title: Adult-repopulating lymphoid potential is not confined to the arterial endothelial cells in yolk sac

first: Gong

last: Yandong

address: DongDaJie #8

institute: the Fifth Medical Center of the PLA General Hospital

summary: During embryogenesis, hematopoietic stem progenitor cells (HSPCs) are believed to  be derived from hemogenic endothelial cells (HECs). Moreover, arterial feature is  proposed to be a prerequisite for the HECs to generate HSPCs with lymphoid potential.  Whereas the molecular basis of the hematopoietic stem cell-competent HECs has been  delicately elucidated within the embryo proper, the functional and molecular  heterogeneity of HECs in the extra-embryonic yolk sac (YS) remains largely  unresolved. In this study, we firstly identified six molecularly different endothelial  populations in the mid-gestational YS through integrated analysis of several single-cell  RNA sequencing (scRNA-seq) datasets, and validated the arterial vasculature  distribution of Gja5+ ECs by using a Gja5-EGFP reporter mouse model. We further  explored the hemogenic potential of different EC populations based on their Gja5-  EGFP and CD44 expression. The lineage differentiation potentials of ECs were  spatiotemporally different and the B lymphoid potential was detected in the YS ECs as  early as embryonic day (E) 8.5 regardless of their arterial feature. Unexpectedly,  capacity of generating hematopoietic progenitors with in vivo lymphoid potential was  found in non-arterial in addition to arterial YS ECs at E10.0-E10.5. Importantly, the  distinct identities of E10.0-E10.5 ECs with a hemogenic potential between those from  YS and from intra-embryonic caudal region were revealed by further scRNA-seq  analysis. Taken together, these findings extend our knowledge about the hemogenic  potential of ECs from anatomically and molecularly different vascular beds, providing  a theoretical basis for better understanding the sources of HSPCs during mammalian  development.

overall_design: Sequencing libraries were prepared following a modified single-cell tagged reverse  transcription (STRT) protocol as previously reported (Li et al., 2017; Picelli et al.,  2013). The cells were first judged by morphology to assess their state, with cells in  good condition being picked and directly placed into lysis buffer. The reverse  transcription reaction was performed using a sample-specific 25-nucleotide (nt) oligo  dT primer containing an 8-nt barcode (TCAGACGTGTGCTCTTCCGATCTXXXXXXXX-  DDDDDDDD-T25, where X represents the sample-specific barcode,  and D stands for the unique molecular identifier (UMI)). After reverse transcription and  second-strand cDNA synthesis, the cDNAs were amplified by 16 cycles of PCR. The barcoded DNAs were then pooled together and purified using AMPure XP beads.  Biotinylated pre-indexed primers were used to further amplify the PCR product by an  additional four cycles of PCR to introduce biotin tags to the 3′ ends of the amplified  cDNAs. Approximately 300 ng cDNA was sonicated into 300-bp fragments using the  Covaris S2 system and enriched with Dynabeads MyOneTM Streptavidin C1 beads.  Libraries were constructed using a Kapa Hyper Prep Kit (Kapa Biosystems) and were  then submitted to150-bp paired-end sequencing on an Illumina Hiseq X Ten  platform (Novogene).

first: Chaojie

last: Wang

first: Yandong

last: Gong


title: RNA-seq of macrophages treated with or without IL-36gamma

status: Public on Jul 12 2021

city: Beijing

first: Jiao

last: Fan

address: Fuxing road

country: China

institute: 301 hospital

type: Expression profiling by high throughput sequencing

summary: Atherosclerosis is chronic inflammation disease and macrophage-derived foam cell formation is a critical early event in atherogenesis. Interleukin(IL)-36 was found to be involved in inflammation. To explore the regulation of IL-36 gamma in macrophages, we performed RNA sequencing (RNA-seq) in mouse bone marrow derived macrophages (BMDMs) treated with or without rIL-36γ.

overall_design: mRNA profiles of macrophages treated with or without IL-36 gamma

first: Minghua

last: Zhang


title: Changes in gene expression after mechanical loading with and without satellite cell.

city: Lexington

first: Vandre

middle: C

last: Figueiredo

state: Kentucky

address: Rose street

country: USA

institute: University of Kentucky

summary: Skeletal muscle is a plastic tissue, adapting to different stimuli. Mechanical overload causes muscle hypertrophy and substantial changes in gene expression. We perform a time course analysis following synergistic ablation surgery to induce compensatory hypertrophy in the plantaris muscle in satellite cell depleted mice and wild-type mice. Microarray was used to determine the different expressed genes in skeletal muscle with or without satellite cell following mechanical overload.

overall_design: Mice were treated with tamoxifen to induce satellite cell (SC) depletion or vehicle (control). Following SC ablation, SC depleted mice (SC-) and satellite cell competent mice (SC+, or wild type) were subjected to mechanical overload of the plantaris muscle induced by synergist ablation surgery (removal of soleus and gastrocnemius tendon). Each experimental group had samples collected after 1, 3, 5 and 7 days post synergistic ablation in addition to a sham surgery control. Total RNA was isolated from n of 5-6 for each group per time point. For microarray analysis, samples were pooled with a total of n=2 per time point.

first: Ivan

middle: J

last: Vechetti

first: Joh

last: Mccarthy


title: MiRNA expression in cerebrospinal fluid of angiogenesis or non-angiogenesis after Encephalo-myo-synangiosis in patients with moyamoya disease

status: Public on Jul 14 2021

city: Guangzhou

first: Gang

state: Guangdong

address: 1023 Guangzhou Avenue North

department: Neurosurgery

institute: Nanfang Hospital of Southern Medical University

type: Non-coding RNA profiling by high throughput sequencing

summary: At present, the treatment for moyamoya disease (MMD) primarily consists of combined direct and indirect bypass surgery. Nevertheless, more than half of indirect bypass surgeries fail to develop good collaterals from the dura and temporal muscle. This study aimed to investigate whether microRNAs (miRNAs) in cerebrospinal fluid (CSF) could serve as biomarkers for the prediction of postoperative collateral formation.

overall_design: We obtained cerebrospinal fluid by lumbar puncture, and performed small RNA sequencing to determine the expression profiles of miRNAs in cerebrospinal fluid of angiogenesis or non-angiogenesis after Encephalo-myo-synangiosis in patients with moyamoya disease

first: Wang

last: Gang

first: Wen

last: Yunyu

first: Feng

last: Wenfeng

first: Qi

last: Songtao


title: Gene expression analysis of collecting duct carcinoma

status: Public on Jul 13 2021

city: Milano

first: Chiara

last: Gargiuli

address: via Amadeo

department: Dept. of Applied Research and Technological Development

country: Italy

institute: Fondazione IRCCS Istituto Nazionale dei Tumori di Milano

summary: We performed a transcriptomic analysis in a cohort of 6 Collecting Duct Carcinoma, 5 Clear Cell Renal Cell Carcinoma and 4 non-matched normal renal tissues to unravel the underlying biological and molecular determinants  and to identifiy specific genes and pathways of this rare tumor type.

overall_design: Gene expression profiles were generated from FFPE tissue of 6 collecting duct carcinoma samples, 5 clear cell renal cell carcinoma and four normal kidney samples (one matched with a CDC patient, three matched with clear cell renal cell carcinoma patients).

first: Giuseppe

last: Procopio

first: Elena

last: Verzoni

first: Matteo

last: Dugo


title: A photoregulatory mechanism of the circadian clock in plants [RNA-seq]

city: fuzhou

first: Lianfeng

last: Gu

address: No.15 Shangxiadian Road, Cangshan District, Fuzhou City, Fujian Province, China

institute: Fujian Agriculture and Forestry University

summary: Circadian clocks are the time-keeping cellular apparatuses that are photoentrained according to the day-night photocycles on Earth 1,2.  Cryptochromes (CRYs) are photoreceptors mediating photoentrainment of the circadian clock in plants and animals but how CRYs mediate light regulation of the molecular clock remains unclear 1,3.  Here we show that CRYs mediate photoresponses of the circadian clock by regulating the activity of N6-methyladenosine (m6A) RNA methyltransferase and photoresponses of the epitranscriptome.  In contrast to the presently known CRY complexome, the CRY2-methyltransferase complex exbibits multivalent interactions and photoresponsive condensation in response to blue light.  We show that photoexcited CRY2 undergoes phosphorylation-assisted demixing to form photobodies with the properties of condensed liquid phase, which facilitates assembly of the CRY2-methyltransferase complex in the condensed liquid phase of CRY2 in vivo.  The mta mutant impaired in m6A methyltransferase and the cry1cry2 mutant missing CRY photoreceptors share common defects of lengthened circadian period, reduced m6A RNA methylation, and accelerated degradation of mRNAs encoding core components of the molecular clock.  These results argue for a photoentrainment mechanism by which blue light elicits liquid-liquid phase separation of the CRY2-methyltransferase complex to regulate m6A mRNA methylation, consequently suppressing mRNA degradation and period lengthening of the circadian clock

overall_design: RNA-seq of WT and cry1cry2 seedlings

first: Xu

first: Chentao

last: Lin


title: A photoregulatory mechanism of the circadian clock in plants

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

overall_design: Refer to individual Series


title: Functional antagonism of chromatin modulators regulates EMT [ChIP-Seq]

status: Public on Jul 16 2021

city: Berlin

first: Gaetano

last: Gargiulo

address: Robert-Rössle-Straße 10

country: Germany

institute: Max-Delbrück-Centrum für Molekulare Medizin

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Genome-wide chromatin analyses to validate the CRISPR interference screen for modulators of mesenchymal signaling reporter in A549 and H1944 cells. ATAC-seq in naive, GSK126- and TGFB-treated A549 cells. ChIP-seq in naive A549 cells for chromatin modulators, ChIP-seq in naive and GSk126-treated cells from RNAPII in A549 cells.

overall_design: Examination of a total six histone modifications and chromatin regulators in naive A549 cells, naive and GSk126-treated cells

first: Michela

last: Serresi

first: Lifei

last: Li


title: A photoregulatory mechanism of the circadian clock in plants [MeRIP-seq]

overall_design: MeRIP-seq of WT and cry1cry2 seedlings

last: Wang


title: Kif5C associated RNAs from mouse hippocampus

city: Jupiter

first: Sathyanarayanan

middle: V

last: Puthanveettil

state: Florida

address: 130 Scripps Way

department: Neuroscience

institute: Scripps Florida

summary: To identify Kif5C transported RNAs, we carried out co-immunoprecipitation of KIf5C-RNA protein complexes from mouse hippocampus. RNAseq analysis reveal ~600 RNAs differentially enriched in the Kif5C complexes suggesting that these are are likely transported to the dendrites by Kif5C. These RNAs code for regulators of structural re-arrangements, translation and synaptic remodeling.

overall_design: Co-immunoprecpitation (Co-IP) of Kif5C from mouse hippocampus using an antibody that can succesfully immunoprecipitate Kif5C from mouse hippocampus. Co-IP using  IgG Ab was used as control.For each Co-IP, we used hippocampi from two adult mice. For the RNAseq analysis, we pooled 6 different Co-IP samples into two samples. Two samples corresponding to Kif5C Co-IP and two for the control Co-IP. Following IP, RNAs were isolated using Trizol method and submitted to Scripps Genomics Core for Processing.

first: Supriya

last: Swarnkar

first: Bindu

last: Raveendra

first: Eddie

last: Grinman


title: Development of novel diagnostic system for pancreas cancer including early stages measuring mRNA of whole blood cells

city: Kanazawa

first: Yoshio

last: Sakai

state: Ishikawa

address: 13-1 Takara-machi

department: Department of Gastroenterology

country: Japan

institute: Kanazawa University

summary: The aim of the study is the assessment of diagnostic efficacy of extracorporeal diagnostic reagent pancreatic cancer diagnosis kit whose principle is the measurement of gene expression affected in pancreatic cancer human patients. Clinical trial registration number: UMIN000020758.

overall_design:
Development of a blood mRNA pancreatic ductal adenocarcinoma (PDAC) screening system using real-time detection PCR to detect the expression of specific genes, in order to discriminate PDAC from healthy volunteers. We performed a clinical study to assess the performance of the developed system. We collected whole blood RNA from PDAC patients and non-cancer subjects. The sensitivity of the system for PDAC diagnosis and the specificity for non-cancer volunteers were determined for the evaluation of the screening system.
Contributed by Hokuriku Liver Study Group

first: Masao

last: Honda

first: Shigeyuki

last: Matsui

first: Osamu

last: Komori

first: Toshinori

last: Murayama

first: Tadami

last: Fujiwara

first: Masaaki

last: Mizuno

first: Yasuhito

last: Imai

first: Kenichi

last: Yoshimura

first: Alessandro

last: Nasti

first: Takashi

last: Wada

first: Noriho

last: Iida

last: Kitahara

first: Rika

last: Horii

first: Tamai

last: Toshikatsu

first: Masashi

last: Nishikawa

first: Hirofumi

last: Okafuji

first: Eishiro

last: Mizukoshi

first: Tatsuya

last: Yamashita

first: Taro

first: Kuniaki

last: Arai

first: Kazuya

last: Kitamura

first: Kazunori

last: Kawaguchi

first: Hajime

last: Takatori

first: Tetsuro

last: Shimakami

first: Takeshi

last: Terashima

first: Tomoyuki

last: Hayashi

first: Koki

last: Nio

first: Shuichi

last: Kaneko


title: Visual experience-dependent expression of Fn14 is required for retinogeniculate refinement (Fn14 KO RNA-Seq)

city: Boston

first: Lucas

middle: Martin

last: Cheadle

state: MA

address: 220 Longwood Ave; Goldenson Bldg 413

department: Neurobiology

institute: Harvard Medical School

summary: Sensory experience influences the establishment of neural connectivity through molecular mechanisms that remain unclear. Here, we employ single-nucleus RNA-sequencing to investigate the contribution of sensory-driven gene expression to synaptic refinement in the dorsal lateral geniculate nucleus of the thalamus, a region of the brain that processes visual information. We find that visual experience induces the expression of the cytokine receptor Fn14 in excitatory thalamocortical neurons. By combining electrophysiological and structural techniques, we show that Fn14 is dispensable for early phases of refinement mediated by spontaneous activity, but that Fn14 is essential for refinement during a later, experience-dependent period of development. Refinement deficits in mice lacking Fn14 are associated with functionally weaker and structurally smaller retinogeniculate inputs, indicating that Fn14 mediates both functional and anatomical rearrangements in response to sensory experience. These findings identify Fn14 as a molecular link between sensory-driven gene expression and vision-sensitive refinement in the brain.

overall_design: Whole-transcriptome RNA-sequencing was performed on microdissected dLGN tissue from male and female Fn14 KO and WT littermates at P27. Differential gene expression analysis was used to compare KO to WT.

first: Christopher

middle: P

last: Tzeng

first: Brian

middle: T

last: Kalish

first: David

middle: A

last: Harmin

first: M

last: Nagy

first: Michael

middle: E

last: Greenberg


title: Visual experience-dependent expression of Fn14 is required for retinogeniculate refinement (stimulus RNA-Seq)

overall_design: Whole-transcriptome RNA-sequencing was performed on microdissected dLGN tissue from C57Bl/6J WT mice (male and female) following dark-rearing and re-exposure to light for 0, 1, or 8 hours. Differential gene expression analysis was performed to compare 1 or 8 hours of stimulation with 0 hours.


title: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes Caused by Dexamethasone Treatment in Cancer Cells

city: Shanghai

first: Zhen

last: Xiang

state: Shanghai

address: No. 197, Ruijin er Road

institute: Department of Surgery of Ruijin Hospital

summary: As commonly used drug in clinical, there is little known about the effects of dexamethasone (Dex) on cancer cells. The goals of this study are to explore the transcriptome caused by Dex in cancer cells. Seven cancer cell lines were used in this project, gastric cancer cell lines SGC-7901 and MKN-45, and colorectal cancer cell lines NCIH-747 and RKO, liver cancer cell line SMMC-7721, pancreatic cancer cell line BxPC3, melanoma cell line MV3. After treated by Dex for 48 hours, total RNAs were extracted for next-generation sequencing profiling.

overall_design: RNA profiles of seven cancer cell lines after DMSO or Dex treatment were generated by deep sequencing, using Illumina HiSeq 2000.

first: Yingyan

last: Yu


title: Pioneer factor Foxa2 enables ligand-dependent activation of type II nuclear receptors FXR and LXRa

city: Charlottesville

first: Irina

last: Bochkis

state: VA

address: 1340 Jefferson Park Ave

department: Pharmacology

institute: University of Virginia

summary: Type II nuclear hormone receptors, such as FXR, LXR, and PPAR, which function in glucose and lipid metabolism and serve as drug targets for metabolic diseases, are permanently positioned in the nucleus regardless of the ligand status. Ligand activation of these receptors is thought to occur by co-repressor/co-activator exchange, followed by initiation of transcription. However, recent genome-wide location analysis showed that LXRα and PPARα binding in the liver is largely ligand-dependent.  We hypothesized that pioneer factor Foxa2 evicts nucleosomes to enable ligand-dependent receptor binding. We show that chromatin accessibility, FXR binding and LXRα occupancy, and ligand-responsive activation of gene expression by FXR and LXRα require Foxa2. Unexpectedly, Foxa2 occupancy is drastically increased when either receptor, FXR or LXRα, is bound by an agonist.  In addition, co-immunoprecipitation experiments demonstrate that Foxa2 interacts with either receptor in a ligand-dependent manner, suggesting that Foxa2 and the receptor bind DNA as an interdependent complex during ligand activation.  Furthermore, PPARα binding is induced in Foxa2 mutants treated with FXR and LXR ligands, leading to activation of PPARα targets.

overall_design:
Chromatin accessibility, binding, and transcriptional analysis (ATAC-Seq, ChIP-Seq, and RNA-seq) of WT and Foxa2 mutant mouse livers after 4 hours after injection of a ligand (FXR agonist GW4064, LXR agonist GW3965, or GW agonist T09) or vehicle control
ATAC-Seq was performed on WT and Foxa2 KO mouse livers  in replicates of 2. For ATAC-Seq analysis, PeakSeq was used to call peaks in the WT ligand conditions against vehicle control .
Foxa2 ChIP-Seq was performed on WT mouse livers  in replicates of 3.  FXR ChIP-Seq was performed on WT and Foxa2 KO mouse livers  in replicates of 2. LXRα ChIP-Seq was performed on WT and Foxa2 KO mouse livers  in replicates of 4. PPARα ChIP-Seq was performed on WT and Foxa2 KO mouse livers  in replicates of 2. For ChIP-Seq analysis, PeakSeq was used to call peaks in the all conditions against input control.
RNA-Seq was performed on WT and Foxa2 mutant mouse livers  in replicates of 3 or 4. For RNA-Seq analysis, EdgeR was used for differential expression.

first: Nihal

last: Reddy

middle: M


title: Visual experience-dependent expression of Fn14 is required for retinogeniculate refinement


title: Visual experience-dependent expression of Fn14 is required for retinogeniculate refinement (development RNA-Seq)

overall_design: Whole-transcriptome RNA-sequencing was performed on microdissected dLGN tissue from C57Bl/6J WT mice (male and female) at 7 developmental timepoints (E18 through P32, listed below). Differential gene expression analysis was used to compare adjacent time points.


title: Visual experience-dependent expression of Fn14 is required for retinogeniculate refinement (stimulus single nucleus RNA-Seq)

overall_design: Single-nucleus RNA-sequencing was performed on microdissected dLGN tissue from C57Bl/6J WT mice (male and female) following dark-rearing and re-exposure to light for 0, 1, or 8 hours. Differential gene expression analysis was performed to compare 1 or 8 hours of stimulation with 0 hours.


title: Concurrent activation of NF-kB and Notch signaling is sufficient to induce B cell transformation and enables B-myeloid conversion

status: Public on Jul 11 2021

city: Iowa City

first: Chen

last: Zhao

state: Iowa

address: 1163 Medical Laboratories

department: Pathology

institute: University of Iowa

summary: Comparison of transcriptome between control, NF-kB, Notch and NF-kB singly- and doubly-activated spleen marginal zone or precursor B cells,  and transformed doubly-activated lymphoma cells

overall_design: Control, NF-kB-activated (Rosa-NIKΔT3flSTOP x CD19Cre), Notch-activated (Rosa-Notch2ICN x CD19Cre), and doubly-activated (Rosa-NIKΔT3flSTOP x Rosa-Notch2ICN x CD19Cre, TriB) mice were used for investigation of the impact of dual activation of NF-kB and Notch signaling on B cell development, transformation and plasticity.  Marginal zone precursor B cells, marginal zone B cells and transformed lymphoma cells were sorted by FACS and used for RNAseq analysis.


title: Effects of Dihydrotanshinone I on proliferation and invasiveness of Paclitaxel-resistant anaplastic thyroid cancer cells

status: Public on Jul 10 2021

city: Udine

first: Giuseppe

last: Damante

address: via chiusaforte, E

department: Medical Area

institute: University of Udine

summary:
ATC is a very rare, but extremely aggressive form of thyroid malignancy, responsible for the highest mortality rate registered for thyroid cancer. In the patients without known genetic aberrations, the current treatment is still represented by palliative surgery and systemic mono- or combined-chemotherapy, which is often not fully effective for appearance of drug resistance. Comprehension of the mechanisms involved in the development of the resistance is therefore an urgent issue to suggest novel therapeutic approaches of this very aggressive malignancy.
In this study, we created a model of anaplastic thyroid cancer (ATC) cells resistant to paclitaxel, to investigate the characteristics of these cells by analyzing the profile of gene expression and comparing with that of paclitaxel-sensitive original ATC cell lines. In addition, we evaluated the effects of Dihydrotanshinone I (DHT) on the viability and invasiveness of paclitaxel-resistant cells.
ATC paclitaxel-resistant cells highlighted an overexpression of ABCB1 and a hyper-activation of the NF-κB compared to sensitive cells. DHT treatment results in a reduction of cell viability, and clonogenic ability of resistant cells. Moreover, DHT induces a decrement of NF-κB activity in SW1736-PTX and 8505C-PTX cells. In conclusion, to the best of our knowledge, the results of the present study are the first to demonstrate the antitumor effects of DHT on ATC cells resistant to Paclitaxel in vitro.

overall_design: mRNA profiles of SW1736 and 8505C paclitaxel-resistant cells.

first: Lorenzo

last: Allegri

first: Federica

last: Baldan


title: Transcriptomic Analysis of High Fat Diet Fed Mouse Brain Cortex

city: Hwasun, Jeollanam-do

first: Young-Kook

last: Kim

address: 264, Seoyang-ro

department: Department of Biochemistry

country: South Korea

institute: Chonnam National University Medical School

summary: High fat diet can lead to metabolic diseases such as obesity and diabetes known to be chronic inflammatory diseases with high prevalence worldwide. Recent studies have reported cognitive dysfunction in obese patients is caused by a high fat diet. Accordingly, such dysfunction is called “type 3 diabetes” or “diabetic dementia.” Although dysregulation of protein-coding genes has been extensively studied, profiling of non-coding RNAs including long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) has not been reported yet. Therefore, the objective of this study was to obtain profiles of diverse RNAs and determine their patterns of alteration in high fat fed brain cortex compared to normal brain cortex. To investigate regulatory roles of both coding and non-coding RNAs in high fat diet brain, we performed RNA sequencing of ribosomal RNA-depleted RNAs and identified genome-wide lncRNAs and circRNAs expression and co-expression patterns of mRNAs in high fat diet mouse brain cortex. Our results showed expression levels of mRNAs related to neurogenesis, synapse, and calcium signaling were highly changed in high fat diet fed cortex. In addition, numerous differentially expressed lncRNAs and circRNAs were identified. Our study provides valuable expression profiles and potential function of both coding and non-coding RNAs in high fat diet fed brain cortex.

overall_design: Male C57BL/6 mice (Orient) were obtained at 8 weeks of age. The mice were fed with either a conventional diet or a diet enriched with fat (60% wt/wt; Bio-Serv) for 8 weeks. At 16 weeks old, the high fat diet fed mice showed increased weight and impaired glucose tolerance. To obtain the brain cortexes, mice were sacrificed under ether anesthesia. We prepared rRNA-depleted total RNAs for brain cortex samples (from 4 normal and 4 high fat diet fed mice) and performed RNA sequencing analysis.

first: Juhyun

last: Song


title: Study the differential gene expression of HEPA1-6 tumors in C57/BL6 Mouse tumors treated with vehicle or EZH2 inhibitor GSK343

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: The study evaluated the differential gene expression in mice tumors treated with or without GSK343, which were then analyzed by RNA-seq for identify differentially regulated genes.

overall_design: Total RNA was extracted from C57/BL6 mouse tumors treated with either vehicle or EZH2 inhibitor GSK343,  followed by poly-A selection and RNA-sequencing using Illumina Hi-Seq 2500 platform, with five biological replicates for each condition.

first: Suresh

last: Bugide


title: Transcriptome analysis of Lactococcus lactis in response to acid stress

city: Wuxi

first: ming

middle: zheng

last: zhu

state: Jiangsu

address: 1800 Lihu Road

department: school of biotechnology

institute: Jiangnan University

summary: Our transcriptome data shows that comparative transcriptomics analysis was performed on L. lactis WH101 and L. lactis NZ9000 to investigated the response mechanisms of microbial cells during acid stress. Carbohydrate metabolism and sugar transporters were strengthened to provide more energy. Amino acids metabolism and transporters were regulated to maintain intracellular pHi homeostasis and generate ATP. Fatty acid metabolism was also regulated to enhance the acid tolerance of cells. Moreover, transcriptional regulators and stress response proteins were also found to be related to acid stress.

overall_design: 4 samples, L. lactis WH101 (acid tolerance strain) at pH 7.0, L. lactis NZ9000 (parent strain) at pH 7.0,L. lactis WH101(acid tolerance strain) at pH 4.0, L. lactis NZ9000 (parent strain) at pH 4.0.

first: Zhengming

last: Zhu

first: Peishan

last: Yang

first: Zhimeng

last: Wu

first: Juan

last: Zhang

first: Guocheng

last: Du


title: T cell-specific deletion of TRAIL-receptor reveals a critical role for pathologic T cell activation and inflammation in experimental autoimmune encephalomyelitis

city: Taipei

first: I-Tsu

last: Chyuan

state: Outside of the US

address: No. 280, Sec. 4, Renai Rd.

department: Internal Medicine

country: Taiwan

institute: Cathay General Hospital

summary: We isolated CD4 T cells from EAE mice with or without TRAIL treatment and analyzed by RNA-seq. We also activated naïve CD4 T cells by anti-CD3/CD28 antibodies in the presence or absence of TRAIL and subsequently analyzed using RNA-seq.

overall_design: Examine the effect of TRAIL on activated T cells in vivo and in vitro

first: Ping-Ning

last: Hsu


title: Histone demethylase SlJMJ7 Integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato [RNA-seq]

city: guangzhou city

first: Ding

last: xiaochun

state: guangdong

address: 723 xingke road, tianhe district

institute: SOUTH CHINA BOTANICAL GARDEN

summary: Combinational analyses of genome-wide transcription, binding sites and histone H3K4 trimethylation profiles revealed that SlJMJ7 directly binds and represses the expression of a series of key ripening-associated factors, including ethylene biosynthesis genes ACS2/4/8 and ACO2, DNA demethylase DML2, as well as the ripening-related transcription factors RIN and NOR by removal the mark of H3K4-trimethylation. Moreover, SlJMJ7 directly and indirectly modulates the transcription of genes related to diverse physiological traits of fruit ripening.

overall_design: RNAseq profiles of  wild type (WT) and transgenic lines (jmj7)  at 38 days after anthesis.

first: Xiaochun

last: Ding

first: Xuncheng

last: Liu

first: Xuewu

last: Duan


title: Expression data from salivary gland cells of NOD/shiLtJ mice and NOD/shiLtJ mice with type 1 diabetes

status: Public on Jul 09 2021

city: Seoul

first: Sun-Hee

last: Hwang

address: Catholic Research Institute of Medical Science, College of Medicine, The Catholic University of Korea, 222, Banpo-daero, Seocho-gu

institute: The Rheumatism Research Center

summary:
Profiles of gene expression in salivary gland cells were compared between NOD/ShiLtJ mice, an animal model or Sjogren's syndrome with or without T1D.
We used microarrays to detail the global programme of gene expression when type 1 diabetes and identified distinct classes of up- or down-regulated genes.

overall_design: Salivary gland tissue from 21-week-old NOD/ShiLtJ mice with or without type 1 diabetes were selected for RNA extraction and hybridization on Affymetrix microarrays.


title: Histone demethylase SlJMJ7 Integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato [ChIP-seq]

overall_design: Tomato histone modification H3K4me3 profiles of  wild type (WT) and transgenic knockout of JMJ7 lines (jmj7) at 38 days after anthesis. JMJ7 target gene identification sample is JMJ7-OE-GFP tomato pericarp at 38 days after anthesis.

first: Zhiwei

last: Li

first: Guoxiang

last: Jiang

first: Yunbo

first: Dandan

first: Jing

last: Zeng

first: Hanzhi

last: Liang

first: Lu

last: Xiao

first: Huiling

last: Yan

first: Hongmei

last: Lai

first: Yueming


title: Transcriptomic Repositioning Analysis Identifies mTOR Inhibitor as Potential Therapy for Epidermolysis Bullosa Simplex

city: Redwood City

first: Kavita

last: Sarin

address: 450 Broadway St, Pavilion C 2nd Fl MC 5334

department: Dermatology

institute: Stanford University

summary: In this study, we characterize significant molecular pathways activated in the blisters that form in EBS and employ a systematic drug repositioning screen to identify promising repositionable drugs for EBS. We implicate the PI3K/AKT/mTOR pathway as central in the EBS disease pathway and further validate our computational repositioning analysis by presenting clinical outcomes of two EBS patients treated with mTOR inhibitors.

overall_design: Drug repositioning analysis using mRNA data on EBS epidermis

first: GunHo

last: Lee

first: Joyce

last: Teng


title: Expression and Function of C1orf132 Long-Noncoding RNA in Breast Cancer Cell Lines and Tissues

city: Turin

first: Andrea

last: Lauria

address: Via Accademia Albertina, 13

department: Life Sciences and Systems Biology

institute: University of Turin

summary: miR-29b2 and miR-29c play a suppressive role in breast cancer progression. C1orf132 (also named MIR29B2CHG) is the host gene for generating both microRNAs. However, the region also expresses longer transcripts with unknown function. We employed bioinformatics and experi-mental approaches to decipher C1orf132 expression and function in breast cancer tissues. We also used the CRISPR/Cas9 technique to excise a predicted C1orf132 distal promoter and followed the behavior of the edited cells by real-time PCR, flow cytometry, migration assay, and RNA-seq tech-niques. We observed that C1orf132 long transcript is significantly downregulated in tri-ple-negative breast cancer. We also identified a promoter for the longer transcripts of C1orf132 whose functionality was demonstrated by transfecting MCF7 cells with a C1orf132 promoter-GFP construct. Knocking-out the promoter by means of CRISPR/Cas9 revealed no expression alteration of the neighboring genes CD46 and CD34, while the expression of miR-29c was reduced by half. Furthermore, the promoter knock-out elevated the migration ability of the edited cells. RNA se-quencing revealed many up- and downregulated genes involved in various cellular pathways, in-cluding epithelial to mesenchymal transition and mammary gland development pathways. Alto-gether, we are reporting here the existence of an additional/distal promoter with an enhancer effect on miR-29 generation and an inhibitory effect on cell migration.

overall_design: RNA-seq transcriptome profiling of wild-type and C1orf132-edited MCF12A cells. 4 samples, 2 biological replicates for each condition.

first: Afsaneh

last: Malekzadeh Shafaroudi

first: Ali

last: Sharifi-Zarchi

first: Saeid

last: Rahmani

first: Nahid

last: Nafissi

first: Seyed

last: Javad Mowla

first: Salvatore

last: Oliviero

first: Maryam

last: M. Matin


title: Transcriptional characterization of bacteria-fungi interaction between Priestia endophytica FH5 and phytopathogen Rhizoctonia solani

city: Groningen

first: Anne

middle: de

last: Jong

address: Nijenborgh 7

department: Molecular Genetics

country: Netherlands

institute: university of Groningen

summary: Priestia endophytica FH5, which was isolated from healthy tomato rhizosphere soil, had biological activity against a variety of plant diseases, including R. solani. We isolated the chemicals generated by strain FH5 to better understand the interaction between strain FH5 and R. solani. A transcriptome study of strain FH5 with and without R. solani exposure was also performed. In response to the fungal pathogen R. solani, strain FH5 changed genes linked to amino acid transport, carbohydrate transport, energy generation and conversion, and inorganic ion transport and metabolism, according to our findings.

overall_design: 2 samples of Priestia endophytica FH5, one treated and oe untreated

last: Zhou

last: de Jong

first: Oscar

last: Kuipers


title: Implications of the use of organic fertilizers for Antibiotic Resistant Gene dissemination in agricultural soils and fresh food products. A plot-scale study

city: Barcelona

first: Claudia

middle: Sanz

last: Lanzas

state: Barcelona

address: Carrer Jordi Girona, 20

department: Environmental Toxicology

country: Spain

institute: IDAEA-CSIC

summary: The spread of antibiotic resistance genes (ARG) into agricultural soils, products, and foods severely limits the use of organic fertilizers in agriculture. In this study, experimental land plots were fertilized, sown, and harvested for two consecutive agricultural cycles using either mineral or three types of organic fertilizers: sewage sludge, pig slurry, or composted organic fraction of municipal solid waste. The analysis of the relative abundances of more than 200,000 ASV (Amplicon Sequence Variants) allowed the identification of a small, but significant  (<10%) overlap between soil and fertilizer microbiomes, particularly in soils sampled the same day of the harvest (post-harvest soils). Loads of clinically relevant ARG were significantly higher (up to 100 fold) in fertilized soils relative to the initial soil. The highest increases corresponded to post-harvest soils treated with organic fertilizers, and they correlated with the extend of the contribution of fertilizers to the soil microbiome.  Edible products (lettuce and radish) showed low, but measurable loads of ARG (sul1 for lettuces and radish, tetM for lettuces). These loads were minimal in mineral fertilized soils, and strongly dependent on the type of fertilizer. We concluded that at least part of the observed increase on ARG loads in soils and foodstuffs were actual contributions from the fertilizer microbiomes. Thus, we propose that adequate waste management and good pharmacological and veterinarian practices may significantly reduce the potential health risk posed by the presence of ARG in agricultural soils and plant products.

sample_organism:
soil metagenome
solid waste metagenome
sludge metagenome
feces metagenome

overall_design:
The nature of the study was to analyse the incorporation rate of Antibiotic Resistance Genes from organic fertilisers (sludge, slurry, USW) to the soil by means of 16s rDNA amplicon sequencing approaches. We used soil fertilised with a chemical fertiliser as our control. We sequenced the organic fertilizers and the soils ammended with these, plus chemically fertilised soils and a couple of "initial soil" with any kind of fertilisation, to have a initial idea fo the ARGs presence in the soil prior to the experiments.

Definitions:

SLUDGE: Soil amended (fertilized) with water treatment plant sludge
SLURRY:  Soil amended (fertilized) with pig slurry
USW:  Soil amended (fertilized) with Urban Solid Waste
MINERAL:  Soil amended (fertilized) with the commonly used chemical fertilizer

last: Sanz

first: Marta

last: Casado

first: Laia

last: Navarro-Martin

first: Núria

last: Cañameras

last: Carazo

first: Víctor

last: Matamoros

first: Josep

last: Martia Bayona

first: Benjamín

last: Piña


title: CC027/GeniUnc mouse strain-derived jejunal epithelial cells before and after peanut sensitization and at 30, 60, and 120 minutes after peanut challenge

city: Chapel Hill

first: Erin

last: Steinbach

state: NC

address: 111 Mason Farm Road, 7314 MBRB

department: Medicine

institute: University of North Carolina at Chapel Hill

summary: Peanut allergy reaction severity correlates with increased intestinal epithelial cell (IEC) barrier permeability. CC027/GeniUnc mice develop peanut allergy by intragastric administration of peanut proteins without adjuvant. We report that peanut-allergic CC027/GeniUnc mice showed increased IEC barrier permeability and systemic peanut allergen Ara h 2 after challenge. Jejunal epithelial cell transcriptomics showed effects of peanut allergy on IEC proliferation, survival, and metabolism, and revealed IEC-predominant angiopoietin like-4 (Angptl4) as a unique feature of CC027/GeniUnc peanut allergy. Peanut-allergic pediatric patients demonstrated significantly higher serum ANGPTL4 compared to non-peanut-allergic but atopic patients, highlighting its potential as a biomarker of peanut allergy.

overall_design: 15 isolated jejunal epithelial cell samples from CC027/GeniUnc mice (n=15) representing 5 experimental conditions: PBS-sensitized & unchallenged (n=3); Peanut-sensitized & unchallenged (n=3); Peanut-sensitized & challenged, 30 minutes post-challenge (n=3); Peanut-sensitized & challenged, 60 minutes post-challenge (n=3); Peanut-sensitized & challenged, 120 minutes post-challenge (n=3).

first: C

first: M

last: Smeekens

first: Satyaki

last: Roy

first: Takahiko

last: Toyonaga

first: Caleb

last: Cornaby

first: Layna

last: Perini

first: Ana

last: Berglind

first: D

last: Kulis

first: H

last: Kim

first: T

last: Ferris

first: S

last: Furey

first: Wesley

last: Burks

first: Z

middle: S

last: Sheikh


title: Distinctive waves of innate immune response in the retina in experimental autoimmune encephalomyelitis

city: San Francisco

first: Sergio

last: Baranzini

state: CA

address: 675 Nelson Rising LN, STE 240

department: Neurology

institute: UCSF

summary: Using transcriptional profiling in retinae of experimental autoimmune encephalitis (EAE) in CX3CR1GFP/+ knock-in mice, we are able to show two distinct waves of innate immune cell activation separated by a marked reduction in number of innate immune cells and change in cell morphology. The first wave is characterized by an inflammatory phagocytic phenotype preceding the onset of EAE whereas the second wave is characterized by a regulatory, anti-inflammatory phenotype during the chronic stage. Additionally, the magnitude of the first wave is associated with neuronal loss. Two transcripts identified - growth arrest-specific protein 6 (GAS6) and suppressor of cytokine signaling 3 (SOCS3) - might be promising targets for enhancing protective effects of microglia in the chronic phase after initial injury.

overall_design: Examination of innate immune cells in EAE and controls at 3 different timepoints (0, 6 and 25 days post induction (dpi)). All samples were WT female C57BL6/J mice.

first: Andrés

last: Cruz-Herranz

first: Frederike

last: Oertel

first: Kicheol

first: Ester

last: Cantó

first: Garrett

last: Timmons

first: Jung

middle: H

last: Sin

first: Michael

last: Devereux

first: Nicholas

last: Baker

first: Brady

last: Michel

first: Ryan

last: Schubert

first: Lakshimisahiti

last: Rani

first: Christian

last: Cordano

first: Ari

last: Green


title: Histone demethylase SlJMJ7 integrates DNA demethylation, ethylene signal and major ripening-related transcription factors in coordination of fruit ripening in tomato.

first: Ding

last: xiaochun

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

overall_design: Refer to individual Series


title: Next generation sequencing of transcriptomic change in NTCP-reconstituted HepG2 cells after hepatocyte maintanace medium treatment

city: Columbus

first: David

last: Brigstock

state: Ohio

address: 700 Children's Drive

institute: Nationwide Children's Hospital

summary: In order to profile the transcriptomic change in NTCP-reconstituted HepG2 cells after the treatment with hepatocyte maintanace medium. HMM-pretreated HepG2/NTCP cells turned to be more susceptible to hepatitis B virus infection.

overall_design: HepG2/NTCP cells were treated with HMM for 24h, DMEM/10%FBS/2%DMSO medium was used as a control. The cells were collected for total RNA extraction and subjected to RNA-seq analysis.

first: Xinlei

last: Li

first: Zongdi

last: Feng

first: Amy

last: Wetzel

first: James

last: Fitch


title: Endogenous Tau deletion affects sex-dependent outcome to traumatic brain injury in Drosophila

status: Public on Jul 15 2021

city: Detroit

first: Ekta

last: Shah

state: Michigan

address: 275 E.  Hancock

institute: Wayne State University

summary: Adult male and female Tau-KO flies were inflicted with traumatic brain injury using high-impact trauma device. Brains were dissected at control, 1, 2 and 4 hours post-TBI. Total RNA was extracted from fly brains and 3'mRNA-seq was performed to assess gene expression changes in response to TBI in both sexes. 3 replicates were sequenced for each condition.

overall_design: To investigate sex-differences in gene expression at control, 1, 2 and 4-hours post-TBI in Tau-deficient Drosophila


title: CARPOOL: A library-based platform to rapidly identify next generation chimeric antigen receptors

city: Cambridge

first: Caleb

middle: R

last: Perez

email: crperez@mit.edu, mbirnb@mit.edu

address: 77 Massachusetts Ave

department: Biological Engineering

institute: MIT

summary: CD19-targeted CAR therapies have successfully treated B cell leukemias, but many responders later relapse or experience toxicities. CAR ICDs are key to converting antigen recognition into anti-tumor effector functions. Despite the many possible immune signaling domain combinations that could be included in CARs, almost all CARs currently rely upon CD3, CD28, and/or 4-1BB signaling. To explore the signaling potential of CAR ICDs, we generated a library of 700,000 CD19 CAR molecules with diverse signaling domains and developed a high throughput screening platform to enable optimization of CAR signaling for anti-tumor functions. Our strategy identifies CARs with novel signaling domains that elicit distinct T cell behaviors from a clinically available CAR, including enhanced proliferation and persistence, lower exhaustion, potent cytotoxicity in an in vitro tumor rechallenge condition, and comparable tumor control in vivo. This approach is readily adaptable to numerous disease models, cell types, and selection conditions, making it a promising tool for rapidly improving adoptive cell therapies and expanding their utility to new disease indications.

overall_design:
Single-cell RNA sequencing data of primary human T cells expressing three different CD19-targeted CAR variants following three tumor challenges with NALM6 leukemia cells. An unstimulated, untransduced control was also included.

Two merged sample records of the following samples:
Untransduced_unstimulated
BBz
Var1
Var3
as detailed in the sample_metadata.txt

first: Taeyoon

last: Kyung

first: Khloe

last: Gordon


title: Transcriptome analysis of NCC-IT-A3 cells by Barasertib treatment

city: Tokushima

first: Takaaki

last: Tsunematsu

address: 3-18-15 Kuramoto

department: Oral Molecular Pathology

institute: Tokushima University

summary: During mitosis, the chromosomal passenger complex (CPC) that is formed by Aurora-B, INCENP, Survivin, and Borealin ensures the faithful segregation of the chromosomes into daughter cells. We previously have shown that CPC activity was terminated by the anaphase promoting complex/cyclosome (APC/C) and its cofactor Cdh1 via ubiquitylation of Borealin and Aurora-B during the G1 phase of somatic cells. On the other hand, protein levels of Borealin and Aurora-B were stable during cell cycle progression due to high levels of Emi1, which keep APC/CCdh1 inactive in embryonal carcinoma (EC) cells. During retinoic acid-induced differentiation of EC cells, these proteins were downregulated by APC/CCdh1-mediated ubiquitylation. Interestingly, CPC proteins form a complex with Aurora-B kinase activity even in interphase of EC cells. Significantly, inhibition of CPC activity by either knockdown of Borealin or Aurora-B and Aurora-B kinase inhibitor treatment induced spontaneous differentiation of EC cells. In conclusion, sustained CPC activity plays a critical role in maintenance of the undifferentiated state of pluripotent stem cells. We therefore propose an interphase role of the CPC in regulating embryonic pluripotency.

overall_design: Embryonal carcinoma cell line NCC-IT-A3 cells were cultured for 4 days with or without 100nM Barasertib, which was Aurora-B specific inhibitor. Collected RNAs were analyzed by RNA-seq


title: Wilson disease: intersecting DNA methylation and histone acetylation mechanisms affect gene expression regulation in a mouse model of hepatic copper accumulation [RNA-Seq]

city: Davis

first: Valentina

last: Medici

address: 451 E. Health Sciences Dr.

department: Department of Internal Medicine, Division of Hepatology/Gastroenterology

institute: University of California, Davis

summary:
Prior investigations of DNA methylation differences in WD liver and blood and in a WD mouse model revealed an epigenetic signature of WD that included the histone deacetylase, HDAC5.
To test the hypothesis that histone deacetylation and acetylation might be altered with respect to copper overload and aberrant DNA methylation in WD, we used the Jackson Laboratory toxic milk model (tx-j) of WD to study the involvement of Class IIa histone deacetylases (HDAC4 and HDAC5) and histone acetylation (H3K9ac and H3K27ac), and the effects of copper chelator D-penicillamine (PCA) and/or methyl group donor choline on histone modification.
Next, we related acetylation profiles of H3K27ac to gene expression changes in wilson disease by ChIP and RNA-seq.

overall_design: Our study represents the liver transcriptomes of tx-j: mice model of WD by RNA-seq technology Coordinately upregulated and downregulated genes with H3K27 acetylation were identified to study the transcription factors and biological pathways involved in WD. We demonstrate a role for histone deacetylases at the interface between nutrition, histone acetylation, DNA methylation, and gene expression regulation affecting liver disease severity in WD

first: Gaurav

last: Sarode


title: Wilson disease: intersecting DNA methylation and histone acetylation mechanisms affect gene expression regulation in a mouse model of hepatic copper accumulation


title: Wilson disease: intersecting DNA methylation and histone acetylation mechanisms affect gene expression regulation in a mouse model of hepatic copper accumulation [ChIP-Seq]

overall_design: Examination of histone modifications specifically H3K9-H3K27 acetylation enriched gene regulation in liver of WD mice models. Co-upregulated and downregulated genes with H3K27 acetylation and transcriptomes analysis (RNA-Seq) were identified to study the transcription factors and biological pathways involved in pathogenesis of WD. We demonstrate a role for histone deacetylases at the interface between nutrition, histone acetylation, DNA methylation, and gene expression regulation affecting liver disease severity in WD.  Number of samples=70: 30 samples per H3K9ac and H3K27ac antibody and 2 input samples per treatment group.  Experiment includes 6 sample per treatment group as 1: C3H-Wildtype, 2: tx-j- Untreated-Mutant (Atp7btx-J), 3: tx-j-PCA- Untreated tx-j+ Penicillamine (copper chelator), 4: tx-j+Choline- Untreated tx-j+ Choline (methyl group doner), 5: tx-j+PCA+Choline- Untreated tx-j+ both PCA and Choline.


title: Transcriptome signature of local native cattle of Ladakh region from high altitude and Sahiwal cattle from low altitude (sea level).

city: Karnal

first: Preeti

last: Verma

state: Haryana

address: GT Road

department: Division of Animal Biotechnology

country: India

institute: National Bureau of Animal Genetics Resources

summary:
The transcriptome signature of peripheral blood mononuclear cells (PBMCs) of Ladakhi cattle adapted to high altitude vis a vis Sahiwal cattle adapted to the arid/semi-arid region at mean sea level was established using bovine expression microarray chips.
The transcriptome analysis of PBMCs from these cattle types living at two distinct altitudes, resulted in identification of several hundred differentially expressed genes, biological processes, molecular functions and pathways.

overall_design: The study has utilized Agilent 4x44K bovine chip using single colour matrix  to generate transcriptome data of Ladakhi cattle from high altitude and Sahiwal cattle from low altitude arid/semi-arid region.

first: Manishi

last: Mukesh

first: Ankita

last: Sharma

first: Vijay

last: Bharti

first: Prabhat

last: Kumar

first: Arup

last: Giri

first: Sahil

last: Kalia

first: Monika

last: Sodhi


title: Integrated Multi-Omics Analysis Reveals Glucose Metabolic Reprogramming and Identifies a Novel Hexokinase in Alcoholic Hepatitis

city: Pittsburgh

first: Ramon

last: Bataller

state: Pennsylvania

address: 200 Lothrop St

department: Gastroenterology Hepatology And Nutrition

institute: University of Pittsburgh

summary:
Purpose: We recently demonstrated that alcoholic hepatitis (AH) is characterized by de-differentiation of hepatocytes and loss of mature functions. Glucose metabolism is tighly regulated in healthy hepatocytes. We hypothesize that AH may lead to metabolic reprogramming of the liver, including dysregulation of glucose metabolism.
Methods: We performed integrated metabolomic and transcriptomic analyses of liver tissue from patients with AH (n=13), alcoholic cirrhosis (n=10) or normal liver tissue from hepatic resection (n=16). Focused analyses of chromatin immunoprecipitation coupled to DNA sequencing (ChIP-seq) was performed. Functional in vitro studies were performed in primary rat and human hepatocytes and HepG2 cells.
Results: Patients with AH exhibited specific changes in the levels of intermediates of glycolysis/gluconeogenesis, the TCA cycle, and monosaccharide and disaccharide metabolism. Integrative analysis of the transcriptome and metabolome revealed the utilization of alternate energetic pathways, metabolite sinks and bottlenecks, and improper glucose storage in AH patients. Among genes involved in glucose metabolism, hexokinase domain containing 1 (HKDC1) was identified as the most up-regulated kinase in AH patients. Histone active promoter and enhancer markers were increased in HKDC1 genomic region. High HKDC1 levels were associated with the development of acute kidney injury and decreased survival. Increased HKDC1 activity contributed to the accumulation of G6P and glycogen in primary rat hepatocytes.
Conclusion: Altered metabolite levels and mRNA expression of metabolic enzymes suggest the existence of profound reprogramming of glucose metabolism in AH. Increased HKDC1 expression may contribute to dysregulated glucose metabolism and may serve as a novel biomarker and therapeutic target for AH.

overall_design: Transcriptome analysis of liver biopsies from 28 patients with alcoholic hepatitis (10 samples), cirrhosis (6 samples) or healthy livers (12 samples).

first: Veronica

last: Massey

first: Austin

last: Parrish

first: Josepmaria

last: Argemi

first: Rajanikanth

last: Vadigepalli

first: Andrew

last: Cameron

first: Phillippe

last: Mathurin


title: Long non-coding RNA expression profile of mouse cementoblasts under compressive force

city: Beijing

first: Yunfei

last: Zheng

state: Beijing

address: 22 Zhongguancun Avenue South, Haidian District

department: Oral and Maxillofacial Surgery

institute: Peking University School and Hospital of Stomatology

summary: To describe the long non-coding RNA (lncRNA) expression profile of cementoblasts under mechanical compression

overall_design: Mouse cementoblasts were exposed to compressive force. RNA sequencing (RNA-seq) was performed to compare the transcriptomes of the compressed and control cells.

first: Yiping

last: Huang

first: Hao

last: Liu

first: Lingfei

last: Jia

first: Weiran

last: Li


title: The long non-coding RNA landscape of periodontal ligament stem cells subjected to compressive force

summary: To explore the lncRNA landscape of periodontal ligament stem cells (PDLSCs) subjected to compressive force.

overall_design: PDLSCs were subjected to static compressive stress. Total RNA was then extracted and sequenced to measure changes in lncRNA and mRNA expression levels. Differential expression analysis, as well as Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses, were also performed.


title: POU4F3 Pioneer Activity Enables ATOH1 to Drive Diverse Mechanoreceptor Differentiation Through a Feed-Forward Epigenetic Mechanism

city: Los Angeles

first: Neil

last: Segil

address: 1425 san pablo st, BCC 503K

department: BCC

institute: University of Southern California

summary: During embryonic development, hierarchical cascades of transcription factors interact with lineage specific chromatin structures to control the sequential steps in the differentiation of specialized cell types. While examples of transcription factor cascades have been well documented, the mechanisms underlying developmental changes in accessibility of cell type-specific enhancers remain poorly understood. Here we show that the transcriptional ‘master regulator’, ATOH1 – which is necessary for the differentiation of two distinct mechanoreceptor cell types, hair cells in the inner ear, and Merkel cells of the epidermis – is unable to access much of its target enhancer network in the progenitor populations of either cell type when it first appears, imposing a block to further differentiation. This block is overcome by a feed-forward mechanism in which ATOH1 first stimulates expression of POU4F3, which subsequently acts as a pioneer factor to provide access to closed ATOH1 enhancers, allowing hair cell and Merkel cell differentiation to proceed. Our analysis also indicates the presence of both shared and divergent ATOH1/POU4F3-dependent, enhancer networks in hair cells and Merkel cells. These cells share a deep developmental lineage relationship, deriving from their common epidermal origin, and suggesting that this feed-forward mechanism preceded the evolutionary divergence of these very different mechanoreceptive cell types.


title: Genome wide gene expression profiling of pre and post treatment breast cancer biopsy

status: Public on Jul 08 2021

city: Baltimore

first: leslie

last: cope

state: MD

address: 550 N. Broadway

institute: leslie cope

summary:
In breast cancer models, combination epigenetic therapy with a DNA methyltransferase inhibitor and a histone deacetylase inhibitor led to reexpression of genes encoding important therapeutic targets, including the estrogen receptor (ER). We conducted a multicenter phase II study of 5-azacitidine and entinostat in women with advanced hormone-resistant or triple-negative breast cancer (TNBC).
Purpose: In breast cancer models, combination epigenetic therapy with a DNA methyltransferase inhibitor and a histone deacetylase inhibitor led to re-expression of genes encoding important therapeutic targets including the estrogen receptor (ER). We conducted a multicenter phase II study of 5-azacitidine (AZA) and entinostat in women with advanced hormone-resistant or triple-negative breast cancer (TNBC). Patients and Methods: Patients received AZA 40 mg/m2 (days 1-5, 8-10) and entinostat  7 mg (days 3,10) of 28 day cycle. Continuation of epigenetic therapy was offered with addition of endocrine therapy at time of progression (optional continuation, OC phase). Primary endpoint was objective response rate (ORR) in each cohort. We hypothesized that ORR would be >20% against null of 5% using Simon two-stage design. At least 1 response was required in 1st of 13 patients per cohort to continue accrual to 27 per cohort. Type I error 4%, power 90%. Results: There was one partial response among 27 women with hormone-resistant disease (ORR=4%, 95% CI=0-19%), and none in 13 women with TNBC. One additional partial response was observed in the OC phase in the hormone-resistant cohort (n=12). Mandatory tumor samples were obtained pre- and post-treatment (58% paired) with either up- or down-regulation of ER  observed in approximately 50% of post-treatment biopsies in the hormone-resistant, but not TNBC cohort. Conclusion: Combination epigenetic therapy was well tolerated but our primary endpoint was not met. OC phase results suggest that some women benefit from epigenetic therapy and/or reintroduction of endocrine therapy beyond progression but further study is needed.

overall_design: Two-condition experiment, pre and post treatment.  Two color array was used as one color by single channel

first: Roisin

last: Connolly

first: Huili

last: Lii

first: Rachel

last: Jankowitz

first: Zhe

last: Zhang

first: Michelle

last: Rudek

first: Stacie

last: Jeter

first: Shannon

last: Slater

first: Penny

last: Powers

first: Antonio

last: Wolff

first: John

last: Fetting

first: Adam

last: Brufsky

first: Richard

last: Piekarz

first: Nita

last: Ahuja

first: Peter

middle: W

last: Laird

first: Hui

last: Shen

first: Daniel

last: Weisenberger

first: Leslie

last: Cope

first: James

middle: G

last: Herman

first: George

last: Somlo

first: Agustin

last: Garcia

last: Jones

first: Stephen

middle: B

last: Baylin

first: Nancy

last: Davidson

first: Cynthia

last: Zahnow

first: Vered

last: Stearns


title: DLBCL patients

city: Reggio Emilia

first: Benedetta

last: Donati

address: Viale Risorgimento, 80

institute: Azienda USL- IRCCS di Reggio Emilia

summary: RNA extracted from diagnostic tumor samples of 52 patients affected by DLBCL was analyzed on the nCounter system using the PanCancer Immune Profiling Panel.

overall_design: Gene expression profile were linked to serum Vitamin D level in DLBCL.

first: Alessia

last: Ciarrocchi

first: Stefano

last: Luminari


title: Genetic Adaptation of C. elegans to Environment Changes II: Multigenerational Analysis of Genome-wide Chromatin Remodeling

city: Newark

first: Irem

last: Celen

state: DE

address: 15 Innovation Way

institute: University of Delaware

summary: Chemical modifications to the tails of histone proteins act as gene regulators that play a pivotal role in adaptive responses to environmental stress. Determining the short and long term kinetics of histone marks is essential for understanding their functions in adaptation. We used Caenorhabditis elegans as a model organism to study the histone modification kinetics in response to environmental stress, taking advantage of their ability to live in both terrestrial and aquatic environments. We investigated the multigenerational genome-wide dynamics of five histone marks (H3K4me3, H3K27me3, H4K20me1, H3K36me1, and H3K9me3) by maintaining P0 animals on terrestrial (agar plates), F1 in aquatic cultures, and F2 back on terrestrial environments.  We determined the distributions of histone marks in the gene promoter regions and found that H4K20me1, H3K36me1, and H3K9me3 showed up to eleven-fold differences in density, whereas H3K4me3 and H3K27me3 remained highly constant during adaptation from terrestrial to aquatic environments. Furthermore, we predicted that up to five combinations of histone marks can co-occupy single gene promoters and confirmed the colocalization of these histone marks by structured illumination microscopy. The co-occupancy increases with environment changes and different co-occupancy patterns contribute to variances in gene expressions and thereby presents a supporting evidence for the histone code hypothesis.

overall_design: In order to elicit an adaptive response, the C. elegans P0 generation was grown on bacteria-seeded agar plates (OP50 NGM), the F1 generation was transferred to liquid, and the F2 generation reverted to agar.  In addition to the changes in the physical environment, i.e., agar to liquid, we examined the effect of the dietary changes in the liquid cultures by using two different growth media: the commonly used bacterial S-Medium and more exotic axenic CeHR medium.  For each generation, ChIP-seq was used to determine the distributions of the five histone modifications across the genome. The ChIP-seq libraries were generated with two replicates. N2 strain was used for all the libraries created.

first: Jung

last: Doh

first: Chandran

last: Sabanayagam


title: Functional and Mechanistic Interrogation of BET Bromodomain Degraders for the Treatment of Metastatic Castration-resistant Prostate Cancer

city: Ann Arbor

first: Pushpinder

middle: Singh

last: Bawa

address: 1500 East Medical Center Drive

department: Pathology

institute: University of Michigan

summary: RNA-seq on VCaP, 22Rv1, and DU145 cells treated with BET-inhibitors and BET-Degradaing molecules

overall_design: RNA-seq was performed on VCaP and 22Rv1 cells treated with 10 nmol/L dBET-2 for 3 and 24 hours.

first: Steven

last: Kregel

first: Arul

last: Chinnaiyan


title: Common and personal target genes of the micronutrient vitamin D in primary immune cells from human peripheral blood

city: Kuopio

first: Andrea

last: Hanel

address: Yliopistonranta 1E, POB 1627

department: Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

summary: In this study, the transcriptome of peripheral blood mononuclear cells (PBMCs) of healthy adults was investigated in response to in vitro treatment with 1,25(OH)2D3.

overall_design: RNA-seq of PBMCs of 12 individuals (#1-12) treated for 24 h in single repeat with the biologically active form of vitamin D, 1,25(OH)2D3 (125D) or solvent (0.1% ethanol (EtOH))

first: Carsten

last: Carlberg


title: DNA methylation analysis of oral  squamous cell carcinoma

city: Rio de Janeiro

first: Sheila

middle: Coelho

last: Soares-Lima

state: Rio de Janeiro

address: Rua André Cavalcanti 37

department: Molecular Carcinogenesis Program

country: Brazil

institute: Brazilian National Cancer Institute

summary: Upper aerodigestive tract (UADT) tumors present different biological behavior and prognosis, suggesting specific molecular mechanisms underlying their development. However, they are rarely considered as single entities (particularly head and neck subsites) and share the most common genetic alterations. Therefore, there is a need for a better understanding of the global DNA methylation differences among UADT tumors. We performed a genome-wide DNA methylation analysis of esophageal (ESCC), laryngeal (LSCC), oral (OSCC) and oropharyngeal (OPSCC) squamous cell carcinomas, and their non-tumor counterparts. The unsupervised analysis showed that non-tumor tissues present markedly distinct DNA methylation profiles, while tumors are highly heterogeneous. Hypomethylation was more frequent in LSCC and OPSCC, while ESCC and OSCC presented mostly hypermethylation, with the latter showing a CpG island overrepresentation. Differentially methylated regions affected genes in 127 signaling pathways, with only 3.1% of these being common among different tumor subsites, but with different genes affected. The WNT signaling pathway, known to be dysregulated in different epithelial tumors, is a frequent hit for DNA methylation and gene expression alterations in ESCC and OPSCC, but mostly for genetic alterations in LSCC and OSCC. UADT tumor subsites present differences in genome-wide methylation regarding their profile, intensity, genomic regions and signaling pathways affected.

overall_design: 7 non-tumor adjacent tissues and 15 tumors from OSCC patients

first: Diego

last: Camuzi

first: Luis

last: Pinto

first: Hisham

last: Mehanna

first: Zdenko

last: Herceg


title: Targeting Hedgehog pathway by Smoothened Antagonist

city: shanghai

first: Jialin

last: Mo

address: South Chongqing Road, Shanghai 200025. P.R. China

institute: Shanghai Jiao Tong University School of Medicine

summary: Aberrant activation of Hedgehog pathway is responsible for initiation and maintenance of various cancers, including medulloblastoma (MB), basal cell carcinoma (BCC), and other solid and hematological tumors. Therefore, targeting Hh pathway represents promising therapeutic prospects for Hh-driven cancers. In recent years, tremendous efforts have been dedicated to the discovery of Hh pathway inhibitor. While the majority of Hh pathway inhibitors target the upstream membrane protein Smoothened (SMO). Here, we performed Next Generation Sequencing to reveal the target genes of Hh pathway by treating mouse SHH-subtype medulloblastoma cells (SmoWT) with SMO inhibitor (GDC0449) or DMSO.

overall_design: mRNA profiling:RNA was prepared from vehicle or GDC0449 (0.1μM) treated mouse SHH-subtype medulloblastoma cells (SmoWT) derived from spontaneous medulloblastoma of Ptch1+/-, Trp53-/- mice for 24 h.   Trim galore was used to automatically detect and trim adapters. Reads were mapped to mm10 reference genome using Hisat2. Read count was generated using HTSeq (version 0.11.1). Differentially expressed genes (DEGs) were calculated using DESeq2 (version 1.26.0). Absolute value of fold change (FC) > 1.5 and false discovery rate (FDR) < 0.05 was used as cut-off value to select significant target genes. FPKM (Fragments per Kilobase Million) was calculated from the number of reads that mapped to each particular gene sequence and the gene length and the sequencing depth were taken into account.

first: Fang

last: Liu

first: Xi

last: Sun

first: Yujie

last: Tang


title: GRSF1 deficiency in skeletal muscle reduces endurance in aged mice

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: GRSF1 is a mitochondrial RNA-binding protein important for maintaining mitochondrial function.  We found that GRSF1 is highly expressed in cultured skeletal myoblasts differentiating into myotubes.  To understand the physiological function of GRSF1 in vivo, we generated mice in which GRSF1 was specifically ablated in skeletal muscle.  The conditional knockout mice (Grsf1cKO) appeared normal until 7-9 months of age.  Importantly, however, a reduction of muscle endurance compared to wild-type controls was observed in 16- to18-month old Grsf1cKO mice.  Transcriptomic analysis revealed more than 200 mRNAs differentially expressed in Grsf1cKO muscle at this age.  Notably, mRNAs encoding proteins involved in mitochondrial function, inflammatory reaction, and ion transport, including Mgarp, Cxcl10, Nfkb2, and Sln, were significantly elevated in aged Grsf1cKO muscle.  Our findings suggest that GRSF1 deficiency exacerbates the functional decline of aged skeletal muscle, likely through multiple downstream genes.

overall_design: Vastus intermedius muscle RNA from three wildtype and three skeletal muscle-Grsf1KO 17 month old (aged) mice were examined by gene expression microarrays.

first: Riley

middle: K

last: Driscoll

first: Linda

last: Krasniewski

first: Samuel

last: Cockey

first: Jen-Hao

last: Yang

first: Yulan

last: Piao

first: Elin

last: Lehrmann

first: Yongqing

last: Zhang

first: Marc

last: Michel

first: JiHeon

last: Noh

first: Chang-Yi

last: Cui

first: Myriam

last: Gorospe


title: Effect of dietary vitamin E on intramuscular fat deposition and transcriptome profile of pectoral muscle in broiler chickens

city: Longyan

first: Yanfa

state: Fujian

address: Dongxiao North Road No. 1, Xinluo District

department: College of Life Science

institute: Longyan University

summary: As an essential micronutrient for animals, vitamin E plays crucial physiological roles in reproduction, antioxidant and immune functions, and lipid metabolism. The objective of this study was to reveal molecular mechanism of vitamin E on intramuscular fat (IMF) deposition through transcriptome sequencing of pectoral muscle in broiler chickens. A total of 240 one-day-old health female chicks were randomly allocated into five dietary treatments with each treatment six replicates. The birds were fed basal diet supplemented with 0 and 100 IU/kg vitamin E in the form of DL-α-tocopheryl acetate, respectively. The body weight, carcass performance and IMF content were measured. Transcriptome profile of pectoral muscle in 35-day-old chickens were sequencing from the control and 100 IU/kg vitamin E treatment. Functional enrichment analyzes of differentially expressed genes (DEGs) based on Gene ontology (GO), KEGG pathway and bio function, and network were performed.  Results shown that IMF content of broiler chickens were significantly increased at 12.89% (P < 0.05) between 100 IU/kg vitamin E treatment and control. Transcriptome sequencing results for pectoralis major muscle of 100 IU vitamin E-supplemented and the control groups identified 57 up-regulated and 102 down-regulated DEGs. These DEGs were significantly enriched (FDR corrected P-value < 0.05) in 13 of 236 GO terms involved in muscle development- and lipid metabolism. Pathway functional enrichment analysis revealed that the DEGs were significantly enriched in three signalling pathways (FDR corrected P-value < 0.05). Two of them, MAPK signaling pathway and FoxO signaling pathway, play key roles in muscular and lipid metabolism. It is worth mentioning that 46 DEGs were significantly enriched in 28 skeletal and muscular system development and function categories and 31 DEGs were significantly enriched in 17 lipid metabolism function categories. Moreover, three lipid metabolism and muscular development-related networks of DEGs were also identified. These DEGEs, pathways, function categories and networks identified in this study provide us new insights for the vitamin E regulation of the IMF deposition in broiler chickens.

overall_design: A total of 240 one-day-old healthy female chicks were randomly allocated into five dietary treatments with each treatment six replicates. The birds were fed basal diet supplemented with 0 and 100 IU/kg vitamin E in the form of DL-α-tocopheryl acetate, respectively. This series includes only control at 100 IU/kg samples.

first: Min

first: Weiming

last: Lin


title: Modulation of energy metabolism and epigenetic landscape in rainbow trout fry by a parental low protein/high carbohydrate diet

city: Saint-Pée-sur-Nivelle

first: Thérèse

last: Callet

country: France

institute: INRA

summary: In rainbow trout (Oncorhynchus mykiss), the effect of a paternal and a maternal high carbohydrate/low protein diet was assessed on progeny. To this purpose, two-year old males and females rainbow trout were fed either a control diet or a high carbohydrate/low protein diet for an entire reproductive cycle for females and for 5  months for males. Crossed-fertilizations were carried out in order to obtain 4 groups of offspring. Before the first feeding, whole fry transcriptomes were compared to detect any impact of the parental diet on offspring metabolism.

overall_design: Two-year old male and female rainbow trout were fed either a control diet (NC, 63.89% protein and 0% carbohydrates) or a high carbohydrate/low protein diet (HC/LP, 42.96% protein and 35.30% carbohydrates) for an entire reproductive cycle for females and for 5 months for males. During the spawning period, spawns from NC and HC/LP females were cross-fertilized with milts from males from each experimental condition. Thus, offspring from 4 different conditions were obtained: NN (offspring from both males and females fed the control NC diet); HN (offspring from only females fed the HC/LP diet and males fed the control NC diet); NH (offspring from only males fed the HC/LP diet and females fed the NC diet); and HH (offspring from both parents fed the HC/LP diet). Whole fry were sampled before the first feeding.

first: T

first: S

last: Panserat

first: L

last: Marandel


title: DNA methylation analysis of laryngeal squamous cell carcinoma

first: Sheila

last: Soares-Lima

overall_design: 11 non-tumor adjacent tissues and 20 tumors from LSCC patients

first: Diego

last: Camuzi

first: Luis

last: Pinto

first: Hisham

last: Mehanna

first: Zdenko

last: Herceg


title: DNA methylation analysis of oropharyngeal squamous cell carcinoma

overall_design: 15 snap-frozen OPSCC samples, 8 FFPE OPSCC samples, and FFPE tonsils from 9 non-cancer patients


title: Collection of RNA-Seq data from early muscle tissue after skeletal muscle injury

city: Jinzhong

first: Jun-hong

last: Sun

state: Shanxi Province

address: 98 University Street, Yuci District, Jinzhong

department: School of Forensic Medicine

institute: Shanxi Medical University

summary: Following skeletal muscle injury (SMI), from post-injury reaction to repair consists of a complex series of dynamic changes.In this study, skeletal muscle tissue in rats was taken at 4h to 48h after injury for next-generation sequencing. We examined the transcriptional kinetics characteristics during above time periods after injury.

overall_design: Male Sprague Dawley rats were randomly divided into different time injury groups (4h, 8h, 12h, 16h, 20h, 24h, 48h) and control group for RNA-seq

first: Junhong

first: Yingyuan

last: Wang

first: Kang

last: Ren

first: Liangliang

first: Liang

first: Qiuxiang

last: Du

first: Jie

last: Cao

first: Qianqian

last: Jin

first: Lihong

last: Dang

last: Li


title: Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes

city: Cambridge

first: Felix

last: Krueger

address: Granta Park

department: Bioinformatics

country: United Kingdom

institute: Altos Labs

type: Methylation profiling by high throughput sequencing

summary: We optimised an in vitro culture model for mouse oocytes starting from immature oocytes to get mature oocytes and investigated the effect of oxygen concentrations on the cultured oocytes (5 % vs 20% oxygen). The cultured oocytes were size-selected in both conditions. We generated expression and methylation profiling (RNA-Seq, RRBS, PBAT) by high throughput sequencing from these size selected oocytes and compared the results with in vivo size oocytes. Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex-vivo culture condition.

overall_design: RNA-Seq, PBAT and RRBS in mouse cultured oocytes at different sizes under 2 different conditions of in vitro culture (5% oxygen vs 20%oxygen)

first: Florence

last: Naillat

first: Lenka

last: Gahurova

first: Joanna

last: Nowacka-Woszuk

first: Shin-ichi

last: Tomizawa

first: Heba

last: Saadeh

first: Gavin

last: Kelsey


title: DNA methylation analysis of esophageal squamous cell carcinoma

first: Sheila

last: Soares-Lima

overall_design: 16 non-tumor adjacent tissues and 24 tumors from ESCC patients

first: Diego

last: Camuzi

first: Luis

last: Pinto

first: Hisham

last: Mehanna

first: Zdenko


title: Microarray analysis to reveal transcriptional differences between a pair of isogenic tobacco cell lines, SL (wild-type) and ALT301 (aluminum-tolerant), under normal growth condition

city: Kurashiki

first: Yoshiyuki

last: Tsuchiya

state: Okayama

department: Institute of Plant Science and Resources

institute: Okayama University

summary: Using our microarray data, we identified 1, 303 probes (680 upregulated; 623 downregulated; with known functions) with changes of at least 2-fold in their differential transcript levels with significance (P < 0.05) in ALT301, compared with SL (note that some probes within the 1,303 probes carry the same TIGR ID and/or UniGene ID). Focusing on the genes related to glycolysis, the TCA cycle, and antioxidant systems, we found several genes differentially expressed between the lines.

overall_design: Differential expression analysis between SL (wild-type) and ALT301 (Al-tolerant) under normal growth condition, 3 different replicate of each lines.

first: Yoko

last: Yamamoto


title: Protein Phosphatase 1 regulates atypical chromosome segregation and cell polarity during mitotic and meiotic division in Plasmodium sexual stages

city: Thuwal

first: AMIT

middle: KUMAR

last: SUBUDHI

state: Thuwal

address: Level4, Builiding, 2, KAUST

department: BESE

country: Saudi Arabia

institute: King Abdullah University of Science and Technology

summary: PP1 is a conserved serine/threonine phosphatase that regulates many aspects of mitosis and meiosis, often working in concert with other phosphatases, such as CDC14 and CDC25, in model eukaryotes. However, the malaria parasite, Plasmodium spp. lacks the CDC14 and CDC25 genes. The proliferative stages of the parasite life cycle include sexual development within the mosquito vector, with male gamete formation characterized by an atypical rapid mitosis, with three rounds of DNA synthesis, successive spindle formation with clustered kinetochore, and a meiotic stage during zygote to ookinete development following fertilization.  It is unclear how PP1 is involved these unusual processes. Using real-time live-cell imaging, conditional gene knockdown, RNAseq and proteomic approaches, we show that Plasmodium PP1 is involved in both chromosome segregation during mitotic exit, and establishment of cell polarity during these sexual stages, suggesting that PP1 inhibitors may block parasite transmission.

overall_design: Gametocytes (non-activated 0 min and activated 30 min-) were collected from from PP1PTD and WT lines. For RNA extraction, parasite samples were passed through a plasmodipur column to remove host DNA contamination prior to RNA isolation. Total RNA was extracted from activated gametocytes and schizonts of WT-GFP and PP1PTD parasites (two biological replicates each) using an RNeasy purification kit (Qiagen). RNA was vacuum concentrated (SpeedVac) and transported using RNA stable tubes (Biomatrica). Strand-specific mRNA sequencing was performed of total RNA and using TruSeq stranded mRNA sample prep kit LT (Illumina), as previously described55.  Libraries were sequenced using an Illumina Hiseq 4000 sequencing platform with paired-end 150 bp read chemistry. The quality of the raw reads was assessed using FATSQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc). Low-quality reads and Illumina adaptor sequences from the read ends were removed using Trimmomatic R56. Processed reads were mapped to the P. beghei ANKA reference genome (release 40 in PlasmoDB- http://www.plasmoddb.org) using Hisat257 (V 2.1.0) with parameter “—rna-strandness FR”. Counts per feature were estimated using FeatureCounts. Raw read counts data were converted to counts per million (cpm) and genes were excluded if they failed to achieve a cpm value of 1 in at least one of the three replicates performed. Library sizes were scale-normalized by the TMM method using EdgeR software59 and further subjected to linear model analysis using the voom function in the limma package. Differential expression analysis was performed using DeSeq.  Genes with a fold-change greater than two and a false discovery rate corrected p-value (Benjamini-Hochberg procedure) < 0.05 were considered to be differentially expressed. Genes with fold change greater than 2 and p-value less than 0.05 were considered as significantly differentially expressed.

first: Mohammad

last: Zeeshan

first: Rajan

last: Pandey

first: Amit

last: Subudhi

first: J

middle: P

last: Ferguson

first: Mathieu

last: Brochet

first: Arnab

last: Pain

first: Anthony

last: Holder

first: David

last: Guttery

first: Rita

last: Tewari


title: Molecular and functional characterization of haematopoietic stem cells (HSCs) in a mouse model of myeloproliferative neoplasm [RNA-seq]

city: Oxford

first: Adam

last: Mead

address: Headley Way

department: Radcliffe Department of Medicine

institute: University of Oxford

summary: We report the characterization of murine HSCs with knock-in of human JAK2V617F, Ezh2 loss, and both hits, through RNA-seq on a limited number of HSCs. We identified Ezh2 loss as being a strong driver of gene expression differences, while gene set enrichment analysis showed unique signatures characterizing mutant HSCs.

overall_design: mRNA profiles of HSCs in four groups: control, JAK2V617F, Ezh2 loss, JAK2V617F + Ezh2 loss.

first: R

last: Norfo

first: A


title: Targeting resistance to Smoothened antagonists by FACT inhibition

first: Jialin

last: Mo

summary: Resistance to clinically available targeted drugs has become a critical issue in hedgehog-driven cancer treatment. Our previous studies have demonstrated two epigenetic/transcriptional targeted therapeutic strategies, BET inhibition and CDK7 inhibition, could overcome both primary and acquired resistance to Smoothened inhibitor (SMOi) drugs, providing a promising direction for novel anti-hedgehog drug development. In this study, we performed CRISPR-Cas9 screening of epigenetic/transcriptional targeted sgRNA library in hedgehog-driven medulloblastoma (SHH-MB) cells and combined with tumor dataset analyses to identify other potential epigenetic/transcriptional targeted strategies for treating aberrant hedgehog pathway and overcoming SMOi-resistance. Our results demonstrated structure specific recognition protein 1 (SSRP1), a subunit of Facilitates Chromatin Transcription (FACT) complex, was a hedgehog-induced essential oncogene and therapeutic target of hedgehog-driven cancer. FACT inhibitor CBL0137, which has entered human clinical trials against cancer, could effectively suppress multiple mouse and human hedgehog-driven cancer models that are either SMOi-responsive or -resistant both in vitro and in vivo. Mechanistically, CBL0137 exerted its anti-hedgehog activity mainly through targeting the transcription of GLI1/2, which are core transcription factors of hedgehog pathway. ChIP-qPCR analyses further revealed SSRP1 could bind to the promoter regions of GLI1/2, while CBL0137 treatment substantially disrupted these interactions. Moreover, CBL0137 could work synergistically with BET inhibitor or CDK7 inhibitor on antagonizing aberrant hedgehog pathway and growth of either SMOi-responsive or -resistant hedgehog-driven cancer models. Taken together, our study identified FACT inhibition as another promising epigenetic/transcriptional targeted therapeutic strategy for treating hedgehog-driven cancer and overcoming SMOi-resistance.

overall_design: mRNA profiling:RNA was prepared from vehicle or CBL0137 (1μM) treated mouse SHH-subtype medulloblastoma cells (SmoWT) derived from spontaneous medulloblastoma of Ptch1+/-, Trp53-/- mice for 24 h.   Trim galore was used to automatically detect and trim adapters. Reads were mapped to mm10 reference genome using Hisat2. Read count was generated using HTSeq (version 0.11.1). Differentially expressed genes (DEGs) were calculated using DESeq2 (version 1.26.0). Absolute value of fold change (FC) > 1.5 and false discovery rate (FDR) < 0.05 was used as cut-off value to select significant target genes. FPKM (Fragments per Kilobase Million) was calculated from the number of reads that mapped to each particular gene sequence and the gene length and the sequencing depth were taken into account.

first: Fang

last: Liu

first: Xi

last: Sun

first: Yujie

last: Tang


title: RNA-seq analysis of cells derived from breast milk

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

summary: We have developed a method to grow breast epithelial cells released into breast milk. RNA from cells of left and right breasts milk were subjected to RNA sequencing in triplicate

overall_design: RNAs from cells of right and left breast milk were sequenced in biological triplicates. RNA was prepared from early passage cells (<5 passages)


title: Regnase-1 suppresses TCF-1+ precursor exhausted T cell formation to limit CAR T cell responses against ALL [Microarray Expression]

city: Memphis

first: Hongbo

last: Chi

state: TN

address: 262 Danny Thomas Place

department: Immunology

institute: St Jude Children's Research Hospital

summary:
transcriptional profiling was performed on WT and KO CAR T cells isolated 7 days after co-transfer into mice with or without tumors.
Regnase-1 KO CAR T cells undergoing a tumor-dependent shift from an effector to memory-like phenotype

overall_design: In total 19 samples were analyzed: (WT CAR with tumor n=5; WT CAR without tumor n=4; KO CAR with tumor n=5, KO CAR without tumor n=5)

first: W

last: Zheng

first: D

last: Yogesh

first: T

last: Geiger


summary:
transcriptional profiling was performed on WT and KO CAR T cells isolated 21 days after co-transfer into tumor bearing mice.
Regnase-1 KO CAR T cell reprogramed to memory-like cells long-term after tumor priming in vivo compared to WT CAR T cells

overall_design: In total 6 samples were analyzed: (WT CAR n=3; KO CAR n=3)

first: Zheng

last: Wenting

first: Yogesh

last: Dhungana

first: Geiger

last: Terrence


title: CD4+ T cells Reject Benign Melanocytic Nevi

city: Charleston

first: Heehwa

last: Son

state: MA

address: 149 13 street

institute: MASSACHUSETTS GENERAL HOSPITAL

summary: Human CD4+ T cells mediate spontaneous rejection of acquired benign melanocytic nevi, in the majority of cases, through a break in peripheral tolerance. For the remaining cases, nevi remain stable and do not progress to malignancy. In this experiment, we compared gene expression of post-transplant rejected nevi to stable nevi in order to better characterize their transcriptional profiles.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: We excised two nevi, contained within peripheral normal skin, and one section of normal skin by means of shave biopsy from each patient.  One of the two nevi (nevus I) was transplanted onto an immunodeficient NOD-SCID mouse and the remaining nevus (nevus II) was used for histological and molecular studies. Nevi I were harvested from mice after a phenotype had been established. RNA to be used for this study was extracted from Nevi I.

first: Erik

last: Schiferle

first: Seokjin

last: Ham

first: Shadmehr

last: Demehri


title: Newfound roles of OLIG2 in the regulation of lncRNAs, epigenetic status and its own expression at transcriptional and post-transcriptional levels during oligodendrocyte lineage formation

city: Houston

first: Haichao

last: Wei

state: TX

address: 1825 Pressler St., SRB 637.C

institute: UTHealth

summary: We performed an integrated study of genome-wide OLIG2 binding and the epigenetic modification status of both coding and non-coding genes during three stages of oligodendrocyte differentiation in vivo: Neural Stem Cells (NSC), Oligodendrocyte Progenitor Cells (OPC), and Newly Formed Oligodendrocytes (NFO). We found that 613 lncRNAs have OLIG2-binding sites and are expressed in at least one cell type, which can potentially be activated or repressed by OLIG2. 48 of them have increased expression in oligodendrocyte lineage cells. Predicting lncRNA functions by using a “guilt-by-association” approach revealed that the functions of these 48 lncRNAs were enriched in ‘oligodendrocyte development and differentiation’. Additionally, bivalent genes are known to play essential roles during embryonic stem cell differentiation. We identified bivalent genes in NSC, OPC, and NFO, and found that some bivalent genes bound by OLIG2 are dynamically regulated during oligodendrocyte development. Importantly, we have identified AU-rich elements (AREs) in the 3’-UTRs of Olig2 mRNAs.  We unveiled a previously unknown mechanism that, in addition to transcriptional regulation via DNA binding, OLIG2 could post-transcriptionally self-regulate expression through interaction with the 3’-UTR of its own mRNA.

overall_design: Oligodendrocyte development from NSC

first: Jiaqian

last: Wu


title: Expression analysis of AtRXR1 overexpressor and mutant

status: Public on Jul 07 2021

city: Ardmore

first: Sheng

last: Ying

state: OK

address: 2510 Sam Noble Pkwy

institute: Noble Research Institute

summary: We used microarrays to detail the global programme of gene expression underlying root hair development and identified distinct classes of changed genes during this process.

overall_design: 7-d-old arabidopsis root tissues that harvested from AtRXR1 overexpressor or mutant, and wild type control were conducted the ATH1 microarray analysis.

first: Wolf

last: Scheible


title: Postnatal memory governs cell function in adult skeletal muscle.

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

institute: Medical Institute of Bioregulation

summary: Skeletal muscle is the contractile tissue that distributes throughout body, with its functionally heterogeneous properties amongst muscles, which may relate to region specific pathology of muscle diseases. Here we found that homeobox (Hox) genes, key regulators of body-plan in the embryo, are region-specifically and robustly maintained as positional memory in both muscle and its associated stem cells named satellite cells in adult mice and humans. Although satellite cell function in adults was unaffected by genetic loss of Hoxa10 in muscle progenitors at the developmental stage, postnatal deletion of Hoxa10 in satellite cells led to genomic instability and mitosis abnormality, resulting in a remarkable decline in regenerative ability of muscles in a region-specific manner. Our results suggest that Hox-based positional memory is flexibly established during embryonic development and governs topographic function of stem cells in adult muscles once it is fixed, potentially influencing the region-specific weakness in muscle diseases

overall_design: Proliferating satellite cell mRNA profiles of CON (Hoxa10f/f) and scKO (Pax7-CreERT2/+;Hoxa10f/f) were generated by RNA-seq.

first: Yoshioka

last: Kiyoshi

first: Nogami

last: Jumpei

first: Ohkawa

last: Yasuyuki

first: Ono

last: Yusuke


title: 16S rDNA (v3-v4 region) sequencing of the cecal bacteria in control (CTL) and chronic nonbacterial prostatitis (CNP) rats

city: guangzhou

first: Ruiqiang

last: Yan

address: 黄埔大道西601号

institute: Jinan University

summary: Prostate of SD rats was injected with 0.1 ml 1% carrageenan to induce chronic nonbacterial prostatitis, and the control rats injected with sterile saline. Then, the cecal contents were collected for 16S rDNA sequencing.

overall_design: Examination of bacterial community in the cecum of CTL and CNP rats (n=6).

first: Junsheng

last: Liu


title: Identification of host tRNAs preferentially recognized by the Plasmodium surface protein tRip

first: Renaud

last: Geslain

state: SC

address: 58 Coming Street

department: Biology

institute: College of Charleston

summary: We used MIST (Microarray Identification of Shifted tRNAs), a previously established in vitro approach, to systematically assess the specificity of complexes between native H. sapiens tRNAs and recombinant P. falciparum tRip. We demonstrate that tRip unexpectedly binds to host tRNAs with a wide range of specificities, suggesting that only a small subset of human tRNAs are preferentially imported into the parasite.

overall_design:
We employed a proven technique where tRip-bound tRNAs isolated from total human tRNA extracts through EMSA were hybridized on tRNA microarrays for systematic identification. This approach named MIST for Microarray Identification of Shifted tRNA was first used to identify non-cognate tRNAs complexed to yeast RRS (Eriani et al., 2015). Since the tRNA binding domain of tRip is located on the parasite surface away from the cytoplasmic content, its binding specificity was tested exclusively against total tRNAs of its human host in absence of any other parasite molecules. To establish the proper experimental conditions for MIST we reasoned that: (i) tRNAs should be in excess to favor competition and allow tRip to naturally select the best interactants from crude human tRNAs (ii) one tRNA molecule is the strict minimum required to saturate one tRip in vitro. Accordingly, different tRNA:tRip ratios were used. While the protein concentration remained constant (2 µM dimer), the amount of tRNA was set to 8, 20, and 40 µM, which corresponds to 4, 10, and 20 times more tRNAs than tRip dimers. In all three conditions tested, both tRNAs present in the complex and the free fraction were recovered from the gel and analyzed with tRNA microarrays. As control experiments, two untreated samples of crude tRNAs purified from HeLa cells were also analyzed, generating a total of 8 different microarrays.
Please note that the 'raw_data.xlsx' contains both sample raw data and raw data processor spreadsheet. The  raw data processor shows the connection between the raw and the processed data and also contains instructions on how to use the processor for any users who wish to regenerate the  processed data from raw data.

first: Marta

last: Cela

first: Magali

last: Frugier


title: Myostain is involved in GINSENOSIDE-Rb1-mediated anti-obesity

city: 济南市

first: li

last: hongshi

state: 山东

address: 山东省济南市历下区文化西路107号山东大学齐鲁医院

institute: 山东大学教育部与卫健委心血管重构与功能研究重点实验室

summary: Obesity, as one of the major public health problems in the world, has attracted more and more attention. Rb1 is the most abundant active component of Panax ginseng and it has been reported to have benefit effects on obesity and diabetes. But the mechanisms of Rb1 in regulation of obesity are not very clear. In this study, by use of obese mice, we found that Rb1 not only reduced body weight but also decreased myostain (MSTN) expression，which plays a key role in the regulation of obesity. In vitro, we found that Rb1 treatment also decreased MSTN expression in differentiated C2C12 cells (Myoblast cells) and 3T3-L1 cells (adipocytes). Fndc5, as the downstream of MSTN, was increased after Rb1 treatment. Our results showed that Rb1 may ameliorate obesity through MSTN/Fndc5 signaling pathway. Our study provides important experimental evidences for the treatment of obesity by Rb1.after Rb1 treated.

overall_design: The expression of differential genes after RB1 acted on adipose tissue was investigated by sequencing.

first: Hong-Shi

last: Li

first: Yuan-Yuan

last: Sun


title: Gene Expresssion Analysis of Myometrium Stem Cells Treated with CDK8/19 Inhibitor

city: San Antonio

first: Thomas

last: Boyer

address: 7703 Floyd Curl Dr.

institute: University of Texas Health San Antonio

summary: We report the gene expression changes in myometrial stem cells after 3hr treatment with CDK8/19 inhibitor (CCT251545).

overall_design: 3 independent samples of myometrial stem cells were treated with either CCT251545 or DMSO for 3hrs. Total RNA was then extracted and subjected to total RNA-sequencing analysis.

first: Lindsey

last: Barron


title: Single-cell transcriptomic analysis of 36 hpf Zebrafish etv2 and jam2b positive cells

city: Tampa

first: Sanjeeva

middle: Sudhakar

last: Metikala

state: FL

address: 560 Channelside Dr

department: Pathology and Cell Biology

institute: University of South Florida

summary: We performed single-cell RNAseq analysis of FACs sorted etv2 and jam2b psoitive cells from etv2Gt(2A-Venus) ; jam2bGt(2A-Gal4);UAS:NTR-mCherry zebrafish embryos at 36 hpf using 10x Genomics' Chromium platform.   18 distinct cell populations were identified including vascular endothelial cells and LPM cells.

overall_design: Transgenic etv2Gt(2A-Venus) fish were crossed to jam2bGt(2A-Gal4);UAS:NTR-mCherry fish. Whole embryos at 36 hpf were then dissociated into a single-cell suspension by cold protease tissue dissociation protocol. Cells expressing Venus only, mCherry only, and both (Venus and mCherry) were sorted using a BD/FACSAria II flow cytometer cell sorter. After sorting, cells expressing both Venus and mCherry were equally divided and added into the Venus only and mCherry only populations manually. Barcoding of cells and and cDNA library construction was carried out using 10X Genomics' Chromium platform.

first: Suman

last: Gurung

first: Saulius

last: Sumanas