title: Comparison of mRNA expression levels in peri-implantitis and periodontitis within the same host environment

city: Beijing

first: Shasha

last: Yuan

address: No.22, Zhongguancun Nandajie, Haidian District

department: Department of Periodontology

institute: Peking University School and Hospital of Stomatology

summary:
Purpose: The aim of this study was to explore whether differences exist and to what an extent of the immune-mediated inflammatory reactions between periodontitis and peri-implantitis at the transcriptional level in the same susceptible host.
Methods: Ligature-induced experimental peri-implantitis and periodontitis in the same mice were established. Gingival tissues of healthy, periodontitis and peri-implantitis sites from the same oral cavity were collected and used for RNA-sequencing. Differentially expressed genes (DEGs) were screened between periodontitis/peri-implantitis sites and healthy sites. The enrichment analysis of DEGs were analyzed. Comprehensive immune landscape was annotated by seq-ImmuCC.
Results: The results showed that 137 and 353 up-regulated DEGs as well as and 670 and 174 down-regulated DEGs were specifically expressed periodontitis/peri-implantitis group compared to the healthy control group, respectively. The pathways of complement and coagulation cascade and osteoclast differentiation were dominating in the peri-implantitis sites. Moreover, peri-implantitis sites exhibited elevated macrophage proportions and relatively enriched macrophage activation and bone loss compared with periodontitis.
Conclusions: Results indicated that peri-implantitis and periodontitis exhibited significantly distinct transcriptional signatures. Additionally, the study suggests that the interplay between macrophages and bone resorption are comparatively more active in peri-implantitis compared with periodontitis. These biological processes may be factors contributing to the pathogenesis of peri-implantitis being distinct from that of periodontitis.

overall_design: Gingival tissues of healthy, periodontitis and peri-implantitis sites from same mice (n=3) were included, and these tissues were sent to the Majorbio Technology Co., Ltd. (Shanghai, China) for sequencing.

first: Cui

last: Wang

first: Ying

first: Wenjie

last: Hu


title: Remodeling of gene regulatory networks underlying thermogenic stimuli-induced adipose beiging

status: Public on Jun 06 2022

city: La Jolla

first: Seoyeon

last: Lee

state: California

address: 9500 Gilman Dr.

country: USA

institute: University of California, San Diego

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Beige adipocytes are induced by cold temperatures or β3-adrenergic receptor (Adrb3) agonists. They create heat through glucose and fatty acid (FA) oxidation, conferring metabolic benefits. The distinct and shared mechanisms by which these treatments induce beiging are unknown. Here, we performed single-nucleus assay for transposase-accessible chromatin sequencing (snATAC-seq) on adipose tissue from mice exposed to cold or an Adrb3 agonist to identify cellular and chromatin accessibility dynamics during beiging. Both stimuli induce chromatin remodeling that influence vascularization and inflammation in adipose. Beige adipocytes from cold-exposed mice have increased accessibility at genes regulating glycolytic processes, whereas Adrb3 activation increases cAMP responses. While both thermogenic stimuli increase accessibility at genes regulating thermogenesis, lipogenesis, and beige adipocyte development, the kinetics and magnitudes of the changes are distinct for the stimuli. Accessibility changes at lipogenic genes are linked to functional changes in lipid composition of adipose. Both stimuli tend to decrease the proportion of palmitic acids, a saturated FA in adipose. However, Adrb3 activation increases the proportion of monounsaturated FAs, whereas cold increases the proportion of polyunsaturated FAs. These findings reveal common and distinct mechanisms of cold and Adrb3 induced beige adipocyte biogenesis, and identify unique functional consequences of manipulating these pathways in vivo.

overall_design: snATAC-seq analysis of iWATs from 8-weeks-old male C57BL/6 mice after cold exposure or CL treatment for 0, 1, 3, and 7 days (n=3 for each)

first: Paul

last: Soloway


title: Characterization and Analysis of Whole Transcriptome of Ningxiang Pig Spleens Reveal Potential Mechanism for Transcriptional Regulation in Immunity [miRNA-Seq]

city: changsha

first: LI

last: Biao

address: Nongda South Road

department: College of Animal Science and Technology

country: China

institute: Hunan Agricultural University

type: Non-coding RNA profiling by high throughput sequencing

summary: we comprehensively analyzed the whole transcriptome of the spleen from three important developmental nodes(30d, 90d and 210d) of Ningxiang pig (a Chinese indigenous breed). A total of 812, 364 and 865 differentially expressed (DE) mRNAs, 98, 37 and 97 DE miRNAs, 278, 220 and 271 DE lncRNAs, and 113, 96 and 96 DE circRNAs were identified between 90d and 30d, 210d and 30d, and 210d and 90d, respectively. And their molecular characterization, spatio temporal expression pattern, potential function and interaction with miRNAs were analyzed. Additionally, co-expression network analysis identified the potential non coding RNAs(ncRNAs) related to immunomodulation, e.g., ssc-miRNA-150, ssc-miRNA-497, MSTRG.24160, MSTRG.18646. Furthermore, our results also revealed that miRNAs and circRNAs may have evolved to regulate a large set of biological processes of Ningxiang pigs spleens, and circRNAs may play the role of miRNA sponges. Our study provides new insights into the expression changes of RNAs during the spleen development process of Chinese indigenous breed Ningxiang pigs, which might contribute to the phenotypic formation of immune function in Chinese native pig breeds. These results greatly improved our understanding of the molecular mechanisms which regulate the immune function of the spleen of Ningxiang pigs.

overall_design: we comprehensively analyzed the whole transcriptome of the spleen from three important developmental nodes(30d, 90d and 210d) of Ningxiang pig (a Chinese indigenous breed)by using Illumina Hiseq 4000.

first: Biao

last: Li

first: Jun

last: He


title: Characterization and Analysis of Whole Transcriptome of Ningxiang Pig Spleens Reveal Potential Mechanism for Transcriptional Regulation in Immunity

type: Expression profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Comparative single-cell RNA-sequencing profiling of BMP4-treated primary glioma cultures reveals therapeutic markers

city: Rotterdam

first: Iris

last: Verploegh

address: Doctor Molewaterplein 40

country: Netherlands

institute: Erasmus MC

summary: We used 10X Chromium single-cell RNAseq to investigate the heterogeneity in response to treatment with BMP4 in glioblastoma.

overall_design: Two primary cultures (one sensitive and one resistant to BMP4) with and without treatment with BMP4.

first: A

last: Conidi

first: I


title: Characterization and Analysis of Whole Transcriptome of Ningxiang Pig Spleens Reveal Potential Mechanism for Transcriptional Regulation in Immunity [RNA-Seq]


title: Chemotherapy response in cholangiocarcinoma

city: Glasgow

first: Chiara

last: Braconi

address: Switchback road

department: Wolfson Wohl Cancer Research Centre

country: United Kingdom

institute: University of Glasgow

summary: CCLP cholangiocarcinoma cells  were transfected with CTRL inhibitor or MIR1249 inhibitor for 48 hours and treated with DMSO or chemotherapy (cisplatin and gemcitabine) for 48 hours before being collected and analysed for gene expression

overall_design: Dual channel microarrays where Cy3 is Experimental sample RNA and Cy5 is Agilent human reference RNA (cat no 740000).


title: IκBζ Regulates the Development of Nonalcoholic Fatty Liver Disease through the Attenuation of Hepatic Steatosis in Mice

status: Public on Jun 05 2022

city: Yakushiji Shimotsuke-shi

first: Morisada

last: Hayakawa

state: Tochigi

country: Japan

institute: Jichi Medical University

summary: IκBζ is a transcriptional regulator that augments inflammatory responses from the Toll-like receptor or interleukin signaling. These innate immune responses contribute to the progression of nonalcoholic fatty liver disease (NAFLD); however, the role of IκBζ in the pathogenesis of NAFLD remains elusive. We investigated whether IκBζ was involved in the progression of NAFLD in mice. We generated hepatocyte-specific IκBζ-deficient mice (Alb-Cre; Nfkbizfl/fl) by crossing Nfkbizfl/fl mice with Alb-Cre transgenic mice. NAFLD was induced by feeding the mice a choline-deﬁcient, L-amino acid-deﬁned, high-fat diet (CDAHFD). CDAHFD-induced IκBζ expression in the liver was observed in Nfkbizfl/fl mice, but not in Alb-Cre; Nfkbizfl/fl mice. Contrary to our initial expectation, IκBζ deletion in hepatocytes accelerated the progression of NAFLD after CDAHFD treatment. Although the increased expression of inflammatory cytokines and apoptosis-related proteins by CDAHFD remained unchanged between Nfkbizfl/fl and Alb-Cre; Nfkbizfl/fl mice, early-stage steatosis of the liver was significantly augmented in Alb-Cre; Nfkbizfl/fl mice. Overexpression of IκBζ in hepatocytes via the adeno-associated virus vector attenuated liver steatosis caused by the CDAHFD in wild-type C57BL/6 mice. This preventive effect of IκBζ overexpression on steatosis was not observed without transcriptional activity. Microarray analysis revealed a correlation between IκBζ expression and the changes of factors related to triglyceride biosynthesis and lipoprotein uptake. Our data suggest that hepatic IκBζ attenuates the progression of NAFLD possibly through the regulation of the factors related to triglyceride metabolism.

overall_design: Microarray analysis were performed on the liver from NAFLD model mice. C57BL/6 mice were were intravenously treated with the AAV8 vector harboring Luciferase or Nfkbiz. Liver RNA was isolated from mice at 4 weeks after the CDAHFD challenge.


title: Transcriptomic profile of TP53 wildtype or knockout cells after treated with mitomycin C or vehicle

city: Shanghai

first: Jingyu

last: Lang

address: 320 Yueyang Road

institute: Shanghai Institutes for Biological Sciences

summary: The goal of this study is to dig out how mitomycin C triggers apoptosis in the sensitive cells

overall_design: mRNA profiles of cell treated with mitomycin C or vehicle for 36 hours  were detected by RNA-sequencing.

first: Xiaomin

last: Chen


title: Bach2 regulates B cell survival to maintain germinal centers and promote B cell memory

city: shanghai

first: Qianwen

address: 重庆南路280号

institute: Shanghai Jiao Tong University School of Medicine

summary: The transcription factor Bach2 serves as a crucial regulator of the germinal center (GC) reaction, which is required for production of high-affinity antibodies and establishment of long-lived B cell memory. However, the stage at which Bach2 controls the GC programs and the precise mechanism underlying these processes remain poorly understood. In this study, we show that genetic ablation of Bach2 in GC B cells of mice impairs their survival and maintenance, and memory B cell formation. These defects can be rescued by enforced expression of anti-apoptotic gene Bcl2. As expected, Bach2-deficient GC B cells are defective in antibody affinity maturation, but have normal somatic hyper mutation and class switch recombination of immunoglobulin genes. Mechanistically, Bach2 controls the GC programs by directly repressing pro-apoptotic gene Bim and a set of genes involved in cell stress response and metabolic processes. Thus, our work reveals the precise roles of Bach2 in the GC biology, and demonstrates that Bach2 acts as a crucial survival regulator of GC B cells, providing a key mechanism underlying GC B maintenance and B cell memory formation.

overall_design: To gain the functions of Bach2 on GC B cells, Bach2-sufficient and -deficient CD19+IgD-CD95+CD38- GC B cells were sorted at day 10 after SRBC immunization and subjected for transcriptional profile analysis.


title: Discovery of small-molecule degraders of the CDK9-cyclin T1 complex for targeting transcriptional addiction in prostate cancer

first: Jiacheng

state: Shanghai

address: 555 Zuchongzhi Road

department: Drug Discovery and Design Center

institute: Shanghai Institute of Materia Medica, Chinese Academy of Sciences

summary: Aberrant hyperactivation of cyclins results in carcinogenesis and therapy resistance in cancers. Direct degradation of the specific cyclin or CDK-cyclin complex by small-molecule degraders remains a great challenge. Here, we applied the first application of hydrophobic tagging to induce degradation of CDK9-cyclin T1 heterodimer which is required to keep productive transcription of oncogenes in cancers. LL-K9-3 was identified as a potent small-molecule degrader of CDK9-cyclin T1. Quantitative and time-resolved proteome profiling exhibited LL-K9-3 induced selective and synchronous degradation of CDK9 and cyclin T1. The expression of androgen receptor (AR) and c-Myc were reduced by LL-K9-3 in 22RV1 cells. LL-K9-3 exhibited enhanced anti-proliferative and pro-apoptotic effects than its parental CDK9 inhibitor SNS032, and suppressed downstream signaling of CDK9 and AR more effectively than SNS032. Moreover, LL-K9-3 inhibited AR and MYC-driven oncogenic transcriptional programs, and exerted stronger inhibitory effects on several intrinsic target genes of AR than the monomeric CDK9 PROTAC (Thal-SNS032).

overall_design: RNA-sequencing was performed using 22RV1 cells that were exposed to DMSO, 2 µM SNS032, 2 µM LL-K9-3, and 2 µM Thal-SNS032 in biological triplicate for 24 hours

first: Ting

last: Liu

first: Yuanli

last: Song

first: Mingyu

first: Liping

first: Hongwen

last: Zhu

first: Qi

first: Jin

last: Lin

first: Hualiang

last: Jiang

first: Kaixian

first: Kehao

last: Zhao

first: Mingliang

first: Hu

last: Zhou

first: Hua

first: Cheng

last: Luo


title: RNA-Seq analysis of Synechocystis sp. PCC 6803 with a deletion of the kaiABC gene cluster in comparison to the wild type.

city: Jena

first: Maximilian

last: Colatz

address: Leutragraben 1

country: Germany

institute: Friedrich-Schiller-University Jena

summary:
We analyzed the gene expression changes in the wild type and the delta kaiAB1C1 mutant at six time points after a 12 hours dark incubation.
RNA-Seq provides a much higher senisitivity and resolution in comparison to previously performed micro array experiments.
We aim to get a better understanding how the circadian oscillator which is encoded by the kaiABC genes regulates the overall gene expression in Synechocystis sp. PCC 6803.

overall_design: Cells were harvested during the first dark period and the following light period. Time is given as zeitgeber time (ZT) with ZT 0.5 being the first sample during dark incubation 0.5 h after the shift from light to dark. Two biological replicates were harvested at ZT={0.5, 5.5, 11.5, 12.5, 17.5, 23.5} and total RNA was isolated

first: Annegret

last: Wilde

last: Collatz

first: Bertram

last: Vogel

first: Franziska

last: Hufsky

first: Manja

last: Marz


title: USP16-mediated Histone H2A Lysine-119 Deubiquitination during Oocyte Maturation is a Prerequisite for Zygotic Genome Activation

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Maternal-to-zygotic transition (MZT) is the first and key step in the control of animal development and is intimately related to changes of chromatin structure and histone modifications. Mono-ubiquitination of histone H2A at lysine-119 (H2AK119ub1), an important epigenetic modification in regulating chromatin configuration and function, is primarily catalyzed by polycomb repressive complex 1 (PRC1) and contributes to resistance to transcriptional reprogramming in mouse embryos. In this study, the genome-wide dynamic distribution of H2AK119ub1 during MZT in mice was investigated by chromosome immunoprecipitation and sequencing. The results indicated that H2AK119ub1 accumulated in fully grown oocytes, enriched at the transcriptional start sequences (TSSs) of maternal genes, but was promptly removed after meiotic resumption, particularly at the TSSs of early zygotic genes, by a previously unidentified mechanism. Genetic evidences indicated that ubiquitin-specific peptidase 16 (USP16) is the major deubiquitinase of H2AK119ub1 in mouse oocytes. Conditional knockout of Usp16 in oocytes did not impair their survival, growth, andor meiotic maturation. However, oocytes lacking USP16 were unable to undergo zygotic genome activation or gain developmental competence after fertilization, due to high levels of H2AK119ub1 deposition on the zygotic genomes. Taken together, this study indicates that H2AK119ub1 is erased during oocyte maturation by an USP16-dependent mechanism, which ensures zygotic genome reprogramming and transcriptional activation of essential early zygotic genes.

overall_design:
WT oocytes at GV and MII stages, WT Zygotes, WT 2-cell stage embryos are collected to perform H2AK119ub1 ChIP sequencing.

WT and Usp16 cKO embryos at zygote and 2-cell stages for two replicates are performed RNA sequencing.

first: Yan

last: Rong

first: Jiali

last: Yu

first: Yezhang

first: Hengyu

last: Fan


title: Analysis of transcriptional changes in cell lines (in vitro) and tumors (in vivo) after treatment with interferon α gene therapy.

city: Houston

first: Ganiraju

last: Manyam

state: TX

address: 1515 Holcombe Blvd

institute: UT MD Anderson Cancer Center

summary: Three bladder cancer cell lines were treated with recombinant IFNα, LV-Ctrl or LV-IFNα and compared with control (Ctrl) samples by RNAseq. Also, vehicle treated, LV-Ctrl and LV-IFNα treated murine MB49 bladder cancer tumor model was compared by RNAseq

overall_design: Murine cell lines BBN975, MB49 and UPPL1541 were treated with recombinant IFNα (100U/ml), LV- Ctrl (MOI2) and LV-IFNα (MOI2) and compared with Ctrl samples.  MB49 cells were instilled into mouse bladder and after tumor cell uptake, mice were randomized and treated with vehicle, LV-Ctrl or LV-IFNα. RNA was extracted using Ambion miRVANA kit (AM1561) and DNAase treated RNA was used to generate cDNA libraries for cell lines and murine tumors.

first: Sharada

last: Mokkapati


title: CircRNA, lncRNA and mRNA expression profiles after spinal cord injury in mouse model

first: Linlin

last: Wang

state: Zhejiang

address: Yuhangtang Road No.866

department: Department of Basic Medicine Sciences

institute: Zhejiang University

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

summary: To further explore the expression of circRNA, lncRNA and mRNA in mice with spinal cord contusion injury, we have employed microarray analysis as a discovery platform to identify circRNAs and lncRNAs with the potential to play role in the pathophysiology process of secondary injuryd after spinal cord injury. Three days after spinal cord injuryI, eight mice (SCI group, n=4; sham group, n=4) were anesthetized and the T9-T10 spinal cord segments centered on and enclosing the injured site were collected.  And then total RNA was extracted and used for microarray detection. Four circRNAs from the top 30 differently expressed circRNAs were selected for real-time PCR. The expression patterns of these circRNAs were consistent with the microarray data validating the expression pattern observed by microarray analysis.

first: Yao

last: Ying

first: Jingyu


title: Mesoderm induction short-timecourse in hESCs

status: Public on Jun 04 2022

city: Cologne

first: Leo

last: Kurian

address: Robert-Kochstr. 21

institute: University of Cologne

summary: To investigate the effect of RBPMS KO on mesoderm commitment we induced WT and RBPMS KO to mesoderm and isolated RNA at 0h (control),3h, 6h and 48h post induction.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HUES hESCs and its RBPMS KO derivatives.

first: Deniz

last: Bartsch


title: Aging exacerbates neuromuscular junction disruption after injury that stimulates pro-inflammatory and diminishes pro-regenerative factor expression in macrophages and fibroadipogenic progenitors.

city: San Francisco

first: Susanna

last: Rosi

state: CA

address: 2200 Island Dr

institute: Altos labs

summary: Aging is associated with delayed skeletal muscle repair and regeneration. Loss of innervation occurs after degenerative muscle injury, however, the extent of denervation, whether the kinetics of reinnervation changes with aging, and the cellular consequences of neuromuscular junction (NMJ) disruption in adult and aged muscle have not been explored. Here we show after degenerative muscle injury progressive denervation and delayed reinnervation in aged compared to adult muscle. Using confocal microscopy and 3-D image rendering we found a relationship between innervation and myofiber size in aged regenerating muscle. Although timely inhibition of pro-inflammatory Ccr2 activity after degenerative muscle injury improved aged regenerated myofiber size, this was not associated with an increase in reinnervation. In contrast, single cell RNA sequencing (scRNASeq) analysis revealed denervation triggers an inflammatory response in target muscles regardless of age; however, pro-inflammatory signaling predominated in aged macrophages and fibroadipogenic progenitors (FAPs) compared to a pro-regenerative response in adult cells. Thus, denervation and delayed reinnervation of NMJs after injury is a feature of persistent pro-inflammatory signals associated with delayed repair and regeneration of aged muscle.

overall_design: Young (3 months) and aged (25 months) C57BL/6J mice were administered nerve crush injury. 5 days post injury, the TA muscles were isolated using surgical scissors, minced and digested with Collagenase type II (0.2%) and Dispase II (2.5U/mL) in 10mL of DMEM per muscle. Samples were placed on rocker in a 37˚C incubator for 1 hour and mixed by pipette every 30 minutes. The enzymes within the slurry were then inactivated by addition of 20% heat-inactivated fetal bovine serum (HI-FBS) in Ham’s F10 media. The solution was passed through a 70um cell strainers, centrifuged, washed, and counted. The isolated cells were then stained with Propidium Iodide (PI) and viable cells isolated using fluorescent-activated cell sorting (FACS). Cells from each mouse were then labeled with cellular hash tags using CellPlex reagents (10x Genomics), pooled from two mice according to age (young and aged) into each lane and 10,000-16,000 cells were loaded into the 10x Genomics chromium single cell controller lane. Single cells were then captured in nanoliter-scale gel bead-in-emulsions (GEMs), lysed, RNA captured, and cDNAs prepared using the single cell 3′ v3 Protocol as per manufacturer’s instructions. Each sample was sequenced on a NovaSeq 6000 (Illumina) with 26 bases for read1 and 98x8 bases for read2.

first: Benjamin

middle: A

last: Yang


title: s3-ATAC landscape of GEMM AML-derived CD8 T cells treated in vivo with JQ1 or vehicle

city: Portland

first: Andrew

last: Adey

state: OR

address: 3181 S.W. Sam Jackson Park Rd, RHH, L103

department: MMG

institute: Oregon Health & Science University

summary: We report the s3-ATAC chromatin landscape of CD8 T cells derived from a FLT3-ITD/TET2 driven GEMM model of AML upon treatment with BET inhibitor JQ1. We find that JQ1 induces chomatin changes specifically in exhausted subsets of CD8 T cells in vivo

overall_design: 10 AML mice were treated daily via i.p injection with either cyclodextrin (5 mice, vehicle control) or JQ1 (5 mice, drug group). Cells were then harvested from the AML mouse spleens and enriched for CD8+ cells by magnetic bead sort prior to sequencing by s3-ATAC

first: Kyle

last: Romine

first: Evan

last: Lind


title: CircEZH2 miR-133b IGF2BP2 aggravates colorectal cancer progression via enhancing the stability of m6A modified CREB1 mRNA [miRNA-seq]

city: Nanjing

first: Bing

last: Yao

state: Jiangsu

address: Longmian Road 101

department: Department of Medical Genetics

institute: Nanjing Medical University

summary: Background: Aberrant expression of circular RNAs contributes to the initiation and progression of human malignancies, but the underlying mechanisms remain largely elusive.    Methods: High throughput sequencing was performed to screen aberrantly expressed circRNAs or miRNAs in colorectal cancer  and adjacent normal tissues. A series of gain and loss of function studies were conducted to evaluate the biological behaviors of CRC cells. RNA pulldown, mass spectrometry, RIP, qRT PCR, western blot, luciferase reporter assays and MeRIP seq analysis were further applied to dissect the detailed mechanisms.    Results: Here, a novel circRNA named circEZH2 , was screened out by RNA seq in CRC tissues, whose expression is related to clinicpathological characteristics and prognosis in CRC patients. Biologically, circEZH2 facilitates the proliferation and migration of CRC cells in vitro and in vivo. Mechanistically, circEZH2 interacts with m6A reader IGF2BP2 and blocks its ubiquitination dependent degradation. Meanwhile, circEZH2 could serve as a competing endogenous RNA for miR 133b, resulting in the upregulation of IGF2BP2. Particularly, circEZH2 IGF2BP2 enhances the stability of CREB1 mRNA, thus aggravating CRC progression.    Conclusions: Our findings not only reveal the pivotal roles of circEZH2 in modulating CRC progression, but also advocate for attenuating circEZH2 miR 133b IGF2BP2 CREB1 regulatory axis to combat CRC.

overall_design: To investigate the role of circRNAs in the progression of CRC, we performed RNA sequencing  analysis of ribosomal RNA depleted total RNA isolated from 6 paired CRC and adjacent normal tissues.

first: Qinglin

last: Zhang

first: Zhou

first: Jing

last: Sun


title: CircEZH2 miR-133b IGF2BP2 aggravates colorectal cancer progression via enhancing the stability of m6A modified CREB1 mRNA


title: A novel 3D co-culture model augmented with single-cell sequencing to study the response of breast cancer cells to cisplatin

city: Foshan

first: Dan

last: Zhou

address: Shiwan Street, Chancheng District, Foshan City

institute: Center, First People's  Hospital of Foshan

summary: Three-dimensional (3D) cell direct co-culture is an essential method for cancer research, which can overcome the limitations of traditional research based on cell lines. Single-cell RNA sequencing can detect the cell heterogeneity of direct co-culture of 3D cells at the single-cell level,However, there is still lack verification. The purpose of this study is to verify the superiority of single-cell RNA sequencing combined with 3D cell direct co-culture in breast cancer research and prove that it can become a powerful solution for cancer cell culture in vitro.In this study ,we found that the different cell culture modes showed very different responses to cisplatin intervention. In MCF-7 alone culture mode, there was a large difference in the transcriptome of MCF-7 after cisplatin intervention compared with the group not given drug intervention; while in direct co-culture mode, there was also a difference between the cisplatin intervention group and the control group, but this difference was relatively small. To further seek evidence that the direct co-culture mode is closer to the real environment in vivo, we analyzed the differential genes in the direct co-culture mode, and the enriched signaling pathways were similar to the results in the CancerSEA database, and the enriched signaling pathways included apoptosis, DNA damage, hypoxia, and metastasis.  Conclusions: Single-cell sequencing can facilitate direct co-culture of 3D cells in tumor research, a model that more closely resembles the real pathophysiological environment in vivo.

overall_design: The experimental samples were divided into four groups: cell co-culture control group, cell co-culture cisplatin-induced group, MCF-7 cultured alone group, and MCF-7 cultured alone cisplatin-induced group. For cell co-culture, MCF-7, HMF, and HUVEC were mixed at a ratio of 1:1:1. All the cells were cultured in the previously prepared Matrigel matrix. The cells in the co-culture cisplatin-induced group and the MCF-7 alone cisplatin-induced group were incubated with cisplatin at a concentration of 1.25 mm/ml. The cells were harvested after 2 days of cisplatin treatment and subjected to single-cell RNA sequencing.

first: Shuqing

first: Peixian

last: Chen

first: Xiaofan

last: Mao

first: KaiRong

last: Lin

first: Wei

last: Li

first: Tiancheng

last: He

first: Huiqi

last: Huang

last: Luo

first: Guolin

last: Ye


title: CircEZH2 miR-133b IGF2BP2 aggravates colorectal cancer progression via enhancing the stability of m6A modified CREB1 mRNA [circRNA-seq]

summary: Background: Aberrant expression of circular RNAs contributes to the initiation and progression of human malignancies, but the underlying mechanisms remain largely elusive.    Methods: High throughput sequencing was performed to screen aberrantly expressed circRNAs or miRNAs in colorectal cancer  and adjacent normal tissues. A series of gain and loss of function studies were conducted to evaluate the biological behaviors of CRC cells. RNA pulldown, mass spectrometry, RIP, qRT PCR, western blot, luciferase reporter assays and MeRIP seq analysis were further applied to dissect the detailed mechanisms.    Results: Here, a novel circRNA named circEZH2 , was screened out by RNA seq in CRC tissues, whose expression is related to clinicpathological characteristics and prognosis in CRC patients. Biologically, circEZH2 facilitates the proliferation and migration of CRC cells in vitro and in vivo. Mechanistically, circEZH2 interacts with m6A reader IGF2BP2 and blocks its ubiquitination dependent degradation. Meanwhile, circEZH2 could serve as a competing endogenous RNA  for miR 133b, resulting in the upregulation of IGF2BP2. Particularly, circEZH2 IGF2BP2 enhances the stability of CREB1 mRNA, thus aggravating CRC progression.    Conclusions: Our findings not only reveal the pivotal roles of circEZH2 in modulating CRC progression, but also advocate for attenuating circEZH2 miR-133b IGF2BP2 CREB1 regulatory axis to combat CRC.


title: Local activation of the complement system mobilizes osteoclast precursors and promotes bone loss

city: Barcelona

first: Carolina

middle: Pimenta

last: Lopes

address: Carrer Feixa Llarga S/N

country: Spain

institute: Univesity of Barcelona

summary: Chemotherapy-induced bone loss depends on cellular senescence and the cell secretory phenotype. To investigate the factors secreted in the senescent microenvironment we have defined a mice model o premature senescence and studied the secreted genes that were differentially expressed in the senescent microenvironment.

overall_design: To define the chemotherapy-induced senescence model, 15-week-old wildtype C57BL/6 male mice were randomly assigned to Control or DoxoR groups. At day 0, mice were injected intraperitoneally with vehicle (saline solution) or 10 mg/kg doxorubicin. 30 days after the treatment mRNA of tibiae and femur (without bone marrow) of 4 Control and 4 Doxorubicin was isolated.

last: Pimenta-Lopes

first: Anna

last: Esteve-Codina

first: Francesc

last: Ventura


title: RNAseq of macrophages from MC38 tumors with PtdSer externalization blockade

city: Pittsburgh

first: Jacob

last: Stewart-Ornstein

state: PA

address: UPMC Hillman Cancer Center, 5117 Centre Avenue

department: computational and systems biology

institute: University of Pittsburgh, School of Medicine

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of tumor associated macrophages from WT MC38 tumors and Xkr8 KO tumors

overall_design: TAMs from the WT or Xkr8 KO tumors were sorted, total RNA was extracted for library construction.

first: Yinan

last: Gong

first: Weihong

last: Wang


title: Genome-scale CRISPR screen reveals inhibitory factors as regulatory module of HIV

city: La jolla

first: Qiong

last: Zhang

address: 9500 Gilman Dr.

department: Pediatrics

institute: UCSD

summary: To identify host factors that restrict HIV replication, we conducted a CRISPR activation screen in a susceptible T cell line using a high-complexity, genome-wide sgRNA library. Our results identified host factors that conferred protection from HIV infection.

overall_design: To identify cellular factors restricting HIV-1 replication, we utilized a previously engineered synergistic activation mediator complex (SAM) for the transcriptional activation of endogenous genes. dCas9 and MS2 expressing CD4 T cells were expanded and 300 million cells were further transduced with the SAM lentiviral library (3 sgRNAs per gene for 70,290 guides in total) at an MOI = 0.3 for 7 days. The gain-of-expression cells were divided into two pools. We challenged the first pool of 60 million transduced cell with HIV at an MOI of 1 for 4 days and then treated cells with GCV for 3 days to further deplete infected cells. Two rounds of infection and GCV selection were performed to enrich HIV resistant cells to identify host genes important in HIV infection. The other pool of 30 million cells were mock infected as control. After 2 weeks, surviving cells were sorted out. Genomic DNA was extracted from harvested cells and sgRNAs were PCR-amplified and deep sequenced. Normalized reads of HIV infected cells were compared to mock infected cells.

first: Shaobo

first: Edwin

last: Yau


title: RNAseq of macrophages and NK cells from MC38 tumors with PtdSer externalization blockade

city: pittsburgh

address: 5117 Centre Ave, lab 2.19

institute: Hillman Cancer Center

summary: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of tumor associated macrophages from WT MC38 tumors and Tmem30a KO tumors; and NK cells from WT and Xkr8 KO MC38 TILs

overall_design: TAMs from the WT or Tmem30a KO MC38 tumors as well as MKs from the WT or Xkr8 KO MC38 tumors  were sorted, total RNA was extracted for library construction.


title: Identification of ENO2-targeted downstream genes by ChIP-seq in Arabidopsis

city: Wuhan

first: Wen-Cheng

last: Liu

address: Bayi Road

department: College of Life Sciences

institute: Wuhan University

summary: ENO2, a bifunctional protein with enolase activity and transcriptional activity, plays a vital role in plant development and responses to environmental stresses. However, only several downstream genes targeted by ENO2 have been reported so far. Our study here identified hundreds of candidates of ENO2 targets with ChIP-seq and our special anti-ENO2 antibody. These results will help us further study the role of ENO2 in plant growth/development and environmental stress responses.

overall_design: Identification of ENO2-binded genes by ChIP-seq with anti-ENO2 antibody in Arabidopsis

first: Ting-Ting


title: Transcriptomic dataset of neural progenitors differentiated from Parkinson's disease patient induced pluripotent stem cells with heterozygous PARK2 junction mutations transduced with a lentivector containing PARK2 cDNA.

status: Public on Jun 03 2022

city: Moscow

first: Daniil

last: Poberezhniy

address: Kurchatov sq. 2

country: Russia

institute: National Research Centre "Kurchatov Institute"

summary: Parkinson's disease (PD) is a neurodegenerative pathology caused by progressive loss of dopaminergic neurons in the substantia nigra. Juvenile PD is known to be strongly associated with mutations in the PARK2 gene encoding E3 ubiquitin ligase Parkin. Despite numerous studies, molecular mechanisms that trigger PD still remain unknown. Here, we presented the transcriptome profile for neural progenitors (NP) which were obtained from iPSCs of Parkinson's disease patient, transduced with lentiviral particles carrying the full-length copy of cDNA PARK2. Transcriptome profiles were generated on an NextSeq 500 System (Illumina). A comparative transcriptome analysis of this data along with transcriptome profiles for NP of healthy donors and other patients with PD will allow determining the contribution of mutations of the PARK2 gene to PD pathogenesis and identifying genes whose expression depends on PARK2 overexpression.

overall_design: iPSCs from PD patient, carrying mutations in PARK2 gene (2 exon (del 202-203 AG) and 1 intron (splicing mutation IVS1+1G/A)), transduced with lentiviral particles carrying the full-length copy of cDNA PARK2 under minimal CMV + TetO promoter, were differentiated into uncommitted neural progenitors. Transcriptome profiles for the obtained samples were generated using NextSeq 500 System.

first: Ekaterina

last: Novosadova

first: Olga

last: Lebedeva

first: Valentina

last: Nenasheva


title: Marker Frequency Analysis of Conchiformibius steedae DSM 2580

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

summary: Investigation of replication dynamics (detection of origin of replication, bidirectionality)

overall_design: 2 conditions (late exponential (OD600 = 0.6), stationary growth (OD600 = 1))

first: Tobias

last: Viehboeck


title: Arsenic toxicity is regulated by queuine availability and oxidation- induced reprogramming of the human tRNA epitranscriptome

city: ALBANY

first: Anwesha

last: Sarkar

state: NY

address: 1400 Washington Ave Albany, 1003K

department: Department of Biological Sciences

institute: University at Albany

summary: Cells respond to environmental stress by regulating gene expression at the level of both transcription and translation. The ~50 modified ribonucleotides of the human epitranscriptome contribute to the latter, with mounting evidence that dynamic regulation of tRNA wobble modifications leads to selective translation of stress response proteins from codon-biased genes. Here we show that the response of human HepG2 cells to arsenite exposure is regulated by the availability of queuine, a micronutrient and essential precursor to the wobble modification queuosine (Q) on tRNAs reading GUN codons. Among oxidizing and alkylating agents at equitoxic concentrations, arsenite exposure caused an oxidant-specific increase in Q that correlated with up-regulation of proteins from codon-biased genes involved in energy metabolism. Limiting queuine increased arsenite-induced cell death, altered translation, increased reactive oxygen species levels, and caused mitochondrial dysfunction. In addition to revealing a new epitranscriptomic facet of arsenite toxicity and response, our results highlight the mechanistic links between environmental exposures, stress tolerance, and micronutrients.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HepG2 cells and its variable media conditions

first: Ulrike

last: Begley

first: Sabrina

last: Huber

first: Thomas


title: Identification of a bile acid-binding transcription factor in Clostridioides difficile using chemical proteomics

city: Boston

first: Aimee

last: Shen

state: MA

address: 136 Harrison Ave

institute: Tufts University

summary: Clostridioides difficile is a Gram-positive anaerobic bacterium that is the leading cause of hospital-acquired gastroenteritis in the US. In the gut milieu, C. difficile encounters microbiota-derived bile acids capable of inhibiting its growth, which are thought to be a mechanism of colonization resistance. While the levels of certain bile acids in the gut correlate with susceptibility to C. difficile infection, their molecular targets in C. difficile remain unknown. In this study, we sought to use chemical proteomics to identify bile acid-interacting proteins in C. difficile. Using photoaffinity bile acid probes and chemical proteomics, we identified a previously uncharacterized MerR family protein, CD3583 (now BapR), as a putative bile acid-sensing transcription regulator. Our data indicate that BapR binds and is stabilized by lithocholic acid (LCA) in C. difficile. Although loss of BapR did not affect C. difficile's sensitivity to LCA, bapR mutant cells elongated more in the presence of LCA than wild-type cells. Transcriptomics revealed that BapR regulates the expression of the gene clusters mdeA-cd3573 and cd0618-cd0616, and cwpV, with the expression of the mdeA-cd3573 locus being specifically de-repressed in the presence of LCA in a BapR-dependent manner. Electrophoretic mobility shift assays revealed that BapR directly binds to the mdeA promoter region. Since mdeA is involved in amino acid-related sulfur metabolism and the mdeA-cd3573 locus encodes putative transporters, we propose that BapR senses a gastrointestinal tract-specific small molecule, LCA, as an environmental cue for metabolic adaptation.

overall_design: RNA-seq from wildtype and ΔbapR 630Δerm C. difficile after 1-hour exposure to 20 μM lithocholic acid or DMSO vehicle. Three biological replicates per strain per condition.

first: Emily

middle: R

last: Forster

first: Xinglin

last: Yang

first: Howard

middle: C

last: Hang


title: Preliminary Interpretations of Epigenetic Profiling of Cord Blood in Preeclampsia

city: Shanghai

first: Xiaonan

last: Wang

address: 227 Chongqing South Road

department: School of Public Health, School of Medicine

institute: Shanghai Jiaotong University

summary: Preeclampsia (PE) is characterized by new-onset hypertension after 20 weeks of pregnancy and results in high maternal and fetal mortality worldwide. It has been reported that PE is associated with abnormalities in the umbilical cord and cord blood. However, previous studies were focused primarily on the transcriptomics level, while the underlying gene regulatory landscapes are still unclear. Thus, we performed the Assay for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) using the umbilical cord blood samples collected from a patient with superimposed PE and three healthy donors to uncover the chromatin accessibility changes attributed to PE. We have identified genes associated with immunomodulation and hypoxia response that have higher chromatin accessibility close to their transcription start sites. Motif analysis indicated that the GATA family transcription factor binding was enriched in PE and may play an essential regulatory role in the disease progression. Overall, our findings provide an overview of gene regulatory programs and the corresponding downstream pathways associated with PE that may influence the placenta function and fetal growth.

overall_design: ATAC-seq of cord blood of healthy pregnancy women and patient with superimposed preeclampsia

first: Junrui

last: Ma

first: Zhongqun

last: Zhan

first: Ning

last: Li

first: Yanli

last: Huang

first: Yan

first: Lu

first: Qi

first: Qiao

last: Chu

first: Benqing

last: Wu

first: Hui


title: The Old Yellow Enzyme OfrA fosters Staphylococcus aureus survival via thiol-dependent redox homeostasis

city: Würzburg

first: Eslam

middle: S.

last: Ibrahim

address: Josef-Schneider-Straße 2, Bau D15

institute: Institut für Molekulare Infektionsbiologie (IMIB)

summary: Old yellow enzymes (OYEs) are widely found in the bacterial, fungal, and plant kingdoms but absent in humans and have been used as biocatalysts for decades. However, OYEs physiological function in bacterial stress response and infection situations remained enigmatic. In the mode of pathogen, the gram-positive bacterium Staphylococcus aureus adapts to numerous stress conditions during pathogenesis. Here we show that in S. aureus genome, two paralogous genes (ofrA and ofrB) encode for two OYEs. We conducted bioinformatic analysis and found that ofrA is conserved among all publicly available representative staphylococcal genomes and some Firmicutes. Expression of ofrA is induced by electrophilic, oxidative, and hypochlorite stress in S. aureus. Furthermore, ofrA contributes to S. aureus survival against reactive electrophilic, oxygen, and chlorine species (RES, ROS, RCS) via thiol-dependent redox homeostasis. At the host-pathogen interface, ofrA mutation affects S. aureus survival in macrophages and whole human blood and the virulence factor staphyloxanthin production. Overall, our results shed the light onto a novel stress response strategy in the bacterial kingdom especially in the important human pathogen S. aureus.

overall_design: 3 replicates of S. aureus JE2 and 3 replicates of JE2ΔofrA in RPMI-1640 medium

middle: S

first: Knut

last: Ohlsen


title: Melatonin inhibits fibroblast cell functions and hypertrophic scar formation by enhancing autophagy through the MT2 receptor-inhibited PI3K/Akt /mTOR signaling

city: Guangzhou

first: Yunxian

last: Dong

address: 58 Zhongshan Road II

department: Department of Burn and Plastic Surgery

institute: The First Affiliated Hospital of Sun Yat-sen University

summary: Hypertrophic scar (HS) is a fibrotic skin condition and characterized by abnormal proliferation of myofibroblasts and accumulation of extracellular matrix. Melatonin, an endogenous hormone, can alleviate fibrosis in multiple models of diseases. This study examined the effect of melatonin on fibrosis in primary fibroblasts from human HS (HSFs) and a rabbit ear model and potential mechanisms. Melatonin treatment significantly decreased the migration and contraction capacity, collagen and α-smooth muscle actin (α-SMA) production in HSFs. RNA-sequencing and bioinformatic analyses indicated that melatonin modulated the expression of genes involved in autophagy and oxidative stress. Mechanistically, melatonin treatment attenuated the AKT/mTOR activation through affecting the binding of MT2 receptor with PI3K to enhance autophagy, decreasing fibrogenic factor production in HSFs. Moreover, melatonin treatment inhibited HS formation in rabbit ears by enhancing autophagy. The anti-fibrotic effects of melatonin were abrogated by treatment with an autophagy inhibitor (3-methyladenine, 3-MA), an Akt activator (SC79), or an MT2 selective antagonist (4-phenyl-2propionamidotetralin, 4-P-PDOT). Therefore, melatonin may be a potential drug for prevention and treatment of HS.

overall_design: RNA-seq of hypertrophic scar fibroblasts were treated with or without melatonin

first: Bing

last: Tang


title: PD-1 checkpoint blockade disrupts CD4 T cell regulated adaptive B cell tolerance to foreign antigengs

city: San Diego

first: Michael

last: McHeyzer-Williams

address: 10550 N Torrey Pines Rd

institute: Scripps Research Institute

summary: We utilized single cell-indexed custom RNA-sequencing to interogate the transcriptomes of IgG1 specific germinal center B cells and Plasma cells at steady state and six days after actue antibody mediated PD1 blockade

overall_design: B cells were isolated from the spleen of C57BL/6 mice at steady state (n=4) or six days after anti-PD1 blockade (n=4) . Phenotypically defined B cell subsets: naïve B cells (Gr1-FceR1a-IgD+IgMlowCD138-GL7-CD79b+CD19+CD38+), IgG1 Plasma Cells (Gr1-FceR1a-IgD-IgM-CD138+IgG1+), IgG1 Germinal Center B (Gr1-FceR1a-IgD-IgM-CD138-  CD79b+CD19+CD38-GL7+IgG1+) were sorted into 384 well plates for library preparation. cDNA was amplied using a nested set of ~500 gene specific targeted primers. Transcriptional data was acquired from 1047 B cells across two experiments.

first: Chad

last: Dufaud

first: Andrew

middle: G

last: Shuparski

first: Brett

middle: W

last: Higgins

first: Louise

middle: J


title: Single-cell RNA-seq uncovers the early alterations of retina in type 2 diabetes mice

city: Beijing

first: Kai

last: Chen

address: 8th Xishiku Street

department: General Surgery

institute: Peking University First Hospital

summary: Diabetic retinopathy (DR) is a complex disease, the early alterations of which remains to be investigated. We isolated retinas from the control and type 2 diabetes (T2D) mice and conducted scRNA-seq analysis using the 10x Genomics platform. We delineated the complete cellular landscape of retina and explored the early alterations of different cell subpopulations of them in T2D.

overall_design: The Lepr knockout mouse model was used. The retinas were isolated from two control (BKS_WT; m/m) and two type 2 diabetes (BKS_DB; db/db) mice at ages of 13 weeks. The isolated retinas were enzymatically digested to generate single-cell suspensions for scRNA-seq.

first: Yinhao


title: MIA-PaCa2 cells treated with Pyrvinium Pamoate, Rotenone, Oligomycin or Control

city: Bethesda

first: Christopher

middle: William

last: Schultz

state: MD

address: 37 Convent Dr, Building 37

institute: NIH

summary: Purpose: To compared Pyrvinium Pamoate induced transcription changes with known mitochondrial inhibitors.  Methods: MIA-PaCa2 cells were treated with Pyrvinium Pamoate at 0.3µM, Oligomycin at 4µM or rotenone at 0.5 µM for 48 hours and then RNA was collected.

overall_design: MIA-PaCa2 cells were treated with Pyrvinium Pamoate, Oligomycin or Rotenone for 48 hours and RNA was collected, all samples were treated in quadruplicate.

first: Jonathan

last: Brody


title: CUT&RUN chromatin profiling of H3K4me2 and H3K79me2 in hPSC-derived cortical neurons

city: New York

first: Emiliano

last: Hergenreder

institute: Memorial Sloan Kettering Cancer Center

summary: Chemical inhibition of histone demethyase LSD1 and histone methyltransferase DOT1L promotes maturation of neurons derived from pluripotent stem cells. We profiled the genome distribution of histone marks targeted by these enzymes in immature hPSC-derived cortical neurons.

overall_design: Examination of histone modifications in immature hPSC-derived neurons

first: Lorenz

last: Studer


title: Ribosome profiling RNA sequencing in zebrafish embryos

first: Bao-Fa

last: Sun

address: Da-Tun Road

institute: Beijing Institute of Genomics (BIG) of Chinese Academy of Sciences (CAS)

summary: We show that liquid-liquid phase separation (LLPS)-mediated zebrafish Ddx3xb condensation facilitates MZT through promoting maternal mRNAs translation. Ddx3xb forms condensates via its N-terminal intrinsically disordered regions (IDRs), and the gradually increased ATP concentration after fertilization promotes its aggregation capability. Ddx3xb-deficiency decelerates the decay of maternal mRNAs and impedes zygotic genome activation, further leading to developmental defect. The phenotype in Ddx3xb-deficiency embryos can be efficiently rescued by condensed Ddx3xb, but not the Ddx3xb without LLPS ability. Mechanistically, the condensation of Ddx3xb is vital for its RNA helicase activity, which is critical for involved in promoting translation efficiency of maternal mRNAs through opening 5’ UTR structures during the MZT process. Our study demonstrates that the condensation of Ddx3xb promotes maternal mRNAs translation via its RNA unwinding activity and further facilitates MZT, highlighting the critical role of protein phase separation in translational control and animal early development.

overall_design:
Ribo-seq of 2 samples from Ddx3xb mutant zebrafish embryos at 4 hpf, 2 samples from Ddx3xb mutant injected with ddx3xbFL zebrafish embryos at 4 hpf and  2 samples from Ddx3xb mutant injected with ddx3xb_deltaN zebrafish embryos at 4 hpf

Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.

first: B

last: Shi

first: J

last: Heng

last: Zhou

first: Y

last: Yang

first: F

last: Liu


title: Nucleolin HITS-CLIP, RNA-Seq and Ribo-Seq upon inhibition of 5'-tRFCys

first: Sohail

last: Tavazoie

address: 1230 York Ave

institute: The Rockefeller University

summary: Expression of 5'-tRFCys is significantly upregulated during breast cancer metastasis and suppression of 5'-tRFCys significantly reduced metastatic lung colonization of breast cancer. We identified Nucleolin (Ncl) as the direct binding partner of 5'-tRFCys. To identify the molecular mechanism underlying 5'-tRFCys promotion of breast cancer, we performed Ncl HITS-CLIP, RNA-Seq, Ribosome profiling (Ribo-Seq) upon inhibition of 5'-tRFCys. These analyses reveal that 5'-tRFCys enhances Ncl binding to a subset of transcripts, resulting in increased transcript stability of those transcripts and expression.

overall_design: To identify tRNA fragments (tRFs) that regulate metastasis, tRFs were profiled from non-metastatic 67NR, poorly-metastatic 4TO7 or highly-metastatic 4T1 breast cancer cells using small RNA-Seq (sRNA-Seq). To identify the direct targets of 5'-tRFCys, Ncl HITS-CLIP was performed upon 5'-tRFCys suppression. To determine the impact of 5'-tRFCys on its target transcripts, 4T1 cells were transfected with a scrambled control or 5'-tRFCys antisense LNA oligo and RNA-Seq as well as Ribo-Seq were performed.

first: Xuhang


title: Transcriptomics analysis of gene expression  in control and Ddx3xb  knockout zebrafish embryos

overall_design: RNA-seq of 6 samples from zebrafish embryos at 2, 4, 6 hpf and 6 samples from Ddx3xb mutant zebrafish embryos at 2, 4, 6 hpf, including two biological replicates.


title: Transcriptomics analysis of gene expression  in control and Ddx3xb  knockdown zebrafish embryos

overall_design: RNA-seq of 6 samples from zebrafish embryos at 2, 4, 6 hpf and 6 samples from Ddx3xb knockdown zebrafish embryos at 2, 4, 6 hpf, including two biological replicates.


title: Transcriptomics analysis of gene expression in Ddx3xb mutant injected with ddx3xbFL or ddx3xb△N

overall_design:
RNA-seq of 6 samples from Ddx3xb mutant injected with ddx3xbFL zebrafish embryos at 2, 4, 6 hpf and 6 samples from Ddx3xb mutant injected with ddx3xb△N zebrafish embryos at 2, 4, 6 hpf, including two biological replicates.
Please note that each processed data was generated from both replicates and is linked to the corresponding rep1 sample records.


title: Comparative transcriptional signatures provide uncovering major molecular processes in early and mature somatic cyst cells of Drosophila testes

first: Alexei

middle: A.

last: Kotov

address: 26 Vavilov Street

institute: Koltzov Institute of Developmental Biology of the Russian Academy of Sciences

summary: Here we employed a FACS-based approach for isolation of early and mature somatic cyst cells from whole testes of adult Drosophila males. We prepared and analyzed RNA-seq libraries to reveal differences in transcriptional patterns of these cells and to uncover protein complexes functioning in cyst cells at different stages of spermatogenesis.

overall_design: Purified PolyA(+) mRNA libraries from  early and mature somatic cyst, and from control unsorted cells of Drosophila testes


title: Genome-Wide Association Study of Hospitalized COVID-19 Patients in the United Arab Emirates

city: Abu Dhabi

first: Habiba

last: Alsafar

address: Al Saada St. Muroor Road

department: Center of Biotechnology

country: United Arab Emirates

institute: Khalifa University

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

summary: The heterogeneity in symptomatology and phenotypic profile attributable to COVID-19 is widely unknown. For the first time, our study provides the unique advantage of obtaining samples from the Middle Eastern population, an underrepresented region in genetic studies, and explore new genotypes in this population that will yield to novel genetic association. Specifically, we studied 646 patients in the United Arab Emirates.  We describe strong association signals from genes on chromosomes 2, 3, 5, 11 and 13, which carry genes that are expressed in the lung, have been associated with tumour progression, emphysema, airway obstruction, and surface tension within the lung. Identifying genetic variants associated to COVID-19 susceptibility and severity may uncover novel biological insights into disease pathogenesis and identify mechanistic targets for therapeutic and vaccine development.

overall_design: The objective of this manuscript is to conduct a genome wide association study (GWAS) of COVID-19 severity to improve the understanding of potentially causal targets for SARS-CoV-2. This cross-sectional study recruited 646 consenting participants that have tested positive for SARS-CoV-2 by Real-Time Polymerase Chain Reaction (RT-PCR) via nasopharyngeal swabs. Participants were prospectively recruited from six collection sites across the UAE including hospitals (3), and quarantine camps (3), from April 1, 2020, to January 31, 2021. The selection criteria were: (1) positive COVID-19 test for a single individual, (2) resident of the UAE, and (3) able to provide an informed consent and complete the survey.

first: Mira

last: Mousa

first: Hema

last: Vurivi

first: Hussein

last: Kannout

first: Maimunah

last: Uddin

first: Nawal

last: Alkaabi

first: Bassam

last: Mahboub

first: Guan

middle: K

last: Tay


title: Bone Marrow Endothelial Cell Progenitor Cell and HUVEC T Cell Irradiation Studies

first: Douglas Scott

last: Merrell

address: 4301 Jones Bridge Road

department: Dept. of Microbiology and Immunology

institute: Uniformed Services University

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

overall_design: Refer to individual Series


title: Gene expression in human abdominal aortic aneurysm wall biopsie with high or low wall stress

status: Public on Jun 02 2022

city: Heidelberg

first: Philipp

last: Erhart

address: Im Neuenheimer Feld 420

department: Vascular and Endovascular Surgery

institute: Heidelberg University Hospital

summary:
This study investigates intra- and inter-individual RNA genome-wide expression profiling differences (Illumina HumanHT-12, BeadCHIP expression) of AAA (abdominal aortic aneurysms) biopsies from 12 patients.
Biopsies were collected during open surgical AAA repair and according to prior finite element analysis (FEA) from regions with highest and lowest wall stress.

overall_design: Twenty-four (12 pairs) biopsies from 12 patients were analysed. RNA-profiles were pairwise (within individuals) compared, as well as between the two groups (high wall stress versus low wall stress).

first: Amelie

last: Behrens


title: Effect of depletion of Nucleoporin Seh1 on gene expression during proliferation and differentiation of neural stem cell

city: xiamen

first: Liu

last: Zhixiong

state: Fujian

address: Xiangan Nanlu 4221-120

department: School of Life Sciences

institute: Xiamen University

summary: To investigate the  function of Nucleoporin Seh1 in the regulation of neural stem cell proliferation and differentiation, we used cmv-cre-ert,seh1 inducible knockout mice's neural stem cell to find out different expression genes

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 4 different cells at proliferation and differentiation stage.

first: Liang

last: Zhang

first: Zhixiong

first: Wenxiu

last: Dai


title: Analysis of metabolic characteristics of peripheral blood mononuclear cells in patients with leukemia at the single cell level

city: Foshan

first: Ying

last: Zhao

address: Shiwan Street, Chancheng District, Foshan City

institute: Department of Hematology, First People’s Hospital of Foshan

summary: We collected peripheral blood from leukemia patients at different stages, including those newly diagnosed as untreated, as well as those in remission on therapy, with a subset of samples including peripheral blood and bone marrow samples. First, mononuclear cells were isolated from the collected peripheral blood, followed by single-cell RNA sequencing and follow-up sequencing results for subgroup classification, focusing on changes such as glycolipid metabolism of B cells as well as T cells. The aim of this project was to explore the changes in metabolic remodeling in leukemia patients with the aid of single-cell technology to provide assistance in the diagnosis and treatment of the disease.

overall_design: The focus of this study was to collect peripheral blood from leukemia patients at different stages of disease onset, followed by single-cell RNA sequencing of peripheral blood mononuclear cells, combined with clinicopathological and other relevant data, to investigate changes in metabolic remodeling in leukemia patients. This project is a study of observational nature and does not involve modification of the treatment regimen to cause adverse effects to patients.

first: Xiaoli

last: Xu

first: Haiyan

last: Ye

first: Yonglei

last: Qi

first: Wenning

first: Yiwen

last: Ling

first: Shaojiang

last: Yang


title: Methylation Based Reclassiﬁcation and Risk Stratiﬁcation of Skull Base Chordoma

first: Xulei

last: Huo

address: Beijing

institute: Beijing tiantan hospital

type: Methylation profiling by genome tiling array

summary:
Epigenome analysis of skull base chordoams
Genome wide DNA methylation profiling of  46 skull base chordomas. The Illumina Infinium 450k  Human DNA methylation Beadchip  was used to obtain DNA methylation profiles across approximately 450,000 CpGs in skull base chorodma samples. Samples included 46 skull base chorodmas

overall_design: Bisulphite converted DNA from the 46 samples were hybridised to the Illumina450k Human Methylation Beadchip

last: Wang

first: Zhen

last: Wu


title: Bone Marrow Endothelial Cell Progenitor Cell Irradiation Study

summary: Question Addressed:  What is the gene expression profile from human bone marrow endothelial cells (BMEC) and human CD34+ stem and progenitor cells (HSPC) after irradiation (IR)?  What, if any, is the effect of co-culturing these two cell types on gene expression? There are eight experimental conditions for this experiment:  (1) non-irradiated BMEC; (2) irradiated BMEC; (3) non-irradiated CD34+; (4) irradiated CD34+; (5) non-irradiated BMEC + non-irradiated CD34+; (6) non-irradiated BMEC + irradiated CD34; (7) irradiated BMEC + non-irradiated CD34+; (8) irradiated BMEC + irradiated CD34+. A common, pooled reference consisting of RNA taken from conditions 1-8 as described above was used for all hybridizations.

first: Douglas


title: HUVEC T Cell Irradiation Study

first: Douglas Scott

summary: Question Addresses:  What is the gene expression profile from human umbilical vein endothelial cells (HUVEC) and human Jurkat T cells after irradiation (IR)?  What, if any, is the effect of co-culturing these two cell types on gene expression? There are eight experimental conditions for this experiment:  (1) non-irradiated HUVEC; (2) irradiated HUVEC; (3) non-irradiated Jurkat; (4) irradiated Jurkat; (5) non-irradiated HUVEC + non-irradiated Jurkat+; (6) non-irradiated HUVEC + irradiated Jurkat; (7) irradiated HUVEC + non-irradiated Jurkat; (8) irradiated HUVEC + irradiated Jurkat. A common, pooled reference consisting of RNA taken from conditions 1-8 as described above was used for all hybridizations.


title: Antigenic determinants of SARS-CoV-2-specific CD4+ T cell lines reveals M protein-driven dysregulation of interferon signaling

first: Eric

last: Dang

state: Maryland

address: 9000 Rockville Pike

department: NIAID

summary: We generated CD4+ T cell lines (TCLs) reactive to either SARSCoV-2 spike (S) or membrane (M) proteins from unexposed naïve T cells from six healthy donor volunteers to understand in fine detail whether the S and M structural proteins have intrinsic differences in driving antigen-specific CD4+ T cell responses. Having shown that each of the TCLs were antigen-specific and antigen-reactive, single cell mRNA analyses demonstrated that SARS-CoV-2 S and M proteins drive strikingly distinct molecular signatures. Whereas the S-specific responses are transcriptionally similar from those responses induced by other viral antigens (e.g. CMV), the M protein-specific CD4+ TCLs have a transcriptomic signature that indicate a marked suppression of interferon signaling, characterized by a downregulation of the genes encoding ISG15, IFITM1, IFI6, MX1, STAT1, OAS1, IFI35, IFIT3 and IRF7 (a molecular signature which is not dissimilar to that found in severe COVID-19). Our study suggests a potential link between the antigen specificity of the SARS-CoV-2-reactive CD4+ T cells and the development of specific sets of adaptive immune responses. Moreover, the balance between T cells of significantly different specificities may be the key to understand how CD4+ T cell dysregulation can determine the clinical outcomes of COVID-19.

overall_design: Naïve CD4+ T cells, as well as monocytes were purified from cryopreserved PBMCs of 6 healthy donor individuals unexposed to SARS-CoV-2 (obtained prior to 2019). Purified monocytes were differentiated into dendritic cells (DCs). Matured DCs were separately seeded in 24 wells plate, and then loaded for 2-4 hours with 1µg/peptide of SARS-CoV-2 peptide megapools (MPs) covering either the entire sequence of SARS-CoV-2 spike protein (MP-S), consisted by a 15-mer peptides overlapping by 10-residues (253 peptides) or covering the complete sequence of SARS-CoV-2 membrane protein (MP-M), consisting of 15-mer sequences with 11 amino acids overlap (PepTivator® SARS-CoV-2 Prot_M, Miltenyi Biotec, USA) and 1µg/peptide of CMV peptide megapools (~500 peptides). On the top of the either MP-S, MP-M or CMV pulsed-DCs, 1x10^6 naïve CD4+ T cells (1:10 ratio) were added and incubated for 12 days in complete R10 media. On days 2, 5 and 8, 60units of human rIL-2 (Cetus, USA) were added at each well. At day 12, cells in culture were washed, counted, and fed (1:1 ratio) with irradiated (40GY) autologous PBMCs (feeder cells) in the presence of either 1µg/peptide of MP-S or MP-M for another 12-day round culture in the same conditions, including the IL-2 stimulation. After three 12-day rounds of peptide pool stimulation/expansion in vitro, we generated a total of 18, 6 MP-S-specific, 6 MP-M-specific and 6 CMV-specific CD4+ TCLs, which were profiled for antigen-specificity and reactivity using multiparameter flow cytometry as well as, for single cell transcriptional analysis.

first: Pedro

middle: H

last: Gazzinelli-Guimaraes

first: Gayatri

last: Sanku

first: Alessandro

last: Sette

first: Daniela

last: Weiskopf

first: Paul

last: Schaughency

first: Justin

last: Lack

first: Thomas

middle: B

last: Nutman


title: Mapping cis-regulatory elements in human excitatory and inhibitory neurons links psychiatric disease heritability and activity-regulated transcriptional programs

first: Matthew

last: Lalli

address: 1 Gustave L. Levy Pl

department: Psychiatry

institute: Icahn School of Medicine at Mount Sinai

summary: Genome-wide association studies (GWAS) have identified hundreds of loci associated with psychiatric diseases, yet there is a lack of understanding of disease pathophysiology. Common risk variants can shed light on the molecular mechanisms underlying these diseases; however, identifying specific causal variants remains challenging. An added complication is that most common risk variants are in non-coding regions. Their impact is likely to be restricted to particular cell types, developmental stages, or cell states. Here, we comprehensively mapped cis-regulatory elements in two defined populations of human excitatory and inhibitory neurons derived from pluripotent stem cells.

overall_design: We performed CUT&RUN (cleavage under targets and release using nuclease) to measure H3K27ac profiles in human induced glutamatergic (Glu) and GABAergic (GABA) neurons derived from human pluripotent stem cells (ES and iPSCs). We exposed neurons to an elevated level of potassium chloride (KCl) to study activity-induced responses, and profiled H3K27ac at various time points after depolarization.

first: Carlos

last: Sanchez-Priego

first: Ruiqi

last: Hu

first: Linda

last: Boshans


title: The role of b2-integrins for the effector functions of polymorphonuclear granulocytes

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

summary:
Background: b2-integrins are heterodimeric surface receptors that are expressed specifically by leukocytes and consist of a variable a (CD11a-d) and a common b-subunit (CD18). Functional impairment of CD18, which causes leukocyte adhesion deficiency type-1 results in an immunocompromised state characterized by severe infections, such as invasive pulmonary aspergillosis (IPA). The underlying immune defects have largely been attributed to an impaired migratory and phagocytic activity of polymorphonuclear granulocytes (PMN). However, the exact contribution of b2-integrins for PMN functions in-vivo has not been elucidated yet, since the mouse models available so far display a constitutive CD18 knockout (CD18-/- or CD18hypo). To determine the PMN-specific role of b2-integrins for innate effector functions and pathogen control, we generated a mouse line with a Ly6G-specific knockdown of the common b-subunit (CD18DLy6G).
Methods: We analyzed expression levels of genes implicated in b2-integrin signaling for treated and untreated PMN derived from CD18DLy6G mice and CD18fl/fl mice using RNA-Sequencing. To determine the most up- or downregulated genes, genes were sorted on the basis of log2 [fold change] maximum-likelihood estimation, and the P-value cut-off was set to 0.05. Results were illustrated using the pheatmap package. Functional interaction networks were visualized using the STRING package in the open-source platform Cytoscape.
Results:  Our results revealed a downregulation of b2-integrins , while genes implicated in NFkB singaling were upregulated. With regard to PMN effector function, we observed a downregulation of genes implicated in PMN chemotaxis and microbicidal functions such as Defb40.

overall_design: We isolated PMN from bone marrow of CD18fl/fl and CD18DLy6G mice (n=3). Each 10^6 PMN were either lysed directly after isolation or cultured overnight with GM-CSF (10ng/ml) plus LPS (1µg/ml). Subsequently RNA was purified and quantified with a Qubit fluorometer in order to compare genotype-dependent expression levels both for untreated and treated conditions.

last: Bros

first: Maximilian

last: Haist


title: Investigating the effects of different HMGB1 redox isoforms on macrophage polarization

city: Solna

first: Heshuang

last: Qu

address: L8:03, visionsgatan 18

country: Sweden

institute: Karolinska Institutet

summary: Macrophages are key inflammatory immune cells that display dynamic phenotypes and functions in response to their local microenvironment. In different conditions, macrophage polarization can be induced by high-mobility group box 1 (HMGB1), a nuclear DNA-binding protein that activates innate immunity. This study investigated the phenotypes of murine bone-marrow-derived macrophages (BMDMs) induced by different HMGB1 redox isoforms via bulk RNA sequencing (RNAseq).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for HMGB1-treated BMDM cells with M1 and LPS-treated BMDM cells, using PBS as control.

first: Rebecka

last: Heinbäck

first: Henna

last: Salo

first: Ewoud

last: Ewing

first: Alexander

last: Espinosa

first: Cecilia

last: Aulin

first: Helena

last: Erlandsson Harris


title: Physiological and transcriptional profiling of surfactin exerted antifungal effect against Candida albicans

city: Debrecen

first: Agnes

last: Jakab

address: Nagyerdei krt 98.

country: Hungary

institute: University of Debrecen

summary: Given the risk of Candida albicans overgrowth in the gut, novel complementary therapies should be developed to reduce fungal dominancy. This study highlights the antifungal characteristics of a Bacillus subtilis-derived secondary metabolite, surfactin with high potential against C. albicans. Surfactin inhibited the growth of C. albicans following a 1-hour exposure, in addition to reduced adhesion and morphogenesis. Specifically, surfactin did not affect the level of reactive oxygen species but increased the level of reduced glutathione. Surprisingly, ethanol production was increased following 2 hours of surfactin exposure. Surfactin treatment caused a significant reduction in intracellular iron, manganese and zinc content compared to control cells, whereas the level of copper was not affected. Alongside these physiological properties, surfactin also enhanced fluconazole efficacy. To gain detailed insights into the surfactin-related effects on C. albicans, genome-wide gene transcription analysis was performed. Surfactin treatment resulted in 1390 differentially expressed genes according to total transcriptome sequencing (RNA-Seq). Of these, 773 and 617 genes with at least a 1.5-fold increase or decrease in transcription, respectively, were selected for detailed investigation. Several genes involved in morphogenesis or related to metabolism (e.g., glycolysis, ethanol and fatty acid biosynthesis) were down-regulated. Moreover, surfactin decreased the expression of ERG1, ERG3, ERG9, ERG10 and ERG11 involved in ergosterol synthesis, whereas genes associated with ribosome biogenesis and iron metabolism and drug transport-related genes were up-regulated. Our data demonstrate that surfactin significantly influences the physiology and gene transcription of C. albicans, and could contribute to the development of a novel innovative complementary therapy.

overall_design: Examination of untreated control and 128 mg/L surfactin-treated Candida albicans cultures in three replicates.

first: Renátó

last: Kovács

first: Ágnes


title: Bruno1 regulates gene expression and splicing that is necessary for proper development of the indirect flight musculature in D. melanogaster.

city: Martinsried-Planegg

first: Maria

middle: Lynn

last: Spletter

state: Bayern

address: Grosshaderner Str. 9

department: Physiological Chemistry

institute: Ludwig-Maximilians-University Munich

summary: Building on a previous study where we examined changes in gene expression and splicing after knockdown of Bruno 1 (Bru1, Aret) in indirect flight muscle, we have now generated a CRISPR allele bru1[M3] that results in a phenotypic null. Here we examine changes in gene expression and alternative splicing in bru1[M3] mutant IFM dissected from 1 d adult flies.

overall_design: Analysis of differential gene expression and exon use between control (w[1118]) IFM and bru1 mutant (bru1[M3]) IFM from 1d adult.

middle: L

first: Elena

last: Nikonova

first: Marc

last: Canela Grimau

first: Tobias

last: Straub


title: Alpha-synuclein supports type 1 interferon signaling in neurons and brain tissue

city: Aurora

first: J.

middle: David

last: Beckham

state: Colorado

address: 12800 East 19th Avenue, RC1N\P18-8404A

department: Microbiology

institute: University of Colorado Anschutz Medical Campus

summary: To investigate broad difference in gene expression in mice wild-type for or knockout for alpha-synuclein during infeciton, we infected mice via footpad infection with West Nile Virus and measured full brain gene expression.

overall_design: comparitive gene expression profiling using data obtained from RNA-seq in two different mouse lines at one timepoint

first: Brendan

last: Monogue

first: Aaron

last: Massey

first: J

middle: D


title: In vitro attachment and symmetry breaking of a human embryo model assembled from primed pluripotent stem cells

first: Mijo

last: Simunovic

state: New York

institute: Columbia University

summary: Human embryonic development after attachment remains elusive due to technical, ethical, and policy challenges of experimenting with early embryonic tissues. We build a model of the post-attachment human embryo by controllably assembling the stem cell model of the human epiblast with stem cell derived extraembryonic tissues. We provide three sets of single cell RNA sequencing data to characterize the system: data from the E10 in vitro attached IVF human embryo, stem cell-derived extraembryonic cells derived by BMP4 induction on soft substrates, and the resulting model of the post-attachment human embryo.

overall_design: Single cell RNA sequencing on the 10x platform of E10 in vitro attached human embryos, embryo models assembled from embryonic stem cells, and extraembryonic tissues derived by direct differentiation of embryonic stem cells.


title: Purine nucleoside phosphorylase enables dual metabolic checkpoints that prevent T cell immunodeficiency and TLR7-associated autoimmunity

city: Los Angeles

first: Caius

middle: Gabriel

last: Radu

address: 650 Charles E. Young Drive, South

department: Molecular and Medical Pharmacology

institute: UCLA

summary: Purine nucleoside phosphorylase (PNP) enables the breakdown and recycling of guanine nucleosides. PNP insufficiency in humans is paradoxically associated with both immunodeficiency and autoimmunity, but the mechanistic basis for these outcomes is incompletely understood. Here we identify two immune lineage-dependent consequences of PNP inactivation dictated by distinct gene interactions. During T cell development, PNP inactivation is synthetically lethal with down-regulation of the dNTP triphosphohydrolase SAMHD1. This interaction requires deoxycytidine kinase activity and is antagonized by microenvironmental deoxycytidine. In B lymphocytes and macrophages, PNP regulates Toll like receptor 7 signaling by controlling the levels of its (deoxy)guanosine nucleoside ligands. Overriding this regulatory mechanism promotes germinal center formation in the absence of exogenous antigen and accelerates disease in a mouse model of autoimmunity. This work reveals that one purine metabolism gene protects against immunodeficiency and autoimmunity via independent mechanisms operating in distinct immune lineages and identifies PNP as a novel metabolic immune checkpoint.

overall_design: RNAseq analysis of murine bone marrow derived macrophages (BMDM) treated with TLR7 agonists. BMDM were treated ± the PNP inhibitor ulodesine (PNPi), guanosine (rG), deoxyguanosine (dG), poly-uridine ssRNA complexed with DOTAP (polyU) or R848.

first: Evan

last: Abt

first: Khalid

last: Rashid

first: Thuc

middle: M

last: Le

first: Suwen

last: Li

first: Hailey

last: Lee

first: Vincent

last: Lok

first: Amanda

last: Creech

last: Labora

first: Hanna

last: Mandl

first: Alex

last: Lam

first: Arthur

last: Cho

first: Valerie

last: Rezek

first: Gabriel

last: Abril-Rodriguez

first: Ethan

last: Rosser

first: Steven

last: Mittelman

first: Willy

last: Hugo

first: Thomas

last: Mehrling

first: Shanta

last: Bantia

first: Antoni

last: Ribas

first: Timothy

last: Donahue

first: Gay

last: Crooks

first: Ting-Ting

last: Wu


title: Real time PCR from expression microdissection (xMD) of epithelial cells

status: Public on Jun 01 2022

city: Baltimore

first: Marc

last: Halushka

address: 720 Ruthand ave Ross 632b

department: Pathology

institute: Johns Hopkins

summary: The goal of this experiment was to determine the extent to which the xMD method can enrich for a specific cell type.  Here we optimized each step of the xMD process from tissue retrieval, tissue transfer, film preparation, and RNA isolation  to increase RNA yields and specficity. Duodenum (small intenstine) tissue was formalin fixed and processed to create routine FFPE slides. Matched RNA from a scrape of a unstained slide and AE1/AE3+ epithelial cells isolated by xMD were compared using TLDA qPCR microRNA array.

overall_design: FFPE slide samples were sectioned at 4um. The samples underwent xMD using AE1/AE3 antibody to select epithelial cells. The epithelial cell samples were matched to a scrape of the FFPE slide or bulk tissue.

first: Ana

middle: E

last: Jenike


title: Condensates induced by transcription inhibition mislocalizes active chromatin to nucleoli

city: CHARLESTOWN

first: Takaaki

last: Yasuhara

department: Cancer Center

institute: Massachusetts General Hospital

summary: The proper function of the genome relies on spatial organization of DNA, RNA, and proteins, but how transcription contributes to the organization is unclear. Here, we show that condensates induced by transcription inhibition (CITIs) drastically alter genome spatial organization. CITIs are formed by SFPQ, NONO, FUS, and TAF15 in nucleoli upon inhibition of RNA polymerase II (RNAPII). Mechanistically, RNAPII inhibition perturbs ribosomal RNA (rRNA) processing, releases rRNA-processing factors from nucleoli, and enables SFPQ to bind rRNA. While accumulating in CITIs, SFPQ/TAF15 remain associated with active genes and tether active chromatin to nucleoli. In the presence of DNA double-strand breaks (DSBs), the altered chromatin compartmentalization induced by RNAPII inhibition increases gene fusions in CITIs and stimulates the formation of fusion oncogenes. Thus, proper RNAPII transcription and rRNA processing prevent the altered compartmentalization of active chromatin in CITIs, suppressing the generation of gene fusions from DSBs.

overall_design:
ChIP-seq for SFPQ and TAF15 in U2OS cells. Cells were treated with THZ1 for 1 hour and prepared for ChIP-seq.
TSA-seq for SFPQ and UBF in U2OS cells. Cells were treated with THZ1 for 1 hour and prepared for TSA-seq.

first: Yu-Hang

last: Xin

first: Nicholas

middle: C

last: Bauer

first: LuKuo

last: Lee

first: Rui

last: Dong

first: Tribhuwan

last: Yadav

first: Roy

last: Soberman

first: Miguel

middle: N

last: Rivera

first: Lee

last: Zou


title: Gene expression profiling of total rat epididymal cells during postnatal development.

city: Laval

first: Daniel

middle: G

last: Cyr

state: QC

address: 531 boul. des Prairies

country: Canada

institute: INRS-Centre Armand-Frappier Santé Biotechnologie

summary:
Immature epididymis is formed of undifferentiated columnar cells which differentiate into the different cell types forming the mature epithelium.
Our goal was to assess the gene expression profiles at different time points in the developping epididymis.

overall_design: RNA was isolated from pools of whole epididymides of 7- (n=3), 18- (n=4), 28- (n=4) and 60-day (n=3) old rats and hybridized on Affymetrix RatGene 2.0 ST array.

first: Julie

last: Dufresne


title: Microarray gene expression profile of primary breast tumour tissue

city: Bratislava

first: Lubos

last: Klucar

address: Dubravska cesta 21

country: Slovakia

institute: Institute of Molecular Biology SAS

summary: Data were used for study of changes in gene expressions in breast primary tumour of patients with circulating tumour cells positive on mesenchymal marker (CTC EMT). Study aimed to identify signaling pathways associated with the presence of CTC_EMT in PBC patients. This translational study included 17 patients with PBC and 5 donors of normal breast tissue. CTC_EMT were detected before surgery by quantitative RT-PCR assay for expression of epithelial-to-mesenchymal transition (EMT) genes (TWIST1, SNAIL1, SLUG, ZEB1). Total RNA was extracted, in parallel, from the fresh frozen primary tumor and whole-transcriptome profiles were obtained using RNA sequencing and by microarray. RNA-seqquencing version of same samples has been submitted to SRA (BioSaples accessions are provided here). Also data under BioProject PRJNA751534 originate from the same samples.

overall_design: 17 patients with primary breast cancer (PBC) tumour tissue and 5 donors of normal breast tissue

first: Andrea

last: Soltysova

first: Michal

last: Mego

first: Dominik

last: Hadzega


title: A TRIM66/DAX1/Dux axis suppresses the totipotent 2-cell-like state in murine embryonic stem cells

city: Beijing

first: Zuo

last: Feifei

address: Zhongguancun Street, Haidian District

institute: Tsinghua University

summary: 2 cell-like cells (2CLCs) resemble blastomeres of the 2-cell stage of embryo and are used as an in vitro model to understand the onset of zygotic genome activation (ZGA). 2CLCs comprise only ~1% of murine embryonic stem cells (mESCs). However, their specification remains unclear. Here, we show that TRIM66 restricts 2CLCs specification by repressing Dux in mESCs. Mutational assays and a solved crystal structure demonstrate that TRIM66’s PHD finger recognizes H3K4K9me3 and Bromo domain recognizes H3K18ac. Moreover, TRIM66 functions as a bridge factor to recruit the transcriptional repressor Dax1 to the Dux promoter preventing expansion of 2CLCs in mESCs. Rrecruitment of Dax1 to the Dux promoter requires TRIM66 and TRIM66’s repressive effect on Dux transcription is dependent on Dax1. Thus, beyond expanding the scope of known regulators of 2CLCs and showing TRIM66 as a chromatin-modification reader, our study suggests multiple strategies for harnessing the biotechnological and medical potential of 2CLCs.

overall_design: Identifiy the transcriptome and histone modification changes in different mouse embryonic stem cells

first: Feifei

last: Zuo

first: Kun

last: Yan

first: Robert

last: Liefke

first: Qiaoran

last: Xi


title: The occupancy of H3K27me3 on chromosomes in glioblastoma cells with radiation treatment

city: Fuzhou

first: Fei

last: Huang

address: No 20 Chazhong Road

institute: First Affiliated Hospital, Fujian Medical University

summary:
We found that radiation treatment enhanced the expression of H3K27me3 in glioblastoma. Thus, we asked whether radiation contributed to the increase of global genomic H3K27me3 occupancy in glioblastoma. The Chip-seq results in GL261 cells showed that irradiation led to the increase of H3K27me3 occupancy ±50kb within the transcription start sites (TSS), especially the promoter sites (peaks±2kb within TSS). Some pathways, in which H3K27me3 peaks significantly enriched, were found.
Chip-seq was conducted for H3K27me3 in glioblastoma cell line GL261 when GL261 cells were treated with or without irradiation.

overall_design: Fei Huang

first: Bing

last: Wu

first: Caihong

last: Wang


title: Use of CRISPR/Cas9 with homology-directed repair to silence the human Topoisomerase IIα intron-19 5' splice site: Generation of etoposide resistance in human leukemia K562 cells

city: Columbus

first: Maciej

last: Pietrzak

state: OH

address: 1800 Cannon Drive, 340C Lincoln Tower

department: Department of Biomedical Informatics College of Medicine

institute: Ohio State University

summary: Results support the important role of both TOP2α/170 and TOP2α/90 as determinants of sensitivity/resistance to TOP2α-targeting agents.

overall_design: CRISPR/Cas9 with homology-directed repair was utilized silencing of the exon 19/intron 19 5′ splice site in parental K562 cells.

first: Jack

last: Yalowich

first: Terry

last: Elton

first: Victor

last: Hernandez


title: Novel targeting of DNA methyltransferase activity inhibits Ewing sarcoma cell proliferation and enhances tumor cell sensitivity to DNA damaging drugs by activating the DNA damage response

city: Badalona

first: IJC

last: Bioinformatics

state: Catalonia

address: Josep Carreras Building, Ctra de Can Ruti, Camí de les Escoles, s/n

institute: Josep Carreras Leukemia Research Institute

summary: Genome wide epigenomic analysis of Ewing Sarcoma human cell lines treated with 5AzadC and MC3343. Samples included 9 x TC-71, 9 x A673 samples, and 8 x PDX samples. For each cell line and condition ( 5AzadC, MC3343, Contol), we created 3 replicates, except PDX with 5AzadC treatment for which only 2 samples were created.

overall_design: Bisulphite converted DNA from the 26 samples were hybridized to the Illumina InfiniumMethylation Epic array

first: C

last: Cristalli

first: K

last: Scotlandi


title: The role of KDM6B in DNA damage repair

city: Dallas

first: Weibo

last: Luo

state: Texas

address: 5323 Harry Hines Blvd.

institute: UT Southwestern Medical Center

summary: KDM6B inhibits DNA repair gene MGMT.

overall_design: HeLa subclones were subjected to mRNA-seq.

first: Mingming

last: Yang

first: Yingfei


title: Indolium 1 Exerts Activity against Vemurafenib-Resistant Melanoma In Vivo

city: Atlanta

first: Yoonhee

last: Jung

state: Georgia

address: 615 Michael Street

department: Human Genetics

institute: Emory university

summary: The development of targeted therapies (Braf/MEK inhibitors) and immunotherapy have had a major impact on the treatment of melanoma. However, the majority of patients with advanced melanomas succumb to their disease. The mechanisms of resistance to both targeted therapies and immunotherapies are numerous and have been well-described. These include the alternative acti-vation of Braf/MEK signaling, novel compensating mutations in additional oncogenes, and loss of neoantigens. There has been limited development of small molecules that target alternative path-ways in melanoma in the last two decades. We have previously identified triphenylmethanes as a class that shows activity against a wide variety of tumors. We have synthesized a novel triphenyl-methane, indolium 1, and demonstrated its efficacy against an aggressive vemurafenib-resistant melanoma in vivo. Indolium 1 has a novel mechanism of action against melanoma, in that it results in induction of the tumor-suppressor EphA3. We believe that pre-IND studies are warranted for this novel compound, given its mechanism of action and ability to inhibit the growth of vemurafenib resistant melanoma in vivo

overall_design: ATAC-seq analysis

first: Rakan

last: Radi

first: Christina

first: Justin

last: Elsey

first: Yoon

last: Corces

last: Arbiser


title: Transplanted human cones incorporate and function in a murine cone degeneration model

city: Dresden

first: Marius

last: Ader

address: Fetscherstrasse 105

department: Center for Regenerative Therapies Dresden

institute: TU Dresden

summary: Once human photoreceptors die, they do not regenerate, thus photoreceptor transplantation has emerged as a potential treatment approach for blinding diseases. Improvements in transplant organization, donor cell maturation and synaptic connectivity to the host will be critical in advancing this technology to clinical practice. Unlike the unstructured grafts of prior cell suspension transplantations into end-stage degeneration models, we describe extensive incorporation of iPSC retinal organoid-derived human photoreceptors into mice with cone dysfunction. This incorporative phenotype was validated in both cone-only as well as pan-photoreceptor transplantations. Rather than forming a glial barrier, Müller cells extended throughout the graft, even forming a series of adherens junctions between mouse and human cells, reminiscent of an OLM. Donor-host interaction appeared to promote polarisation as well as development of morphological features critical for light detection, namely formation of inner and well stacked outer segments oriented towards the RPE. Putative synapse formation and graft function was evident both at a structural and electrophysiological level. Overall, these results show that human photoreceptors interact readily with a partially degenerated retina. Moreover, incorporation into the host retina appears to be beneficial to graft maturation, polarisation and function.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from human retinal organoid cells cultured in vitro (cone-reporter positive versus cone-reporter negative) and cone-reporter positive cells retrieved at different timepoints after subretinal transplantation into the cone degeneration mouse host line Cpfl1.

first: Sylvia

last: Gasparini

first: Karen

last: Tessmer

first: Miriam

last: Reh

first: Stephanie

last: Wieneke

first: Madalena

last: Carido

first: Manuela

last: Völkner

first: Oliver

last: Borsch

first: Anka

last: Swiersy

first: Marta

last: Zuzic

first: Olivier

last: Goureau

first: Thomas

last: Kurth

first: Volker

last: Busskamp

first: Günther

last: Zeck

first: Mike

middle: O

last: Karl


title: Differences in the epigenetic modification of somatic cloned cattle from different types of donors still exist after reprogramming and differentiation

city: kaifeng

first: haoqiang

last: ma

state: henan

address: Jinming Revenue

institute: henan university

summary: To investigate the differences in the epigenetic modification of somatic cloned cattle from different types of donors after reprogramming and differentiation,we established Six cell lines of cloned cattle from different donor nuclei (three strains derived from fetal fibroblasts, numbered FFB1, FFB2, and FFB3, and another three strains derived from fetal oviduct epithelial cells, numbered FOV1, FOV2, and FOV3)

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different types of donors(Each type contains three cell lines, respectively).

first: Gengsheng

last: Cao

first: Haoqiang

last: Ma


title: RNAseq-based bladder cancer subtyping and IPA analysis with the xenografts from C57 BL/6J

city: Pittsburgh

first: Bowen

last: Dong

state: Pennsylvania

address: 4200 Fifth Ave, Pittsburgh, PA 15260

institute: University of Pittsburgh

summary: To subtype the Triple gene knockout tumor we generated and assess the similiarities with widely used MB49 cells, TKO cells were injected into bladder wall orthtopically and bladder lumen by catheter intravesically in C57 BL/6J, while MB49 intravesical injection as a control. TKO intravesical tumors, TKO orthotopic tumors and MB49 intravesical tumors were collected and sent for RNA-seq analysis. In results, both intravesical TKO and orthotopic TKO tumors demonstrates transcriptome profiles that closely resembled human basal like muscle invasive bladder cancer using a luminal/basal/neuronal classifier. Principal Component Analysis (PCA) across samples demonstrated that MB49 cells had transcriptome profiles that differed significantly from TKO tumors. Hence, this study suggest that the TKO tumors closely resemble basal like human bladder cancer and MB49 exhibited no expression of urothelial markers.

overall_design:
transcriptome profiling analysis of bladder intravesical and orthotopic tumors on C57 BL/6J

The knock out genes for TKO samples are Trp53, Pten, Rb1

first: Dongbo

last: Xu

first: Yali

last: Zhang

first: Jianmin

last: Wang

first: Prashant

last: Singh

first: Qiang

last: Li


title: Redundant effects of Pirfenidone against fibroblast activation and severe fibrotic lung disease

city: Cincinnati

first: Anil

last: Jegga

address: 240 Albert Sabin Way

department: Biomedical Informatics

institute: Cincinnati Children's

summary: Idiopathic Pulmonary Fibrosis (IPF) is a progressive chronic lung disease characterized by excess deposition of extracellular matrix (ECM) proteins in the lung. TGFα is a is a ligand for the epidermal growth factor receptor, and found elevated in several fibrotic lung diseases including IPF. Notably, lung-specific overexpression of TGFα alone in adult mice can cause progressive and extensive adventitial and subpleural fibrosis similar to IPF. Pirfenidone, an FDA approved drug has been shown to improve the decline in lung function in IPF patients. However, the mechanism of action of pirfenidone largely unknown. In the current study, we investigated the effects of pirfenidone using a mouse model of TGFα-induced pulmonary fibrosis and fibroblasts isolated from IPF lungs. Total lung transcriptome analysis suggest a significant overlap in dysregulated gene transcripts between TGFα model and IPF. In vivo studies demonstrate a significant improvement in lung function with pirfenidone therapy compared to vehicle-treated TGFα mice on Dox for six wks. However, pirfenidone treatment did not affect fibroproliferation, myofibroblast transformation, and ECM deposition during TGFα-induced pulmonary fibrosis. In summary, pirfenidone treatment improved lung function but had a limited or no effect on the expression of collagen, ECM genes, fibroproliferation and migration of lung-resident fibroblasts.

overall_design: mRNA profiles of control and TGFalpha mice on Dox for 6weeks and treated with eaither vehicle or pirfenidone for the last 3 weeks and measured changes in total lung transcripts

first: Satish

last: Madala


title: Single cell sequencing of anti-PD-1 treated xenograft from mice bladder urothelium with Trp53, Rb1, PTEN mutations on C57 BL/6J

summary: To determine the immune mechanism of anti-PD1 therapy, we carried out an anti-PD1 treatment on C57 BL/6J mice bearing mouse bladder urothelial carcinoma with three gene knockout. Anti-PD-1 immunotherapy resulted in a mixed pattern of treatment responses in individual tumors. Then, we performed single cell transcriptome profiling for tumor xenografts from Control IgG, anti-PD-1 non-responders and anti-PD-1 responders group. Duplicate tumors in each group were mixed and sequenced together as one representative sample. In results, we captured 4762 cells from Control IgG group, 4459 cells from anti-PD-1 non-responders group and 4861 cells from anti-PD-1 responders group.  identified 8 clusters of immune cells in treated samples (basophils, B cells, dendritic cells, macrophages, monocytes, neutrophils, NK cells, and T cells). Responder xenografts displayed significantly increased immune cell infiltration (15.2%, 742 immune cells / 4861 total cells) compared to the non-responder tumors (10.1%, 452 immune cells/ 4459 total cells, Fisher Exact Test p<0.0001). Specifically, there were more T cells (46/4861 vs 18 /4459, p=0.002), and macrophages (420/4861 vs 287/4459, p=0.002) in responder xenografts than in non-responder xenografts. Compared to control IgG tumors, response tumors exhibited an immune-inflamed phenotype with significant infiltration of T cells and NKT cells, whereas non-responder tumors showed no significant change. The higher percentage of T cells and macrophages tumor infiltration in responders suggests a potential role of innate immune microenvironment for the Immune checkpoint inhibitor (ICI) treatment response. This study provides the insights of immune environments in ICI-treated bladder tumor xenograft on C57 mice.

overall_design: Single cell transcriptome profiling of control IgG or anti-PD-1 treated xenograft on C57 BL/6J