title: Zebrafish caudal fin amputation induces a metabolic switch necessary for cell identity transitions and cell cycle re-entry to support blastema formation and bone regeneration

city: Caparica

first: Patricia

middle: H.

last: Brito

address: Rua Câmara Pestana

country: Portugal

institute: NOVA School of Science and Technology

summary: Regeneration depends on the ability of mature cells at the injury site to respond to injury, generating tissue-specific progenitors that incorporate the blastema and proliferate to reconstitute the original organ architecture. The metabolic microenvironment has been tightly connected to cell function and identity during development and tumorigenesis. Yet, the link between metabolism and cell identity at the mechanistic level in a regenerative context remains unclear. The adult zebrafish caudal fin, and bone cells specifically, have been crucial for the understanding of mature cell contribution to tissue regeneration. Here, we use this model to explore the relevance of glucose metabolism for the cell fate transitions preceding new osteoblast formation and blastema assembly. We show that injury triggers a shift in the metabolic profile at early stages of regeneration, enhancing glycolysis at the expense of mitochondrial oxidation. This metabolic switch mediates transcriptional changes that make mature osteoblast amenable to be reprogramed into pre-osteoblasts and induces cell cycle re-entry and progression. Manipulation of the metabolic profile led to severe reduction of the pre-osteoblast pool, diminishing their capacity to generate new osteoblasts, and to a complete abrogation of blastema formation. Overall, our data indicate that metabolic alterations have a powerful instructive role in regulating genetic programs that dictate fate decisions and stimulate proliferation, thereby providing a deeper understanding on the mechanisms regulating blastema formation and bone regeneration.

overall_design: Total of 5 samples: two control samples from uninjured condition (GrU_U2.300 and GrU_U3.300) and three samples at 6 hours post-amputation (Gr6H_6H1.300; Gr6H_6H2.300; and Gr6H_6H3.300)

first: Ana

last: Brandão

first: Jorge

last: Borbinha

first: Telmo

last: Pereira

first: Patrícia

first: Raquel

last: Lourenço

first: Anabela

last: Bensimon-Brito

first: António

last: Jacinto


title: Alzheimer’s disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment [N40K neuron RNA-seq]

status: Public on Aug 11 2022

city: Memphis

first: Yingxue

last: Fu

state: Tennessee

address: 262 Danny Thomas Place

country: USA

institute: St. Jude Children's Research Hospital

type: Expression profiling by high throughput sequencing

summary: Recent proteome and transcriptome profiling of Alzheimer's disease (AD) brains reveals RNA splicing dysfunction and U1 small nuclear ribonucleoprotein (snRNP) pathology containing U1-70K and its N-terminal 40-KDa fragment (N40K). Here we present a causative role of U1 snRNP dysfunction to neurodegeneration in primary neurons and transgenic mice (N40K-Tg), in which N40K expression exerts a dominant-negative effect to downregulate full-length U1-70K. N40K-Tg recapitulates N40K insolubility, neuronal degeneration, cognitive impairment, and erroneous splicing events in synaptic pathways.

overall_design: Mouse primary cortical neuronal culture at DIV 7 treated with lentiviral particles of vector control FCK1.3GW or FCK1.3GW-N40K for 3 days (three replicates).

first: Ping-Chung

last: Chen

first: Xian

last: Han

first: Timothy

middle: I

last: Shaw

first: Gang

last: Wu

first: Junmin

last: Peng


title: Alzheimer’s disease-associated U1 snRNP splicing dysfunction causes neuronal hyperexcitability and cognitive impairment [N40K mice RNA-seq]

overall_design:
1. RNA-seq of stranded mRNA of 6-month old of wild-type, N40K-Tg, 5XFAD, dTg (N40K-Tg and 5xFAD) mice generated by crossing N40K-Tg and 5xFAD mice.
2. RNA-seq of stranded mRNA of 12-month old of wild-type and Tau P301S mice.


title: Neuronal expression of Alzheimer's disease-associated U1-70K cleavage product causes splicing dysfunction and cognitive impairment in mice

address: 262 Danny Thomas PL

department: Structural Biology

institute: St Jude Children's Research Hospital

summary: Alzheimer's disease (AD) displays progressive cognitive decline that is associated with protein ß-amyloid and tau aggregation, but the causative mechanisms are not fully understood. Recent proteomics profiling has identified, in sporadic and familial cases, a tangle-like pathology of U1 small nuclear ribonucleoprotein complex (snRNP), containing U1-70K and its N-terminal cleavage product (N40K), with RNA splicing alteration. To determine whether U1 snRNP dysfunction may play a causative role in AD, we generate a transgenic mouse model (N40K-Tg) by neuronal expression of N40K. Deep transcriptomic analysis of N40K-Tg mice was performed to evaluate intron-retaining mRNAs. Tissue was extracted from hippocampus at three month and twelve month comparing N40K-Tg vs WT mice.

overall_design: Three month comparison of N40K-TG (n = 3) vs WT (n = 3); Twelve month comparison of N40K-TG(n = 3) vs WT (n = 3)

first: Yuxin

last: Li


title: Heat- and wound-responsive genes in Nicotiana benthamiana

status: Public on Aug 10 2022

city: Daejeon

first: Hyo-Jun

last: Lee

address: Gwahak-ro

department: Plant Systems Engineering Research Center

country: South Korea

institute: Korea Research Institute of Bioscience and Biotechnology

summary: Nicotiana benthamiana is a widely used organism for expression of foreign proteins. To increase protein abundance, overexpression promoters have been developed. However, several proteins cause negative effects on plant growth and development when they are overexpressed. Therefore, overexpression promoters cannot be widely used to generate transgenic plants that produce foreign proteins. In this study, we tried to find stress-inducible promoters which specifically express downstream genes when plants were exposed to stress conditions. By RNA-sequencing analysis of heat- and wound-treated plants, we found that NbHSP20 promoters can be used as a heat-inducible promoters to express foreign proteins in N. benthamiana.

overall_design:
For analyzing heat-responsive genes, N.benthamiana plants were incubated at 37oC for 1 h. For wound-responsive genes, N.benthamiana plants were wounded and then incubated at 23oC for 1 h.
Three biological replicates for mock, heat, and wound samples were analyzed. Control: mock

first: Seung

middle: Y

last: Shin

first: Ah

first: Suk

last: Kwon

first: Ki-Beom

last: Moon

first: Hyun-Soon

last: Kim

first: Jae

middle: H

last: Jeon


title: TMAO Suppresses Megalin Expression and Albumin Uptake in Human Proximal Tubular Cells Via PI3K and ERK Signaling

city: örebro

first: isak

last: demirel

address: campus usö

country: Sweden

institute: örebro University

summary: Trimethylamine-N-oxide (TMAO) is a uremic toxin, which has been associated with chronic kidney disease (CKD). Renal tubular epithelial cells play a central role in the pathophysiology of CKD. Megalin is an albumin-binding surface receptor on tubular epithelial cells, which is indispensable for urine protein reabsorption. To date, no studies have investigated the effect of TMAO on megalin expression and the functional properties of human tubular epithelial cells. The aim of this study was first to identify the functional effect of TMAO on human renal proximal tubular cells and second, to unravel the effects of TMAO on megalin-cubilin receptor expression. We found through global gene expression analysis that TMAO was associated with kidney disease. The microarray analysis also showed that megalin expression was suppressed by TMAO, which was also validated at the gene and protein level. High glucose and TMAO was shown to downregulate megalin expression and albumin uptake similarly. We also found that TMAO suppressed megalin expression via PI3K and ERK signaling. Furthermore, we showed that candesartan, dapagliflozin and enalaprilat counter-acted the suppressive effect of TMAO on megalin expression. Our results may further help us un-ravel the role of TMAO in CKD development and to identify new therapeutic targets to counteract TMAOs effects.

overall_design: HK-2 cells were stimulated with TMAO (300 µM) for 6 h at 37 °C in 5% CO2 and the gene expression was evaluated.

first: Stefania

last: Kapetanaki

first: Ashok

middle: K

last: Kumawat

first: Katarina

last: Persson

first: Isak

last: Demirel


title: Immune cell distribution in the decidua and myometrium of pregnant mice at E7.5.

city: Newark

first: Alexander

last: Lemenze

state: New Jersey

address: 185 South Orange Ave

institute: Rutgers

summary: We used single cell RNA sequencing (scRNA-seq) with TotalSeq-A (BioLegend) cell hashing to investigate the immune cell distribution in the decidua and myometrium of pregnant mice at E7.5.

overall_design: C57BL6 (Hashtag A0306) and Il33cit/cit (IL-33-deficient) (Hashtag A0309) dams were mated with C57BL6 studs. At E7.5, live CD45.2+ cells from the decidua and myometrium of pregnant were stained separately with TotalSeq-A (BioLegend) cell hashing antibodies, isolated by fluorescence-activated cell sorting (FACS), pooled at 1:1 ratio, and analyzed by scRNA-seq.

first: Aimee

middle: M

last: Beaulieu

first: Nuriban

last: Valero-Pacheco


title: IL-33+ cell subsets in the decidua and myometrium of pregnant mice at E7.5.

summary: We used single cell RNA sequencing (scRNA-seq) to investigate the IL-33+ cell types present in the decidua and myometrium of pregnant mice at E7.5.

overall_design: Il33cit/wt reporter dams were mated with C57BL6 studs. At E7.5, live Citrine+ cells from the decidua and myometrium were isolated by fluorescence-activated cell sorting (FACS) and analyzed using scRNAseq.


title: Static Magnetic Fields Regulate T-Type Calcium Ion Channels and Mediate Mesenchymal Stem Cells Proliferation

city: Guangzhou

first: Jing

last: Liu

state: Guangdon

address: 190 Kai Yuan Avenue, Science Park,Guangzhou

department: CAS Key Laboratory of Regenerative Biology

country: China

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou 510530, China

summary: The static magnetic fields (SMFs) impact on biological systems, induce a variety of biological responses, and have been applied to the clinical treatment of diseases. However, the underlying mechanisms remain largely unclear. In this report, by using human mesenchymal stem cells (MSCs) as a model, we investigated the biological effect of SMFs at a molecular and cellular level. We showed that SMF exposure promotes MSC proliferation and activates the expression of transcriptional factors such as FOS (Fos Proto-Oncogene, AP-1 Transcription Factor Subunit) and EGR1 (Early Growth Response 1). In addition, the expression of signal-transduction proteins p-ERK1/2 and p-JNK oscillate periodically with SMF exposure time. Furthermore, we found that the inhibition of the T-type calcium ion channels negates the biological effects of SMFs on MSCs. Together, we revealed that the SMFs regulate T-type calcium ion channels and mediate MSC proliferation via the MAPK signaling pathways.

overall_design: all the data sequenced by illumina nextseq 500

first: Haokaifeng

last: Wu


title: CRISPR screens for synthetic rescue of cFLIP depletion in primary effusion lymphoma cell lines

city: Chicago

first: Eva

middle: Henriette

last: Gottwein

state: IL

address: 320 E Superior St., Tarry building, Room 6-752

department: Microbiology-Immunology

institute: Northwestern University

summary: Kaposi’s sarcoma-associated herpesvirus (KSHV) causes the B cell malignancy primary effusion lymphoma (PEL). We have previously shown that cultured PEL cell lines require expression of the cellular FLICE inhibitory protein (cFLIP) for survival (Manzano et al., Nat Comm 2018), although KSHV encodes a viral homolog of this protein (vFLIP). Here we employed genome-wide CRISPR/Cas9 synthetic rescue screens to identify loss of function perturbations that can compensate for cFLIP knockout/knockdown.

overall_design: BCBL1 lentiCas9-Blast cells clonally selected for high Cas9 editing activity were transduced with the genome-wide Brunello (Doench et al., Nature Biotechnology 2016) CRISPR library followed by a second challenge with either lentiviral sgRNAs (sgAAVS1, sgCFLIP) or lentiviral shRNAs (shRen308, shRen713, sh1-cFLIP, shM-cFLIP, or shN-cFLIP). Experiments utilizing sgAAVS1 and sgAAVS1 were repeated in BC2 lentiCas9-Blast (no clonal selection for Cas9 activity) cells.

first: Neil

last: Kuehnle

first: Mark

last: Manzano


title: Deconstructing cold-induced brown adipocyte neogenesis in mice [bulk RNA-seq]

city: Detroit

first: Rayanne

middle: B

last: Burl

address: 42 W. Warren Ave

institute: Wayne State University

summary: Cold-exposure triggers neogenesis in classic interscapular brown adipose tissue (BAT) that involves activation of b1-adrenergic receptors, proliferation of PDGFRA+ adipose tissue stromal cells (ASCs), and recruitment of immune cells whose phenotypes are presently unknown. Single-cell RNA-sequencing (scRNA-seq) identified three ASC subpopulations that occupied distinct tissue locations. Of these, interstitial ASC1 were found to be direct precursors of new brown adipocytes (BA). Surprisingly, knockout of b1-adrenergic receptors in ASCs did not prevent cold-induced neogenesis, whereas pharmacological activation of the b3-adrenergic receptor on BAs was sufficient, suggesting that signals derived from mature BAs indirectly trigger ASC proliferation and differentiation. In this regard, cold exposure induced the delayed appearance of multiple macrophage and dendritic cell populations whose recruitment strongly correlated with the onset and magnitude of neogenesis across diverse experimental conditions. High resolution immunofluorescence and single molecule fluorescence in situ hybridization demonstrated that cold-induced neogenesis involves dynamic interactions between ASC1 and recruited immune cells that occur on the micrometer scale in distinct tissue regions. Our results indicate that neogenesis is not a reflexive response of progenitors to b-adrenergic signaling, but rather is a complex adaptive response to elevated metabolic demands within brown adipocytes.

overall_design: Whole-tissue RNA-sequencing of mouse interscapular brown adipose tissue (iBAT) after a cold-exposure time course. Data includes iBAT RNA-seq from mice housed at room temperature, or six cold-exposure time points: 6 hours, 1 day, 2 days, 3 days, 4 days, and 5 days. Cold exposure corresponds to housing at 6 degrees Celsius. Five mice were collected for each time point, totaling 35 RNA-seq libraries.

first: Elizabeth

middle: A

last: Rondini

first: Hongguang

last: Wei

first: Roger

last: Pique-Regi

first: James

middle: G

last: Granneman


title: Deconstructing cold-induced brown adipocyte neogenesis in mice [scRNA-seq]

overall_design: Single-cell RNA-sequencing of mouse interscapular brown adipose tissue (iBAT).


title: mRNA Sequencing of BC-1 Cells

summary: Kaposi’s sarcoma-associated herpesvirus (KSHV) causes the B cell malignancy primary effusion lymphoma (PEL). Here we performed mRNA sequencing to characterize the mRNA expression profile of the primary effusion lymhoma (PEL) cell line BC-1.

overall_design: BC-1 cells (ATCC CRL-2230) submitted for standard mRNA sequencing


title: Deconstructing cold-induced brown adipocyte neogenesis in mice

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

overall_design: Refer to individual Series


title: Profiling of gene expression in the brain associated with anxiety-related behaviors in the chronic phase following cranial irradiation

city: Seoul

first: Yeonghoon

last: Son

address: 75, Nowon-ro

institute: Korea Institute of Radiological & Medical Sciences (KIRAMS)

summary: By using RNA sequencing (RNA-seq), we analyzed gene expression profiles in the cortex and hippocampus of the adult brain to demonstrate the molecular mechanisms of radiation-induced brain dysfunction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data in hippocampus and cortex of mice brain at 3 months after cranial irradiation

first: Hae-June

last: Lee

first: Joong-Sun

last: Kim

first: Changjong

last: Moon


title: Cross-comparison of high-throughput platforms for circulating mcroRNA in non small cell lung cancer -QiAseq

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

type: Non-coding RNA profiling by high throughput sequencing

summary: This study focuses on platform comparison to assess performance variability in circulating microRNA (ct-miR) detection, agreement in assignment of a miR signature classifier (MSC) and concordance for the identification of cancer-associated miRs in plasma samples from non‐small cell lung cancer (NSCLC) patients.   A plasma cohort of 10 NSCLC patients and 10 healthy donors matched for clinical features and MSC risk level was profiled for miRs expression using two sequencing- and three quantitative PCR (qPCR)-based platforms.   Intra- and inter-platform variations were examined by correlation and concordance analysis. MSC risk levels were compared to those estimated using a reference method. Differentially expressed ct-miRs were identified among NSCLC patients and donors and the diagnostic value of those dysregulated in patients was assessed by receiver operating characteristic curve analysis. Downregulation of miR-150-5p was verified by qPCR. The Cancer Genome Atlas (TCGA) lung carcinoma dataset was used for validation at tissue level.  Intra-platform reproducibility was consistent whereas the highest values of inter-platform correlations were among qPCR-based platforms. MSC classification concordance was >80% for four platforms. Dysregulation and discriminatory power of miR-150-5p and -210-3p were documented. Both were significantly dysregulated also on TCGA tissue-originated profiles from lung cell carcinoma in comparison to normal samples.   Overall, our studies provide a large performance analysis between five different platforms for miRs quantification, indicate the solidity of MSC classifier and identify two noninvasive biomarkers for NSCLC

overall_design: A total of 20 human specimens were employed for this study, which included plasma from NSCLC patients (n=10) and, as control, healthy subjects (n=10), matched for age, sex, smoking status and MSC risk score RNA aliquots from these samples, including duplicates, one from a patient and two for donors, obtained from two independent RNA extractions from aliquots of the same plasma, were profiled by the following four high-throughput technological platforms: Taqman OpenArray Human miR and Taqman OpenArray Human Advanced miR Panels (Thermo Fisher Scientific); miRCURY LNA miR miRNome PCR Panels (Qiagen); QiaSeq miRNA Library (Qiagen). The fifth platform, EdgeSeq miR Whole Transcriptome Assay (HTG Molecular Diagnostics) employed, instead, crude blood plasma as starting material. All the statistical and bioinformatic analysis were performed using the R statistical program v 3.6.1. Annotation was performed according to the miRBase v21 available for each platform and downloaded from each manufacturers’ website. We studied: i) performance of miR expression profiling within platforms; ii) reproducibility of miR profiling intra-platform; iii) cross-platform comparison; iv) Cross-platform concordance in the assignement of a clinical validated miR risk score; v) differential ct-miR expression in NSCLC patients compared to control group; vi) fidelity of fold-change across platforms; vii) identification and validation of potential NSCLC biomarkers.


title: miR-182-5p Promotes Hepatocyte-Stellate Cell Crosstalk to Facilitate Liver Regeneration

city: Changsha

first: Wen

last: Meng

state: Outside the United States or Canada

address: The Second Xiangya Hospital of Central South University, Changsha 410011, Hunan, China.

institute: Central South University

summary: A unique feature of the liver is its high regenerative capacity, which is essential to maintain liver homeostasis. However, key regulators of liver regeneration (LR) remain ill-defined. Here, we identify hepatic miR-182-5p as a key regulator of LR. Suppressing miR-182-5p, whose expression is significantly induced in the liver of mice post two-thirds partial hepatectomy (PH), abrogates PH-induced LR in mice. In contrast, liver-specific overexpression of miR-182-5p promotes LR in mice with PH. Overexpression of miR-182-5p failed to promote proliferation in hepatocytes, but stimulates proliferation when hepatocytes are cocultured with stellate cells. Mechanistically, miR-182-5p stimulates Cyp7a1-mediated cholic acid production in hepatocytes, which promotes hedgehog (Hh) ligand production in stellate cells, leading to the activation of Hh signaling in hepatocytes and consequent cell proliferation. Collectively, our study identified miR-182-5p as a critical regulator of LR and uncovers a Cyp7a1/cholic acid-dependent mechanism by which hepatocytes crosstalk to stellate cells to facilitate LR.

overall_design: Briefly, 8- to 10-week-old male mice were anesthetized with isoflurane, followed by a ventral midline incision. The left lateral, left middle, and right middle lobe of the liver (70% of the liver) were removed from the anesthetized mice after pedicle ligation with prolene 6/0. After surgery, the mice were placed on a warming pad for recovery until completely conscious. All partial hepatectomies were performed at early hours in the morning.


title: Foxm1 haploinsufficiency drives clonal hematopoiesis in vivo and promotes the transition to hematologic malignancy under stress

city: Charlottesville

first: Yong

last: Huang

state: VA

address: 1340 Jefferson Park Ave

department: Medicine

institute: University of Viginia

summary: Clonal hematopoiesis plays a critical role in the initiation and development of hematologic malignant diseases. FOXM1, a well-known transcription factor, is often downregulated in CD34+ cells from patients with del(5q) Myelodysplastic Syndrome (MDS).      Here we show that Foxm1 haploinsufficiency disturbs normal hematopoiesis and confers a competitive repopulation advantage to hematopoietic stem cells (HSCs) for a short period, but disrupts the long-term self-renewal capacity of HSCs, recapitulating the phenotypes of abnormal HSCs in MDS patients. Moreover, heterozygous inactivation of Foxm1 leads to an increase in DNA damage in hematopoietic stem/progenitor cells (HSPCs). Foxm1 haploinsufficiency induces an MDS-like disease in a mouse model with LPS-induced chronic inflammation, and accelerates AML-ETO9a-mediated leukemogenesis. We also identified PARP1, an important enzyme responding to various kinds of DNA lesions, as a previously unrecognized target of Foxm1.  Foxm1 haploinsufficiency inhibits DNA damage response (DDR) in HSCs by downregulating PARP1 expression in HSPCs. Given that PARP1 inhibitors increase the risk of MDS and AML in clinical therapy for solid tumors, our results suggest that downregulation of the Foxm1-PARP1 molecular axis plays a pivotal role in the pathogenesis of MDS by promoting clonal hematopoiesis and reducing genome stability.

overall_design: BM cells from Foxm1 heterozygous mice or control mice were harvested, followed by HSCs staining described above. Total RNA extracted from sorted LT-HSC cells (CD150+CD48-LSK) was isolated by Trizol (Invitrogen). RNA-seq was performed by UC (San Francisco, California).

first: Chunjie

last: Yu

first: Yue

last: Sheng

first: Hongyu

last: Ni

first: Alan

last: Qiu

first: Zhijian

last: Qian


title: Cross-comparison of high-throughput platforms for circulating mcroRNA in non small cell lung cancer- miRCURY LNA

first: Marialuisa

last: Sensi


title: ADAR1 mutation causes ZBP1-dependent immunopathology II

city: Seattle

first: Andrew

last: Oberst

state: WA

address: 750 Republican street

institute: University of Washington

summary: The RNA editing enzyme ADAR1 is essential for suppression of innate immune activation and pathology caused by aberrant recognition of self-RNA, a role it carries out by disrupting the duplex structure of endogenous double-stranded RNA species. A point mutation in the Z-nucleic-acid binding domain (ZBD) of ADAR1 is associated with severe autoinflammatory disease. ZBP1 is the only other ZBD-containing mammalian protein and its activation can trigger both cell death and transcriptional responses via the kinases RIPK1 and RIPK3, and the protease caspase-8. Here, we show that the pathology caused by ADAR1 ZBD mutation is driven by activation of ZBP1. We found that ablation of ZBP1 fully rescued the overt pathology caused by ADAR1 mutation, without reversing the underlying inflammatory program caused by this mutation. While loss of RIPK3 partially phenocopied the protective effects of ZBP1 ablation, combined deletion of caspase-8 and RIPK3, or of caspase-8 and MLKL, unexpectedly exacerbated the pathogenic effects of ADAR1 mutation. These findings indicate that ADAR1 is a negative regulator of sterile ZBP1 activation, and that ZBP1-dependent signaling underlies the autoinflammatory pathology caused by mutation of ADAR1.

overall_design: Mouse embryonic fibroblasts derived from mice of the indicated genotypes were treated with zVAD for 4 hours to compare the effect of genotype and ADAR1 deficiency on inflammatory signatures. 3 biological replicates were analyzed for each group. Transcripts were measured using the Mouse inflammation v2 nCounter panel commercially availible from Nanostring Technologies Inc.

first: Nicholas

middle: W

last: Hubbard

first: Joshua

last: Ames

first: Megan

last: Maurano

first: Lan

last: Chu

first: Kim

last: Somfleth

first: Nandan

middle: S

last: Gokhale

first: Margo

last: Werner

first: Jessica

last: Snyder

first: Katrina

last: Lichauco

first: Ram

last: Savan

first: Daniel

last: Stetson


title: Cross-comparison of high-throughput platforms for circulating mcroRNA in non small cell lung cancer - TaqMan OpenArray

first: Loris

last: De Cecco


title: Cross-comparison of high-throughput platforms for circulating mcroRNA in non small cell lung cancer -HTG


title: ADAR1 mutation causes ZBP1-dependent immunopathology I

overall_design: Mouse embryonic fibroblasts derived from mice of the indicated genotypes were treated with an siRNA targeting ADAR1 (siADAR) or a non-targeting siRNA (siNT) to compare the effect of genotype and ADAR1 deficiency on inflammatory signatures. 3 biological replicates were analyzed for each group. Transcripts were measured using the Mouse inflammation v2 nCounter panel commercially availible from Nanostring Technologies Inc.


title: A multiomics disease progression signature of low-risk ccRCC

city: Bergen

first: Philipp

last: Strauss

address: Haukeland Universitetssykehus Laboratoriebygget, 7. etg. Heis øst

country: Norway

institute: University of Bergen

summary:
Background:  Clear cell renal cell carcinoma (ccRCC) is the most common renal cancer. Identification of ccRCC likely to progress, despite an apparent low risk at the time of surgery, represents a key clinical issue.
Methods:   From a cohort of adult ccRCC patients (n=443), we selected low-risk tumors progressing within a 5-years average follow-up (progressors: P, n=8) and non-progressing (NP) tumors (n=16). Transcriptome sequencing, miRNA sequencing and proteomics were performed on tissues obtained at surgery.
Our work suggests that LXR, FXR and macrophage activation pathways   could be critically involved in the inhibition of the progression of low-risk ccRCC. Furthermore, a 10-component classifier could support an early identification of apparently low-risk ccRCC patients.

overall_design:
Next-generation sequencing of microRNA from formalin-fixed samples obtained at initial surgery from 8 low-risk patients with progressing tumours and 16 patients with similar Leibovich score, tumour stage and size, creatinine levels and surgical treatment, not progressing to recurrence with metastasis. Key results were confirmed with qPCR, immunohistochemistry and in external data.
*** Raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns****
Expression profiling by high throughput sequencing; part of mulitomics dataset; This is microRNAseq dataset which is linked to mRNAseq data from GSE171955 and proteomics mass-spec data posted on PRIDE (https://www.ebi.ac.uk/pride (ongoing submission process))

first: Strauss

last: Philipp

first: Rivedal

last: Mariell

first: Scherer

last: Andreas

first: Eikrem

last: Oystein

first: Nakken

last: Sigrid

first: Beisland

last: Christian

first: Bostad

last: Leif

first: Flatberg

last: Arnar

first: Skandalou

last: Eleni

first: Beisvag

last: Vidar

first: Furriol

last: Jessica

first: Marti

last: Hans-Peter


title: A SOX2 engineered epigenetic silencer factor represses the glioblastoma genetic program

city: Milano

first: Luca

last: Massimino

state: MI

address: Via Olgettina, 58

department: Gastroenterology

institute: Ospedale San Raffaele

type: Genome binding/occupancy profiling by high throughput sequencing

type: Methylation profiling by high throughput sequencing

summary: By rational engineering of the transcription factor SOX2, a key promoter of GBM malignancy, we generated a synthetic repressor named SOX2 Epigenetic Silencer (SES), which maintains the ability to bind to a large group of its original targets. Data from RNAseq, ATACseq, MeDIPseq, ChIPseq in GBM cells indicate that SES, through the KRAB and DNA methyltransferase 3A/L catalytic domains, epigenetically inhibits the SOX2 tumorigenic molecular network (rather than activating it as SOX2 does). This epigenetic long-term transcriptional silencing includes genes crucial for tumor maintenance and growth.  Conversely, transcriptomic and epigenomic data show that SES is ineffective (thus not harmful) in healthy neural cells.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Human SNB19 cells: 3x SOX2 ATAC; 3x SES ATAC; 2x Mock H3K9me3; 2x SES H3K9me3; 2x Mock MeDIP; 2x SES MeDIP; 2x SOX2 V5 ChIP; 2x SES V5 ChIP; 3x SOX2 V5 Cut-n-Tag; 3x SES V5 Cut-n-Tag; 3x Mock RNA; 3x SES RNA. Mouse cortical neurons: 3x Mock RNA; 3x SES RNA

first: Alessandro

last: Sessa

first: Mattia

last: Zaghi

first: Vania

last: Broccoli


title: Cross-comparison of high-throughput platforms for circulating mcroRNA in non small cell lung cancer - TaqMan OpenArray Advanced

first: Loris

last: De Cecco

first: Marialuisa

last: Sensi


title: Cross-comparison of high-throughput platforms for circulating mcroRNA in non small cell lung cancer


title: Next Generation Sequencing of Asymptomatic and Symptomatic Carotid Atherosclerotic Plaques

city: New Orleans

first: Thomas

middle: Cooper

last: Woods

state: LA

address: 1430 Tulane Avenue

department: Physiology

institute: Tulan

summary: Atherosclerotic plaque rupture is the etiology of ischemic stroke and myocardial infarction. Ribosome-depleted total RNA was sequenced from carotid plaques obtained from patients undergoing carotid endarterectomy with high-grade stenosis and either 1) a carotid-related ischemic cerebrovascular event within the previous 5 days ('recently ruptured,' n=6) or 2) an absence of a cerebrovascular event ('asymptomatic,' n=5). Examination of the differentially expressed genes supported the importance of inflammation and inhibition of proliferation and migration coupled with an increase in apoptosis. Thus, the transcriptome of recently ruptured plaques is enriched with transcripts associated with inflammation and fibrous cap thinning and support further examination of the role of B lymphocytes and interferons in atherosclerotic plaque rupture.

first: T

middle: C

first: Hernan

last: Bazan


title: Developmental modeling of hepatogenesis using obese iPSCs-hepatocyte differentiation uncovers pathological features

city: Philadelphia

first: Priyankara

middle: J

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Obesity is a multigene disorder. However, in addition to genetic factors, environmental determinants also participate in developing obesity and related pathologies. Thus, obesity could be best described as a combination of genetic and environmental perturbations often having its origin during the early developmental period. Environmental factors such as energy-dense food and sedentary lifestyle are known to be associated with obesogenicity. However, the combinatorial effects of gene-environment interactions are not well understood. Understanding the role of multiple genetic variations leading to subtle gene expression changes is not practically possible in monogenic or high fat-fed animal models of obesity. In contrast, human induced pluripotent stem cells (hiPSCs) from individuals with familial obesity or an obesogenic genotype could serve as a good model system. Herein, we have used hiPSCs generated from normal and genetically obese subjects and differentiated them into hepatocytes in cell culture. We show that hepatocytes from obese-iPSCs store more lipids and show increased cell death than normal-iPSCs. Whole transcriptome analyses in both normal and obese-iPSCs treated with palmitate compared to control revealed LXR-RXR and hepatic fibrosis pathways were enriched among other pathways in obese iPSCs compared to normal iPSCs. Among other genes, increased CD36 and CAV1 expression and decreased expression of CES1 in obese-iPSCs could have been responsible for excess lipid accumulation resulted in differential expression of genes associated with hepatic fibrosis a key feature of non-alcoholic fatty liver disease (NAFLD). Our results demonstrate that iPSCs derived from genetically obese subjects could serve as an excellent model to understand the effects of this multigene disorder on organ development and may uncover pathologies of NAFLD, which is highly associated with obesity.

overall_design: RNAseq of induced pluripotent stem cells from normal and obese individuals.

first: Suraiya

last: Ansari


title: Transcriptomic changes in F9 tumors after EDA-CART cell therapy

city: Pamplona

first: Juan

middle: Jose

last: Lasarte

state: Navarra

address: Avda Pio XII, 55

department: Inmunología e Inmunoterapia

country: Spain

institute: Centro de Investigación Médica Aplicada

summary: Transcriptomic analysis of tumor tissues isolated from  animals bearing F9 teratocarcinoma. 129Sv mice were challenged with F9 tumor cells and, when tumors were palpable, mice were treated with EDA CAR-T s (a mixture of 1×107 CD4+ and 2×106 CD8+ CAR-T cells)or left untreated. 14 days after adoptive transfer, RNA was isolated from tumors for their transcriptomic analysis.

overall_design: 129Sv mice were challenged with F9 tumor cells and, when tumors were palpable, mice were treated with EDA CAR-T s (a mixture of 1×10^7 CD4+ and 2×10^6 CD8+ CAR-T cells) or left untreated.

first: Teresa

last: Lozano

first: Celia

last: Martin-Otal


title: Intrarenal Single-Cell Sequencing of Hepatitis B Virus-Associated Membranous Nephropathy

city: CHANG SHA

first: YONG

last: ZHONG

address: XIANGYA ROAD

institute: XIANGYA HOSPITAL

summary: This study aimed to decipher the etiopathogenesis of HBV-associated MN by performing single-cell RNA sequencing (scRNA-seq) of kidney biopsy specimens from a patient with HBV-associated MN and two healthy individuals.

overall_design: scRNA-seq of one sample from human kidney from patient with HBV-associated MN

first: Yong

last: Zhong

first: Xiangcheng

last: Xiao

first: Leilin

last: Yu

first: Wei

last: Lin


title: Absence of major epigenetic and transcriptomic changes accompanying the interspecific cross between peach and almond

city: Cerdanyola del Vallès

first: Carlos

last: de Tomás

state: Barcelona

address: Carrer de la Vall Moronta

institute: CRAG

summary: We analysed the DNA methylation and transcription levels of transposable elements and genes in leaves of Prunus persica and Prunus dulcis and in their F1 hybrid using high-throughput sequencing tecnhologies. We can conclude that the merging of the two parental genomes in the P. persica x P. dulcis hybrid does not result in a “genomic shock” with significant changes in the DNA methylation or in the transcription.

sample_organism:
Prunus dulcis
Prunus persica
Prunus persica x Prunus dulcis

overall_design: Leaves of Prunus dulcis cv Texas, Prunus persica cv Early Gold and one interspecific F1 hybrid were collected. For the analysis of DNA methylation, we used two biological replicates per genotype. For RNA-seq analysis, we used three biological replicates per genotype.

first: Amélie

last: Bardil

first: Raúl

last: Castanera

first: Josep

last: Casacuberta

last: Vicient


title: Expression data from murine colon tumors induced by azoxymethane. Tumors from control, obese, formerly obese, or sulindac-treated mice.

city: Chapel Hill

first: Stephen

middle: D

last: Hursting

state: North Carolina

address: 215B MHRC

institute: University of North Carolina - Chapel Hill

summary: Obesity is associated with an increased risk of colon cancer. Our current study examines whether weight loss and/or treatment with the non-steroidal anti-inflammatory drug (NSAID) sulindac suppresses the protumor effects of obesity in a mouse model of colon cancer. Azoxymethane-treated male FVB/N mice were fed a low-fat diet (LFD) or high-fat diet (HFD) for 15 weeks, then HFD mice were randomized to remain on HFD (obese) or switch to LFD (formerly obese (FOb-LFD)). Within the control (LFD), obese, and FOb-LFD groups, half the mice were also randomized to start sulindac treatment (140 ppm in the diet). All mice were euthanized seven weeks later. FOb-LFD mice had intermediate levels of body weight, lower than obese but higher than control mice (P<0.05). Sulindac did not affect body weight. Obese mice had greater tumor multiplicity and burden than all other groups (P<0.05). Transcriptomic profiling indicated that both weight loss and sulindac modulate the expression of tumor genes related to invasion and may promote a more anti-tumor immune landscape. Furthermore, the fecal microbes Prevotella and Akkermansia muciniphila, both known to be elevated in colorectal cancer patients, were positively correlated with tumor multiplicity and reduced by sulindac in obese mice. In sum, either moderate weight loss or sulindac treatment completely reversed the effects of chronic obesity on colon tumorigenesis. Our findings suggest that an investigation regarding the effects of NSAID treatment on colon cancer risk and/or progression in obese individuals is warranted, particularly for those unable to achieve moderate weight loss.

overall_design: 22 samples were analyzed

first: Elaine

last: Glenny


title: Effects of excessive FSH dose on granulosa cell, cumulus cell and oocyte transcriptomes in small ovarian reserve heifers

city: East Lansing

first: Peter

last: Schall

address: 474 S. Shaw Lane

department: CMIB ANS

institute: Michigan State University

summary: To evaluate the mechanisms by which excessive FSH doses during ovarian stimulation are detrimental to ovarian follicle function and assisted reproduction outcomes, small ovarian reserve (SOR) heifers were subjected to ovarian stimulation with either a standard, 70 IU, or excessive, 210 IU, dose of commercial porcine FSH (cpFSH) preparation, per injection. The ovaries were recovered at the end of the ovarian stimulation protocol, consisting of eight cpFSH injections at 12 h intervals. In excessive dose treated heifers, heterogeneity was observed with regards to follicle phenotype including cumulus cell-oocyte complex (COC) morphology and intrafollicular steroid hormone milieu. In contrast, standard-dose treated heifers exhibited one predominant follicle phenotype which was selected as the control follicle type for all comparisons herein. RNA-seq analyses of granulosa, cumulus cells and the oocyte from individual follicles of these defined phenotypes was used to identify changes in the transcriptomes of these cell types in excessive dose treated individuals.

overall_design: RNA-sequencing of the oocyte, cumulus and granulosa cells collected from individual ovulatory-size (≥ 10 mm) follicles from the ovaries of small ovarian reserve (SOR) heifers subjected to an ovarian stimulation protocol with either 70 IU (n = 7 heifers) or 210 IU (n = 6 heifers) cpFSH per injection. Follicles were classified into follicle types and one follicle per follicle type per heifer was randomly selected and RNA-libraries prepared. Samples from Type 1 follicles were treated as controls for subsequent comparisons because these follicles displayed the published characteristics (e.g., estrogen-active with a compact COC) of the ovulatory follicle in cattle and the fact that these samples were collected from standard, 70 IU, cpFSH dose-treated heifers.

first: Latham

middle: E

last: Keith

first: Clark

middle: L

last: Zaramasina

first: Karl

middle: R

last: Kaitlin

first: Schall

middle: Z

last: Peter

first: Ireland

last: James


title: Skeletal stem/progenitor cells in periosteum and skeletal muscle share a common molecular response to bone injury

city: Creteil

first: Celine

last: Colnot

state: Val de Marne

address: 8 rue du Général Sarrail

department: INSERM U955, IMRB

country: France

institute: Univ Paris Est Créteil, INSERM

summary: Periosteum is a major source of skeletal stem/progenitor cells (SSPCs) during bone repair. However, the cellular composition of the periosteum is poorly characterized. Here, we provide single-cell RNAseq data of periosteal cells isolated by explant culture at steady state and at day 3 post-tibial fracture. We found that periosteal cell populations are heterogeneous containing several sub-populations of SSPCs. Upon fracture, SSPCs are activated by leaving their mesenchymal state, and engaging into fibrogenesis prior to chondrogenesis.

overall_design: Periosteal cells from Prx1Cre;mTmG mice were isolated by explant culture without expansion. Periosteal cells at P0 were directly used for single cell RNAseq analyses.

first: Colnot

last: Celine

first: Perrin

last: Simon


title: Study the differential gene expression in A375 cells treated with DMSO or XL413 or GSK343 or GSK343 and XL413 combination

city: Birmimgham

first: Romi

last: Gupta

state: Alabama

address: 720, 20th street south

institute: University of Alabama at Birmingham

summary: The study evaluated the differential gene expression in A375 cells treated with DMSO when compared to XL413 or GSK343 or GSK343 and XL413 combination using RNA-seq

overall_design: Total RNA was extracted from A375 cells that were treated with  either DMSO or XL413 or GSK343 or GSK343 and XL413 combination for 24 hours , followed by poly-A selection and RNA-sequencing using Illumina Hi-Seq 4000 platform, with three biological replicates for each transformed sample.

first: Suresh

last: Bugide


title: Hepatic ARID3A facilitates liver cancer malignancy by cooperating with CEP131 to regulate an embryonic stem cell-like gene signature

city: Shanghai

first: Xianghuo

last: He

address: No 270, Dong An Road

institute: Fudan University

summary: Huh 7 cells were infected with lentivirus or transfected with siRNA using Lipofectamine RNAiMAX to overexpress or knockdown indicated genes. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) was performed using indicated antibodies to study the H3K9me2 status after certain treatment in Huh7 cells. Cleavage Under Targets and Tagmentation (CUT&Tag) was performed to explore the chromatin binding sites of ARID3A. Whole-transcriptome sequencing (RNA-Seq) was performed to identify the downstream target genes regulated by ARID3A or KDM3A in Huh 7 cells.

first: Mengting

last: Shen

first: Zhiao

last: Chen


title: High-Frequency Repetitive Transcranial Magnetic Stimulation (rTMS) Protects Against Ischemic Stroke by Inhibiting M1 Microglia Polarization through Let-7b-5p/HMGA2/NF-κB Signaling Pathway

city: Nanjing

first: Ye

last: Hong

address: No.68, Changle Road, Nanjing, Jiangsu Province, China

department: Department of Neurology

institute: Nanjing First Hospital

summary: Modulating M1/M2 polarization is a potential therapy for treating ischemic stroke. Repetitive transcranial magnetic stimulation (rTMS) held the capacity to regulate astrocytic polarization, but little is known about rTMS effects on microglia. Therefore, the present study aimed to investigate whether and how rTMS influence microglia polarization in ischemic stroke models. The 10-Hz rTMS was applied to transient middle cerebral artery occlusion (MCAO) rats and oxygen and glucose deprivation/ reoxygenation injured BV2 cells. Western blot, immunofluorescence and ELISA were used to detect M1/M2 markers. High-throughput sequencing, RT-PCR and FISH staining were adopted to test microRNA changes. The 10-Hz rTMS inhibited ischemia/reperfusion induced M1 microglia and significantly increased let-7b-5p. HMGA2 was proved to be the target protein of let-7b-5p and its downstream NF-κB signaling pathway were inhibited by rTMS. Microglia culture medium (MCM) collected from rTMS treated microglia had low TNF-α but high IL-10 concentration, leading to reduced neural death, minor ischemic volumes and improved functional recovery of MCAO animals. However, knockdown of let-7b-5p by antagomir reversed rTMS effects on microglia. In conclusion, high-frequency rTMS could improve functional recovery through inhibiting M1 microglia polarization via regulating let-7b-5p/HMGA2/NF-κB signaling pathway in cerebral ischemic stroke models.

overall_design: microRNA profiles of peri-infarct cortex tissue derived from the MCAO male SD rats (250-270g)  and MCAO rats with  rTMS treatment

first: Mengyi

last: Xu

first: Jinfeng

last: Lv


title: Gene expression profiling for spaceflight induced-neuroinflammation in the mouse brain

city: Loma Linda

first: Xiao Wen

last: Mao

state: CA

address: 11175 Campus Street

institute: Loma Linda University

summary: The health risk from spaceflight-induced neuronal damage and potential adverse neurovascular effects is a chief concern. More recently, it has been proposed that neuroinflammatory response plays an important role in the neurovascular remodeling in the brain after stress. The goal of the present study was to characterize changes in the gene expression of neuroinflammation panel for inflammation, neuronal function, metabolism and stress in mouse brain tissue. Ten-week old male C57BL/6 mice were launched to the International Space Station (ISS) on Space-X 12 for a 35-day mission. Within 38+4 hours of splashdown, mice were returned to Earth alive. Brain tissues were collected for analysis. Habitat ground control (GC) mice were maintained on Earth in flight hardware cages. A novel digital color-coded barcode counting technology (NanoStringTM) was used to evaluate gene expression profiles in the spaceflight mouse brain. The Neuroinflammation panel includes 757 genes covering the core pathways and processes that define neuroimmune interactions. A set of 54 differently expressed genes (p<0.05) significantly segregates the GC group from flight (FLT) group. Many pathways associated with cellular stress, inflammation, apoptosis, and metabolism were significantly altered by flight conditions. Genes supporting neuronal synaptic signaling and migration were significantly downregulated in FLT compared to the GC mice. A decrease in the expression of genes important for oligodendrocyte differentiation and myelin sheath maintenance was observed.  Moreover, mRNA expression of many genes related to antiviral signaling, reactive oxygen species (ROS) generation, and bacterial immune response were significantly downregulated. These data indicate that neuroinflammation and altered immune reactions may be closely associate with spaceflight-induced stress response and have an impact on the neuronal function that may result in chronic neuroinflammation and late neurodegeneration.

overall_design: A total of 12 frozen right caudal half hemispheres containing mid- and hindbrain from GC and FLT mice (n=6 per group), were used for analysis

first: Jacob

last: Holley

first: Seta

last: Stanbouly

first: Jeffrey

last: Willey

first: Michael

last: Pecaut

last: Delp

first: Xiao


title: Global histone H3 lysine 9 trimethylation (H3K9me3) landscape changes in response to TGF-β1

city: Ahmedabad

first: Noopur

last: Thakur

state: Gujarat

address: Navrangpura

department: Biological and Life Sciences

country: India

institute: Ahmedabad University

summary: TGF-β plays an important part in the Epithelial to Mesenchymal Transition (EMT) in many malignancies. TGF-β may have pro- and anti-tumour effects in cancer cells, depending on the context and microenvironment. On the other hand, epigenetic alterations are becoming increasingly significant in a variety of biological activities. Aberrations in epigenetic processes can cause gene function to be disrupted, as well as malignant cellular change. Understanding the role of H3K9me3 in cancer survival is becoming increasingly popular. A worldwide drop in the heterochromatin mark H3 Lys9 dimethylation (H3K9me2), an increase in the euchromatin mark H3 Lys4 trimethylation (H3K9me3), and an increase in the transcriptional mark H3 Lys36 trimethylation were discovered during TGF-β induced EMT (H3K36me3). Our study focuses on locating globally H3K9me3 related regions in response to TGF-β since TGF-β and H3K9me3 play an essential role in carcinogenesis. To further understand the role and process of H3K9me3 alteration in TGF-β induced EMT, ChIP-Sequencing was done in PC-3 prostate cancer cells.

overall_design: We performed Chromatin-Immunoprecipitation followed by Next-Generation Sequencing (ChIP-Seq) in PC-3 cells stimulated with TGF-β1 for different duration. We used anti-H3K9me3 antibody to immunoprecipitate DNA fragment associated with H3K9me3. We found that a number of regions associated with H3K9me3 decreased in a time-dependent manner upon TGF-β1 stimulation. Further the regions were classified into different Functional annotations.

first: Ankit

last: Naik


title: NELL-1 regulates the matrisome to alter osteosarcoma disease progression

city: Baltimore

first: Aaron

last: James

state: Maryland

address: 720 Rutland Avenue, Ross Bldg., Room 529

department: Pathology

institute: Johns Hopkins University

summary: Sarcomas produce abnormal extracellular matrix (ECM) which in turn provides instructive cues for cell growth and invasion. Neural EGF Like-Like molecule 1 (NELL-1) is a secreted glycoprotein characterized by its non-neoplastic osteoinductive effects, yet highly expressed in skeletal sarcomas. Here, NELL1 gene deletion markedly reduced invasive behavior across human osteosarcoma (OS) cell lines. This resulted in reduced OS disease progression, inhibited metastatic potential and improved survival in a xenograft model. These observations were recapitulated with Nell1 conditional knockout in mouse models of p53/Rb driven sarcomagenesis, including reduced tumor frequency, and extended tumor free survival.  Transcriptomic and phospho-proteomic analysis demonstrated NELL1 loss skews the expression of matricellular proteins associated with reduced FAK signaling. Culture on OS enriched matricellular proteins reversed phenotypic and signaling changes among NELL1 knockout sarcoma cells. These findings in mouse and human models suggest that NELL-1 expression alters the sarcoma matrix, thereby modulating cellular invasive potential and prognosis.  Disruption of NELL-1 signaling may represent a novel therapeutic approach to short circuit sarcoma disease progression.

overall_design: There are 8 samples: 4 biological replicates each of  NELL1 knockout compared to vector control cells

first: Qizhi

last: Qin


title: Next Generation Sequencing Facilitates Quantitative Analysis of NP1 and NP1/CRTCHA Gut Transcriptomes

first: HANSONG

last: DENG

address: RM 5O1, BLDG 1, # 817 ZHENGLI RD, YANGPU DISTRICT

institute: Tongji University

summary: Differential expression analysis used the DESeq2 Bioconductor package, a model based on the negative binomial distribution. the estimates of dispersion and logarithmic fold changes incorporate data-driven prior distributions, Padj of genes were setted <0.05 to detect differential expressed ones.Our study represents the detailed analysis of of NP1 and NP1/CRTCHA drosophila gut transcriptomes, with biologic replicates, generated by RNA-seq technology.Transcriptome analysis indicated that the genes involved in proteasome assembly, ROS scavengers, and protein folding were highly enriched among those differentially expressed genes (DEGs) in CRTC overexpressing (CRTCOE) intestines.

overall_design: Gut mRNA profiles of 3-5-day old NP1/+ and NP1/+;UASCRTCHA/+ drosophila

first: Hansong

last: Deng

first: Youjie

last: Yin


title: Study the differential gene expression in A375 cells treated with DMSO or XL413 or OF1 or OF1 and XL413 combination.

first: Romi

last: Gupta

summary: The study evaluated the differential gene expression in A375 cells treated with DMSO when compared to XL413 or OF1 or OF1 and XL413 combination using RNA-seq

overall_design: Total RNA was extracted from A375 cells that were treated with either DMSO or  XL413 or OF1 or OF1 and XL413 combination for 24 hours, followed by poly-A selection and RNA-sequencing using Illumina Hi-Seq 4000 platform, with three biological replicates for each transformed sample.

first: Suresh

last: Bugide


title: lncRNA-GM polarizes Th17 differentiation to mediate autoimmune inflammation by targeting Foxo1 activity

city: Hangzhou

first: Yali

last: Chen

address: 66 Yuhangtang Road

department: School of Medicine

institute: Zhejiang University

summary: Purpose: RNA-sequencing analysis of Th17 signature genes. The goals of this study are to compared the gene expression between wild type (WT) and lncRNA-GM-/- Th17 cells by RNA-seq analysise.

overall_design: Th17 cells were collected at 3 days under Th17 differentiation conditions, and then subjected to RNA seq.

first: Xuetao

last: Cao

first: Kun


title: MYCN directly regulates TET1 expression to control 5-hmC distribution and enhance neuroblastoma cell migration in hypoxia [RNA-Seq]

city: Stanford

first: Anastasia

last: Hains

email: hainsa@uchicago.edu, hains@stanford.edu

address: 269 Campus Drive

institute: Stanford University

summary: We performed RNA-sequencing on inducible MYCN cell line SHEPTET21n on Day 4 post MYCN induction

overall_design: RNA was extracted from SHEPTET21n cells that had been induced for 4 days. RNA was extracted from controls that had not been induced

first: Sakshi

last: Uppal

first: John

first: Helen

last: Salwen

first: Mark

last: Applebaum

first: Susan

last: Cohn

first: Lucy

last: Godley


title: MYCN directly regulates TET1 expression to control 5-hmC distribution and enhance neuroblastoma cell migration in hypoxia [ChIP-Seq]

summary: We performed HIF-1alpha ChIP-seq in SK-N-BE(2) cells cultured in normoxia vs. hypoxia for 48 hrs. We identified two new HIF-1alpha binding sites in TET1 that control TET1expression in hypoxia

overall_design: SK-N-BE(2) cells were cultured in normoxia or hypoxia for 48 hours. HIF-1alpha ChIP were performed on fixed chromatin


title: The role of CDC7 in Melanoma cancer growth and progression

summary: Disruptor of Cell Division Cycle 7 (CDC7) expression is elevated in many cancer types including melanoma. Therefore, we analyzed the role of CDC7 in melanoma. Pharmacological inhibition of CDC7 expression in Melanoma cancer cell lines resulted in decreased proliferation, and increased cell death.

overall_design: A375  and SK-MEL-28 cells were treated with  CDC7 inhibitor (10 micomolar) XL-413 for 48 hours, samples were harvested and were used to prepare the total RNA, followed by RiboRNA depletion with random priming and RNASeq Illumina Hi-Seq 2500 platform, with three biological replicates for each sample.

last: Chava


title: MYCN directly regulates TET1 expression to control 5-hmC distribution and enhance neuroblastoma cell migration in hypoxia [hMe-SEAL]

summary: We characterized genome-wide 5-hydroxymerhylcytosine (5-hmC) distribution at 0,6,12,24, 48, 72 hours in hypoxia in SK-N-BE(2) neuroblastoma cell line.5-hmC increases over time in hypoxic but especially between 0 and 6 and 24 to 48 hours.

overall_design: DNA was extracted from SK-N-BE(2) neuroblastoma cell line cultured in normoxia or hypoxia at various times. 5-hmC containing DNA was pulled-down and submitted for deep sequencing


title: ZNF165 as a potential novel immunotherapeutic target for gastric cancer

status: Public on Aug 09 2022

city: Lanzhou

first: Fan

last: Zhang

state: Gansu Province

address: 82 Cuiyingmen

department: Department of Oncology Surgery

institute: Lanzhou university

summary: Background: Cancer testis antigens (CTAs) are an extensive gene family with a unique expression pattern restricted to testis tissues, but aberrantly high expressed in a variety of cancer tissues. In view of this, CTAs are typically considered as efficient biomarkers and targets of immunotherapy. However, limited information is available regarding CTAs as immunotherapeutic targets for gastric cancer (GC) patients. Herein, we evaluated the expression levels of CTAs in both Eastern and Western GC patients and elucidate the expression pattern and functions of a novel CTAs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MKN28/MKN45 cells with knockdown and overexpressed ZNF165.

first: Yumin

last: Li


title: Single-cell RNA-seq of mouse peripheral iNKT cells

city: Detroit

first: Indra

last: Adrianto

address: 1 Ford Place

department: Public Health Sciences

institute: Henry Ford Health System

summary: Invariant natural killer T cells (iNKT) cells are differently distributed in various immune organs. However, it remains unclear whether iNKT cells exhibit phenotypical and functional differences in different peripheral organs and how thymic iNKT migrate to peripheral organs. Hence, characterizing iNKT cells in peripheral organs is important.

overall_design: We profiled the transcriptome patterns of individual mouse peripheral iNKT cells from liver, lymph node, and spleen using a droplet-based single-cell RNA-sequencing (scRNA-seq) approach.

first: Jie

last: Wang

first: Ian

last: Loveless

first: Tingting

last: Liu

first: Subedi

last: Kalpana

first: Xiaojun

last: Wu

first: Li

last: Zhou

first: Qing-Sheng

last: Mi


title: Transcriptional analysis of chemically induced hepatocyte-like cells from mouse fibroblasts

city: Beijing

first: yunfei

last: bai

address: No.5 Yiheyuan road

institute: Peking University

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

overall_design: Refer to individual Series


title: Duplicated ribosomal protein paralogs promote alternative translation and drug resistance

city: Montréal

first: Frédérick

last: Mallette

state: QC

address: 5415 boulevard de L'Assomption

department: Médecine

country: Canada

institute: Université de Montréal

summary: Ribosomes are often seen as monolithic machines produced from uniformly regulated genes. However, in yeast most ribosomal proteins come from duplicated genes. Here, we demonstrate that gene duplication may serve as an adaption mechanism modulating the global proteome through the differential expression of ribosomal proteins paralogs after exposure to stress. Our data indicate that the yeast paralog pair of the ribosomal protein L7/uL30 produces two differentially acetylated proteins. Under normal conditions most ribosomes incorporate the hypo-acetylated major form favoring the translation of genes with short open reading frames. Exposure to drugs, on the other hand, increases the production of ribosomes carrying the hyper-acetylated minor paralog that increases translation of long reading frames. Many of these long genes encode cell wall proteins that increase drug resistance in a programed change in translation equilibrium. Together the data reveal a mechanism of translation control through the differential fates of near-identical ribosomal protein isoforms.

overall_design: Total RNA and ribosome associated RNA from wild type cells and cells carrying a copy of either uL30A or uL30B on plasmid was sequenced.

first: Mustafa

last: Malik-Ghulam

first: Mathieu

last: Catala

first: Gaspard

last: Reulet

first: Michelle

last: Scott

first: Sherif

last: Abou Elela


title: Gene expression signatures for anti-glioma therapy with Ad-SGE-REIC and bevacizumab

city: Okayama

first: Yasuhiko

last: Hattori

address: 2-5-1 Shikata-cho, Kita-ku

country: Japan

institute: Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences

summary: We investigated the gene expression profile of tumor-bearing mouse brain treated with PBS(control), Ad-SGE-REIC(SGE), or combination of Ad-SGE-REIC and bevacizumab (SGE+BEV).

overall_design: Gene expression in mouse brain treated with PBS, Ad-SGE-REIC, Ad-SGE-REIC and bevacizumab were evaluated

first: Kazuhiko

last: Kurozumi


title: Transcriptional profiling of two muscadine grape cultivars ‘Carlos’ and ‘Noble’ to reveal new genes, gene regulatory networks, and pathways that involved in grape berry ripening

city: Gainesville

first: Tongjun

last: Gu

state: FL

address: 2033 Mowry Road

department: ICBR

institute: The University of Florida

summary: In commercial fruit production, synchronized ripening and stable shelf life are important properties. The loosely clustered or non-bunching muscadine grape has unrealized potential as a disease resistant cash crop, but requires repeated hand harvesting due to its unsynchronized or long or heterogeneous maturation period. Genomic research can be used to identify the developmental and environmental factors that control fruit ripening and postharvest quality.  This study coupled the morphological, biochemical, and genetic variations between ‘Carlos’ and ‘Noble’ muscadine grape cultivars with RNA-sequencing analysis during berry maturation. The levels of antioxidants, anthocyanins, and titratable acids varied between the two cultivars during the ripening process. We also identified new genes, pathways, and regulatory networks that modulated berry ripening in muscadine grape. These findings may help develop a large-scale database of the genetic factors of muscadine grape ripening and postharvest profiles and allow the discovery of the factors underlying the ripeness heterogeneity at harvest. These genetic resources may allow us to combine applied and basic research methods in breeding to improve table and wine grape ripening uniformity, quality, stress tolerance, and postharvest handling and storage.

overall_design: In the present study, we aimed to decipher the genetics and developmental differences between two cultivars of muscadine grape using morphological characterization as well as physiological and transcriptional analysis. The transcriptional profiles of grape berry were characterized at the last three stages of ripening in the muscadine grape cultivars ‘Carlos’ and ‘Noble’.  We identified new genes and molecular networks that are involved in the transition of berry ripening in both cultivars as well as in just one cultivar.

first: Yuru

last: Chang

first: Yogesh

last: Ahlawat

first: Ali

last: Sarkhosh

first: Tie


title: Spatial transcriptomics revealing host-microbe interactions

first: seqcore

last: sii

address: Southern Chongqing Road

institute: Shanghai Jiao Tong University School of Medicine

summary: We developed an analysis pipeline that can extract microbial sequences from Spatial Transcriptomic (ST) data and assign taxonomic labels, generating a spatial microbial abundance matrix in addition to the default host expression matrix, enabling simultaneous analysis of host expression and microbial distribution. We called the pipeline Spatial Meta-transcriptome (SMT) and applied it on both human and murine intestinal sections and validated the spatial microbial abundance information with alternative assays. Biological insights were gained from this novel data that that demonstrated host-microbe interaction at various spatial scales. Finally, we tested experimental modification that can increase microbial capture while preserving host spatial expression quality and, by use of positive controls, quantitatively demonstrated the capture efficiency and recall of our methods. This proof of concept work demonstrates the feasibility of Spatial Meta-transcriptomic analysis, and paves the way for further experimental optimization and application.

sample_organism:
Mus musculus
mouse gut metagenome

platform_organism:
Mus musculus
mouse gut metagenome

overall_design: Six-week-old male C57BL/6 mice were ordered from Shanghai SLAC Laboratory Animal Co.,Ltd. All mice were maintained under 12hr:12hr light-dark（LD）cycles and fed ad libitum in the Specific Pathogen Free(SPF) mouse facilities at Fudan University. All experimental procedures described in the study were approved by the Institutional Animal Care and Use Committees(IACUC) of Fudan University. 10-12 days later, feces and serum were collected and stored at −80℃.Intestine and colon tissue were washed in cold PBS and embedded in optimal cutting temperature(O.C.T) sectioning media(Thermo Scientific) by submersion in isopentane(2-methylbutane,Sigma Aldrich) pre-cooled to −80℃ in dry ice for ST.

first: Lin

last: Lyu

first: Xue

last: Li

first: Ru

last: Feng

first: Lei

last: Chen


title: Manipulation of  Long-Range Chromatin Interactions through CTCF Phase Separation for Cell Fate Control

first: lumeng

last: Jia

address: Yiheyuan

summary: Gene expression is controlled under spatial chromatin structures with short-range in topologically associating domains (TAD) and long-range chromatin interactions between TADs, compartments or chromosomes, and disruption of chromatin structure leads to human diseases. The mechanism of short-range chromatin interactions has been well characterized by loop-extrusion model, but little is known about how long-range chromatin interactions are organized. Here, we demonstrate that CTCF contributes to long-range chromatin interactions via phase separation. Surprisingly, RYBP is required for the phase separation and long-range chromatin organization of CTCF. Artificial CTCF phase seperation restores the long-range chromatin interactions and corresponding gene expression which were eliminated by RYBP depletion, and manipulation of CTCF phase separation also maintains pluripotency and inhibits differentation of embryonic stem cells. These findings support a model that long-range chromatin interactions are organized through phase sepearation of architectural protein, and further reveals the distinct mechanisms of architectural protein in organizing short-range and long-range chromatin interactions.

overall_design: Examination of  RNA-seq, Hi-C, CTCF HiChIP, RYBP HiCHIP NGS data before or/and after RYBP knock out.

first: Chao

last: Wei

first: Lumeng

first: Xiaona

last: Huang

first: Jin

last: Tan


title: K. pneumoniae induced metabolic stress promotes immunotolerance [single-cel RNA-seq]

city: Newark

first: Tania

last: Wong

state: New Jersey

address: 205 South Orange Avenue

department: Microbiology, Biochemistry and Molecular Genetics

institute: Rutgers NJ Medical School

summary: Metabolites generated in response to infection have a major role in shaping the nature of the immune response. We predicted that the metabolic response to the highly prevalent Klebsiella pneumoniae sequence type 258 (Kp ST258) strains is responsible for their ability to persist in the lungs, despite the expected proinflammatory signaling evoked by LPS. By combining in situ metabolic imaging and comprehensive transcriptional analyses, we demonstrate that Kp ST258 activates host glutaminolysis and fatty acid oxidation (FAO), generating an oxidant-rich microenvironment predisposed to the accumulation of anti-inflammatory monocyte populations. In a setting not unlike that generated by some tumors, metabolically active Kp ST258 elicits an immunotolerant, instead of a proinflammatory response. The bacteria in turn adapt to airway oxidants by upregulation of the Type VI Secretion System (T6SS), which is highly conserved across these strains worldwide. The global success of Kp ST258 can be explained, to a major extent, by their metabolic activity that promotes a permissive immune response to which the bacteria adapt.

overall_design: Single cell RNA-seq experiment: Intranasal administration of wild type BL/6 mice with metabolically active (viable) K. pneumoniae MKP103 or purified MKP103 LPS or PBS as control and an Irg1-/- mouse with metabolically active MKP103.

last: Wong Fok Lung

first: Kristin

last: Beaumont


title: Transcriptomics of chemically induced hepatocyte-like cells from mouse fibroblasts [RNA-seq]

first: yunfei

last: bai

summary: Here, we chemically induced hepatocyte-like cells (CiHeps) from mouse fibroblasts using a new protocol. To compare the transcriptional profiles between different cocktail-induced cells and primary hepatocytes  (pHeps), we profiled the transcriptomes of induced cells and freshly isolated primary mouse hepatocytes. CiHeps' function and maturation-related gene expression was validated as well as the similarity it shares with pHeps.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Mouse embryonic fibroblasts (MEFs), MEFs induced with chemical cocktails, including C6FAE, C6F(L), C6FAE-C6F(L), C6F5UE-C6F(L)V, NSF-derived CiHeps (induced by C6F5UE-C6F(L)V), or pHeps.

first: Yunfei

last: Bai

first: Xiaochan

last: Xu

first: Yang

last: Zhao


title: Next Generation Sequencing  of wild type (WT) and K14 conditional Il9ra-/- mice  ear epidermal cell layers

city: Sapporo

first: Ippei

last: Ikegami

state: Hokkaido

address: S1 W17, Chuo-ku

department: Department of Human Immunology

institute: Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine

summary: Complex interactions of keratinocytes with various cells like inflammatory cells and stromal cells contribute to the pathogenesis of chronic inflammatory dermatoses. In proinflammatory cytokines mediating such ill settings, interleukin (IL)-9 plays a pathological role in inflammatory dermatoses. However, IL-9-related mechanisms in such diseases are still incompletely understood. In this study, we established tamoxifen-induced keratinocyte-specific IL-9 receptor alpha-chain-deficient mice (K14CRE/ERTIl9ra∆/∆ mice) to examine the role of IL-9 in multicellular interactions under the condition of chronic skin inflammation. Studies using an imiquimod-induced psoriasis-like model showed that K14CRE/ERTIl9ra∆/∆ mice significantly reduced the severity of dermatitis and mast cell infiltration compared to K14WTIl9rafl/fl mice as controls. The transcriptome analyses of psoriasis-like lesions showed that the level of peptide tyrosine-tyrosine (Pyy), a member of neuropeptide Y family, was markedly downregulated in K14CRE/ERTIl9ra∆/∆ epidermis. Blockade of Pyy suppressed thickening of the epidermis and mast cell number in imiquimod-treated wild-type mice. Together with in vitro studies indicating a capacity of Pyy to induce IL-9 production and chemotactic activity of bone marrow-derived mast cells (BMMCs), these suggest that Pyy-mediated interplay of keratinocytes and mast cells induces psoriasiform inflammation. Further investigation focusing on the IL-9-Pyy axis would provide a new modality for treatment of chronic inflammatory dermatoses.

overall_design: Epidermal RNA profiles of IMQ treated wild type (WT) and K14 conditional Il9ra-/- mice

first: Shiori

last: Kamiya

first: Shingo

last: Ichimiya


title: Blood pressure changes PVAT function and transcriptome: use of the mid-thoracic aorta coarcted rat

city: East Lansing

first: Genaro

middle: Andres

last: Contreras

address: 736 Wilson Road Room D202, Michigan State University

department: Large Animal Clinical Sciences

institute: Michigan State University

summary: A mid-thoracic aorta coarcted rat was created to generate a stable pressure difference above versus below the coarctation ligature. This study determined that the PVAT around the thoracic aorta exposed to a higher pressure has a significantly reduced ability to assist stress relaxation versus that below the ligature and appears to retain the ability to be anticontractile. At the same time, the PVAT around the thoracic aorta exposed to higher pressure had a reduced adipogenic potential versus that below the ligature. Transcriptomics analyses indicated that PVAT below the coarctation showed the greatest number of DEGs with an increased profile of the synaptic neurotransmitter gene network.

overall_design: Male Sprague-Dawley Rats coarcted in the mid-thoracic aorta created PVAT tissues that would exemplify pressure-dependent changes (above vs. below coarctation); a sham rat was used as a control. Radiotelemetry revealed a ∼20 mmHg systolic pressure gradient across the coarctation 4 wk after surgery. Four measures (histochemical, adipocyte progenitor proliferation and differentiation, isometric tone, and bulk mRNA sequencing) were used to compare PVAT above versus below the ligature in sham and coarcted rats.

first: G

first: Yongliang

last: Yang

first: Emma

last: Flood

first: Hannah

last: Garver

first: Sudin

last: Bhattacharya

first: Gregory

last: Fink

first: Stephani

last: Watts


title: K. pneumoniae induced metabolic stress promotes immunotolerance

first: Tania

last: Wong

sample_organism:
Mus musculus
Klebsiella pneumoniae subsp. pneumoniae

overall_design: Dual RNA-seq experiment: Infection of wild type BL/6 and Irg1-/- (no itaconate produced) mice with K. pneumoniae MKP103 or PBS as control, Transcriptional data from bacteria isolated directly from murine lungs were compared to those from bacteria grown in Luria broth (control).

first: Shwetha

middle: H

last: Sridhar


title: RNA-seq Analysis of sibling and dhx38-- zebrafish

city: WuHan

first: Jiayi

last: Tu

address: LUOYU ROAD

institute: Huazhong university of science and technology

summary: Purpose: Loss of dhx38 disrupts the proliferation and differentiation balance of hematopoiesis. Notably, the mitosis of both EMPs and HSPCs are blocked in the pre-metaphase with abnormal chromatin karyotype in the dhx38--zebrafish. RNA-seq analysis screened abnormal splicing and aberrant expression genes that are likely to explain the dysfunction of mitosis.

overall_design: Tail tissue mRNA profiles of 36 hpf sibling (WT) and dhx38--zebrafish

first: Jingzhen

last: Li

first: Jiong

last: Luo


title: Osteoclast response to low extracellular sodium

city: Washington

first: Julianna

last: Barsony

state: DC

address: 4000 Reservoir Rd D/233

department: Medicine

institute: Georgetown University

summary:
RAW 264.7 murine osteoclastic cells were cultured with recombinant cytokines (RANKL and M-CSF) in culture medium with normal sodium (NS; Na=140 mmol/l) and low sodium and reduced sodium (Na=120 mmol.l) while maintaining normal ostmolality with the addition of mannitol. After 24 hours, total RNA was extracted using PureLink kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions, and purified using the Rneasy Mini Kit (Invitrogen). 5 µg RNA from each sample was converted into biotin-labeled cDNA and hybridized to GeneChip Mouse Genome 430 2.0 arrays containing 45,101 probe sets corresponding to known genes and expressed sequence tags.
Total RNA was extracted using PureLink kit (Invitrogen, Carlsbad, CA) according to manufacturer’s instructions, and purified using the Rneasy Mini Kit (Invitrogen). 5 µg RNA from each sample was converted into biotin-labeled cDNA and hybridized to GeneChip Mouse Genome 430 2.0 arrays containing 45,101 probe sets corresponding to known genes and expressed sequence tags.

overall_design: Growing evidence indicated that chronic hyponatremia causes osteoporosis by increasing osteoclastic bone resorption, thereby liberating stored sodium from bone. Cell culture studies suggested that low extracellular sodium directly increases osteoclast function, but the underlying mechanisms remained to be defined.

first: Julia


title: Single cell transcriptional analysis of chemically induced hepatocyte-like cells from mouse fibroblasts [scRNA-seq]

first: yunfei

last: bai

summary: Here, we chemically induced hepatocyte-like cells (CiHeps) from mouse embryonic fibroblasts (MEFs) using a new protocol. To illustrate the transcriptomic landscape of hepatocyte cell formation by chemical induction, scRNA-seq was performed in C6F5UE-C6F(L)V-induced MEFs at 60 days of induction. The analysis of scRNA-seq data revealed that gastrointestinal-like and keratinocyte-like cells were induced along with CiHeps and these induced epithelial cells closely resembled that of their primary counterparts.

overall_design:
scRNA-seq was performed in C6F5UE-C6F(L)V-induced MEFs at 60 days of induction.
Differentially expressed genes (DEGs) between different samples or consecutive clusters were identified with the FindMarkers function. Monocle (https://github.com/cole-trapnell-lab/, R package,v.2.20.0) was then employed for ordering cells based on progress through differentiation stages (pseudo-time), SCENIC (Single Cell Regulatory Network Inference and Clustering) was employed to define gene regulatory networks (GRN) in chemically induced cells, and Cellchat was used to analyze potential cell-cell communication

first: Yunfei

last: Bai

first: Wanqiu

last: Ding

first: Juntian

last: Qi

first: Yang

last: Zhao


title: ER, mitochondria and ISR regulation by mt-HSP70 and ATF5 upon procollagen misfolding (proximal tibia srRNASeq)

status: Public on Aug 08 2022

city: Bethesda

first: Sergey

last: Leikin

department: NICHD

institute: National Institutes of Health

summary: We used spatially resolved RNA sequencing (srRNA-seq) to identify trabecular osteoblast cell stress response pathway to misfolding of type I procollagen with Gly610->Cys substitution in the triple helical region of alpha2(I) chain (trabecular region of proximal tibia adjacent to the growth plate).

overall_design: Cryosections of fresh frozen proximal tibia were examined by srRNASeq as described in Gorrell et al, Adv Sci, 2022

first: Laura

last: Gorrell


title: Deficiency of the bZIP transcription factors Mafg and Mafk causes misexpression of genes in distinct pathways and results in lens embryonic developmental defects

first: Deepti

last: Anand

state: Delaware

address: 351 Wolf Hall, University of Delaware

department: Biological Sciences

institute: University of Delaware

summary: Deficiency of the small Maf proteins Mafg and Mafk cause multiple defects, namely, progressive neuronal degeneration, cataract, thrombocytopenia and mid-gestational/perinatal lethality. Previous data shows Mafg-/-:Mafk+/- compound knockout (KO) mice exhibit cataracts age 4-months onward. Strikingly, Mafg-/-:Mafk-/- double KO mice develop lens defects significantly early in life, during embryogenesis, but the pathobiology of these defects is unknown, and is addressed here. At embryonic day (E)16.5, the epithelium of lens in Mafg-/-:Mafk-/- animals appears abnormally multilayered as demonstrated by E-cadherin and nuclear staining. Additionally, Mafg-/-:Mafk-/- lenses exhibit abnormal distribution of F-actin near the “fulcrum” region where epithelial cells undergo apical constriction prior to elongation and reorientation as early differentiating fiber cells. To identify the underlying molecular changes, we performed high-throughput RNA-sequencing of E16.5 Mafg-/-:Mafk-/- lenses and identified a cohort of differentially expressed genes that were further prioritized using stringent filtering criteria and validated by RT-qPCR. Several key factors associated with the cytoskeleton, cell cycle or extracellular matrix (e.g. Cdk1, Cdkn1c, Camsap1, Col3A1, Map3k12, Sipa1l1) were mis-expressed in Mafg-/-:Mafk-/- lenses. Further, the congenital cataract-linked extracellular matrix peroxidase Pxdn was significantly overexpressed in Mafg-/-:Mafk-/- lenses, which may cause abnormal cell morphology. These data also identified the ephrin signaling receptor Epha5 to be reduced in Mafg-/-:Mafk-/- lenses. This likely contributes to the Mafg-/-:Mafk-/- multilayered lens epithelium pathology, as loss of an ephrin ligand, Efna5 (ephrin-A5), causes similar lens defects. Together, these 35 findings uncover a novel early function of Mafg and Mafk in lens development and identify their new downstream regulatory relationships with key cellular factors.

overall_design: For RNA-sequencing (RNA-Seq) experiments, mouse embryonic lenses at stage E16.5 (n = 8 lenses per biological replicate) were collected from  collected from control (Mafg+/-:Mafk+/-), compound (Mafg-/-:Mafk+/-) and double KO (Mafg-/-:Mafk-/-).  RNA isolation was performed using the mirVanaTM RNA isolation kit (Life Technologies, Grand Island, NY).  Total RNA isolation, followed by removal of small molecular weight RNA was performed according to manufacturer’s instructions.  Sequencing was performed on a 2x101 paired end run using standard protocols on an NovaSeq 6000 sequencing system and FASTQ sequence files were obtained

first: Anand

last: Deepti

first: Lachke

last: Salil


title: Single-cell microglial transcriptomics during demyelination defines a microglial state required for lytic carcass clearance

city: Edmonton

first: Jason

middle: R.

last: Plemel

state: Alberta

address: 5-64 Heritage Medical Research Centre

department: Department of Medicine

institute: University of Alberta

summary: How microglia respond and regulate demyelination is not fully understood. To understand how microglia respond during demyelination, we fed mice cuprizone and assessed the response of genetically fate-mapped microglia. Cuprizone-induced demyelination generated a robust microglial response. We conducted single-cell RNA sequencing and identified several cuprizone-associated microglia (CAM) clusters during demyelination. These clusters expressed a transcriptomic signature indicative of cytokine regulation and reactive oxygen species production with altered lysosomal and metabolic changes consistent with ongoing phagocytosis. To understand how microglia contribute to the clearance of dead oligodendrocytes, we ablated microglia starting at the peak of cell death. We used the viability dye acridine orange and monitored apoptotic and lytic cell morphologies after microglial ablation and found that microglia preferentially phagocytose lytic carcasses. In culture, microglia exposed to lytic carcasses partially recapitulated the CAM state, suggesting that phagocytosis contributes to this distinct microglial state during cuprizone demyelination.

overall_design: Microglia and Macrophages of the cuprizone-treated  and control C57BL/6 mice were isolated by Fluorescence-activated cell sorting (FACS) according to the presence  of Cd11b-FITC signal and analyzed using scRNAseq.

first: Sameera

last: Zia

first: Brady

middle: P

last: Hammond

first: Martin

last: Zirngibl

first: Anastasia

last: Sizov

first: Charbel

last: Baaklini

first: Sharmistha

last: Panda

first: Kelly

middle: V

last: Lee

first: Apurba

last: Mainali

first: Mena

middle: K

last: Burr

first: Sioned

last: Williams

first: Andrew

last: Caprariello

first: Thomas

last: Simmen

first: Bradley

last: Kerr


title: Differential gene expression in iPSC-derived human intestinal epithelial cell layers following exposure to two concentrations of the Short Chain Fatty Acids butyrate, propionate and acetate

city: Wageningen

first: Menno

last: Grouls

address: Postbus 8000

department: Toxicology

country: Netherlands

institute: Wageningen University & Research

summary: Intestinal epithelial cells and the intestinal microbiota are in a mutualistic relationship that is dependent on communication. This communication is multifaceted, but one aspect is communication through compounds produced by the microbiota such as the short-chain fatty acids (SCFAs) butyrate, propionate and acetate. Studying the effects of SCFAs and especially butyrate in intestinal epithelial cell lines like Caco-2 cells has been proven problematic. In contrast to the in vivo intestinal epithelium, Caco-2 cells do not use butyrate as an energy source, leading to a build-up of butyrate. Therefore, we used human induced pluripotent stem cell derived intestinal epithelial cells, grown as a cell layer, to study the effects of butyrate, propionate and acetate on whole genome gene expression in the cells. For this, cells were exposed to concentrations of 1 and 10 mM of the individual short-chain fatty acids for 24 hours. Unique gene expression profiles were observed for each of the SCFAs in a concentration-dependent manner. Evaluation on both an individual gene level and pathway level showed that butyrate induced the biggest effects followed by propionate and then acetate. Several known effects of SCFAs on intestinal cells were confirmed, such as effects on metabolism and immune responses. The changes in metabolic pathways in the intestinal epithelial cell layers in this study demonstrate that there is a switch in energy source from glucose to SCFAs, thus induced pluripotent stem cell derived intestinal epithelial cell are responding in a similar manner to SCFAs as in vivo intestinal tissues.

overall_design: Induced pluripotent stem cell derived intestinal epithelial cells were exposed to butyric acid (NaB; 1 or 10mM), acetic acid (NaA 1 or 10 mM), propionic acid, (NaP 1 or 10 mM) or control treatment (water) for 24 hours, and subjected to gene expression profiling by RNA-sequencing.

first: Aafke

middle: F

last: Janssen

first: Loes

middle: M

last: Duivenvoorde

first: Guido

last: Hooiveld

first: Hans

last: Bouwmeester

first: Meike

last: van de Zande


title: Gene expression profile at single cell level of mononuclear cells from the liver sinusoid

city: Seocho-gu

first: June-Young

last: Koh

state: Seoul

address: 2575 Nambusunhwan-ro,

institute: GENOME INSIGHT

summary: This study identified a distinct liver sinusoidal NK-like CD56hiCD161-CD8+ T-cell population that expands in the liver with hepatitis B virus-associated chronic liver disease. CD56hiCD161-CD8+ T cells exert NKG2C-mediated NK-like effector functions even without TCR stimulation.

overall_design:
We obtained liver sinusoidal mononuclear cells from the liver perfusate of healthy donors and recipients with hepatitis B virus (HBV)-associated chronic liver disease (CLD) during liver transplantation. We performed a CITE-seq analysis of liver sinusoidal CD45+ cells in combination with TCR-seq of liver sinusoidal mononuclear cells.

Please note that several samples were pooled into 1 GEM, and hashtags were used to distinguish each sample;
lsmc1_1: hashtag1 (HBV 1)
lsmc1_2: hashtag4 (HBV 2)
lsmc2_1: hashtag1 & hashtag4  (HC1 & 2)
lsmc2_2: hashtag2 & hashtag3  (HC3 & 4)
lsmc2_3: hashtag1 & hashtag4  (HBV 3 & 4)
lsmc2_4: hashtag2 (HBV 5)

first: Eui-Cheol

last: Shin


title: Transcriptomic analysis in hippocampus of C57BL/6 and DBA/2 mice

city: Nantong

first: He

last: Lichun

address: 9 Seyuan Road

institute: Nantong University

summary: Background: Previous studies have shown that significant difference in learning and memory ability existed between C57BL/6 and DBA/2 mouse. Identification of behavioral and genetic differences between these two strains is typically important for neuroscience research, indicating that they can be used to identify candidate genes for learning and memory. Objective: This study was conducted to identify candidate genes for learning and memory using C57BL/6 and DBA/2 mouse. Methods: We conducted a transcriptomic analysis in hippocampus of C57BL/6 and DBA/2 mouse using high throughput RNA deep sequencing (RNA-seq) technology to detect differentially expressed genes (DEGs). Differentially expressed genes were then functionally annotated. Results: We found a total of 31,714 genes from hippocampi of C57BL/6 and DBA/2 mice, which comprised 4,241 to 4,599 known genes with new isoforms and, 4,023 to 4,451 structurally optimized known genes. Among these genes, a total of 458 genes showed different expression in the two strains of mouse. Eight genes were randomly selected to be validated by qRT-PCR, and the expression levels of all genes were consistent with the RNA sequencing. Conclusion: Our data indicated that there were different gene expression patterns between hippocampi of C57BL/6 and DBA/2 mice. The genes associated with learning and memory discovered in the study may enhance the explanation of the behavioral differences between the two mice.

first: Lichun

last: He

first: Lvqing

last: Miao

first: Lulu

last: Yu

first: Jiahong

last: Xia


title: Altered gene expression profiles impair the nervous system development in patients with 15q13.3 microdeletion

city: Leipzig

first: Diana

last: Le Duc

address: Deutscher Platz 6

department: Department of Evolutionary Genetics

country: Germany

institute: Max Planck Institute for Evolutionary Anthropology

summary:
Background: The 15q13.3 microdeletion has pleiotropic effects ranging from apparently healthy to severely affected individuals with intellectual disability, epilepsy, and neuropsychiatric disorders. Previous studies have investigated several genes within the deletion as potential drivers, but the pathomechanism and the underlying basis of the variable phenotype remain elusive.
Methods: We analyzed the effects of the 15q13.3 microdeletion on genome-wide gene expression using native RNA-seq data from blood of 3 probands with the 15q13.3 microdeletion and 4 sex- and age-matched control subjects. We assessed differentially expressed genes (DEGs), gene ontology (GO) enrichment, protein-protein interaction (PPI) functional modules, as well as gene expression in different brain developmental stages.
Results: The haploinsufficiency of genes within the deleted region was not transcriptionally compensated, suggesting that a dosage effect may contribute to the pathomechanism. Although GO and PPI showed that regulation of gene expression is perturbed, we could not identify a singular driving transcription factor. We observed network-wide dysregulatory effects suggesting that the phenotype is not caused by a singular critical gene. A significant proportion of DEGs, which are silenced in the adult brain, have maximum expression during the prenatal stage of brain development. Based on DEGs and their PPI partners we identified altered functional modules related to immune and inflammatory processes, as well as nervous system development.
Conclusions: We show that the 15q13.3 microdeletion has a ubiquitous impact on transcriptome pattern, especially dysregulation of genes involved in brain development. The effect on immune and inflammatory responses cannot be fully assessed based on the test material, i.e. blood. Possibly, the high phenotypic variability seen in 15q13.3 microdeletion could stem from an increased vulnerability during brain development, instead of a specific pathomechanism.

overall_design: RNAseq data of whole blood samples from three 15q13.3 microdeletion patients and four controls

first: Marek

middle: B

last: Körner

first: Akhil

last: Velluva

first: Linnaeus

last: Bundalian

first: Maximilian

last: Radtke

first: Chen-Ching

last: Lin

first: Pia

last: Zacher

first: Tobias

last: Bartolomaeus

first: Achmed

last: Mrestani

first: Nicole

last: Scholz

first: Konrad

last: Platzer

first: Anne

last: Teichmann

first: Julia

last: Hentschel

last: Langenhan

first: Johannes

last: Lemke

first: Antje

last: Garten

first: Rami

last: Abou Jamra


title: Oligodendrocyte differentiation alters tRNA modifications and codon-dependent mRNA decay  [QuantM-seq II]

city: Baltimore

first: Jeff

last: Coller

address: 725 N. Wolfe St PCTB 505

institute: Johns Hopkins University

summary: Oligodendrocytes are specialized cells that confer neuronal myelination. Leukodystrophies associated with oligodendrocyte and hypomyelination are known to result when a number of tRNA metabolism genes are mutated. Thus, for unknown reasons, oligodendrocytes may be hypersensitive to perturbations in tRNA biology. In this study, we survey the tRNA transcriptome in the murine oligodendrocytes cell lineage in an effort to understanding the molecular underpinning for human disease. We find that specific tRNAs are hypomodified in oligodendrocytes within or near the anticodon. This hypomodified state may be the result of differential expression of key modification enzymes during oligodendrocyte differentiation. Moreover, we observe a concomitant relationship between tRNA hypomodification and tRNA decoding potential; observing oligodendrocyte specific alterations in codon optimality-mediated mRNA decay and ribosome transit. Our results reveal that oligodendrocytes naturally maintain a delicate, hypersensitized tRNA/mRNA axis. We suggest this axis underlies disease etiology when further insult to tRNA metabolism is introduced.

overall_design: tRNA sequencing data (QuantM-seq) of S. cerevisiae WT (2 replicates), TYW1 deletion (tyw1∆) (2 replicates) and WT/tyw1∆ mixes with ratio 1:3 or 3:1 (2 replicates each)

first: Sophie

last: Martin

first: Kevin

middle: C

last: Allan

first: Otis

last: Pinkard

first: Thomas

last: Sweet

first: Paul

last: Tesar


title: Human Sensory Neurons Modulate Melanocytes Through Secretion of RGMB

city: Meguro

first: Yoshiho

last: Ikeuchi

state: Tokyo

address: 4-6-1 Komaba

department: Institute of Industrial Science

institute: The University of Tokyo

summary: Melanocytes are surrounded by diverse cells including sensory neurons in our skin, but their interaction and functional importance has been poorly investigated. In this study, we found that melanocytes and nociceptive neurons contact more in human skin color patch tissue than control. Co-culture with human iPS cell-derived sensory neurons significantly induced morphogenesis and pigmentation of human melanocytes. To reveal melanocytes-stimulating factors secreted from neurons, we performed proteomic analyses and identified RGMB in the sensory neuron-conditioned media. RGMB protein induced morphogenesis and melanin production of melanocytes, demonstrating that RGMB is a melanocyte-stimulating factor released from sensory neurons. Transcriptome analysis suggested that the melanosome transport machinery could be controlled by RGMB, which led us to identify vesicle production response of melanocytes upon RGMB treatment. This study discovered a role of sensory neurons to modulate multiple aspects of human melanocytes through secretion of a key factor RGMB.

overall_design: RNA-seq of melanocytes upon recombinant RGMB treatment and RGMB depleted IPSC-derived sensory neuron conditioned media.

first: SiuYu

middle: A

last: Chow

first: Kazuki

last: Nakayama

first: Tatsuya

last: Osaki

first: Maki

last: Sugiyama

first: Maiko

last: Yamada

first: Hirotaka

last: Takeuchi


title: Ablation of NLRP3 inflammasome rewires MDSC function and promotes tumor regression

city: Athens

first: Maria

last: Grigoriou

state: Papagou

address: Soranou Efesiou 4

country: Greece

institute: BRFAA

summary: Myeloid-derived suppressor cells (MDSCs) are myeloid precursors which exert potent immunosuppressive properties in cancer. Despite the extensive knowledge on mechanisms implicated in mobilization, recruitment and function of MDSCs, still their therapeutic targeting remains an unmet need in cancer immunotherapy suggesting that unappreciated mechanisms of MDSC-mediated suppression exist. Herein, we demonstrate an important role of NLRP3 inflammasome in the functional properties of MDSCs in tumor-bearing hosts. Specifically, Nlrp3-deficient mice exhibited reduced tumor growth compared to wild-type animals and induction of robust anti-tumor immunity, accompanied by re-wiring of the MDSC compartment. Interestingly, both monocytic (M-MDSCs) and granulocytic (G-MDSCs) subsets from Nlrp3-/- mice displayed impaired suppressive activity and demonstrated significant transcriptomic alterations supporting the loss-of-function and associated with metabolic re-programming. Finally, therapeutic targeting of NLRP3 inhibited tumor development and re-programmed the MDSC compartment. These findings propose that targeting NLRP3 in MDSCs could overcome tumor-induced tolerance and may provide new checkpoints of cancer immunotherapy.

overall_design: The role of NLRP3 inflammasome in the functional properties of MDSCs in tumor-bearing hosts.

first: Iosif

last: Papafragkos

first: Panayotis

last: Verginis


title: Distinct ribosome states trigger diverse mRNA quality control pathways

first: Anthony

middle: John

last: Veltri

address: 725 N. Wolfe St

department: Molecular Biology and Genetics

summary: Key protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on nonoptimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully-designed reporter mRNAs to perform genetic screens and functional assays in S. cerevisiae. We characterize the roles of Hel2 and Syh1 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 acts as the primary link to mRNA decay in NGD. Importantly we, observe that these NGD factors are not involved in the degradation of mRNAs enriched in nonoptimal codons. Further, we establish that key factors previously implicated in COMD, Not5 and Dhh1 , contribute modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new mechanistic insight into the role of Syh1 in NGD and define the molecular triggers that determine how distinct pathways target mRNAs for degradation in yeast.

overall_design: Monosome and disome footprint profiling was performed on yeast strains containing one of three different translation reporters (minOPT, minNONOPT, or minCGA) and in one of three different genetic backgrounds (wild-type, hel2∆ and syh1∆). Two or three replicates per reporter/background pair were performed.

middle: J

first: Rachel

last: Green