongro 335, Seongnam-Si, Kyounggido, Republic of Korea

department: Department of biological sciences

institute: CHA university

summary: Intrauterine administration of BoTA might be a potential therapeutic strategy to promote endometrial regeneration via elevation of insulin-like growth factor binding protein 3 mediated osteopontin proteolytic cleavage

overall_design: To investigate differentially expressed genes in EtOH-treated thin endometrium compared to saline-treated control gourp, 3 independent uteri from EtOH-treated and saline-treated endometrium were obtained and compared.

first: Youn-Jung

last: Kang

first: Hwa-Seon

last: Koo

first: Jungho

last: Ahn


title: Musashi1 is a master regulator of aberrant translation in Group 3 medulloblastoma

status: Public on Jul 19 2022

city: La Jolla

first: En-Ching

last: Luo

address: 9500 Gilman St

institute: UCSD

summary: Pediatric medulloblastoma (MB) is the most common solid malignant brain neoplasm, with group 3 (G3) MB representing the most aggressive subgroup associated with a poor prognosis and a remarkable ability to resist upfront multimodal therapy. Despite a low mutational burden of disease and MYC amplification identified as a independent factor associated with poor survivorship, efforts to target the MYC has met with limited therapeutic success. Consequently alternative mediators associated with the aggressive phenotype of G3 MB continues as a common goal within the MB community. Here we show how the neural stem cell determinant Musashi 1 (MSI1) is a central and vital moderator of G3 MB in both a MYC amplified mouse model of G3 MB and patient derived xenografts (PDX). Specifically, we modified the MYC amplified and p53 mutated (MP) mouse model of G3 MB to generate Msi1 conditional knockout mice (Msi1flox/flox), which led to the observation that MSI1 is required for tumor initiation of MP tumors. To identify the translational potential of these findings, we employed shRNA against Msi1 in multiple PDX lines, observing a striking deficit in multiple key stem cell features including self-renewal, proliferation, and failure to progress through the cell cycle. Notably, Msi1 inhibition resulted in a failure of tumor initiation, translating to a significantly prolonged survival, reaffirming the essential role for MSI1 in G3 MB. To determine how MSI1 symphonizes the anarchic post-transcriptional landscape of G3MB, we differentially analyzed the MSI1 binding sites in normal neural stem cells and G3 MB and subsequently compared the MSI1-binding transcriptome, and proteome following Msi1 inhibition. Comparative analysis suggested an integral role for post-transcriptional regulators, such as MSI1 and its binding prey mRNA, as a therapeutic target. Here we propose the neural RNA binding protein MSI1, as a master regulator, hijacked from its normal neural developmental function, orchestrating the aberrant translational landscape of G3 MB.

overall_design: shRNA against Msi1 in a patient-derived xenograft line.

first: Michelle

last: Kameda

first: En

middle: C

first: Gene

last: Yeo

first: Sheila

last: Singh


title: Identification of extremely GC-rich micro RNAs for RT-qPCR data normalization in human plasma

status: Public on Jul 25 2022

city: Vienna

first: Angelos

last: Athanasiou

address: Veterinaerplatz 1

country: Austria

institute: University of Veterinary Medicine Vienna

summary: We aimed at extending the repertoire of high-quality miRNA normalizers for reverse transcription-quantitative PCR (RT-qPCR) of human plasma with special emphasis on the extremely guanine-cytosine-rich portion of the miRNome. For high-throughput selection of stable candidates, microarray technology was preferred over small-RNA sequencing (sRNA-seq) since the latter underrepresented miRNAs with a guanine-cytosine (GC) content of at least 75% (p = 0.0002, n = 2). miRNA abundances measured on the microarray were ranked for consistency and uniformity using nine normalization approaches. The eleven most stable sequences included miRNAs of moderate, but also extreme GC content (45%–65%: miR-320d, miR-425-5p, miR-185-5p, miR-486-5p; 80%–95%: miR-1915-3p, miR-3656-5p, miR-3665-5p, miR-3960-5p, miR-4488-5p, miR-4497 and miR-4787-5p). In contrast, the seven extremely GC-rich miRNAs were not found in the two plasma miRNomes screened by sRNA-seq. Stem-loop RT-qPCR was employed for stability verification in 32 plasma samples of healthy male Caucasians (age range: 18–55 years). In general, inter-individual variance of miRNA abundance was low or very low as indicated by coefficient of variation (CV) values of 0.6%–8.2%. miR-3665 and miR-1915-3p outperformed in this analysis (CVs: 0.6 and 2.4%, respectively). The eight most stable sequences included four extremely GC-rich miRNAs (miR-1915-3p, miR-3665, miR-4787-5p and miR-4497). The best-performing duo normalization factor (NF) for the condition of human plasma, miR-320d and miR-4787-5p, also included a GC-extreme miRNA. In summary, the identification of extremely guanine-cytosine-rich plasma normalizers will help to increase accuracy of PCR-based miRNA quantification, thus raise the potential that miRNAs become markers for psychological stress reactions or early and precise diagnosis of clinical phenotypes. The novel miRNAs might also be useful for orthologous contexts considering their conservation in related animal genomes.

overall_design: Sequencing of the small RNA transcriptome was performed by a sequencing-by-synthesis approach on the HiSeq 2500 System.

first: Volker

last: Baumann

middle: T

first: Omid

middle: R

last: Faridani

first: Andreas

last: Schwerdtfeger

first: Bernard

last: Wallner

first: Ralf

last: Steinborn


title: TGS1 controls snRNA 3' end processing, prevents neurodegeneration and ameliorates SMN-dependent neurological phenotypes in vivo (Illumina)

city: Rome

first: Grazia Daniela

last: Raffa

address: P.le Aldo Moro 5

country: Italy

institute: Sapienza Università di Roma

summary: Trimethylguanosine synthase 1 (TGS1) is a highly conserved enzyme that converts the 5' mono-methylguanosine cap of snRNAs to a trimethylguanosine cap. Here, we show that loss of TGS1 in C. elegans, D. melanogaster and D. rerio results in neurological phenotypes similar to those caused by Survival Motor Neuron (SMN) deficiency. Importantly, expression of human TGS1 ameliorates the SMN-dependent neurological phenotypes in both flies and worms, revealing that TGS1 can partly counteract the effects of SMN deficiency. TGS1 loss in HeLa cells leads to the accumulation of immature U2 and U4atac snRNAs with long 3' tails that are often uridylated. snRNAs with defective 3' terminations also accumulate in Drosophila Tgs1 mutants. Consistent with defective snRNA maturation, TGS1 and SMN mutant cells also exhibit partially overlapping transcriptome alterations that include aberrantly spliced and readthrough transcripts. Together, these results identify a neuroprotective function for TGS1 and reinforce the view that defective snRNA maturation affects neuronal viability and function.

overall_design: Exploring transcriptome alterations induced by TGS1 and SMN deficiency in human cells using Illumina.

first: Lu

first: Caitlin

last: Roake

first: Paolo

last: Maccallini

first: Francesca

last: Bavasso

first: Roozbeh

last: Dehghannasiri

first: Pamela

last: Santonicola

first: Natalia

last: Mendoza-Ferreira

first: Livia

last: Scatolini

first: Ludovico

last: Rizzuti

first: Alessandro

last: Esposito

first: Ivan

last: Gallotta

first: Sofia

last: Francia

first: Stefano

last: Cacchione

first: Alessandra

last: Galati

first: Valeria

last: Palumbo

first: Gian

last: Tartaglia

first: Alessio

last: Colantoni

first: Gabriele

last: Proietti

first: Yunming

last: Wu

first: Matthias

last: Hammerschmidt

first: Cristiano

last: De Pittà

last: Sales

first: Julia

last: Salzman

first: Livio

last: Pellizzoni

first: Brunhilde

last: Wirth

first: Elia

last: Di Schiavi

first: Maurizio

last: Gatti

first: Steven

middle: E

last: Artandi

first: Grazia

middle: D


title: tRNA-m1A modification promotes T cell expansion via efficient MYC protein synthesis

status: Public on Jul 23 2022

city: Hangzhou

first: Xiaoyu

last: Li

state: Zhejiang

address: 866 Yuhangtang Road

department: SCHOOL OF BASIC MEDICAL SCIENCES

institute: Zhejiang University

summary:
Using genetic mouse models, high-throughput sequencing, transcriptome-wide m1A profiling and ribosome profiling, we find:
(1) Translation is the most active process of these genetic information processing in early T cell activation.
(2) T cells upregulate tRNA-m1A58 “writer” proteins TRMT61A and TRMT6 to install m1A58 modification to a specific subset of early expressed tRNAs during the early stage of activation.
(3) m1A58 modifications in tRNA support rapid and adequate synthesis of MYC and other key functional proteins, guide the exit of naïve T cells from quiescence state into a proliferative state, and promote rapid T cell expansion after activation.

overall_design:
For RNA-seq, there are 0h,3h,6h,18h,48h for WT samples and 0h,3h,6h,48h for Trmt61A-cKO samples.
For m1A-seq,there are 6h WT/cKO samples.
For tRNA-seq,  naïve CD4+ T cells were isolated from WT mice and activated with plate-bound anti-CD3 plus anti-CD28 in a 96-well plate for 0,6,18,48 hours.
For RiboTag-seq, 500 million naïve CD4+ T cells were isolated from WT (RiboTagflox/floxCd4Cre) and Trmt61a-KO (Trmt61aflox/floxRiboTagflox/floxCd4Cre) mice (activated with plate-bound anti-CD3 plus anti-CD28 in 96-well plate for 6 hours).

first: Yongbo

last: Liu

first: Jing

last: Zhou

first: Xiaoting

last: Zhang


title: HDAC inhibition suppresses telomerase activity in neuroblastoma cells harboring TERT rearrangements [ChIP-Seq]

city: Berlin

first: January

last: Weiner

address: Charitéplatz 1

department: CUBI

institute: Berlin Institute of Health, Charité Medical University of Berlin

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of histone modifications in mammalian cells. The three histone marks acetylation of histone 3 at lysine residue 27 (H3K27ac), trimethylation of histone 3 at lysine residue 4 (H3K4me3) and trimethylation of histone 3 at lysine residue 36 (H3K36me3) were selected, representing marks for an open chromatin structure and enable gene transcription. The two histone marks standing for a condensed chromatin state and disabled gene transcription trimethylation of histone 3 at lysine residue 27 (H3K27me3) and trimethylation of histone 3 at lysine residue 9 (H3K9me3) were chosen. ChIP sequencing of the five histone marks was investigated in high-risk TERT-rearranged neuroblastoma GI-ME-N cells treated with solvent or HDAC inhibitor panobinostat. Exemplary samples include solvent-treated and panobinostat-treated samples after 18 h of treatment.

overall_design: Characterization of histone modifications in the TERT-rearranged neuroblastoma cell line GI-ME-N treated with panobinostat or solvent control

first: Sabine

last: Finkler

first: Konstantin

last: Helmsauer

first: Annika

last: Sprüssel

first: Birte

last: Arlt

first: Annette

last: Kuenkele

first: Johannes

middle: H

last: Schulte

first: Kerstin

last: Haase

first: Benedikt

last: Obermayer

first: Dieter

last: Beule

last: Fischer

first: Nils

last: Bluethgen

first: Anton

last: Henssen

first: Marco

last: Lodrini

first: Angelika

last: Eggert

first: Hedwig

last: Deubzer


title: ATAC-Seq for control and Huntington's disease mouse models for neun+ and neun- cells

status: Public on Jul 14 2022

city: Cambridge

first: Maxwell

last: Gold

state: MA

address: 21 Ames St

institute: MIT

summary: Data collected from HD and control mouse models for multiple brain regions (striatum vs. cortex), time points (8 weeks vs. 12 weeks), and cell types (NeuN+ vs. Neun-)

overall_design: ATAC-Seq profiles to compare HD and control mouse brains for the conditions described above

last: P. Gold

first: Miriam

last: Adam

first: Ernest

last: Fraenkel


title: HDAC inhibition suppresses telomerase activity in neuroblastoma cells harboring TERT rearrangements

first: January

last: Weiner

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

overall_design: Refer to individual Series


title: The Role of FOXO4/NFAT2 Signaling Pathway in Dysfunction of Human Coronary Endothelial Cells and Inflammatory Infiltration of Vasculitis in Kawasaki Disease

status: Public on Aug 02 2022

city: Suzhou

first: Hongbiao

last: Huang

address: Zhongnan street 92

institute: Children’s Hospital of Soochow University

summary:
Aims: The Ca+/NFAT (Nuclear factor of activated T cells) signaling pathway activation is implicated in the pathogenesis of Kawasaki disease (KD); however, we lack detailed information regarding the regulatory network involved in the human coronary endothelial cell dysfunction and cardiovascular lesion development. Herein, we aimed to use mouse and endothelial cell models of KD vasculitis in vivo and in vitro to characterize the regulatory network of NFAT pathway in KD.
Methods and Results: Among the NFAT gene family, NFAT2 showed the strongest transcriptional activity in peripheral blood mononuclear cells (PBMCs) from patients with KD. Then, NFAT2 overexpression and knockdown experiments in Human coronary artery endothelial cells (HCAECs) indicated that NFAT2 overexpression disrupted endothelial cell homeostasis by regulation of adherens junctions, whereas its knockdown protected HCAECs such dysfunction. Combined analysis using RNA sequencing and transcription factor (TF) binding site analysis in the NFAT2 promoter region predicted regulation by Forkhead box O4 (FOXO4). Western blotting, chromatin immunoprecipitation, and luciferase assays validated that FOXO4 binds to the promoter and transcriptionally represses NFAT2. Moreover, Foxo4 knockout increased the extent of inflamed vascular tissues in a mouse model of KD vasculitis. Functional experiments showed that inhibition NFAT2 relieved Foxo4 knockout exaggerated vasculitis in vivo.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TNFα stimulated human coronary artery endothelial cells and its overexpression and knockdown derivatives (OE-NFAT2, KnD-NFAT2).

first: Jinfeng

last: Dong

first: Jiaqi

last: Jiang

first: Lei

last: Gu

first: Haitao

last: Lv


title: Engineering large-scale perfused tissues via synthetic 3D soft microfluidics

city: Heverlee

first: Adrian

last: Ranga

state: Flanders

address: Celestijnenlaan 200F - Room 03.349

department: Mechanical Engineering

country: Belgium

institute: KU Leuven

summary: The vascularization of engineered tissues and organoids has remained a major unresolved challenge in regenerative medicine. While multiple approaches have been developed to vascularize in vitro tissues, it has thus far not been possible to generate perfusable vessels in sufficiently close proximity and at sufficient small scale to perfuse large de novo tissues. Here, we achieve the perfusion of multi-mm3 tissue constructs by generating perfusable synthetic capillary-scale 3D channels. Our 3D soft microfluidic strategy is uniquely enabled by a 3D-printable 2-photon-polymerizable hydrogel formulation, which allows for precise microvessel printing at scales below the diffusion limit. We demonstrate that these large-scale engineered tissues are viable, proliferative and exhibit complex morphogenesis during long-term in-vitro culture, while avoiding hypoxia and necrosis. We show by scRNAseq and immunohistochemistry that neural differentiation is significantly accelerated in perfused neural constructs. Additionally, we illustrate the versatility of this platform by demonstrating long-term perfusion of developing liver tissue. This fully synthetic vascularization platform opens the door to the generation of human tissue models at unprecedented scale and complexity.

overall_design: 3 samples are analyzed to compare the effect of perfusion on human brain tissue. 1x day 8 brain organoids in suspentions (chip control), 1x day 8 brain tissue in non-perfused chip (perfusion control), and 1x day 8 brain tissue in a perfused chip.

first: Sergei

last: Grebenyuk

first: Abdel

last: Abdel Fattah

first: Gregorius

last: Rustandi

first: Manoj

last: Kumar

first: Burak

last: Toprakhisar

first: Idris

last: Salmon

first: Catherine

last: Verfaillie


title: Knockdown of ZIP11 impairs growth in HeLa cells.

status: Public on Jul 11 2022

city: Farmington

first: Sabriya

last: Syed

state: CT

address: 10 Discovery Dr

institute: The Jackson Laboratory for Genomic Medicine

summary: We report the effect of knocking down a nuclear Zn transporter, ZIP11, in HeLa cells

overall_design: Gene expression profiles of proliferating HeLa cells transduced with either the scramble, or two different ZIP11 shRNAs.

first: Teresita

last: Padilla-Benavides

first: Julia

last: Kan

first: Monserrat

last: Olea-Flores


title: MiDAS in BRCA2-deficient cells originate at early S-phase transcription-replication conflicts

city: Oxford

first: Madalena

last: Tarsounas

address: The Old Road Campus Research Building

country: United Kingdom

institute: Oxford Univerity

summary: Multiple replication abnormalities cause cells lacking BRCA2 to enter mitosis with under-replicated DNA and to activate mitotic DNA synthesis (MiDAS). However, the precise position of these MiDAS sites, as well as their origin, remains unknown. Here we labelled mitotic nascent DNA and performed high-throughput sequencing to identify at high-resolution the sites where MiDAS occurs in the absence of BRCA2. This approach revealed 150 genomic loci affected by MiDAS, which map within regions replicating during early S-phase and are therefore distinct from the aphidicolin-induced common fragile sites. Moreover, these sites largely localise near early firing origins and within genes transcribed in early S, suggesting that they stem from transcription-replication conflicts (TCRs). Inhibiting transcription with 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) during early S-phase abrogates MiDAS. Strikingly, MiDAS sites co-localise with genomic loci where R-loops form in unchallenged conditions, suggesting that R-loop accumulation caused by BRCA2 inactivation leads to DNA lesion which are repaired by MiDAS. RAD52 is required in this process, as its abrogation in BRCA2-deficient cells reduces the rate of MiDAS and causes DNA damage accumulation in G1. Furthermore, MiDAS sites triggered by BRCA2 inactivation are hotspots for genomic rearrangement in BRCA2-mutated breast tumours. These results indicate that BRCA2 acts in early S-phase to protect TRC- and R-loop-induced DNA lesions, thereby preventing them from becoming a source of genomic instability and tumorigenesis.

overall_design: MiDAS-seq in BRCA2-proificent and -deficient cells, and wt +aphidicolin treated cells, and H1299 Repli seq

first: Rebecca

last: Dagg


title: Chromatin-bound RB targets promoters, enhancers, and CTCF-bound loci.

city: Charlestown

first: Ioannis

last: Sanidas

department: Cancer Center

institute: Massachusetts General Hospital

summary: RB’s interaction with chromatin is key to understanding its molecular functions. Using a novel ChIP-sequencing protocol, we identify the precise chromatin loci bound by various forms of human RB. RB targets three fundamentally different types of loci (promoters, enhancers, CTCF-sites), that are largely distinguishable by the mutually exclusive presence of E2F1, c-JUN and CTCF. E2F/DP facilitates RB association with promoters, whereas AP-1 recruits RB to enhancers. RB’s association with promoters and enhancers fluctuates: G1-arrest enriched RB at promoters, while S-phase progression redistributed RB towards enhancers. RB binding to RB/CTCF sites was unaltered by cell cycle progression. RB-bound promoters include the classic E2F targets and are similar between cell types. However, RB-bound enhancers are associated with different gene categories, including, notably, MAPK signaling, and they vary between cell types. We propose that RB has a well-preserved role controlling E2F in G1, and cell type-specific effects at enhancers when cells enter S-phase.

overall_design: Analysis of the genomic distribution of human RB.  1. ChIP-seq data for RB wild-type, RB∆CDK and the 14 mono-phosphorylated forms of RB in human RPE1 epithelial cells.  2. ChIP-seq data for E2F1, H3K4me3, H3K4me1 and H3K27ac in RPE1 cells expressing RB wild-type or RB∆CDK.  3. ChIP-seq data for c-JUN and CTCF in RPE1 cells expressing shControl or shRB1.  4. ChIP-seq data for FLAG-RB in RPE1 cells expressing dominant-negative FOS (A-FOS) or dominant-negative DP1 (DNDP1) or GFP.  5. ChIP-seq data for E2F1 in RPE1 cells expressing DNDP1 or GFP.  6. ChIP-seq data for FLAG-RB in G1 accumulated RPE1 cells by contact inhibition for 6 days and S-phase accumulated RPE1 cells after release from contact inhibition for 24 hours.   7. ChIP-seq data for c-JUN and H3K4me1 in RB wild-type and RB knock-out RPE1 cells.   8. ChIP-seq data for wild-type RB and RB∆CDK in human BJ fibroblasts.  9. ChIP-seq data for RB in RPE1 wild-type and RPE1 RB1 knock-out cells.  10. ChIP-seq data for wild-type RB and RB∆CDK in MCF10A human breast epithelial cells.  11. ChIP-seq data for wild-type RB and RB∆CDK in T47D human breast cancer cell line.

first: Michael

last: Lawrence

first: Nicholas

last: Dyson


title: RNA-seq analysis of MCF-10A human mammary epithelial cells following MYC activation

first: Olga

last: Anczukow

address: 10 Discovery Drive

summary: We profiled gene expression and splicing changes in MCF-10A human mammary epithelial cells expressing MYC fused to a portion of estrogen receptor (MYC-ER) (Eilers et al., 1989; Littlewood et al., 1995).   We performed RNA-seq, in triplicate, on 3D-grown MCF-10A MYC-ER cells at 0, 8, and 24 hours (h) after 4-OHT-induced MYC activation.   As a control for 4-OHT-induced effects, 3D-grown parental MCF-10A cells lacking the MYC-ER fusion protein were treated with 4-OHT at the same timepoints.

overall_design: For 3D culture assays, MCF-10A and MCF-10A MYC-ER cells were seeded at a density of 10,000 cells per well in triplicate on a 4-well glass chamber slide coated with Matrigel Growth Factor Reduced (BD Biosciences) as described (Debnath et al., 2003; Liberzon et al., 2015). Media was replaced at 72h. Starting on day 3, cells were treated with 1μM 4-hydroxy tamoxifen (4-OHT) (Sigma) for 48h, 24h, 8h, or 0h, prior to collection. All samples were collected at the same time on day 5.  Cells were washed with PBS (1X) and the Matrigel was dissolved by incubating slides at 4°C in Cell Recovery Solution (BD Biosciences). Total RNA was extracted using the RNeasy kit (Qiagen) including DNase I treatment per manufacturer instructions.   Barcoded RNA libraries were prepared starting with 1ug for MCF-10A of total RNA using the TrueSeq stranded mRNA kit with polyA selection (Illumina), and quantified using a Bioanalyzer DNA 1000 chip (Agilent).   Libraries were sequenced as 150bp paired-end reads at 100-200 million reads per library on an Illumina HiSeq, equal amounts of 3 libraries were pooled per lane.

first: Laura

last: Urbanski

first: Mattia

last: Brugiolo

first: SungHee

last: Park

first: Brittany

last: Angarola

first: Nathan

middle: K

last: Leclair

last: Anczuków


title: scRNA-seq study of Eed-deleted cerebellar granule neuron progenitors (CGNPs)

status: Public on Jul 08 2022

city: Atanta

first: Tim

last: Gershon

state: GA

address: Emory University School of Medicine

department: Pediatrics

institute: Emory University

summary: We studied CGNPs with conditional deletion of Eed using scRNA-seq. Eed was deleted in CGNPs by crossing Math1-Cre mice with Eed floxed mice. scRNA-seq seq was performed by Drop-seq. The results may be compared to our prior published data on scRNA-seq in normal CGNPs (GEO accession number GSE129730)

overall_design: Cerebella  were dissociated from 3 replicate P7 mice of genotype Math1-Cre/Eed fl/fl. Each dissociated cerebellum was separately subjected to Drop-seq, as in or prior published work. For controls, we suggest comparing to the WT P7 cerebella subjected to Drop-seq and deposited in GEO accession number GSE129730.

first: Daniel

last: Malawsky

first: Abigail

last: Cleveland

first: Timothy


title: Bulk RNAseq of HUVECs

status: Public on Jul 30 2022

city: Guangzhou

first: lei

last: zeng

address: No. 74, Zhongshan 2nd Road, Yuexiu District

institute: SUN YAT-SEN UNIVERSITY

summary: Bulk RNAseq was performed using P4 human umbilical vein endothelial cells (HUVECs)

overall_design: Untreated cells were detached and lysed. Total RNAs were extracted and then subjected to RNAseq analysis

first: Feng

last: Zhang

first: Yangxin

last: Chen

first: Weibin

last: Zhou

first: Keli

last: Liu

first: Lei

last: Zeng


title: RNA sequencing of endoscopic biopsies from patients with esophageal adenocarcinoma

status: Public on Jul 05 2022

city: Amsterdam

first: Sanne

last: Hoefnagel

state: Noord-Holland

address: Meibergdreef 9

department: Gastroenterology

country: Netherlands

institute: Academic Medical Centre Amsterdam


title: The effect of extreme hyperglycemia on islet cell expression program

city: Jerusalem

first: Dana

last: Tzfati

address: Jerusalem

country: Israel

institute: hebrew university

summary: Our in vivo Insulin-rtTA;TET-DTA mouse model of severe hyperglycemia revealed that proloned exposure to very high glucose levels inhibits cell cycle entry and progression of pancreatic beta cells. To investigation of the molecular mechanisms responsible for this observation we   performed ex vivo experiment on wild-type ICR mouse islets mimiking the in vivo conditions and subjected them to RNAseq analysis.

overall_design: we incubated wild-type mouse islets for 3 days in basal glucose levels (11.8mM, 20mM (360mg/dl) or 35mM (630mg/dl) glucose, simulating normoglycemic, hyperglycemic and extreme hyperglycemic conditions respectively and subjected the islets and cells to RNAseq analysis

first: Judith

last: Furth-Lavi

last: Avrahami


title: Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers [Repli-seq]

status: Public on Jul 01 2022

city: Worcester

first: George

last: Spracklin

state: Massachusetts

address: 368 Plantation Street

department: Systems Biology

institute: University of Massachusetts Medical School

summary: Two dominant processes organizing chromosomes are loop extrusion and the compartmental segregation of active and inactive chromatin. The molecular players involved in loop extrusion during interphase, cohesin and CTCF, have been extensively studied and experimentally validated. However, neither the molecular determinants nor the functional roles of compartmentalization are well understood. Here, we distinguish three inactive chromatin states using contact frequency profiling, comprising two types of heterochromatin and a previously uncharacterized inactive state exhibiting a neutral interaction preference. We find that heterochromatin marked by long continuous stretches of H3K9me3, HP1α and HP1β correlates with a conserved signature of strong compartmentalization and is abundant in HCT116 colon cancer cells. We demonstrate that disruption of DNA methyltransferase activity dramatically remodels genome compartmentalization as a consequence of the loss of H3K9me3 and HP1 binding. Interestingly, H3K9me3-HP1α/β is replaced by the neutral inactive state and retains late replication timing. Furthermore, we show that H3K9me3-HP1α/β heterochromatin is permissive to loop extrusion by cohesin but refractory to CTCF, explaining a paucity of visible loop extrusion-associated patterns in Hi-C. Accordingly, CTCF loop extrusion barriers are reactivated upon loss of H3K9me3-HP1α/β, not as a result of canonical demethylation of the CTCF binding motif but due to an intrinsic resistance of H3K9me3-HP1α/β heterochromatin to CTCF binding. Together, our work reveals a dynamic structural and organizational diversity of the inactive portion of the genome and establishes new connections between the regulation of chromatin state and chromosome organization, including an interplay between DNA methylation, compartmentalization and loop extrusion.

overall_design: We compare genome structure and chromatin state genome-wide using Hi-C, ChIP-seq, Repli-seq, and Protect-seq in HCT116 colon cancer cells with its genetic derivative DKO cells which lack DNMT3B and DNMT1 activity and HCT116 cells treated with the DNA methylation inhibitor 5-Azacytidine (5Aza).

first: Nezar

last: Abdennur


title: Melanoma Brain Metastasis Atlas [single-cell/nuclei RNA-sequencing (sc/snRNA-seq)]

status: Public on Jul 06 2022

city: New York

first: Jana

last: Biermann

state: New York

address: 622 W168th Street

institute: Columbia University

summary: We performed single-cell/nuclei RNA-sequencing (sc/snRNA-seq) of 22 treatment-naïve melanoma brain metastases (MBM; 5 samples using scRNA-seq and 17 snRNA-seq) from 21 patients and 10 treatment-naïve extracranial (peripheral) metastases (MPM; all snRNA-seq) from 10 patients . In total, we recovered 145,555 cell transcriptomes in 32 samples including 73,369 cells from MBM and 72,186 from MPM.

overall_design:
Single-cell/nuclei RNA sequencing of 145,555 cells from 22 treatment-naïve melanoma brain metastses (MBM) and 10 treatment-naïve extracranial (peripheral) metastases (MPM).
>>>Submitter states: Due to patient privacy concerns the raw data will be submitted to dbGAP.<<<

first: Benjamin

last: Izar

first: Johannes

last: Melms


title: Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers.


title: TGS1 controls snRNA 3' end processing, prevents neurodegeneration and ameliorates SMN-dependent neurological phenotypes in vivo (Nanopore)

first: Grazia Daniela

last: Raffa

overall_design: Exploring transcriptome alterations induced by TGS1 and SMN deficiency in human cells using Oxford Nanopore Sequencing.

first: Lu

first: Caitlin

last: Roake

first: Paolo

last: Maccallini

first: Francesca

last: Bavasso

first: Roozbeh

last: Dehghannasiri

first: Pamela

last: Santonicola

first: Natalia

last: Mendoza-Ferreira

first: Livia

last: Scatolini

first: Ludovico

last: Rizzuti

first: Alessandro

last: Esposito

first: Ivan

last: Gallotta

first: Sofia

last: Francia

first: Stefano

last: Cacchione

first: Alessandra

last: Galati

first: Valeria

last: Palumbo

first: Gian

last: Tartaglia

first: Alessio

last: Colantoni

first: Gabriele

last: Proietti

first: Yunming

last: Wu

first: Matthias

last: Hammerschmidt

first: Cristiano

last: De Pittà

last: Sales

first: Julia

last: Salzman

first: Livio

last: Pellizzoni

first: Brunhilde

last: Wirth

first: Elia

last: Di Schiavi

first: Maurizio

last: Gatti

first: Steven

last: Artandi

first: Grazia


title: RNA-seq analysis of Metastatic and Localized human Pancreatic Neuroendocrine Tumors

status: Public on Jun 30 2022

first: Akanksha

last: Verma

address: 1300, York Avenue

department: Department of Physiology and Biophysics

institute: Weill Cornell Medical College

summary: We report the application of single-molecule-based sequencing technology for high-throughput profiling of RNAs in human pancreatic neuroendocrine tumor (PNET) tissues. We analyzed the transcriptome maps of primary tumor sites from patients that presented metastasis or not (localized). This analysis revelaed that the immune cell and pathway-related molecular signatures were enriched in metastatic compared to  localized tumors. Given the wide change of gene expression in metastatic PNETs, we analyzed the RNA-seq data using a L1000 drug-induced signature to identify pharmacologic agents that might preferentially target metastatic disease. In a separate study, we analyzed our RNA-seq data to understand the molecular basis of sexual dimorphisms in PNETs. We found that PNETs are associated with the emergence of unique sex-specific transcriptomic differences that are not observed in non-neoplastic  pancreatic islet tissues.

overall_design: A total of 22 PNET cases were sequenced with 7 from tumors associated with metastasis and 15 localized tumors.

first: Jessica

last: Limberg

first: Olivier

last: Elemento

first: Irene

last: Min

first: Nikolay

last: Ivanov


title: The IRE1α/XBP1 pathway expression is impaired in pediatric cholestatic liver disease explants

status: Public on Jun 23 2022

city: Chicago

first: Alyssa

last: Kriegermeier

state: IL

address: 225 E. Chicago

department: GI/Hepatology/Nutrition

institute: Ann and Robert H. Lurie Children's Hospital of Chicago

summary: Background/Aims: Cholestatic liver diseases (CLD) are the leading indication for pediatric liver transplantation. Increased intrahepatic bile acid concentrations cause endoplasmic reticulum (ER) stress and the unfolded protein response (UPR) is activated to maintain homeostasis. UPR dysregulation, including the inositol-requiring enzyme 1α/X-box protein 1 (IRE1α/XBP1) pathway, is associated with several adult liver diseases. We evaluated hepatic UPR expression in pediatric patients with end-stage CLD and hypothesize that an inability to appropriately activate the hepatic IRE1α/XBP1 pathway is associated with the pathogenesis of CLD.   Methods: We evaluated 34 human liver explants. Cohorts included: pediatric CLD (Alagille, ALGS, and progressive familial intrahepatic cholestasis, PFIC), pediatric non-cholestatic liver disease controls (autoimmune hepatitis, AIH), adult CLD, and normal controls. We performed RNA-seq, quantitative PCR, and western blotting to measure expression differences of the hepatic UPR and other signaling pathways.   Results: Metascape pathway analysis demonstrated that the KEGG ‘protein processing in ER’ pathway was downregulated in pediatric CLD compared to normal controls. Pediatric CLD had decreased hepatic IRE1α/XBP1 pathway gene expression and decreased protein expression of p-IRE1α compared to normal controls. These CLD changes were not disease-specific to ALGS or PFIC. IRE1α/XBP1 pathway gene expression was decreased in pediatric CLD compared to AIH disease controls.   Conclusion: Pediatric CLD explants have decreased gene and protein expression of the protective IRE1α/XBP1 pathway and down-regulated KEGG protein processing in the ER pathways. IRE1α/XBP1 pathway expression differences occur when compared to both normal and non-cholestatic disease controls. Attenuated expression of the IRE1α/XBP1 pathway is associated with cholestatic diseases and could be targeted to treat pediatric CLD.

overall_design: Samples are human explanted livers: 9 pediatric (<18 years of age) normal livers, 10 pediatric cholestatic liver disease (CLD) livers (5 with Alagille syndrome, 5 with progressive familial intrahepatic cholestasis), 5 pediatric autoimmune hepatitis livers, 3 adult cholestatic liver disease livers (1 with primary sclerosing cholangitis and 2 with primary biliary cholangitis), and 7 adult (>18 years of age) normal  livers

first: Angela

last: Hyon

first: Brian

last: LeCuyer

first: Susan

last: Hubchak

first: Xiaoying

last: Liu

first: Richard

last: Green


title: Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers [ChIP-seq]

first: George

last: Spracklin

first: Nezar

last: Abdennur


title: Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification. [RNA-Seq]

status: Public on Jun 22 2022

city: Knoxville

first: Rachel

middle: Patton

last: McCord

state: Tennessee

address: 1311 Cumberland Avenue

department: Department of Biochemistry & Cellular and Molecular Biology

institute: University of Tennessee Knoxville

summary:
Purpose: A systematic analysis of the transcriptomic profile of HGPS patient-derived fibroblasts, stratifying the analysis by comparing defined age groups to  matched controls
Methods: Total mRNA, acquired from Coriell Institute for Medical Research was submitted for RNA-seq library preparation and sequencing at Genewiz.  Libraries were prepared using Illumina, RNA with PolyA selection approach, and then sequenced on a HiSeq instrument using 2x150 bp sequencing.
Results: We observe that these fibroblasts carry abnormal transcriptional signatures, centering around five main functional hubs: DNA maintenance and epigenetics, bone development and homeostasis, blood vessel maturation and development, fat deposition and lipid management, and processes related to muscle growth. Stratification of patients by age revealed that a cohort of genes related to endochondral ossification and chondrogenic commitment show altered expression patterns in children aged four to seven years old, where this differentiation program starts in earnest, related to the growth of long bones.  We further report changes in lamin associated domains and 3D genome organization around a cohort of genes of interest, identified in this study.

overall_design: Purified mRNA from skin fibroblasts derived from HGPS patients was acquired from Coriell Insitute, at the earliest passage number available, prepared, and sequenced with PolyA selection and 2x150 bp reads.

first: Rebeca

last: San Martin

first: Priyojit

last: Das

first: Jacob

last: Sanders

first: Ashtyn

last: Hill


title: Epigenomic and transcriptomic profiles a of prostate cancer cell line with and without androgen stimulation

status: Public on Jun 14 2022

city: Brookline

first: Sylvan

last: Baca

address: 450 Brookline Ave

institute: Dana–Farber Cancer Institute, Dana-704

summary: We performed H3K27ac ChIP-seq, ATAC-seq, and RNA-seq in LNCaP with and without androgen stimulation

first: M

last: Freedman


title: RNA-seq analysis of human TNBC cells overexpressing three splicing factor genes (SRSF2-SRSF3-SRSF7) or MYC

first: Olga

last: Anczukow

summary: We profiled gene expression and splicing changes in HCC1806 human TNBC cells overexpressing three splicing factor genes (SRSF2-SRSF3-SRSF7), all three splicing factors (called 3xSR) or MYC.   We performed RNA-seq, in triplicate on 3xSR, MYC-OE, triple plasmid control, SRFS2, SRSF3, SRSF7, or single plasmid control HCC1806 cells.

overall_design: 2D-grown HCC1806 cells were harvested by scraping adherent cells in PBS once ~90% confluence was reached.  Total RNA was extracted using the RNeasy kit (Qiagen) including DNase I treatment per manufacturer instructions.  Barcoded RNA libraries were prepared starting with 500ng of total RNA using the TrueSeq stranded mRNA kit with polyA selection (Illumina), and quantified using a Bioanalyzer DNA 1000 chip (Agilent).   Libraries were sequenced as 150bp paired-end reads at 100-200 million reads per library on an Illumina NovaSeq, equal amounts of 18 libraries were pooled per lane.

first: Laura

last: Urbanski

first: Mattia

last: Brugiolo

first: SungHee

last: Park

first: Brittany

last: Angarola

first: Nathan

last: Leclair

first: Marina

last: Yurieva

first: Phil

last: Palmer

first: Sangram

last: Sahu

last: Anczuków


title: Transcriptomic analysis of homoserine-evolved MG1655 strain (wild type) and of homoserine -treated wild type, mutant deleted for thrL and mutant bearing thrL* allele

status: Public on Jun 18 2022

city: Toulouse

first: JEAN MARIE

last: FRANCOIS

address: 135 avenue de Rangueil

country: France

institute: Toulouse Biotechnology Institute

summary: The growth of E. coli is inhibited by millimolar concentrations of L-homoserine, which may be problematic for the industrial production of this compound or for products derived from it. In this work, an adapted laboratory evolution (ALE) was applied, which resulted in the isolation of an E. coli strain at least 10-fold more tolerant to L-homoserine than the original (MG1655) strain. Only four genomic modifications were identified after genome sequencing of this evolved strain (designed 4E), including a 49 bp truncation starting from the codon stop of thrL and leading to a modified thrL locus carrying a thrL* allele encoding a 30 amino acids polypeptide, which is 9 amino acids more than the leader peptide encoded by thrL. Replacement of thrL with thrL* enabled the initial strain to be as or slightly more tolerant to L-homoserine than the evolved 4E strain, which is explained by the rapid metabolization of L-homoserine to threonine resulting from ThrL*-dependent transcriptional activation of the threonine thrABC operon. Interestingly, in 4E strain, L-homoserine degradation went beyond threonine degradation, as tdh and kbl encoding threonine degradation pathway II and genes of the glycine cleavage system were strongly upregulated. To infer about the toxicity of L-homoserine, a transcriptomic analysis of wild-type MG1655 in the presence of 10 mM L-homoserine was performed, which identified a potent repression of locomotion-motility-chemotaxis process. Since the magnitude of this repression was reduced in a ΔthrL mutant concomitantly with a twofold lower sensitivity of this mutant to L-homoserine, one could argue that the repression of this biological process contributed to growth inhibition by L-homoserine. Furthermore, in both wild type and thrl mutant, a strong repression of the branched-chain amino acids synthesis and transport, as well as activation of the sulphate assimilation pathway process to cysteine synthesis were observed in the presence of L-homoserine, which may also contribute to toxic effect of this compound. How this non-canonical amino acid triggers these transcriptomic changes is discussed.

platform_organism: Escherichia coli str. K-12 substr. MG1655

overall_design: Transcriptomic analysis implicated 4 strains, namely MG1655 (WT), strain deleted of thrl (Dthrl), strain bearing thrL* allele (thrL*) and strain obtained after adapted laboratory evolution on homoserine (4E). Agilent microarray platfprm GPL13359 was used for microarray analysis . The four strains were inoculated at 0D600 of 0.2 in M9 minimal medium containing 10 g/L glucose in the absence or presence of 10 mM L-homoserine. When cultures reached OD600 of around 1.0, samples were taken for RNA was extraction. Notice that strain 4E is referred in the transcriptomic samples as E4

first: Ceren

last: Alkim

first: Daniela

last: Farias

first: Julie

last: Fredonnet

first: Helene

last: Serrano-Bataille

first: Pauline

last: Herviou

first: Marc

last: Picot

first: Nawel

last: Slama

first: Sebastien

last: Dejean

first: Nicolas

last: Morin

first: Brice

last: Enljalbert

first: Jean

last: Francois


title: Transcriptomic profiling of lung adenocarcinoma associated alleles in A549s

status: Public on Jul 10 2022

city: Seattle

first: Alice

last: Berger

state: Washington

address: 1100 Fairview Ave N, Mailstop C2-023

department: Human Biology

institute: Fred Hutchinson Cancer Research Center

summary: Based on the previous eVIP study (Cancer Cell, 2016), we profiled the transcriptomes of lung adenocarcinoma cell lines expressing oncogenes to compare methods and investigate the effects of these oncogenes on the cells' whole transcriptomes, differential expression, and alternative splicing

overall_design: mRNA profiles

first: April

last: Lo


title: Transcriptomic analysis of myogenesis in human myoblasts

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: The goals of this study are to compare differentially expressed RNAs during human myogenesis and further investigate functional regulatory network of those RNAs in myogenesis in vitro and in vivo.

overall_design: Examination of proliferating and differentiated human myoblasts

first: Jen-Hao

last: Yang

first: Myriam

last: Gorospe


title: Gene expression by BTF3 knocked down in MDA-MB-231 cells

city: Jinan

first: Jing

last: Hu

address: Wenhua xi road

department: Department of Pathology

institute: Shandong University

summary: The aim of this research was to confirm the regulatory effect of BTF3 on gene expression in the development of TNBC.

overall_design: In this research, there were two samples examed including sample of negtive control cells (231-NC) and sample of BTF3 knocked down cells (231-siBTF3).

first: Bo

last: Han


title: Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers [Protect-seq]

first: George

last: Spracklin

first: Nezar

last: Abdennur


title: LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis

status: Public on Jun 13 2022

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

overall_design: Refer to individual Series


title: Heterochromatin diversity modulates genome compartmentalization and loop extrusion barriers [HiC]


title: Single cell profiling of γδ hepatosplenic T-cell lymphoma unravels tumor cell heterogeneity associated with disease progression

city: Beijing

first: Ruoyu

last: Zhang

address: Life Science Park building 1 B220

institute: Innovec Biotherapeutics

summary: Hepatosplenic T-cell lymphoma (HSTCL) is a rare but very aggressive lymphoma mostly derived from γδ T cells. The molecular pathogenesis driving HSTCL is largely unknown while only limited treatment options are available with poor outcomes. In this study, we performed paired single cell RNA-seq and T cell receptor (TCR) sequencing on biopsies collected from a HSTCL patient pre- and post- chemotherapy treatments. We characterized unique gene expressing signatures of malignant γδ T cells with a set of marker genes were newly identified in HSTCL (AREG, PLEKHA5, VCAM1 etc.). Although the malignant cells were expanded from a single TCR clonotype according to their TCR sequences, they evolved into two transcriptional distinct tumor subtypes during the disease progression. The Tumor_1 subtype was dominant in pre-treatment samples with highly aggressive phenotypes. The Tumor_2 had relative mild cancer hallmark signatures but expressed genes associated with survival and drug resistance (IL32, TOX2, AIF1, AKAP12 etc.), and finally became the major tumor subtype post-treatment. We further dissected the tumor microenvironment of the HSTCL and found CD8 memory T cells were clonal expanded post-treatment. In addition, we discovered dynamically rewiring cell-cell interaction networks during the treatment. The tumor cells had reduced interactions with the microenvironment post-treatment. Our study reveals heterogenous and dynamic tumor and microenvironment underlying pathogenesis of HSTCL and may contribute to identify novel targets for diagnosis and cure of HSTCL in the future.

overall_design: Bone marrow and PBMC biopsies were collected from a HSTCL patient pre- and post- chemotherapies. Samples were proceed for single cell RNA-seq and T cell receptor sequencing

first: Wei

last: Song

first: Keqian

last: Shi

first: Haixi


title: Loss of the long non-coding RNA, Malat1, accelerates premature aging and mortality

status: Public on Jul 02 2022

city: Mölndal

first: Ramy

last: Elgendy

state: Göteborg

address: Pepparedsleden 1

institute: AstraZeneca

summary: Here we show that the 5’ end and 3’ end of Malat1 are dependently and independently expressed. Loss of 5’ Malat1 up-regulates Neat1 in cis, while loss of 3’ Malat1 globally regulated gene expression in trans. Furthermore, loss of 3’ Malat1 accelerates premature aging and shortens the lifespan in mice, but loss of 5’ Malat1 produces no phenotypic changes. Mechanistically, 3’ Malat1 exerts a tight regulation of P21 that is drastically up-regulated in brain and retina upon its deletion in mice. This is very likely mediated at two different levels. One is at the mRNA level since Malat1 interacts with hnRNP A1 and hnRNP A2/B1. This is independently of P53 since it is significantly decreased upon 3’ Malat1 KO, probably due to the down-regulation of hnRNP C which has been shown to maintain P53 mRNA stability in our cell line model. The other is at the protein level through NPM, which is significantly up-regulated in 3’ Malat1 KO and which was known to decrease P21 ubiquitination and hence stabilizing of P21. These observations reveal previously unknown functions of 3’ Malat in the brain and indicates the need for more detailed understanding of highly abundant conserved lncRNAs, such as Malat1, and alarms for detailed understanding before therapeutic targeting in the future.

overall_design: Comparison of 5' and 3' knockout of the lncRNA Malat1 in a mouse model.

first: Amr

last: Ghanam

first: Xiaoyuan


title: miRNAs expression of Gleason 3+4 Prostate Cancer

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

summary: The aim of this research was to identification of miRNAs that is associated with bone metastasis of gleason 3+4 prostate cancer.

overall_design: miRNA expression profiling  was performed on prostate cancer with bone metastasis (n=4) and prostate cancer with good prognosis (n=4). All sample was Gleason 3+4 prostate cancer.

first: Hongwei

last: Guo


title: The Heterogeneous Nuclear Ribonucleoprotein U (HNRNPU) is the Safeguard of Neural Stem Cell Viability

status: Public on Jun 07 2022

city: Rehovot

first: Tsviya

last: Olender

address: 234 Herzl St.

department: Molecular Genetics

institute: The Weizmann Institute

summary:
To study Hnrnpu function during cortical development we preformed single-cell RNA sequencing (scRNA-seq) on mouse neutrosphere cultures derived from E13 ICR cortices, 24 hours following treatment with CRISPR/CAS9 and two sgRNA sequences targeting mouse Hnrnpu.
In parallel, we analyzed bulk RNA-seq from dissected cortices of E13 embryos in which Hnrnpu conditional truncation in the telencephalon was driven by Emx1::Cre.
Additionally, we analyzed MARS-Seq trancriptomal profiles of cortices of E13 embryos carrying homozygous heterozygous or wildtype alleles of Hnrnpu truncation (Emx1::Cre driver) in combination with homozygous or heterozygous conditional deletion of Tp53

overall_design:
For scRNA seq, neurospheres were prepared from E13 ICR cortices, cultured for two days in the presence of EGF (20ng/ml), and bFGF (20ng/ml). Neurospheres were dissociated using Accutase and electroporated with a DNA mixture containing 4ug of pX330 CRISPR/CAS9 Hnrnpu Guide A,  4ug of pX330 CRISPR/CAS9 Guide B,  and , 1ug of pCAG::GFP. Cells were collected 24 hours post electroporation, dissociated using Accutase and passed through a 40 micron strainer. The 10x Genomics© Chromium system was used to capture 5000 single cells. The sequencing library was generated using the 10x Genomics© Single Cell 3′ Solution kit and subjected to Illumina NextSeq 550.
For Bulk RNA seq and MARS seq, embryos (E13) were collected, their cortices were dissected in cold PBS, flush frozen in liquid nitrogen and kept in -80°C. RNA of desired genotypes was prepared using RNeasy Mini kit, Quiagen.

first: Tamar

last: Sapir

first: Aditya

last: Kshirsaga

first: Anna

last: Gorelik

first: Ingrid

last: Scheffer

first: David

middle: B

last: Goldstein

first: Orrin

last: Devinsky

first: Orly

last: Reiner


title: Foxa2 overexpression is sufficient to establish the p3 neural progenitor chromatin landscape

status: Public on Jun 06 2022

city: London

first: M Joaquina

last: Delas

address: 1 Midland Road

department: Briscoe Lab

institute: The Francis Crick Institute

summary: In many developing tissues the spatial and temporal pattern of gene expression is organised by secreted signals functioning in a graded manner over multiple cell diameters. Cis Regulatory Elements (CREs) interpret these graded inputs to control gene expression. How this is accomplished remains poorly understood. The morphogen Sonic hedgehog (Shh) acts in a graded manner to direct neural progenitor specification in the neural tube. Here, we uncover two distinct ways in which CREs translate graded Shh signaling into differential gene expression. A common set of CREs are used to control gene activity in the majority of ventral neural progenitors. These CREs integrate cell type specific inputs to control gene expression. By contrast, the most ventral progenitors use a unique set of CREs. These are established by the pioneer factor FOXA2, paralleling the role of FOXA2 in endoderm. Moreover, FOXA2 binds a subset of the same sites in neural and endoderm cells. Together the data identify distinct cis regulatory strategies for the interpretation of morphogen signaling and raise the possibility of an evolutionarily conserved role for Foxa2-mediated cell specification across tissues.

overall_design: ATAC-seq was performed after overexpression of control of Foxa2 constructs under 0 nM SAG conditions. Biological triplicates (independent differentiations)

first: M

middle: J

first: James

last: Briscoe


title: Regulatory strategies in mouse ventral neural tube progenitors


title: Cell type specific RNAseq from crosslinked and and TF-Sorted ventral neural tube cell types

overall_design: RNAseq timecourse of a cellular model of spinal cord differentiation covering specification of four neural progenitor cell types. Biological triplicates (independent differentiations)


title: Effect of diptoindonesin G on T47D cells overexpressing the Y537S ER mutation

status: Public on Jun 11 2022

city: Madison

first: Kristine

last: Donahue

state: WI

address: 1111 Highland Ave.

institute: University of Wisconsin

summary: To investigate the effect of diptoindonesin G on breast cancer cells expressing the estrogen receptor Y537S ligand binding domain mutation, we treated T47D cells overexpressing the ER Y537S mutation and treated them with vehicle or diptoindonesin G and performed differential gene expression analysis and gene set enrichment analysis

overall_design: Gene expression profiling, differential gene expression analysis, and gene set enrichment analysis for T47D cells treated with DMSO or diptoindonesin G

first: Yidan

last: Wang


title: Principles of gene regulation quantitatively connect DNA to RNA and proteins in bacteria

city: La Jolla

first: Igor

last: Segota

address: 9500 Gilman Drive

institute: University of California, San Diego

summary: To understand the contribution of mRNA synthesis and degradation rates towards setting protein concentrations, we performed RNA-sequencing based measurements of mRNA abundance and degradation to facilitate comparisons with recently collected proteomic datasets (Mori 2021) in the same E. coli strain.

overall_design: For mRNA abundance determination, we grew E. coli exponentially in several different growth media and extracted total RNA. To determine mRNA degradation rates, Rifampicin was added to inhibit transcription initiation in exponentially growing E. coli and RNA was extracted from different samples over the next 11 minutes for sequencing.

first: Rohan

last: Balakrishnan

first: Matteo

last: Mori

first: Terence

last: Hwa


title: spKAS-seq reveals R-loop dynamics using low-input materials by detecting single-stranded DNA with strand specificity

first: Ruitu

last: Lyu

address: 929 E 57th Street

department: Chemistry

institute: The University of Chicago

summary: R-loops impact transcription and genome stability and are related to human diseases. Genome-wide R-loop mapping typically uses the S9.6 antibody or inactive RNase H, both requiring a large number of cells with varying results observed depending on the approach applied. Here, we present strand-specific KAS-seq (spKAS-seq) to map R-loops by taking advantage of the presence of a single-stranded DNA (ssDNA) in the triplex structure. We show that spKAS-seq detects R-loops and their dynamics at coding sequences, enhancers, and other intergenic regions with as few as 50,000 cells and eliminates potential bias towards open chromatin and RNase H-sensitive regions. A joint analysis of R-loops and chromatin-bound RNA-binding proteins (RBPs) suggested that R-loops can be RBP-binding hotspots on the chromatin.

overall_design: Identification of genome-wide R-loops using strand-specific KAS-seq in HEK293, HepG2 and K562 cells.

first: Tong

last: Wu

first: Chuan

last: He


title: Restoring a homeostatic microglia state by combination antiretroviral therapy in SIV-infected rhesus macaques

city: OMAHA

first: Meng

last: Niu

state: NE

address: 42nd and Emile

department: Department of Neurological sciences

institute: University of Nebraska Medical Center

summary: Although modern therapies like cART have transformed HIV from a lethal disease to a manageable condition, associated neurocognitive consequences remain a concern. Paradoxically, microglia and macrophages, which comprise the innate defense system in the brain and are crucial for CNS homeostasis, are targets for HIV and key players in its neuropathogenesis. In addition, these infected cells can serve as viral reservoirs even in effectively treated infection. Here using an scRNA-seq approach in the SIV-NHP model, we demonstrate differential transcriptional programs in brain myeloid cells from monkeys under four conditions: uninfected, chronically SIV-infected, chronically SIV-infected treated with combination antiretroviral therapy (cART), and SIVE. Our study reveals alterations in composition (both lineage and gene expression profiles) of the cell populations between groups. Importantly, treatment with cART largely restored the homeostatic microglia profile present in uninfected animals that was disrupted in SIV-infected untreated animals

overall_design: Microglia/Macrophages were isolated and cryopreserved from the rhesus monkey brains of 3 saline-treated (control), 3 saline-treated SIV-infected, 3 saline-treated SIV-infected treated with cART and 1 saline-treated SIV-infected with encephalitis. They were subsequently thawed and immunomagnetically enriched for CD11b+ cells, and further purified by flow cytometry, sorted for CD11b positive, live events, and processed for scRNA by the 10xGenomics platform.

first: Howard

last: Fox

first: Andrew

last: Trease

first: Brenda

middle: M

last: Morsey


title: PI3K-mediated crosstalk between angiopoietin and vascular endothelial growth factor C signaling pathways is required for lymphangiogenesis

status: Public on Jun 29 2022

city: Helsinki

first: Sawan

middle: KUMAR

last: Jha

state: Haartmaninkatu 8

address: Haartm

department: Research Program Unit

country: Finland

institute: University of Helsinki

summary: The aim of the study was to invetigate the crosstalk between VEGF-C/VEGFR3 and Ang2/Tie pathway

overall_design: ScRNA sequence analysis contains two experiments.In first experiment, lymphatic endothelial cells from Tie1 and Tie1;Tie2 deleted lymphatic endothelial cell. The control for deletion experiments were Tamoxifen treated littermate controls, and the deleted sample had Prox1-CreERT2.

first: Emilia

middle: A

last: Korhonen

first: Kari

last: Alitalo

first: Aino

last: Murtomaki

first: Taija

last: Mäkinen

first: Simon

last: Stritt


title: Modulation of behavioral and hippocampal transcriptomic responses in rat prolonged chronic unpredictable stress model by fluoxetine, eicosapentaenoic acid and lipopolysaccharide

city: St Petersburg

first: Konstantin

middle: Andreevich

last: Demin

address: University Embankment, 7/9

country: Russia

institute: Saint Petersburg State University

summary: Here, we examine behavioral and brain transcriptomic (RNA-seq) responses in rat prolonged chronic unpredictable stress (PCUS) model, and their modulation by 4-week treatment with fluoxetine, eicosapentaenoic acid (EPA), lipopolysaccharide (LPS) and their combinations.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for hippocampus of wistar male rats (n=3) subjected to 12 weeks of chronic unpredictable stress (CUS; 1) or rats also subjected to fluoxetine (2), lipopolysacharide (3), eicosapentaenoic acid (4), fluoxetine + eicosapentaenoic acid (5), and fluoxetine + lipopolysacharide (6) for last 4 weeks of CUS or experimentally naive rats (7).

first: Tatiana

middle: O

last: Kolesnikova

first: David

middle: S

last: Galstyan

first: Nataliya

last: Krotova

first: Nikita

middle: P

last: Ilyin

first: Ksenia

last: Derzhavina

first: Maria

last: Seredinskaya

first: Yuriy

last: Kositsyn

first: Dmitry

last: Sorokin

last: Nerush

first: Abubakar-Askhab

last: Khaybaev

first: Sofia

last: Pushkareva

first: Tatyana

last: Strekalova

first: Alexey

last: Masharsky

first: Allan

last: Kalueff


title: Cell type specific ATACseq (Crosslinked and TF-Sorted ATAC-seq (CaTS-ATAC)) reveals two distinct cis regulatory strategies for Shh interpretation in the mouse ventral neural tube

first: M Joaquina

last: Delas

overall_design: CaTS-ATAC timecourse of a cellular model of spinal cord differentiation covering specification of four neural progenitor cell types. Biological triplicates (independent differentiations)

first: M

first: James

last: Briscoe


title: Comparison of dual sgRNA library versus Dolcetto by Perturb-seq

status: Public on Jun 04 2022

city: Cambridge

first: Joseph

last: Replogle

state: Massachussetts

address: 455 Main St

institute: UCSF / Whitehead Institute / MIT

summary: CRISPR interference (CRISPRi) genetic screens use programmable repression of gene expression to systematically explore questions in cell biology and genetics. However, wider adoption of CRISPRi screening has been constrained by the large size of single guide RNA (sgRNA) libraries and lack of consensus on the choice of CRISPRi effector proteins. Here, we address these challenges to present next-generation CRISPRi sgRNA libraries and effectors. First, we combine empiric sgRNA selection with a dual sgRNA library design to generate an ultra-compact, highly active CRISPRi sgRNA library. Next, we rigorously compare CRISPRi effectors to show that the recently published Zim3-dCas9 provides an optimal balance between strong on-target knockdown and minimal nonspecific effects on cell growth or the transcriptome. Finally, we engineer a suite of cell lines which stably express Zim3-dCas9 and demonstrate robust on-target knockdown across these cell lines. Our results and publicly available reagents establish best practices for CRISPRi genetic screening.

overall_design: Comparative on-target gene knockdown using scRNA-seq data for K562 cells expressing dCas9-KRAB. Cells were transduced with a dual sgRNA library or Dolcetto library targeting 132 genes and profiled on day 7 post-transduction.

first: Angela

last: Pogson

first: Jonathan

last: Weissman

first: Marco

last: Jost


title: Single cell transcriptome analysis of non-neuronal cell populations in mouse brain cortex

status: Public on Jun 24 2022

city: Muenster

first: Hyun-Woo

last: Jeong

state: NRW

department: Dept. Tissue Morphogenesis

institute: Max-Planck-Institute for Molecular Biomedicine

summary: Single cell RNA-Seq analysis for myelin-depleted brain cortex cell populations of juvenile, adult, aged and Experimental Autoimmune Encephalomyelitis (EAE) mice

overall_design: Myelin-depleted mouse brain cortex samples were analyzed for single cell RNA-Seq using 10X Genomics Chromium droplet based system

first: Ralf

last: Adams


title: LncRNA OIP5-AS1-directed miR-7 degradation promotes MYMX production during human myogenesis

first: Supriyo

last: De

summary: The goals of this study are to compare differentially expressed RNAs during  OIP5-AS1:MIR-7 TSB treated myoblasts  and control myoblasts during myogenesis and further investigate functional regulatory network of those RNAs in myogenesis in vitro and in vivo.

overall_design: Examination OIP5-AS1:MIR-7 TSB affect the myogenesis

first: Jen-Hao

last: Yang

first: Ming-Wen

last: Chang

first: Dimitrios

last: Tsitsipatis

first: Xiaoling

first: Jennifer

middle: L

last: Martindale

first: Rachel

last: Munk

first: Aiwu

last: Cheng

first: Elizabeth

last: Izydore

first: Poonam

last: Pandey

first: Yulan

last: Piao

first: Krystyna

last: Mazan-Mamczarz

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: Bulk RNA sequencing in SARS-CoV-2-infected hamsters

status: Public on May 26 2022

city: Seoul

first: Hyun Jik

last: Kim

address: 101 Daehak-ro, Jongno-gu

department: Department of otorhinolaryngology

institute: Seoul National University

summary: We report the application of bulk RNA sequencing technology for high-throughput profiling of SARS-CoV-2 infection in the lung of Syrian golden hamsters (Mesocricetus auratus).

overall_design: Examination of SARS-CoV-2-induced RNA expression in the lung of Syrian golden hamsters.

first: Hyun

first: Haeun

last: Shin


title: NECTIN1 controls an IGF1-dependent adhesion switch in melanoma spreading

city: Boston

first: Leonard

last: Zon

state: MA

address: 1 Blackfan Circle

department: Oncology/Hematology

institute: Boston Children's Hospital

summary: Defects in cell-cell contacts have been proposed to participate in early steps of tumor metastasis1 but little is known about the signals from the cancer cell niche that influence this process. Here, we show that the lack of adherens junctions caused by genetic loss of the adhesion molecule NECTIN1 in melanoma promotes tumor dissemination specifically under growth factor deprivation. We found that NECTIN1 was deleted in 53% of human melanomas and that its loss was enriched in metastases. NECTIN1 inactivation in zebrafish melanomas stimulated cancer cell spreading in vivo, while in human cell lines, it increased cell migration specifically in response to serum starvation. We further identified IGF1 as the serum component responsible for this effect. Serum withdrawal or IGF1 inhibition induced formation of strong adherens junctions between NECTIN1-wild-type melanoma cells. In contrast, NECTIN1-deficient cells were unable to establish adherens junctions and instead activated integrin-mediated motility through a FAK/SRC axis. During melanoma dissemination, NECTIN1 loss thus causes a cellular phenotypic switch from cell-cell adhesion to cell-matrix adhesion triggered by IGF1 signaling. Our study uncovers a mechanism by which cancer cells integrate information from the tumor microenvironment and cell-cell contacts to regulate their migratory behavior during spreading.

overall_design: In order to identify secreted factors that may be responsible for the formation of adherens junctions between melanoma cells upon serum depletion, we examined the transcriptional response of human melanoma cells to serum withdrawal by RNA-sequencing. We analyzed gene expression in 4 lines derived from the A375 human melanoma cell line by single-cell cloning and cultured in DMEM in the presence or absence of 10% FBS for 12 hours.

first: Julien

last: Ablain

first: Song


title: Frequent loss of adhesion gene NECTIN1 triggers melanoma dissemination upon local IGF1 depletion [RNA-Seq]

summary: Defects in cell-cell contacts participate in early steps of tumor metastasis, but the mechanism regulating the staying-at-home or leaving decision has not been molecularly defined. We found the adherens junction gene NECTIN1 deleted in 55% of human melanomas. Inactivation of NECTIN1 stimulated cancer cell spreading in zebrafish melanomas in vivo, and increased cell migration in human cell lines specifically in response to decreased IGF1 signaling. IGF1 inhibition induced robust formation of adherens junctions between NECTIN1-wildtype melanoma cells, while NECTIN1-deficient cells were unable to establish these junctions and instead activated integrin/FAK-mediated motility. In 20 human melanoma biopsies, adherens junctions were seen exclusively in areas with low IGF1 levels, but not in NECTIN1-deficient tumors. Our study uncovers a mechanism by which the status of cell-cell contacts modulates the cellular response to microenvironmental signals, effecting a decision switch between leaving and staying in the cancer cell niche.

overall_design: In order to define the cell state associated with the loss of NECTIN1 under conditions of serum depletion, we examined the transcriptional profiles of A375 human melanoma cells wildtype or knockout for NECTIN1 in response to serum withdrawal by RNA-sequencing. We analyzed gene expression in 4 NECTIN1-wildtype and 4 NECTIN1-knockout lines derived from the A375 human melanoma cell line by single-cell cloning and cultured in DMEM in the absence of 10% FBS for 12 hours.


title: Transcriptional profiles of neural crest-derived progenitor cells from the small bowel and subcutaneous adipose tissue

status: Public on May 31 2022

first: Rhian

last: Stavely

address: 185 Cambridge Street, CPZN, 6100

department: Pediatric Surgery

institute: Massachusetts General Hospital

summary: Neural stem cells (NSCs) are most commonly sourced from neural tissue such as the central nervous system or the enteric nervous system (ENS) of the gut. Emerging evidence has shown that adipose tissue contains its own complex nervous system consisting of sympathetic and sensory innervation. The entirety of the peripheral nervous system is the progeny of Wnt1-expressing cells of the embryonic neural crest. This includes the ENS, autonomic neurons, and Schwann cell precursors that provide peripheral glial cells. Counterintuitive to their name, however, embryonic Schwann cell precursors represent multipotent stem cells that migrate along embryonic nerve fibers and contribute to glial and non-glial cell populations, including melanocytes, neuroendocrine chromaffin cells, enteric neurons, sympathetic neurons and mesenchymal stem cells from the bone marrow, depending on local environmental cues. However, no equivalent progenitors are known to exist postnatally in the nerve fiber niche. Schwann cells have been demonstrated to give rise to enteric neurons postnatally, suggesting they retain neuronal progenitor properties and offer a potential source of NSCs for regenerative therapies. In this study, we compare the transcriptomic properties of neural crest-derived NSCs from the intestine (enteric neural progenitors) and the nerve fibers of the subcutaneous adipose tissue and evaluate the effects of different methods of NSC culture and isolation.

overall_design: Examination of mRNA profiles in neural crest cells isolated from the intestine and adipose tissue

first: Ryo

last: Hotta

first: Nicole

last: Picard

first: Ahmed

last: Rahman

first: Weikang

last: Pan

first: Sukhada

last: Bhave

first: Meredith

last: Omer

first: Wing-Lam

middle: N

last: Ho

first: Richard

last: Guyer

first: Allan

last: Goldstein


title: Comparison of non-specific transcriptional effects of CRISPRi effector proteins by RNA-seq

status: Public on Jun 03 2022

first: Joseph

last: Replogle

overall_design: Comparative gene expression profiling analysis of RNA-seq data for K562 cells transduced to express dCas9-KOX1, Zim3-dCas9, SID-dCas9-Kox1, dCas9-Kox1-MeCP2, or an empty vector in triplicate.

first: Jessica

last: Bonnar

first: Jonathan

last: Weissman

first: Marco

last: Jost


title: INRI-seq enables global cell-free analysis of translation initiation and off-target effects of antisense inhibitors

status: Public on May 23 2022

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

institute: University of Würzburg

summary: Ribosome profiling (Ribo-seq) is a powerful method for the transcriptome-wide assessment of protein synthesis rates and the study of translational control mechanisms. Yet, Ribo-seq also has limitations. These include difficulties with detection of low abundance transcripts and analysis of translation-modulating molecules such as antibiotics, which are often toxic or challenging to deliver into living cells. Here, we have developed in vitro Ribo-seq (INRI-seq), a cell-free method to analyze the translational landscape of a fully customizable synthetic transcriptome. Using Escherichia coli as an example, we show how INRI-seq can be used to analyze the translation initiation sites of a transcriptome of interest. We also study the global impact of direct translation inhibition by antisense peptide nucleic acid (PNA) to analyze PNA off-target effects. Overall, INRI-seq presents a scalable, sensitive method to study translation initiation in a transcriptome-wide manner without the potentially confounding effects of extracting ribosomes from living cells.

overall_design: Examination of control and PNA-treated samples of different concentrations before applying INRI-Seq

first: Jens

last: Hör

first: Svetlana

last: Ðurica-Mitić

first: Lars

last: Barquist

first: Jörg

last: Vogel


title: Divergent BRAF Inhibitor Resistance Mechanisms Revealed through Epigenetic Mapping

status: Public on May 25 2022

first: Hensin

last: Tsao

address: 50 Blossom St

summary: In this report, we generated eight matched pairs of vemurafenib sensitive/resistant melanoma lines and subjected these to concurrent RNA-seq and H3K27Ac ChIP-seq analysis. Globally, we identified two classes of epigenetic profiles that correlate with resistance. Class 1 resistance involves fewer RNA expression alterations accompanied by fewer enhancer mark changes with H3K27Ac. Class 2 resistance shows widespread alterations in transcription and enhancer profiles, which converge on EMT and hypoxia-related pathways. We also observed significant and dynamic changes in super-enhancers that underpin these transcriptomic patterns. We subsequently verified the 2-class structure in pre-BRAFi and post-relapse human melanoma specimens. Our findings reveal a broad and underappreciated spectrum of epigenetic plasticity during acquired BRAFi resistance.

overall_design: Eight pairs of melanoma cell lines were subjected to RNAseq and ChIPseq.

first: Yuanyuan

last: Kang

first: Zhenyu

last: Ji

first: He

last: Li


title: Frequent loss of adhesion gene NECTIN1 triggers melanoma dissemination upon local IGF1 depletion

first: Leonard

last: Zon

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

overall_design: Refer to individual Series


title: Divergent BRAF Inhibitor Resistance Mechanisms Revealed through Epigenetic Mapping [RNA-seq]


title: Hyperglycemic conditions induce rapid cell dysfunction-promoting transcriptional alterations in human aortic endothelial cells.

status: Public on May 21 2022

city: Abu dhabi

first: Youssef

last: Idaghdour

state: Abu dhabi

address: Saadiyat Marina District

department: Biology

country: United Arab Emirates

institute: NYUAD

summary: We report the first deep RNASeq time-series dataset (n=96 samples) of human aortic endothelial cells (HAECs) following exposure to normal (NG) and high glucose (HG) conditions over a time course from baseline to 24 hours (0, 0.5, 1, 4, 8 and 24 hours). We identify rapid and transient transcriptomic changes, alteration of molecular networks, and document temporal transcriptional dynamics of in HAECs.

overall_design: RNA-seq time series analysis in HAECs under normal or high glucose conditions.

first: Odmaa

last: Bayarra

first: Claire

last: Inman

first: Sneha

last: Thomas

first: Fatima

last: AlJalaf

first: Louise

last: Ashall


title: AGAP3: a novel BRAF-fusion partner in pediatric pancreatic acinar cell carcinoma

status: Public on May 18 2022

city: NICE

first: Thibault

last: FABAS

address: 28 av Valombrose

institute: CHU Nice

summary: Most available molecular data on pancreatic acinar cell carcinoma (PACC) are provided by studies of adult cases. BRAF, RAF1 or RET rearrangements have been described in approximately 30% of cases. To the best of our knowledge, only seven cases with molecular data have been reported in pediatric PACC. We report here the comprehensive study of a PACC from a 6-year-old patient. We detected a novel AGAP3-BRAF fusion. This result showing a BRAF rearrangement demonstrates a molecular link between adult and pediatric PACC. Moreover, it identifies AGAP3, a gene located at 7q36.1 that encodes a major component of the N-methyl-D-aspartate (NMDA) receptor signaling complex, as a new partner gene of BRAF.  The variability of BRAF partners is consistent with a driver role of BRAF alterations in PACC. The identification of such alterations is noteworthy for considering the use of MEK inhibitors in metastatic cases. We did not detect associated genomic instability. The better outcome of pediatric cases might be related to their stable genomic background.

overall_design: one sample: pancreatic acinar cell carcinoma

first: Charlotte

last: Paoli

first: Fanny

last: Burel-Vandenbos

first: Florence

last: Pedeutour

first: Bérengère

last: Dadone-Montaudié


title: Context-dependent genetic effects on gene expression

status: Public on Jun 30 2022

city: Nashville

first: Amanda

middle: Jeanne

last: Lea

state: TN

address: Box 351634 Station B

country: USA

institute: Vanderbilt University

summary: We profiled genome-wide gene expression levels across 12 cellular environments using 544 immortalized B cell (lymphoblastoid) lines from the 1000 Genomes Project.

overall_design: mRNA-seq of RNA extracted from lymphoblastoid cell lines