title: ZMYND11-MBTD1 induces leukemogenesis through hijacking NuA4/TIP60 acetyltransferase complex and a PWWP-mediated chromatin association mechanism

summary: Recurring chromosomal translocation t(10;17)(p15;q21) present in a subset of human acute myeloid leukemia (AML) patients creates an aberrant fusion gene termed ZMYND11-MBTD1 (ZM); however, its function remains undetermined. Here, we show that ZM confers primary murine hematopoietic stem/progenitor cells indefinite self-renewal capability ex vivo and causes AML in vivo. Genomics profilings reveal that ZM directly binds to and maintains high expression of pro-leukemic genes including Hoxa, Meis1, Myb, c-Myc and Sox4. Mechanistically, ZM recruits NuA4/Tip60 histone acetyltransferase complex to cis-regulatory elements, sustaining an active chromatin state enriched in histone acetylation and devoid of repressive histone marks. Systematic mutagenesis of ZM demonstrates essential requirements of TIP60 interaction and an H3K36me3-binding PWWP domain for oncogenesis. Inhibitor of histone acetylation-‘reading’ bromodomain proteins, which act downstream of ZM, is efficacious in treating ZM-induced AML. Collectively, this study demonstrates AML-causing effects of ZM, examines its gene-regulatory roles, and reports an attractive mechanism-guided therapeutic strategy.

overall_design: Mapping the genome-wide binding sites of 3XHA-3XFLAG-tagged ZMYND11-MBTD1 (ZM), ZM∆M (ZM with the MBTD1 part deleted) and ZM∆Z (ZM with the ZMYND11 part deleted) in HEK293T cells.


title: Transcriptomic profile of ovarian tissue of third generation PCOS-like mice versus control animals

status: Public on Jan 14 2021

city: Illkirch

first: Damien

last: PLASSARD

address: 1 rue Laurent Fries

country: France

institute: IGBMC

type: Expression profiling by high throughput sequencing

summary: The aim of this study is to investigate ovarian transcriptomic changes by RNA-seq between 2 experimental groups, control (CNTR) and the third generation of PCOS-like mice (PAMH F3).

overall_design: mRNA profiles of controls and third generation PCOS-like mice (PAMH F3) ovaries, in triplicates and quadruplicates, respectively.

first: Paolo

last: Giacobini


title: Transcriptional profiling of senescent A549 cells

status: Public on Jan 13 2021

city: Pittsburgh

first: Jonathan

middle: K.

last: Alder

state: PA

address: 3459 Fifth Ave, NW 628

department: Medicine

country: USA

institute: University of Pittsburgh

summary: Telomere dysfunction is the most common identifiable cause of pulmonary fibrosis. Cellular senescence of epithlial cells is thought to play a signfiicant role in disease pathogensis. We established a model of cellular senescence using a human alveolar epithelilial-like cell lines (A549) and profiled the transcriptional changes that occur in response to telomere dyfunction. Telomere dysfunction was induced by expressing a dominant-negative form TRF2, the shelterin binding protein.

overall_design: RNA-seq was performed on 12 samples from 4 groups (3 biologic replicates each). The four groups are as follows; 1) A549 cells. 2) A549 cells cultured with 2 microgram per mL doxicycline for 10 days. 3) A549 cells stably expressing a doxicylcine-inducible TRF2-DN protein that induces telomere dysfunction and cellular scenescence when expressed. And 4) TRF2-DN cells cultured with 2 micrograms per mL  doxicycline for 10 days. RNA was isolated using RNAeasy kits (Qiagen) and total RNA was sent to Novagen for paired end RNA-sequencing. At least 20 million reades were sequenced per sample.

middle: K


title: 10X single-cell RNASeq profiling of human CD8+ T cells from advanced metastatic melanoma tumor samples and paired peripheral blood

city: Boston

first: Osmaan

last: Shahid

state: MA

address: 77 Avenue Louis Pasteur

department: Department of Immunology

institute: Harvard Medical School

summary: The ability to monitor anti-tumor CD8+ T cell responses in the blood has tremendous therapeutic potential. However, tracking tumor antigen-specific CD8+ T cells in the blood is challenging due to their small number and limited reagents to track these cells. We asked whether paired single-cell RNA and T cell receptor (TCR) sequencing could be used to detect and characterize “tumor matching” (TM) CD8+ T cells in the blood of advanced melanoma patients using the TCR as a molecular barcode. By leveraging the transcriptome, we characterized these cells, and identified candidate cell surface markers for to enrich this population. These data show that the TCR can be used to identify tumor-relevant cells for characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells.

overall_design:
10X 5' single cell RNASeq and paired TCR sequencing was performed on human CD8+ T cells from advanced metastatic melanoma as well as paired peripheral blood. A paired blood and tumor sample was taken from four different patients prior to checkpoint immunotherapy (treatment naive). For two patients, we also obtained a follow up blood sample after initiating checkpoint therapy. Using the TCR sequence as a molecular barcode, we identified matching T cell receptor clones between the peripheral blood and tumor, characterized the matching versus non-matching T cell populations, and compared these populations within a tissue compartment and between tissue compartments.

Please note that the processed data file generated from both GEX and VDJ/TCR samples is linked to the corresponding GEX sample records.

first: Kristen

middle: E

last: Pauken

first: Kelly

middle: M

last: Mahuron

first: Meromit

last: Singer


title: Maturation of human induced pluripotent stem cell-derived cardiomyocytes for modeling hypertrophic cardiomyopathy

status: Public on Jan 12 2021

city: Augusta

first: Hongyan

last: Xu

state: GA

department: Population Health Sciences

institute: Augusta University

summary: We describe a combination of methods to induce a more mature phenotype in hiPSC-CMs.  RNA-seq analysis was performed to compare gene expression between hiPSC-CMs cultured under standard conditions (GLUC) and those cultured under semi optimized (MM) and fully optimized (MPAT) conditions

overall_design: Examination of gene expression in less and more mature stem cell derived cardiomyocytes

first: Walter

last: Knight

first: Yuanbiao

last: Zhou

first: Kunhua

last: Song


title: BACH1 Recruits NANOG and Histone H3 Lysine 4 Methyltransferase MLL/SET1 Complexes to Regulate Enhancer-promoter Activity and Maintains Pluripotency

city: Philadelphia

first: Siqing

last: Wang

state: PENNSYLVANIA

address: 3401 Civic Center Blvd

department: Department of Pediatrics, Division of Hematology

institute: Children’s Hospital of Philadelphia

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Maintenance of stem-cell identity requires proper regulation of enhancer activity. Both transcription factors OCT4/SOX2/NANOG and histone methyltransferase complexes MLL/SET1 were shown to regulate enhancer activity, but how they are regulated in embryonic stem cells (ESCs) remains further studies. Here, we report a transcription factor BACH1, who which directly interacts with OCT4/SOX2/NANOG (OSN) and MLL/SET1 methyltransferase complexes and maintains pluripotency in mouse ESCs (mESCs). BTB domain and bZIP domain of BACH1 are required for these interactions and pluripotency maintenance. Loss of BACH1 reduced the interaction between NANOG and MLL1/SET1 complexes, and decreased their occupancy on chromatin, and further decreased H3 lysine 4 trimethylation (H3K4me3) level on gene promoters and (super-) enhancers, leading to decreased enhancer activity and transcription activity, especially on stemness-related genes. Moreover, BACH1 recruited NANOG through chromatin looping and regulated remote NANOG binding, fine-tuning enhancer-promoter activity and gene expression. Collectively, these observations suggest that BACH1 maintains pluripotency in ESCs by recruiting NANOG and MLL/SET1 complexes to chromatin and maintaining the trimethylated state of H3K4 and enhancer-promoter activity, especially on stemness-related genes.

overall_design: Bach1 knock-out (Bach1-KO) mESCs were generated by CRISPR/Cas9.  DoxBach1 mESCs expressing dox inducible Bach1 with C-terminal Flag tag were generated by piggyBac (PB) transposon system. We performed ChIP-seq of Nanog, H3K4me1, H3K4me3, and H3K27ac in wild-type (WT) mESCs and Bach1-KO mESCs, and also the ChIP-seq of Flag tagged Bach1 in DoxBach1 mESCs. We also perfromed the RNA-seq of WT mESCs and Bach1-KO mESCs. RNA-seq for each cell line had biological triplicates.

first: Dan

last: Meng


title: Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [BS-seq]

city: Beijing

first: Zhiqiang

last: Yan

address: No.5 Yiheyuan Road Haidian District

country: China

institute: Peking University

type: Methylation profiling by high throughput sequencing

summary: In mammals, drastic epigenomic reprogramming occurs during preimplantation development. However, the functional associations between different epigenetic layers and transcriptional regulation remains unclear, and to what extent, the dynamic epigenomics contribute to the lineage segregation remains to be elucidated. Here, we developed a single cell multi-omics sequencing technology, and provided the first single cell multi-comics map of chromatin accessibility, DNA methylation and RNA transcription during mouse preimplantation development.

overall_design: Mouse blastomeres from seven time points of preimplantation embryos were collected. For each single cell, scRNA-seq was performed using cell lysate supernatant, and scNOME-seq was performed with cellular nucleus precipitates.

first: Yang

first: Peng

last: Yuan

first: Jie

last: Qiao


title: Single-cell analyses identify circulating anti-tumor CD8 T cells and markers for their enrichment

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: 10X single-cell RNASeq profiling of CD8+ T cells from wildtype MC38 tumors and paired peripheral blood

summary: The ability to monitor anti-tumor CD8+ T cell responses in the blood has tremendous therapeutic potential. However, tracking tumor antigen-specific CD8+ T cells in the blood is challenging due to their small number and limited reagents to track these cells. We asked whether paired single-cell RNA and T cell receptor (TCR) sequencing could be used to detect and characterize “tumor matching” (TM) CD8+ T cells in the blood of mice with MC38 tumors using the TCR as a molecular barcode. By leveraging the transcriptome, we characterized these cells, and identified candidate cell surface markers for to enrich this population. These data show that the TCR can be used to identify tumor-relevant cells for characterization, reveal unique transcriptional properties of TM cells, and develop marker panels for tracking and analysis of these cells.

overall_design: 10X 5' single cell RNASeq and paired TCR sequencing was performed on sorted CD8+ T cells from wildtype MC38 tumors in C57BL/6 mice, as well as on sorted CD8+ CD44+ T cells from the peripheral blood of paired mice. Using the TCR sequence as a molecular barcode, we identified matching CD8+ T cell clones between the peripheral blood and tumor, and characterized the matching versus non-matching T cell populations within a tissue compartment and between tissue compartments. For some samples, we also performed CITE seq to detect protein expression of CD39, CX3CR1, and NKG2D.


title: Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [NOME-seq]


title: Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing [RNA-seq]


title: A high-resolution protein architecture of the budding yeast genome

city: Ithaca

first: B. Franklin

last: Pugh

state: New York

address: 465 Biotechnology Building

department: Molecular Biology and Genetics

institute: Cornell University

summary: The genome-wide architecture of chromatin-associated proteins that maintains chromosome integrity and gene regulation is ill defined. Here we use chromatin immunoprecipitation, exonuclease digestion and DNA sequencing (ChIP–exo/seq) to define this architecture in Saccharomyces cerevisiae. We identify 21 meta-assemblages consisting of roughly 400 different proteins that are related to DNA replication, centromeres, subtelomeres, transposons, and transcription by RNA polymerase (Pol) I, II and III. Replication proteins engulf a nucleosome, centromeres lack a nucleosome, and repressive proteins encompass three nucleosomes at subtelomeric X-elements. We find that most promoters associated with Pol II evolved to lack a regulatory region, having only a core promoter. These constitutive promoters comprise a short nucleosome-free region (NFR) adjacent to a +1 nucleosome, which together bind the transcription-initiation factor TFIID to form a preinitiation complex (PIC). Positioned insulators protect core promoters from upstream events. A small fraction of promoters evolved an architecture for inducibility, whereby sequence-specific transcription factors (ssTFs) create a nucleosome-depleted region (NDR) that is distinct from an NFR. We describe structural interactions among ssTFs, their cognate cofactors and the genome. These interactions include the nucleosomal and transcriptional regulators RPD3-L, SAGA, NuA4, Tup1, Mediator and SWI–SNF. Surprisingly, we do not detect interactions between ssTFs and TFIID, suggesting that such interactions do not stably occur. Our model for gene induction involves ssTFs, cofactors and general factors such as TBP and TFIIB, but not TFIID. By contrast, constitutive transcription involves TFIID but not ssTFs and cofactors. From this, we define a highly integrated network of gene regulation by ssTFs.

overall_design: Genome-wide analysis of hundreds of yeast proteins using ChIP-exo

first: Matthew

middle: J

last: Rossi

first: Prashant

last: Kuntala

first: William

last: Lai

first: Naomi

last: Yamada

first: Nitika

last: Badjatia

first: Chitvan

last: Mittal

first: Guray

last: Kuzu

first: Kylie

last: Bocklund

first: Nina

middle: P

last: Farrell

first: Thomas

middle: R

last: Blanda

first: Joshua

middle: D

last: Mairose

first: Ann

middle: V

last: Basting

first: Katelyn

middle: S

last: Mistretta

first: David

last: Rocco

first: Emily

last: Perkinson

first: Gretta

last: Kellogg

first: Shaun

last: Mahony

first: B

middle: F


title: Patient-Derived Nasopharyngeal Cancer Organoids for Disease Modelling and Radiation Dose Optimization

city: Singapore

first: Lucky

middle: Swarnalatha

last: Sasidharan

state: Singapore

address: 31 Biopolis Way

department: Institute of Bioengineering and Nanotechnology

country: Singapore

institute: A*STAR Research Entities

type: Non-coding RNA profiling by high throughput sequencing

summary: Background:  Effective radiation treatment (RT) for recurrent nasopharyngeal cancers (NPC), featuring an intrinsic hypoxic sub-volume, remains a clinical challenge. Lack of disease‐specific in-vitro models, together with difficulties in establishing patient derived xenograft (PDX) models, have further hindered development of personalized therapeutic options.   Methods: Here in, we established two NPC organoid lines from recurrent NPC PDX models and further characterized and compared these models with original patient tumors using RNA sequencing analysis. Organoids were cultured in hypoxic conditions to examine the effects of hypoxia and radioresistance. These models were then utilized to determine the radiobiological parameters, such as α/β ratio and oxygen enhancement ratio (OER), characteristic to radiosensitive normoxic and radioresistant hypoxic NPC, using simple dose-survival data analytic tools. The results were further validated in-vitro and in-vivo, to determine the optimal boost dose and fractionation regimen required to achieve effective NPC tumor regression.   Results: Despite the differences in tumor microenvironment due to the lack of human stroma, RNA sequencing analysis revealed good correlation of NPC PDX and organoid models with patient tumors. Additionally, the established models also mimicked inter-tumoral heterogeneity. Hypoxic NPC organoids were highly radioresistant and had high α/β ratio compared to its normoxic counterparts. In-vitro and in-vivo fractionation studies showed that hypoxic NPC was less sensitive to RT fractionation scheme and required a large bolus dose or 1.4 times of the fractionated dose that was effective against normoxic cells in order to compensate for oxygen deficiency.   Conclusion: This study is the first direct experimental evidence to predict optimal RT boost dose required to cause sufficient damage to recurrent hypoxic NPC tumor cells, which can be further used to develop dose-painting algorithms in clinical practice.

overall_design: RNA sequencing data of 8 NPC patient tumors, 2 PDXs lines 296T and 250T and corresponding organoid lines from the 2 PDXs

first: Tan

last: Han


title: Regulatory landscape of early embryos development revealed by parallel single-cell multi-omics sequencing

first: Zhiqiang

last: Yan


title: Comprehensive single-cell sequencing reveals the stromal dynamics and tumor-specific characteristics in the microenvironment of nasopharyngeal carcinoma

status: Public on Jan 11 2021

city: Hong Kong

first: Xin-Yuan

last: Guan

address: L10-56, Laboratory Block, LKS Faculty of Medicine

department: Clinical Oncology

country: Hong Kong

institute: The University of Hong Kong

summary: The tumor microenvironment (TME) of nasopharyngeal carcinoma (NPC) harbors a heterogeneous and dynamic stromal population. A comprehensive understanding of this tumor-specific ecosystem is necessary to enhance cancer diagnosis, therapeutics, and prognosis. However, recent advances based on bulk RNA sequencing remain insufficient to construct an in-depth landscape of infiltrating stromal cells in NPC. Here we apply single-cell RNA sequencing to 66,627 cells from 14 patients, integrated with clonotype identification on T and B cells. We identify and characterize five major stromal clusters and 36 distinct subpopulations based on genetic profiling. By comparing with the infiltrating cells in the non-malignant microenvironment, we report highly representative features in the TME, including phenotypic abundance, genetic alternations, immune dynamics, clonal expansion, developmental trajectory, and molecular interactions that profoundly influence patient prognosis and therapeutic outcome. The key findings are further independently validated in two single-cell RNA sequencing cohorts and two bulk RNA-sequencing cohorts. In the present study, we reveal the correlation between NPC-specific characteristics and progression-free survival. Together, these data facilitate the understanding of the stromal landscape and immune dynamics in NPC patients and provides deeper insights into the development of prognostic biomarkers and therapeutic targets in the TME.

overall_design: Single-cell transcriptome analysis and immune profiling of the NPC microenvironment

first: Lanqi

last: Gong


title: L1 retrotransposons exploit RNA m6A modification as an evolutionary driving force

status: Public on Jan 09 2021

city: Seoul

first: Sung-Yeon

last: Hwang

address: School of Biological Sciences, Seoul National University

country: South Korea

summary: To investigate the m6A profiles of full-length L1 RNA, we use MeRIP-seq in HeLa cells expressing reporter L1. We find that L1 RNA contains functional m6A sites, predominantly in 5'UTR.

overall_design: Study of m6A in L1 RNA using two MeRIP-seq replicates for HeLa cells expressing reporter L1.

first: Sung

middle: Y

first: Hyunchul

last: Jung

first: Jung

last: Choi

first: Kwangseog

last: Ahn


title: Single-molecule long-read sequencing reveals a conserved intact long RNA profile in sperm

city: Rochester

first: Xin

last: Li

state: NY

address: 601 Elmwood Ave.

department: Biochemistry and biophysics

institute: University of Rochester Med Center

summary: Sperm contributes diverse RNAs to the zygote. While sperm small RNAs have been shown to impact offspring phenotypes, our knowledge of the sperm transcriptome, especially the composition of long RNAs has been limited by the lack of sensitive, high-throughput experimental techniques that can distinguish intact RNAs from fragmented RNAs, known to abound in sperm. Here, we integrate single-molecule long-read sequencing with short-read sequencing to detect sperm intact RNAs (spiRNAs). We identify 3,440 spiRNA species in mice and 4,100 in humans. The spiRNA profile consists of both mRNAs and long non-coding RNAs, is evolutionarily conserved between mice and humans, and displays an enrichment in mRNAs encoding for ribosome. In sum, we characterize the landscape of intact long RNAs in sperm, paving the way for future studies on their biogenesis and functions. Our experimental and bioinformatics approaches can be applied to other tissues and organisms to detect intact transcripts.

overall_design:
We used PacBio IsoSeq and Oxford Nanopore Technologies to sequence mouse sperm and testis RNAs, as well as human sperm RNAs. We also used Illumina short reads to sequence human sperm RNAs and mouse sperm RNAs.

The Summary.MousePacBio.ONT.xlsx table contains both PacBio and ONT data for mouse:
Mouse Sperm and Testis PacBio: Summary.MousePacBio.ONT.xlsx
Mouse Sperm ONT: Summary.MousePacBio.ONT.xlsx

The following three data files are linked to the corresponding sample records:
HumanSpermPacBio: Summary.HumanPacBio.xlsx
RNAseq.HumanSperm.cauda: RNAseq.HumanSperm.cauda.salmon.sf
RNAseq.MouseSperm.cauda.adult: RNAseq.MouseSperm.cauda.adult.salmon.sf

The following three GTF files are results of our PacBio assembly. They were based on both PacBio and Illumina sequencing data:
TranscriptomeAssembly.MouseTestis.mm10.gtf
TranscriptomeAssembly.spiRNA.HumanSperm.hg38.gtf
TranscriptomeAssembly.spiRNA.MouseSperm.mm10.gtf

These three fasta files are the full-length non-chimeric (FLNC) CCS reads for downstream analysis:
SpermPacBio_FLNC.fasta
TestisPacBio_FLNC.fasta
HumanSpermPacBio_FLNC.fasta

middle: Z

first: Kin

last: Au

first: Yu

middle: H

last: Sun

first: Anqi

last: Wang


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Elf4fl/fl-Villin-Cre distal colon Transcriptomes

status: Public on Jan 07 2021

city: beijing

first: Tongtong

last: Liu

address: Peking University Health Science Center, 38 Xueyuan Road, Haidian District, Beijing

summary: Conclusion: Elf4fl/fl-Villin-Cre mice are more sensitive to Dextran sulfate (DSS) induced colon tumorigenesis

overall_design: six-week-old WT and Elf4fl/fl-Villin-Cre C57BL/6 female mice were treated with 2% DSS for 5 days. At Day 5, the distal colon was taken out and the RNA was extracted by Trizol method, followed by eukaryotic RNA-seq and associated analysis

first: Fuping

last: You


title: Gene expression profiling of drug-persistent breast and prostate cancer cells derived from treatment of organoids or PDX with cytotoxic agents

first: Eugen

last: Dhimolea

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

summary: Cancer treatments often fail to achieve complete and sustained responses due to persistent residual tumor foci with acquired drug refractoriness, the “seed” for eventual relapse. The biological underpinning of this in situ resistance is not clear, while faithful in vitro models of this cancer cell state are lacking. We observed that the in vitro cytotoxic treatment of breast and prostate cancer patient-derived cells and cell lines cultured as 3D organoids generates persistent tumor cell subpopulations that phenotypically and molecularly simulate the in vivo emergence of drug-refractory residual tumors in preclinical and clinical settings. Here we provide RNAseq gene expression profiling data from drug-persistent cancer cells generated after longitudinal treatment of cancer organoids or PDX/xenograft tumors with chemotherapeutic (docetaxel, vinblastine) or targeted (afatinib) agents. These data can be used to identify genes and pathways which are upregulated in residual drug-persistent tumors.

overall_design: RNA profiles of drug-persistent cancer cells in 3D organoid cultures or in vivo tumors treated with chemotherapeutics and/or targeted agents

first: Ricardo

last: de Matos Simoes

first: Constantine

last: Mitsiades


title: Antagonistic control of myofiber size and muscle protein quality control by the ubiquitin ligase UBR4 during aging

city: Memphis

first: Yong-Dong

state: TN

address: 262 Danny Thomas Pl, MS1135

institute: St. Jude Children's Research Hospital

summary: Sarcopenia is a degenerative condition that consists in the age-induced atrophy and functional decline of skeletal muscle cells (myofibers). A common hypothesis is that inducing myofiber hypertrophy should also reinstate myofiber contractile function but such model has not been extensively tested. Here, we find that the levels of the ubiquitin ligase UBR4 increase in skeletal muscle with aging, and that muscle-specific UBR4 loss rescues age-associated myofiber atrophy in mice. However, UBR4 promotes proteolysis by the proteasome and consequently UBR4 loss reduces the muscle specific force and accelerates the decline in muscle protein quality that occurs with aging in mice. Similarly, hypertrophic signaling induced via muscle-specific loss of UBR4 and of several other ubiquitin ligases consistently compromises muscle function and shortens lifespan in Drosophila by reducing protein quality control. Altogether, these findings indicate that ubiquitin ligases regulate in opposite fashion myofiber size and muscle protein quality control during aging.

overall_design: Expression profile of RNA-seq samples from tibialis anterior muscles from male mice at 6 and 24 months of age.

first: Liam

middle: C

last: Hunt

first: Bronwen

last: Schadeberg

first: Jared

last: Stover

first: Benard

last: Haugen

first: Vishwajeeth

last: Pagala

first: Jason

last: Puglise

first: Elisabeth

last: Barton

first: Junmin

last: Peng

first: Fabio

last: Demontis


title: Stretch-activated ion channels identified in the touch-sensitive structures of carnivorous Droseraceae plants.

city: La Jolla

first: Carl

last: Procko

state: CA

address: 10010 N Torrey Pines Rd

institute: Salk Institute for Biological Studies

summary: We compare isolated trigger hairs from Venus flytrap leaves to whole trap tissue (with trigger hairs removed) to find differentially-expressed transcripts.

overall_design: Paired trigger hair and whole trap samples were collected in triplicate, and stranded mRNA libraries sequenced and compared.

first: Swetha

last: Murthy

first: William

middle: T

last: Keenan

first: Seyed-Ali-Reza

last: Mousavi

first: Tsegaye

last: Dabi

first: Adam

last: Coombs

first: Erik

first: Lisa

last: Baird

first: Ardem

last: Patapoutian

first: Joanne

last: Chory


title: Long terms effects of very low dose particle radiation on the gene expression in the mouse heart

status: Public on Jan 05 2021

city: New York

first: David

last: Goukassian

address: 1470 Madison Ave

department: Cardiovascular Research Center

institute: Icahn School of Medicine at Mount Sinai

summary:
We sought to determine the long-term effects of radiation (IR) on gene expression in the whole heart as a function of IR type and dose. We hypothesize that compared to low doses of gamma-IR, high charge and energy (HZE) particle-IR may have different biological response thresholds in cardiac tissue at lower doses, and these effects may be IR type- and dose-dependent.
We provide for the first time the transcriptome analysis of mouse hearts exposed to low and very low doses of gamma- (137Cs), silicon- (14Si), and titanium- (22Ti) irradiation. Our results show that 16 months after low and very low dose IR exposure, the gene expression in the heart tissue is significantly differentially regulated, suggesting there are long-term effects on dysregulation of varying molecular pathways that are associ-ated with various degrees of cardiovascular, pulmonary and metabolic diseases, as well as biological processes, including abnormal circadian rhythm, cancer, Hutchinson-Gilford progeria syndrome, etc.

overall_design: 72 female CB6F1/Hsd mice were irradiated with a single, full-body HZE dose (≤0.5 Gy) of 260 MeV/n silicon (14Si, LET ~ 70 keV/µm) and 1,000 MeV/n titanium (22Ti, LET ~ 100 keV/µm) Another group of animals were also irradiated with 137Cs gamma-ray that served as a low-LET reference. Control sham-treated animals were placed in clear plastic holders for equivalent exposure times but were not irradiated. Animals were eutanazied 16 months after a single dose of full-body IR with the corresponding ions and doses. Total RNA was isolated with total RNA isolation kit from heart organs (n=4-5 per group) according to manufacturer’s instructions. Gene expression profiling was performed using Affymetrix Clariom S Mouse Array according to the manufacturer’s instructions (Affymetrix, Inc., Santa Clara, CA). Chips were scanned with an Affymetrix GeneChip Scanner using 3000 Command Console Software. Signal intensities were converted to log2 RMA expresson values.

middle: A

first: Sankar

last: Addya


title: Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing

status: Public on Jan 06 2021

city: Wuhan

first: Jingzhen

last: Li

address: Wuhan, Hubei 430074, PR China

institute: Huazhong University of Science and Technology

summary: Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis, especially in neural tissues. Mutations in pre-mRNAs processing factor 31 (PRPF31) cause autosomal dominant retinitis pigmentosa, a progressive retinal degeneration disease. The transcriptome-wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here, we showed that the differentiation and viability of retinal progenitor cells (RPCs) are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level, significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild-type human PRPF31 rather than the disease-associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak 5′ splicing site. Moreover, genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events, which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis.

overall_design: Head mRNA profiles of 36 hpf sibling (wild type) and prpf31-/- zebrafish were generated by deep sequence in three independent biological replicates.

first: Fei

last: Liu

first: Yuexia

last: Lv

first: Kui

last: Sun

first: Yuntong

last: Zhao

first: Jamas

last: Reilly

first: Yangjun

last: Zhang

first: Shanshan

last: Yu

first: Jiayi

last: Tu

first: Xiliang

first: Yayun

last: Qin

first: Yuwen

last: Huang

first: Pan

last: Gao

first: Danna

last: Jia

first: Xiang

last: Chen

first: Yunqiao

last: Han

first: Xinhua

last: Shu

first: Daji

last: Luo

first: Zhaohui

last: Tang

first: Mugen


title: Transcriptome Analysis Reveals a Promotion of Carotenoid Production by Copper Ions in Recombinant Saccharomyces cerevisiae

city: Guangzhou

first: Li

middle: Bu

last: Su

address: No. 100, Xianlie Middle Road, Guangzhou, 510070, PR China

institute: Guangdong Institute of Microbiology

summary: When using YPM media, the carotenoid yield was increased 10-fold compared to using the YPD media. To elucidate the hidden mechanism, the transcriptome analysis was performed and showed that 464 genes changed significantly in YPM media. Furthermore, inspired by the differential gene expression analysis which indicated that ADY2, HES1, and CUP1 showed the most remarkable changes, we found that the improvement of carotenoid accumulation in YPM media was mainly due to the copper, since supplementation of 80 µM CuSO4 in YPD media could increase carotenoid yield 9.2-fold

overall_design: RNA-seq for Recombinant Saccharomyces cerevisiae in YPD and YPM media.

first: Buli

first: Honghui

last: Zhu

first: Anzhang

last: Li

first: Ming-Rong

last: Deng


title: Changes in gene expression of H. pylori 26695 and ∆dppA cells

city: Fuzhou

first: Xiaohong

last: xu

address: Antai Street

institute: Fujian Medical University Union Hospital

summary: To further examine the roles of DppA, we performed RNA-seq analysis and investigated the genes expressed differentially between H. pylori 26695 and a ΔdppA strain.We found that 253 genes were differentially expressed with a |Log2 (fold change)| > 1, including 116 genes that were upregulated and 137 genes that were downregulated in ∆dppA (P < 0.05). We also performed functional classification of the genes upregulated and downregulated in ∆dppA. We found that those genes involved in energy metabolism, transportation, and translation were significantly downregulated in ∆dppA, which might contribute to the decreased growth rate of H. pylori in this genetic background. Genes involved in DNA metabolism, bacterial pathogenesis, and motility were upregulated in this strain, and they might contribute to the virulence of H. pylori.

overall_design: To prepare total RNA for transcriptomic study, H. pylori 26695 and ∆dppA cells were cultivated in Brucella broth containing 10% FBS for 20 h until exponential phase in a shaker at 120 rpm in a microaerobic environment (5% O2, 10% CO2, and 85% N2) at 37°C.Two replicates was done per sample

last: Xu


title: Integration of Alzheimer's disease genetics and myeloid genomics identifies disease risk regulatory elements and genes [RNA-seq]

first: Alison

last: Goate

address: Icahn (East) Building Floor 10 Room 10-70C, 1425 Madison Ave

department: Department of Genetics and Genomic Sciences

summary: Genome-wide association studies (GWAS) have identified more than 40 loci associated with Alzheimer’s disease (AD), but the causal variants, regulatory elements, genes and pathways remain largely unknown, impeding a mechanistic understanding of AD pathogenesis. Previously, we showed that AD risk alleles are enriched in myeloid-specific epigenomic annotations. Here, we show that they are specifically enriched in active enhancers of monocytes, macrophages and microglia. We integrated AD GWAS with myeloid epigenomic and transcriptomic datasets using analytical approaches to link myeloid enhancer activity to target gene expression regulation and AD risk modification. We identify AD risk enhancers and nominate candidate causal genes among their likely targets (including AP4E1, AP4M1, APBB3, BIN1, MS4A4A, MS4A6A, PILRA, RABEP1, SPI1, TP53INP1, and ZYX) in twenty loci. Fine-mapping of these enhancers nominates candidate functional variants that likely modify AD risk by regulating gene expression in myeloid cells. In the MS4A locus we identified a single candidate functional variant and validated it in human induced pluripotent stem cell (hiPSC)-derived microglia and brain. Taken together, this study integrates AD GWAS with multiple myeloid genomic datasets to investigate the mechanisms of AD risk alleles and nominates candidate functional variants, regulatory elements and genes that likely modulate disease susceptibility.

overall_design: We generated RNA-seq in 4 hiPSC-derived microglia lines to evaluate allele specific expression at the candidate causal variant in the MS4A locus

first: Gloriia

last: Novikova

first: Yiyuan

last: Liu

first: Edoardo

last: Marcora


title: Integration of Alzheimer's disease genetics and myeloid genomics identifies disease risk regulatory elements and genes [ATAC-seq]

overall_design: We generated ATAC-seq in 3 hiPSC-derived microglia lines to evaluate allele specific chromatin accessiblity at the candidate causal variant in the MS4A locus


title: Integration of Alzheimer's disease genetics and myeloid genomics identifies disease risk regulatory elements and genes

overall_design: Refer to individual Series


title: Nascent RNA sequencing identifies a widespread sigma70-dependent pausing regulated by Gre factors in bacteria

city: Tianjin

first: Zhe

last: Sun

address: 32 West 7th Ave

institute: Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences

summary: Promoter-proximal pausing regulates eukaryotic gene expression and serves as checkpoints to assemble elongation/splicing machinery. Little is known how broadly this type of pausing regulates transcription in bacteria. We apply nascent elongating transcript sequencing combined with RNase I footprinting for genome-wide analysis of σ70-dependent transcription pauses in Escherichia coli. Retention of σ70 induces strong backtracked pauses at a 10-20-bp distance from many promoters. The pauses in the 10-15-bp register of the promoter are dictated by the canonical -10 element, 6-7 nt spacer and “YR+1Y” motif centered at the transcription start site. The promoters for the pauses in the 16-20-bp register contain an additional -10-like sequence recognized by σ70. Our in vitro analysis reveals that DNA scrunching is involved in these pauses relieved by Gre cleavage factors. The genes coding for transcription factors are enriched in these pauses, suggesting that σ70 and Gre proteins regulate transcription in response to changing environmental cues.

sample_organism: Escherichia coli str. K-12 substr. W3110

overall_design: To identify the genome-wide σ70-dependent pause sites, RNET-seq were performed using the E. coli strains σ70-WT, σ70-greAB-, β'-WT and β'-greAB- with His-tag fusion to RpoD (σ70) and RpoC (β’) in parallel. The RNAP-DNA-RNA ternary complex immobilized by Ni-NTA agarose beads was treated by DNase I and RNase I to obtain the RNA footprints protected by RNAP. RNA-seq were performed using the same strains and conditions to monitor the changes of gene transcription.

first: Mikhail

last: Kashlev


title: Remodeling of Neurotransmission and Chemokine Signaling Genomic Fabrics in Neuropsychiatric Systemic Lupus Erythematosus

status: Public on Jan 03 2021

city: Prairie View

first: Dumitru

middle: Andrei

last: Iacobas

state: TX

address: Ann Preston St

department: Undergraduate Medical Academy

institute: Prairie View A&M University

summary: Cognitive dysfunction and mood changes are prevalent and especially taxing issues to patients with systemic lupus erythematosus (SLE). TNF-like weak inducer of apoptosis (TWEAK) and its cognate receptor Fn14 have been shown to play an important role in neurocognitive dysfunction in murine lupus. We profiled and compared gene expression in the cortices of MRL/+, MRL/lpr and MRL/lpr-Fn14 knockout (Fn14ko) adult female mice to determine the transcriptomic impact of TWEAK/Fn14 on cortical gene expression in lupus. We found that the TWEAK/Fn14 pathway strongly affects the expression level, variability and coordination of the genomic fabrics responsible for neurotransmission and chemokine signaling. Dysregulation of the PI3K-Akt pathway in the MRL/lpr lupus strain compared with the MRL/+ control and Fn14ko mice was particularly prominent and therefore promising as a potential therapeutic target, although the complexity of the transcriptomic fabric highlights important considerations in in vivo experimental models.

overall_design: Comparison of gene expression profiles in cortices of MRL/lpr, Fn14ko and MRL/MpJ adult female mice

first: Jing

last: Wen

first: Sanda

first: Noa

last: Schwartz

first: Chaim

last: Putterman


title: Comprehensive analysis of single cell ATAC-seq data with SnapATAC

first: Rongxin

last: Fang

institute: Ludwig Institute for Cancer Research

summary: Identification of the cis-regulatory elements controlling cell-type specific gene expression patterns is essential for understanding the origin of cellular diversity. Conventional assays to map regulatory elements via open chromatin analysis of primary tissues is hindered by sample heterogeneity. Single cell analysis of accessible chromatin (scATAC-seq) can overcome this limitation. However, the high-level noise of each single cell profile and the large volumes of data pose unique computational challenges. Here, we introduce SnapATAC, a software package for analyzing scATAC-seq datasets. SnapATAC dissects cellular heterogeneity in an unbiased manner and map the trajectories of cellular states. Using the Nyström method, SnapATAC can process data from up to a million cells. Furthermore, SnapATAC incorporates existing tools into a comprehensive package for analyzing single cell ATAC-seq dataset. As demonstration of its utility, SnapATAC is applied to 55,592 single-nucleus ATAC-seq profiles from the mouse secondary motor cortex. The analysis reveals candidate regulatory elements in 31 distinct cell populations in this brain region and inferred candidate cell-type specific transcriptional regulators.

overall_design: Profling of single cell chromatin accessibility in the mouse secondary motor cortex.

first: Bing

last: Ren


title: Stimulation with M.tb peptide pool induces multiple signaling pathways involved in providing protection during M.tb infection

city: New Delhi

first: Ashima

last: Bhaskar

state: Delhi

address: Aruna Asaf Ali Marg

country: India

institute: National Institute of Immunology

summary: M.tb Peptide pool induces an intricate network of signaling pathways in DCs and T cells which leads to enhanced cytokine production and T cell activation.

overall_design: To understand the host changes at the transcription levels leading to an increased T cell activation and an augmented pro-inflammatory cytokine upon M.tb peptide pool treatment, we performed comparative transcriptome analysis of unstimulated dendritic cells DCs (Un-DC) vs peptide pool pulsed DCs (Pep-DC) and T cells co-cultured with unstimulated DCs (Un-TC) vs T cells co-cultured with peptide pool pulsed DCs (Pep-TC).

first: Ved

last: Dwivedi


title: Pretreatment of aged mice with retinoic acid restores alveolar regeneration via upregulation of reciprocal PDGFRA signaling

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: Reciprocal PDGFA signaling activates regenerative fibroblasts that support alveolar epithelial cell differentiation and repair, providing a potential therapeutic strategy to influence the pathogenesis of IPF.

overall_design:
PNX of mice, with or without RA pretreatment, followed by RNA Sequencing of the Epithelial (Epcam+) or Fibroblast (Pdgfra+) lung cells was used to study lung repair and regeneration.
Pdgfra+ Lung Cells from inidividuals with idiopathic pulmonary fibrosis (IPF).

first: Jason

last: Gokey

first: Jenna

last: Green

first: Marion

last: Waltamath

first: Jillian

last: Spinney

first: Katharine

middle: E

last: Black

first: Lida

last: Hariri

first: Yan

first: Anne-Karina

last: Perl


title: The metabolite methylglyoxal-mediated gene expression is associated with histone methylglyoxalation

first: Zheng-Wei

last: Fu

state: Hubei

address: Bayi road

department: College of Life Sciences

institute: Wuhan University

summary:
RNA-seq analysis of Arabidopsis wild-type, glyI2, 35S::GLYI2 35S::GLYII4 seedlings suggested that MG mediates salt stress responsive gene expression.
ChIP-seq analysis of MG-treated Arabidopsis wild-type seedlings with anti-MMP and anti-H3K4MG suggested that MG-mediated gene expression is associated with histone methylglyoxalation.

overall_design: Total mRNA and ChIP DNA profiles were generated by deep sequencing using BGISEQ-500

first: Ying-Tang

last: Lu


title: Transcriptome profiling of Amazon molly and F1 interspecies hybrid

city: San Marcos

first: Yuan

address: university drive

institute: Xiphophorus Genetic Stock Center

summary: The Amazon molly is a unique clonal fish species that originated from an interspecies hybrid between Poecilia species P. mexicana and P. latipinna. It reproduces by gynogenesis, which eliminates paternal genomic contribution to offspring. Earlier study showed that Amazon molly exhibits bi-allelic expression for a large portion of the genome, leading to two main questions: 1. Are the allelic expression patterns from the initial hybridization event stabilized or changed during establishment of the asexual species and its further evolution? 2. Is allelic expression biased toward one parental allele a stochastic or adaptive process? To answer these questions, the allelic expression of P. formosa siblings was assessed to investigate intra- and inter-cohort allelic expression variability. For comparison, interspecies hybrids between P. mexicana and P. latipinna were produced in the laboratory to represent the P. formosa ancestor. We have identified inter-cohort and intra-cohort variation in parental allelic expression. The existence of inter-cohort divergence suggests functional P. formosa allelic expression patterns do not simply reflect the atavistic situation of the first interspecies hybrid but potentially result from long-term selection of transcriptional fitness. In addition, clonal fish exhibit a transcriptional trend representing minimal intra-clonal variability in allelic expression patterns compared to the corresponding hybrids. The intra-clonal similarity in gene expression translates to sophisticated genetic functional regulation at the individuum level. These findings suggest the parental alleles inherited by P. formosa form tightly regulated genetic networks that lead to a stable transcriptomic landscape within clonal individuals.

sample_organism:
Poecilia formosa
Poecilia mexicana x Poecilia latipinna

overall_design: Brain, liver and ovary transcriptome profiling were assessed in siblings of clonal Amazon molly, and siblings of one brood of F1 hybrid between P. mexicana and P. latipinna.

first: Manfred

last: Schartl


title: Targeting IL-21 to tumor-reactive T cells enhances memory T cell responses and anti-PD-1 antibody therapy

status: Public on Jan 01 2021

city: Beijing

first: Ying

last: Li

address: Datun Road #15, Chaoyang District

institute: Institute of Biophysics, Chinese Academy of Sciences

summary: T cell rejuvenation by PD-1/PD-L1 blockade, despite emerging as a highly promising therapy for advanced cancers, is only beneficial for a minority of treated patients. There is evidence that a lack of efficient T cell activation may be responsible for the failure. Here, we demonstrate that IL-21 can be targeted to tumor-reactive T cells by fusion of IL-21 to anti-PD-1 antibody. To our surprise, the fusion protein PD-1Ab21 promoted the generation of TSCM-like CD8+ T cells with enhanced cell proliferation. A transcriptome analysis of isolated TN, activated and PD-1Ab-cultured CD44highCD62Lhigh T cells, IL-2-generated TE/TEM, IL-15-generated TCM as well as PD-1Ab21 and IL-21-generated CD44lowCD62Lhigh T cells provides corroborating evidence that PD-1Ab21 induces conversion of activated CD8+ T cells back to a memory subset that is distinct from TCM cells, but similar to TSCM. PD-1Ab21 treatment showed potent antitumor effects in established tumor-bearing mice accompanied with an increased frequency of TSCM and robust expansion of tumor-specific CD8+ T cells with a memory phenotype, and was superior to a combination of PD-1 blockade and IL-21 infusion. Therefore, we have developed a potential strategy to improve the therapeutic effects of immune checkpoint blockade by simultaneously targeting cytokines to tumor-reactive T cells.

overall_design: mRNA profiles of naïve, OVA-activated, IL-2-,IL-15-, IL-21-, PD-1Ab-, PD-1Ab-21-differentiated OT-1 T cells in vitro. Totally 21 samples were sequencing, 3 replicates per group.

first: Mingming

last: Jia

first: Shengdian

last: Wang


title: The chromatin accessibility of circulating CD8+ T cells predicts immune-therapeutic response of PD-1 blockade in gastric cancer

first: Hyun Mu

last: Shin

address: Biomedical Science Building 202, 103 Daehakro, Jongro-gu

department: Biomedical Sciences

institute: Seoul National University College of Medicine

summary: We hypothesized that there are distinct signatures in chromatin of circulating CD8+ T cells depending on their response to anti-PD-1 therapy due to their long-term interaction with the internal stimuli, such as with tumor and its microenvironment, and external stimuli, such as with infectious diseases. To identify unique chromatin regions predicting the clinical outcome of PD-1 therapy, we performed an assay for transposase-accessible chromatin sequencing (ATAC-seq) using blood samples of patients enrolled in PD-1 therapy. From the analysis of ATAC-seq data, we identified quantitatively distinct open regions of chromatin that distinguishes responders from non-responders to PD-1 therapy. We demonstrated for the first time that epigenetic characteristics of pre-treatment CD8+ T cells further identifies GC patients who may benefit from immune checkpoint inhibitors (ICIs) in addition to tumor profiling status.

overall_design: All CD8+ T cells isolated from blood samples of metastatic gastric cancer patients were used for ATAC-seq

first: H

middle: M

first: G

last: Kim


title: The effects of postmortem delay on mouse microglia gene expression

city: Groningen

first: Bart

last: Eggen

state: Groningen

address: Antonius Deusinglaan 1

department: Department of Biomedical Sciences

country: Netherlands

institute: UMCG Groningen

summary: Microglia are specialized macrophages of the central nervous system (CNS) and first to react to pathogens or injury. Transcriptional profiling significantly contributed to our understanding of microglia functions. In the case of human CNS samples, a postmortem delay (PMD) in tissue access and collection is the potential factor that might affect microglia gene expression profiles. However, the direct analysis of effects of PMD on human microglia transcriptome is challenging due to many confounding factors such as sex, aging, nutrition, lifestyle, medication and medical history. To determine the effects of PMD on the microglia transcriptome. Here, we analyzed mouse microglia, where ante-mortem conditions and post-mortem delay can be tightly controlled. PMD had very limited effect on mouse microglia gene expression, only 50 genes (out of 15,554 detected genes) were differentially expressed between different PMDs.

overall_design: 4 experimental groups with different postmortem intervals  (0, 4, 6, 12 h), with 4 replicates per group. In total, 16 mouse samples for bulk RNAseq.

middle: W

last: Boddeke

first: B

middle: J


title: Kynurenine treatment of herpesivrus stimulated iCD103 dendritic cells

city: Ann Arbor

first: Stephen

middle: J.

last: Gurczynski

state: MI

address: 109 Zina Pitcher Pl, Room 4062

department: Internal Medicine

institute: University Of Michigan

summary: We report the gene expression (obtained by next generation RNAseq) of inducible CD103+ dendritic cells, iCD103 cells, stimulated with both murine herpesvirus-68 and the immunomodulatory tryptophan derivative kynurenine (kyn).  This study provides data on how tryptophan derivatives can modulate pro-inflammatory cytokine expression in virus treated dendritic cells.

overall_design: iCD103+ DCs were treated with γHV-68 w/ or w/o co-incubation with kyn.  Cells treated with a DMSO vehicle serve as control.

first: Bethany

middle: B

last: Moore


title: Microarray analysis of human articular chondrocytes stimulated with Wnt3a in presence/absence of the CaMKII inhibitor KN93

city: Guildford

first: Giovanna

last: Nalesso

address: Daphne Jackson Road

country: United Kingdom

institute: University of Surrey

summary: The scope of the analysis was to discriminate between CaMKII-dependent and independent targets of Wnt3a stimulation in human articular chondrocytes. Chondrocytes were isolated from preserved areas of the articular cartilage removed from 4 patients affected by osteoarthritis. The samples were stimulated with KN92 (inactive analogue of the CaMKII inhibitor KN93), KN92+Wnt3a and KN93+Wnt3a.

overall_design: 4 human donors, each condition tested either in singulate or duplicate within the individual biological samples. Total of 20 samples. KN92 stimulation used as control.

first: Francesco

last: Dell'Accio

first: Kevin

last: Blighe

first: Sharmila

last: Rana


title: Influence of 3HP and PDO on cell metabolism at the transcriptional level in Halomonas bluephagenesis

city: Chongqing

first: Xiao-Ran

last: Jiang

address: No.30 Gaotanyan Main Street, Shapingba District

department: Department of Microbiology

institute: Army Medical University

summary: To investigate degradation genes in the 3HP degradation pathway, transcriptome sequencing was performed under culture conditions with and without 3HP as the carbon source. Overall, in the presence of 3HP as a sole carbon source, 384 genes were upregulated while 210 downregulated. Among them, we identified two 3HP degradation genes, GME_RS01260 encoding choline dehydrogenase (RefSeq. Accession: WP_009721523) and GME_RS01255 encoding CoA-acylating methylmalonate-semialdehyde dehydrogenase (RefSeq. Accession WP_009721522). Subsequently, transcriptome sequencing was performed under the culture condition with or without addition of PDO as a carbon source. Overall, 292 genes were upregulated while 285 downregulated with the addition of PDO. Among them, we identified an alcohol dehydrogenases AdhP (RefSeq. Accession: WP_039868491.1).

overall_design: We compared the differential gene expression in H. bluephagenesis under culture conditions with and without 3HP/PDO as the carbon source.

first: Guo-Qiang

last: Chen


title: Effect of iodine on Arabidopsis thaliana (Col-0) trancriptome

city: San Giuliano Terme

first: Pierdomenico

last: Perata

state: Pisa

address: Via Guidiccioni 8-10

department: Institute of Life Sciences

country: Italy

institute: Sant'Anna School of Advanced Studies

summary: Iodine treatments specifically regulated the expression of several genes in shoot and root tissues, mostly involved in the plant defence response, suggesting the protective role of iodine against both biotic and abiotic stresses.

overall_design: Each sample consisted of a pool of rosettes (leaves) or roots, sampled from three different plants. Analysis was performed on 3-week-old Arabidopsis plants hydroponically grown. To identify genes whose expression was specifically altered by iodine, Arabidopsis plants were treated by adding 10 µM of NaI, KI or KBr to the basal nutrient solution, compared to the untreated control plants (iodine concentration in the basal nutrient solution was 8 nM, as a contaminant). To identify genes whose expression was specifically altered by iodine, we searched the microarray dataset for genes that responded to KI and NaI, but not to KBr.  Plant material was collected 48 h after the beginning of the treatment. Plants were grown 22 °C day/18 °C night with a 12-h photoperiod, a quantum irradiance of 100 μmol photons m-2 sec-1 and a relative humidity close to 35%.

first: Claudia

last: Kiferle


title: ATF3 drives senescence by reconstructing accessible chromatin profiles

city: Kunming

first: Chao

last: Zhang

state: Yunnan

address: No.17 Longxin Road

department: Kunming Institute of Zoology

institute: Chinese Academy of Sciences

summary: We depicted the landscapes of both chromatin accessibility and gene expression to reveal gene regulatory networks in human umbilical vein endothelial cell (HUVEC) senescence and found that chromatin accessibilities are re-distributed during senescence.

overall_design:
ATAC-seq during HUVEC senescence
RNA-seq during HUVEC senescence

first: Wei

last: Tao


title: Effect of NSD3 on MDA-MB-231 breast cancer cells (RNA-seq)

city: Seoul

first: Gu

last: Kong

address: 17 Haengdang-dong, Seongdong-gu

department: Department of Pathology

institute: College of Medicine, Hanyang University

summary: RNA-sequencing analysis of control (shCon) and NSD3-knockdown (shNSD3) MDA-MB-231 cell lines. NSD3 (also known as WHSC1L1), a histone H3 lysine K36methyltransferase, is highly amplificated in several human cancers, including breast carcinomas. Results provide insight into the transcriptional regulation of NSD3 in breast cancer.

overall_design: MDA-MB-231 cells were stably infected with lentiviruses encoding either shControl (pGIPZ vectror) or NSD3 shRNA (pGIPZ-shNSD3) and selected using puromycin. Total RNA was isolated from shControl- and NSD3-knockdown MDA-MB-231 stable cells using Trizol reagent. For each of the 2 conditions, 3 biological replicates were included. In total, 6 RNA-sequencing samples were analyzed; 3 shControls and 3 NSD3 knockdown MDA-MB-231 cells.

first: Ga-Young

last: Jeong

first: Mi

middle: K

last: Park


first: Yingying

last: Lei

state: China

address: NO. 1 shizishan Street, Hongshan District

institute: Huazhong Agricultural University

summary: RAW-Rv3722c and RAW-Vector cells were collected for RNA extraction and subject to transcriptome sequencing. Expression levels of all genes in the two cell lines were determined by Next Generation Sequencing (NGS)

overall_design: Transcriptome information of RAW-Rv3722c and RAW-Vector cell lines, three replicates per sample

first: Gang

last: Cao

first: Xi


title: The effect of fructose on the inflammatory response of human monocytes

status: Public on Dec 31 2020

city: Swansea

first: Nick

last: Jones

state: Swansea

address: ILS1 Floor 2, Swansea University, Singleton Park

institute: Swansea University

summary: The purpose of this study was to determine whether any genes were differentially regulated in human monocytes exposed to glucose or fructose in the presence of lipopolysaccharide stimulation for 24 hours.

overall_design: Examination of the effects of fructose v glucose on the human monocyte response following LPS-stimulation

first: N

first: D

last: Avancini


title: Cepharanthine shows antiviral activities by modulating cellular stress responses triggered by a SARS-CoV2 related coronavirus

city: ANN ARBOR

first: Shasha

last: Li

address: 1109 Maiden Ln, ct apt 104

institute: University of Michigan

summary: Antiviral therapies targeting the pandemic coronavirus disease 2019 (COVID 19) are urgently required. We studied an already approved botanical drug cepharanthine (CEP) in a cell culture model of GX_P2V, a severe acute respiratory syndrome coronavirus 2 (SARS CoV 2) related virus. RNA sequencing results showed the virus perturbed the expression of multiple cell stress responses such as endoplasmic reticulum (stress and HSF1 mediated heat shock response related genes and signaling pathways, of which heat shock response related genes and pathways were at the core. CEP was potent to reverse most dysregulated genes and pathways in infected cells mainly by interfering with cellular stress responses including ER stress unfolded protein response and HSF 1 mediated heat shock response . Additionally, single cell transcriptomes from COVID 19 patients (GSE150728 and GSE148829) also confirmed that cellular stress responses and stress induced autophagy play an important role in the development of COVID 19. In summary, this study uncovered the potential mechanisms of the anti-viral activities of CEP, providing evidence for CEP as a promising therapeutic option and modulating cellular stress could be a promising therapy for SARS CoV 2 infection.

overall_design: Vero E6 cells (1.5×10e7 cells/flask) were plated in T75 culture flasks for 24h. Cells were treated with GX_P2V, CEP, or CEP and virus, and then cultured for another 72h. Cells were harvested and mRNA was isolated by using TRIzon (Invitrogen). The libraries were constructed by using the NEBNext Ultra™ RNA Library Prep Kit for Illumina (NEB) standard protocols. The libraries were sequenced on HiSeq 2500 sequencing system (Illumina)

first: Wenli

last: Liu

first: Huahao

last: Fan

first: Chenyang

last: Lu

first: Yigang

last: Tong


title: Microglia control the formation of brain small vessel calcfication via TREM2

city: Zurich

first: Annika

last: Keller

address: Frauenklinikstrasse 10

department: Department of Neurosurgery

country: Switzerland

institute: University Hospital Zürich

summary: The role of microglia in the formation of brain capillary calcification was investigated in a platelet-derived-growth factor B (PDGFB) hypomorph - Pdgfb ret/ret mouse model of human primary familial brain calcification.

overall_design: RNA-seq was performed on brain tissue developing vessel-associated calcifications (n=4 thalamus) and on brain tissue lacking calcifications (n=4 cortex) of Pdgfb ret/ret animals. Control animals (Pdgfb wt/ret) do not develop calcifications in any of the analyzed regions (n=4 thalamus and n=4 cortex).

first: Sina

last: Nassiri

first: Yvette

last: Zarb


title: Pericardial fluid exosome miRNA profiling

city: Philadelphia

first: Sezin

last: Aday

state: Pennsylvania

address: 210 South 33rd Street, Skirkanich Hall

institute: University of Pennsylvania

summary: Pericardial sac surrounding the heart contains pericardial fluid (PF), which is rich in exosomes. PF exosomes increase angiogenesis in hypoxic endothelial cells and in animal model of hindlimb ischemia by passing the proangiogenic miRNAs to recipient cells. However, under pathological conditions such as diabetes, exosome cargo composition changes and harmful miRNAs can be transferred to the recipient cells and induce more deleterious effects in target tissues. In order to check cargo composition of different PF exosomes, we used PF exosomes from non-diabetic aortic valve replacement (AVR),  mitral valve replacement (MVR), coronary artery bypass grafting (CABG) patients and CABG patients with diabetes.

overall_design: PF samples were collected from non-diabetic aortic valve replacement (AVR),  mitral valve replacement (MVR), coronary artery bypass grafting (CABG) patients and CABG patients with diabetes (n=4 for each group) and exosomes were isolated from these samples using a commercially available kit. miRNA profiles of exosomes were determined using Exiqon human V4 microRNA PCR panel I+II.


title: Methylation and gene expression data obtained from Dnmt3b+/- peripheral T-cell lymphomas.

city: Gainesville

first: Rene

last: Opavsky

state: FL

address: 2033 Mowry rd, CGRC r..265

department: Anatomy and cell biology

institute: University of FLORIDA

summary: Dnmt3b is a tumor suppressor in oncogene-driven lymphoid and myeloid malignancies in mice. However, it is poorly understood whether reduced Dnmt3b activities can initiate malignant hematopoiesis. We modulated Dnmt3b activity in vivo by generating Dnmt3b+/− mice expressing one wild-type allele. Here, we analyzed methylation and gene expression in Dnmt3b+/- peripheral T-cell lymphomas (PTCLs).

overall_design: We performed WGBS and RNA-seq analysis on Dnmt3b+/- peripheral T-cell lymphoma samples isolated from lymph nodes of terminally sick mice. WGBS experiments were performed in biological duplicates, RNA-seq experiments in triplicates. In addition we performed WGBS of Dnmt3a -/- PTCL.

first: Katarina

last: Lopusna

first: Pawel

last: Nowialis

first: Jana

last: Opavska

first: Ajay

last: Abraham

first: Alberto

last: Riva

first: Staci

middle: L

last: Haney


title: Foxc1 establishes enhancer accessibility for craniofacial cartilage differentiation

city: Los Angeles

first: Gage

last: Crump

address: 1425 San Pablo St.

department: Stem Cell

institute: USC

summary: The specification of cartilage requires Sox9, a transcription factor with broad roles for organogenesis outside the skeletal system. How Sox9 gains selective access to cartilage-specific cis-regulatory regions during skeletal development had remained unclear. By analyzing chromatin accessibility during the differentiation of neural crest cells into chondrocytes of the zebrafish head, we find that cartilage-associated chromatin accessibility is dynamically established. Cartilage-associated regions that become accessible after neural crest migration are co-enriched for Sox9 and Fox transcription factor binding motifs. In zebrafish lacking Foxc1 paralogs, we find a global decrease in chromatin accessibility in chondrocytes, consistent with a later loss of dorsal facial cartilages. Zebrafish transgenesis assays confirm that many of these Foxc1-dependent elements function as enhancers with region- and stage-specific activity in facial cartilages. We propose that Foxc1-dependent chromatin accessibility helps directs the versatile Sox9 protein to a chondrogenic program in the face.

overall_design: Wildtype embryos double positive for  fli1a:GFP; sox10:DsRed (36 hpf and 48 hpf), col2a1a:GFP; sox10:DsRed (72hpf )and foxc1a; foxc1b mutant embryos  and sibling controls double positive for pou3f3b>GFP; sox10:Dsred (36 hpf and 48 hpf) were selected under a fluorescent dissecting microscope, dechorionated, and dissociated. Cells were sorted based on GFP and DsRed expression on a MoFlo Astrios instrument. Approximately 5,000 cells were collected into PBS with 5% FBS and used to construct μATACseq libraries.

first: Pengfei

last: Xu

first: Haoze

middle: V

last: Yu

first: Kuo-Chang

last: Tseng

first: Mackenzie

last: Flath

first: Peter

last: Fabian

first: Neil

last: Segil

first: J

middle: G


title: An integrated analysis of lncRNAs and mRNAs expression profiles in the kidney of mice with lupus nephritis

status: Public on Dec 30 2020

city: Wuhan

first: Dong

last: Chen

address: 388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone

department: Center for Genome Analysis

institute: ABLife, Inc.

summary: Long non-coding RNAs (lncRNAs) are pervasively expressed and have been reported as potential biomarkers and therapeutic targets in various diseases, including systemic lupus erythematosus (SLE). However, there was limited information about lncRNAs expression in kidney tissue with lupus nephritis (LN), a serious complication of SLE. To explore the underlying molecular and cellular mechanisms of lncRNAs during pathogenesis of LN, RNA sequencing (RNA_seq) was performed to determine the lncRNAs and mRNAs expression of kidney tissues from LN (MRL/lpr) and control mouse. We identified 12, 979 novel lncRNAs in mouse. The expression profiles of both mRNA and lncRNA were significant different between LN and control mouse. In particular, both upregulated lncRNAs and mRNAs were more than downregulated ones in kidney tissue of LN mouse. However, GO analysis showed that more downregulated genes were enriched in immune and inflammatory response associated pathway. KEGG analysis showed that both downregulated and upregulated genes were enriched in pathway including SLE pathway, about half of these SLE-assocaited genes were inflammatory factors. Moreover, we found that 2, 181 DElncRNAs potential targeted and regulated expresison of 778 mRNA in kidney tissues of LN. The results showed that 11 DE-LncRNAs targeted and co-expressed with six immune and SLE-assocaited genes. qPCR confirmed that lncRNA Gm20513 would positively regualte the expression of SLE-associated gene H2-Aa. In conclusion, our study demonstrates that lncRNA will influence the progression of LN and will provide some cues for further study of lncRNAs in LN. LncRNA-mRNA regulation network may have important value in LN diagnosis and therapy.

first: Juan

last: Wang


title: Splicing factor SF3B1 promotes endometrial cancer progression via regulating KSR2 RNA maturation

city: ST LOUIS

first: RAMAKRISHNA

last: KOMMAGANI

state: Missouri

address: 425 S. Euclid Avenue, CB 8064

department: OB/GYN

institute: WASHINGTON UNIVERSITY

summary:
The goal of this study is to compare transcriptome profiling of SF3B1 depleted Ishikawa endometrial cancer cells by RNA-sequencing
Methods: SF3B1 depleted mRNA profiles of control siRNA treated and SF3B1 siRNA treated Ishikawa endometrial cancer cells were generated by deep sequencing, in triplicate using Illumina HiSeq 3000 sequencers with 2×150 paired-end reads. Basecalls and demultiplexing were performed with Illumina’s RTA version 1.9 and bcl2fastq2 software with a maximum of one mismatch in the indexing read. RNA-seq reads were then aligned to the Ensembl release 76 primary assembly with STAR version 2.0.4b. qRT–PCR validation was performed using TaqMan assays
Results: Using a 2.5-fold cutoff and Benjamini-Hochberg false discovery rate (FDR) of <0.01 threshold for inclusion, we identified 1,992 differentially expressed genes (DEGs) between Control and SF3B1 depleted Ishikawa cells
Conclusions: Our study represents the first detailed analysis of SF3B1 depleted Ishikawa endometrial cancer cells  transcriptomes, with biologic replicates, generated by RNA-seq technology.

overall_design: Transcriptome profiling of Control siRNA and SF3B1 siRNA depleted Ishikawa cells

first: POOJA

last: POPLI

first: SANGAPPA

last: CHADCHAN

first: ERIC

last: TYCKSEN


title: Global transcriptional response of Methylorubrum extorquens to formaldehyde stress includes both overlapping and unique gene sets in comparison to antibiotic translational inhibition and expands the role of EfgA

city: Austin

first: Jeffrey

middle: E.

last: Barrick

address: 2500 Speedway, Stop A4800

department: Molecular Biosciences

institute: The University of Texas at Austin

summary: The potency and indiscriminate nature of formaldehyde reactivity upon biological molecules make it a universal stressor. However, some organisms such as Methylorubrum extorquens possess means to rapidly and effectively mitigate formaldehyde-induced damage. EfgA is a recently identified formaldehyde sensor predicted to halt translation in response to elevated formaldehyde as a means to protect cells. Herein, we investigate growth, formaldehyde consumption, and changes in gene expression to better understand how M. extorquens responds to formaldehyde with and without the EfgA-formaldehyde-mediated translational response, and how this mechanism compares to other forms of translation inhibition. These distinct mechanisms of translation inhibition have notable differences: they each involve different specific players and in addition, formaldehyde also acts as a general, multi-target stressor and a potential carbon source. Here, we present findings demonstrating that in addition to its characterized impact on translation, functional EfgA also allows for a rapid and robust transcriptional response to formaldehyde and that removal of efgA leads to heightened proteotoxic and genotoxic stress in the presence of increased formaldehyde levels. As our previous work suggested that formaldehyde is proteotoxic in M. extorquens, we accurately predicted that strains lacking efgA would experience increased protein damage. We also found that many downstream consequences of translation inhibition were shared by EfgA-formaldehyde- and kanamycin-mediated translation inhibition. Our work to modularize the transcriptional response uncovered additional layers of regulatory control enacted by functional EfgA upon experiencing formaldehyde stress, and further demonstrate the importance this protein plays at both transcriptional and translational levels in this model methylotroph.

overall_design: Time courses of gene expression after treatment with two different translational inhibitors (kanamycin and formaldehyde).  The responses of wild type and an ΔefgA mutant of Methylorubrum extorquens were compared.

first: Jannell

last: Bazurto

first: Siavash

last: Riazi

first: Simon

last: D’Alton

first: Daniel

last: Deatherage

first: Christopher

last: Marx


title: Cytoplasmic cleavage of IMPA1 3’UTR is necessary for maintaining axon integrity.

city: Martigny

first: Raphaelle

last: Luisier

state: Valais

address: Rue Marconi 19, PO Box 592

institute: Idiap Research Institute

summary: The 3’ untranslated regions (3’UTRs) of messenger RNAs (mRNA) are non-coding  sequences involved in many aspects of mRNA metabolism, including intracellular  localisation and translation. Incorrect processing and delivery of mRNA causes severe  developmental defects and has been implicated in many neurological disorders. Here,  we use deep sequencing to show that in sympathetic neuron axons, the 3’UTRs of  many transcripts undergo cleavage, generating isoforms that express the coding  sequence with a short 3’UTR, and stable 3’UTR-derived fragments of unknown  function. Cleavage of the long 3’UTR of Inositol Monophosphatase 1 ( IMPA1 ),  mediated by a protein complex containing the endonuclease Ago2 and the RNA  binding protein HuD, generates a translatable isoform that is necessary for maintaining  the integrity of sympathetic neuron axons. Thus, our study provides a new mechanism  of mRNA metabolism that simultaneously regulates local protein synthesis and  generates a yet undescribed class of non-coding RNAs.

overall_design: Bulk 3' end sequencing data from cell body and distal axons of post-mitotic rat sympathetic neurons which distal axons have been exposed either to NGF or to NT3.

first: Catia

last: Andreassi

first: Raphaëlle

first: Hamish

last: Crerar

first: Sasja

last: Blokzijl-Franke

first: Nicholas

last: Luscombe

first: Giovanni

last: Cuda

first: Marco

last: Gaspari

first: Adolfo

last: Saiardi

first: Antonella

last: Riccio


title: Blood transcriptome indicates different disease etiology in pediatric ANCA-associated vasculitis subtypes.

city: Richmond

first: Maren

middle: Lydia

last: Smith

state: Virginia

address: 1217 E Marshall St

department: Pharmacology and Toxicology

institute: Virginia Commonwealth University

summary:
Purpose: The goal of this study was to compare gene expression profiles from whole blood RNA-Seq data from pediatric ANCA-associated vasculitis patients to identify mechanistic endotypes.
Methods: Whole blood mRNA profiles were generated from pediatric and adult vasculitis patients using Illumina GAIIx or Hi Seq 2500 RNA-Seq. Fastq files were alinged to human genome version GRC38.91 using STAR v2.6 and count data was generated with HTSEQ v0.61p1. Counts that passed quality and minimum expression filteres were anlayzed by hierarchical clustering based on Euclidean distance, and then for differential expression with DESeq2.
Results: Our workflow identified 14,156 transcripts consistently expressed in vasculitis patients. Distance hierarchcial clustering identified three groups within these pediatric samples, and two groups plus one outlier in the adult samples. The two largest pediatric clusters were used as groups for differential expression analysis with the DESeq2 package for R. DE analysis identified 3,809 differentially expressed genes between clusters. Between the two adult groups, 1,682 genes were differentially expressed. DE genes were anlayzed for enrichment using ReatomePA as the reference database. This analysis revealed that genes involved in T-cell mediated immunity are more highly expressed in pediatric patients that fell into one endotype and those involved in neutrophil and Toll-like receptor mediated inflammation are more highly expressed in pediatric patients that fell into the other endotype group. Similar results were also seen in adults.
Conclusions: This study utilizes RNA-Seq data to investigate the etiologies of ANCA-associated vasculitis. Using this approach we have identified T-cell mediated immunity and Toll-like receptor mediated inflammation as potentially differing inflammatory mechanisms in both pediatric and adult vasculitis patients that do not fall along normal diagnostic criteria.

overall_design: Whole blood mRNA expression profiles generated from pediatric vasculitis patients using RNA-Seq.

first: Erin

last: Gill

first: Kristen

last: Gibson

first: Kim

last: Morishita

first: Amy

middle: H

last: Lee

first: Reza

last: Falsafi

first: Jinko

last: Graham

first: Dirk

last: Foell

first: Susanne

last: Benseler

first: Raashid

last: Luqmani

first: Colin

last: Ross

first: David

last: Cabral

first: Kelly

last: Brown

first: Robert

last: Hancock


title: Microarray gene expression analysis of HNSCC- and BM- derived mesenchymal stromal cells

city: Firenze

first: Matteo

last: Ramazzotti

address: viale Morgagni 50

department: Experimental and Clinical Biomedical Sciences

institute: University of Florence

summary: Head Neck Squamous Cell Carcinoma (HNSCC)- or Bone Marrow (BM)- derived mesenchymal stromal cells (MSC) were analyzed either resting or following stimulation with IFN-g and TNF-a cytokines.

overall_design: HNSCC- and BM- MSC were expanded in vitro from the original tissue and then stored for transcriptome analysis either resting or following IFN-g and TNF-a stimulation.

first: Alessio

last: Mazzoni

first: Laura

last: Maggi

first: Raffaele

last: De Palma

first: Francesco

last: Liotta

first: Lorenzo

last: Cosmi

last: Annunziato


title: RNA sequencing of Mus musculus thymic lymphomas [ATM and RAG2]

city: Paris

first: Ludovic

last: Deriano

address: 25-28 Rue du Docteur Roux

department: Immunology

institute: Institut Pasteur

overall_design: We performed transcriptome sequencing of T-cell lymphomas originating from mice harbouring a C-terminus truncation in RAG2 in a p53-deficient context (Rag2 352/352 p53-/-) or lacking Atm activity (Atm-/-). We sequenced five different mice from each genotype and we also sequenced thymus from three wild type mice (re-used from GSE85894).

first: Valentine

last: Murigneux

first: Joy

last: Bianchi

first: Marie

last: Bedora-Faure

first: Chloé

last: Lescale


title: RNA-seq during occlusion myopia induction and recovery

city: Melbourne

first: Loretta

last: Giummarra

state: Victoria

address: c/o Psychological Science

department: Psychology & Counselling

country: Australia

institute: La Trobe University

summary: We sequenced mRNA from 16 retina/RPE/choroid samples taken from the right eyes of male chicks across control, form-deprivation occlusion, and recovery from form deprivation conditions.

overall_design: Examination of mRNA levels in individual retina/RPE/choroid samples across 4 groups (control, 7 days form deprivation (FDM), 6 hours recovery and 24 hours recovery from form deprivation (FDMR)).

first: Nina

last: Riddell


title: PTEN DEFICIENCY LEADS TO PROTEASOME ADDICTION, A NOVEL VULNERABILITY IN GLIOBLASTOMA

status: Public on Dec 29 2020

city: La Jolla

first: Tao

last: Long

state: CA

address: 9500 Gilman Dr

department: Medicine

institute: University of California at San Diego

summary: We found that GSCs were highly sensitive to proteasome inhibition due to an underlying dependency on an increased protein synthesis rate, and loss of autophagy, associated with PTEN loss and activation of the PI3K/mTOR pathway. In contrast, combinatory inhibition of autophagy and the proteasome, resulted in enhanced cytotoxicity specifically in GSCs that did express PTEN. Finally, proteasome inhibition specifically increased cell death markers in 3D glioblastoma organoids, suppressed tumor growth, and increased survival of mice orthotopically engrafted with GSCs. As perturbations of the PI3K/mTOR pathway occur in nearly 50% of GBMs, these findings suggest that a significant fraction of these tumors could be vulnerable to proteasome inhibition.

overall_design: High throughput drug screening was performed on 5 GSCs followed by a dose response assay of the 5 identified original “hits” in 15 samples. A PI3K/mTOR dependency to a proteasome inhibitor (carfilzomib), was confirmed by genetic and pharmacologic experiments. Proteasome inhibition response signatures were derived from proteomic and bioinformatic analysis. Molecular mechanism of action was determined using 3-dimensional (3D) GBM organoid models and preclinical orthotopic GBM models

first: Jorge

last: Benitez

first: Darren

last: Finlay

first: Anthony

last: Castanza

first: Alison

middle: D

last: Parisian

first: Jianhui

last: Ma

first: Ciro

last: Longobardi

first: Alex

last: Campos

first: Raghavendra

last: Vadla

first: Alejandro

last: Izurieta

first: Gianluca

last: Scerra

first: Tomoyuki

last: Koga

first: Lukas

last: Chavez

first: Jill

middle: P

last: Mesirov

first: Kristiina

last: Vuori

first: Frank

last: Furnari


title: AP-2γ is Required for Maintenance of Multipotent Mammary Stem Cells

city: Iowa City

first: Ronald

last: Weigel

state: IA

address: 200 Hawkins Drive

department: Surgery

institute: University of Iowa

summary: Mammary gland ductal morphogenesis depends on the differentiation of mammary stem cells (MaSCs) into basal and luminal lineages. The AP-2γ transcription factor, encoded by Tfap2c, has a central role in mammary gland development but its effect in mammary lineages and specifically MaSCs is largely unknown. Herein, we utilized an inducible, conditional knockout of Tfap2c to elucidate the role of AP-2γ in maintenance and differentiation of MaSCs. Loss of AP-2γ in the basal epithelium profoundly altered the transcriptomes and decreased the number of cells within several clusters of mammary epithelial cells, including adult MaSCs and luminal progenitors. AP-2γ regulated the expression of genes known to be required for mammary development including Cebpb, Nfkbia, and Rspo1. As a result, AP-2γ-deficient mice exhibited repressed mammary gland ductal outgrowth and inhibition of regenerative capacity. The findings demonstrate that AP-2γ can regulate development of mammary gland structures potentially regulating maintenance and differentiation of multipotent MaSCs.

overall_design: Tfap2c fl/fl / Krt5-Cre mice were treated with either intraperitoneal corn oil or 4OHT for one week at four weeks postnatally determine effect of conditional knockout of Tfap2c on mammary stem cells. The fourth mammary glands of the mice were harvested at 9 weeks age. Two mice of each condition were submitted for sequencing using the manufacturer recommended Chromium (10x Genomics) and Illumina technologies. The amplified cDNA was constructed into 3’ expression libraries and pooled together in separate lanes of a 150 base-pair, paired-end chemistry flow cell. The Illumina HiSeq 4000 was used with Agilent Bioanalyzer, and average library sizes ranged from 329 bp to 432 bp in length. The adapter sequence of the library was 124 bases in length. Basecalls were converted into FASTQ files by the University of Iowa Genomics Division using the Illumina bcl2fastq software. These samples captured an estimated 3,546 to 5,545 number of cells with mean reads per cell ranging from 63,842 to 94,776. Transcripts were mapped using Cell Ranger Version 3.0.1 and mm10 reference genome (GRCm38.91).

first: Vivian

last: Gu

first: Edward

last: Cho

first: Dakota

middle: T

last: Thompson

first: Victoria

middle: C

last: Cassady

first: Nicholas

last: Borcherding

first: Kelsey

last: Koch

first: Vincent

last: Wu

first: Allison

last: Lorenzen

first: Dana

last: van der Heide

first: Jeffrey

middle: R

last: White

first: Mikhail

last: Kulak

first: Trevor

last: Williams

first: Weizhou

last: Zhang


city: SEATTLE

first: THOMAS

middle: A

last: REH

state: WA

address: 1959 NE PACIFIC STREET

department: BIOLOGICAL STRUCTURE

institute: UNIVERSITY OF WASHINGTON

summary: The innate immune system plays key roles in tissue regeneration. For example, microglia promote neurogenesis in Müller glia in birds and fish after injury. Although mammalian retina does not normally regenerate, neurogenesis can be induced in mouse Müller glia by Ascl1, a proneural transcription factor. We show that in mice, microglia inhibit the Ascl1-mediated retinal regeneration, suggesting the innate immune system limits the regenerative response to injury.

overall_design: Five samples were created for the publication Microglia suppress Ascl1-induced retinal regeneration in mice. One sample contains Cd45+/Cd11b+ cells from ANT treated mice seven days after injury. These contain immune cells in the mouse retina. The remaining four samples are ANT reprogrammed FAC-sorted Muller Glia at 2 days and 7 days post ANT treatment with and without the CSF1R inhibitor PLX5622. For more details see the associated manuscript.

first: Levi

last: Todd

first: Connor

last: Finkbeiner

first: Claire

last: Wong

first: Marcus

last: Hooper

first: Thomas

last: Reh


title: Transcriptomic analysis of hepatic genes in DEN-treated wildtype and Sesn3 knockout mice

city: Indianapolis

first: Xiaocheng

middle: Charlie

last: Dong

state: IN

address: 635 Barnhill Drive, MS1021D

department: Biochemistry and Molecular Biology

institute: Indiana University School of Medicine

summary: RNA-seq was performed on mRNA samples purified from the liver of wildtype (WT) and Sesn3 knockout (KO) mice.

overall_design: Two genotypes (WT and KO) were used for this study. Each genotype had three liver mRNA samples.

first: X


title: Impact of the menstrual cycle and ethinyl estradiol/etonogestrel contraceptive vaginal ring on granulysin and other mucosal immune mediators

city: Seattle

first: Sean

last: Hughes

address: 850 Republican St

institute: University of Washington

summary:
We conducted a prospective, open-label study to determine the effect of the NuvaRing on gene expression in the endocervix and immune-related protein expression in cervicovaginal secretions. Women provided endocervical cytobrush samples during the luteal and follicular phases of the menstrual cycle (as determined by progesterone levels) as well as during NuvaRing use. Gene expression was measured using Illumina Human HT12 v4 BeadChip microarrays. We compared the NuvaRing visit to each phase of the menstrual cycle separately, as well as follicular and luteal phase samples to each other, adjusting for technical batch, presence of blood in vaginal discharge, and BV status by Nugent score, and blocking on participant.

We found that gene expression in the endocervical canal changed across the menstrual cycle and in response to NuvaRing use. In particular, we observed a continuum of expression of immune-related genes and gene sets in the endocervical canal: highest during NuvaRing use, intermediate in the follicular phase, and lowest in the luteal phase.

overall_design: We compared endocervical gene expression at three time points: the follicular phase, the luteal phase, and during use of the ethinyl estradiol and etonogestrel contraceptive vaginal ring (NuvaRing, Merck). Repeated samples were obtained from most participants. Menstrual cycle phase was determined based on serum progesterone levels. In a few cases, samples that were expected to follicular or luteal based on the date of the participant’s last menstrual period had discordant progesterone levels. In those cases, menstrual phase was switched and assigned based on progesterone level. Samples were run in two batches. Women were also tested for HSV-2-seropositivity and bacterial vaginosis by Nugent score.

first: Florian

last: Hladik

middle: M


title: Small RNAs during seed development in a small-seeded chickpea

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

institute: Jawaharlal Nehru University

summary: In this study, we sequenced small RNAs at seven successive stages of seed development and leaf tissue in a small-seeded chickpea cultivar (Himchana 1) using Illumina platform. More than 500 million reads were generated in all the samples combined together with an average of 34 million reads in each sample. Data obtained in FASTQ files were pre-processed and unique reads representing small RNAs were identified at different stages of seed development.

overall_design: Total RNA was isolated from the seed stages and leaf tissues followed by preparation of small RNA libraries and sequencing using Illumina platform. The reads were pre-processed using modified perl scripts. After quality control, the identical reads were collapsed into a unique read and read count for each sequence was recorded. All the filtered unique reads from each sample were mapped on the chickpea genome to find their location.

first: Rohini

last: Garg

first: Niraj

last: Khemka

first: Mohan

middle: S

last: Rajkumar


title: A non-radioactive, improved PAR-CLIP and small RNA cDNA library preparation protocol

city: Bethesda

first: Markus

last: Hafner

state: MD

address: 50 South Drive

department: NIAMS

institute: NIH

summary: Streamlined protocol for fluorescence-based PAR-CLIP (fPAR-CLIP) that eliminates the need to use radioactivity. Protocol is based on direct ligation of a fluorescently labeled adapter to the 3’end of crosslinked RNA on immobilized ribonucleoproteins, followed by isolation of the RNA and efficient conversion into cDNA without the previously needed size fractionation on denaturing polyacrylamide gels. These improvements cut the experimentation time from 4-5 to 2 days and increases sensitivity by 10-100-fold.

overall_design: Elimination of radioactivity and optimization of PAR-CLIP library preparation protocol

first: Dimitrios

last: Anastasakis

first: Alexis

last: Jacob

first: Parthena

last: Konstantinidou

first: Kazuyuki

last: Meguro

first: Duncan

last: Claypool

first: Pavol

last: Cekan

first: Astrid

last: Haase


title: Spliceostatin A limits U1 snRNP availability and leads to premature poly(A)-tailing

city: Toyoake

first: Rei

last: Yoshimoto

state: Aichi

address: 1-98 Dengakugakubo, Kutsukake

department: Institute for Comprehensive Medical Science

country: Japan

institute: Fujita Health University

summary: RNA-Seq analysis of SSA treated cells

overall_design: Cytoplasmic Poly(A)+ RNA was prepared from the exact same sample of rRNA-depleted RNA (GEO: GSE72156)


title: Comprehensive circRNA expression profile and construction of circRNAs-related ceRNA network in a mouse model of autism

city: Harbin

first: Yanan

last: Jiang

address: 157 Baojian Road

department: Pharmacology

institute: Harbin Medical University

summary:
Purpose: We aimed to detected the circRNA expression profile and constructed a circRNA-based competing endogenous RNA (ceRNA) network in autism.
Methods:Valproate acid was used to establish an in vivo model of autism in mice. circRNAs  in autism group was identified by RNA sequencing. The expression of circRNAs were detected by real-time PCR. Module analysis was conducted followed by GO and KEGG pathway enrichment analysis.
Results: A total of 1059 differentially expressed circRNAs (477 upregulated and 582 downregulated) in autism group. The expression of novel_circ_015779 and novel_circ_035247 were detected by real-time PCR. A ceRNA network based on altered circRNAs was established, with 9715 nodes and 150408 edges. The top three modules were all correlated with autism-related pathways involving ‘TGF-beta signaling pathway’, ‘Notch signaling pathway’, ‘MAPK signaling pathway’, ‘long term depression’, ‘thyroid hormone signaling pathway’, etc.
Conclusions: The present study reveals a novel circRNA involved mechanisms in the pathogenesis of autism.

overall_design: Brain circRNA profiles in a mouse model of autism.

first: Ji

last: Wang


title: An in-vivo screen of noncoding elements reveals that Daedalus is a gatekeeper of a novel Ikaros-dependent checkpoint during haematopoiesis [GRO-seq]

city: New Haven

first: Christian

last: Harman

state: Connecticut

address: 300 Cedar Street, The Anlyan Center

department: Genetics/Immunobiology

institute: Yale University

summary: The development of all lymphoid lineages relies on a tightly-controlled series of gene expression patterns as development proceeds through a series of progenitors1-8. These gene expression patterns are understood to be controlled by lineage-specifying transcription factors, however these factors often are found to have broad expression patterns and activities across lineages. Given their role in regulating cell-type specific gene expression, noncoding loci are thought be important in the lineage-specific regulation of this complex process6,9-16. To identify transcripts that might mark such loci, we performed transcriptomic analysis in terminally differentiated murine CD4 effector T lymphocytes. Our analysis identified a variety of loci containing dynamically expressed noncoding RNAs and we tested their role in the lymphoid lineage using an in-vivo CRISPR knockout-mouse screen. This approach revealed that a non-coding locus proximal to the haematopoietic transcription factor Ikaros17,18, named Daedalus, exerted control over the earliest fate decisions during lymphoid lineage commitment. Deletion of Daedalus led to a cell-autonomous reduction in bone marrow and thymic lymphoid progenitor populations, phenocopying Ikaros deficient strains. Strikingly, loss of Daedalus resulted in a loss of Ikaros protein expression without impacting total Ikaros transcript levels. Finally, we identify a novel Ikaros regulated erythroid-lymphoid checkpoint that is governed by Daedalus in a lymphoid-lineage specific manner. Daedalus appears to act as a gatekeeper of Ikaros’s broad lineage specifying functions, selectively stabilizing Ikaros activity in the lymphoid lineage and permitting diversion to the erythroid fate in its absence. To our knowledge, these findings represent the first illustration of how a transcription factor with broad lineage expression must work in concert with non-coding elements to orchestrate haematopoietic lineage specification and commitment.

overall_design: 2 GRO-Seq (2 replicates)

first: Hiromi

last: Tagoh

first: Louisa

last: Hill

first: Meinrad

last: Busslinger


title: Relaxed initiation pausing of ribosomes drives oncogenic translation

city: Hangzhou

first: Yuanhui

last: Mao

state: Zhejiang

address: 1369 West Wenyi Road

institute: Zhejiang University

summary: Using quantitative profiling of initiating ribosomes, we found that ribosomal pausing at the start codon serves as a “brake” to restrain the translational output. In response to oncogenic RAS signaling, the initiation pausing relaxes and contributes to the increased translational flux. Intriguingly, mRNA m6A modification in the vicinity of start codons influences the behavior of initiating ribosomes. Under oncogenic RAS signaling, the reduced mRNA methylation leads to relaxed initiation pausing, thereby promoting malignant transformation and tumor growth. Restored initiation pausing by inhibiting m6A demethylases suppresses RAS-mediated oncogenic translation and subsequent tumorigenesis. Our findings unveil a new paradigm of translational control that is co-opted by RAS mutant cancer cells to drive malignant phenotypes.

overall_design: We took advantage of a human TtH cell line stably expressing a 4-hydroxytamoxifen (4-OHT)-inducible ER:HRASG12V fusion protein. QTI-seq, Ribo-seq, RNA-seq, m6A-seq and corresponding experiments were performed on the ER:HRASG12V cells with or without 4-OHT treatment and METTL3 or FTO knockdown.

first: Leiming

last: Dong

first: Shu-Bing

last: Qian


title: Comparative analysis of gene expression between PBMCs  from TB patients and healthy individuals.

city: Bhopal

first: Himanshu

last: Kumar

state: MADHYA PRADESH

address: Indore bypass road

department: Biological Sciences

institute: IISER Bhopal

summary: Total RNA from PBMCs isolated from TB patients and healthy individuals was subjected to RNASeq analysis. The samples among two groups were compared to analyze differentially expressed genes.

overall_design: Transcriptome from 5 TB patients and 4 healthy individuals were compared by RNASeq.

first: Ranjeet

last: Mahla

first: Akhilesh

last: kumar

first: Helena

middle: J

last: Tutill

first: Charlotte

last: Williams

first: Rachel

first: Evi

last: Tasaliki

first: Mahdad

last: Noursadeghi

first: Judith

last: Breuer


title: Plant roots employ cell-layer specific programs to respond to pathogenic and beneficial microbes

city: Wuerzburg

first: William

middle: Andrés

last: López Arboleda

state: Bavaria

address: Klara-Oppenheimer-Weg 32

department: Biology

country: Germany

institute: University of Wuerzburg

summary: As plant roots are built of concentric cell-layers, it is anticipated that these respond to microbial infection by employing specific, genetically defined programs. Due to cell-type specific expression of tagged ribosomes, ribosome-bound mRNA was isolated to obtain cell-layer translatomes. After inoculation with the vascular pathogen Verticillium longisporum, the pathogenic oomycete Phytophthora parasitica and the mutualistic endophyte Serendipita indica, we determined root responses on a cell-layer resolution. These data reflect the fundamentally different colonization strategies of the microbes. Mining the data-set, we identified a Verticillium specific suppression of the endodermal barrier restricting fungal progression, localized biosynthesis of antimicrobial compounds, and observed a pathogen-specific arrest of root meristems correlated with ethylene biosynthesis. These examples highlight the power of this approach in generating testable hypotheses to gain insights into Root-microbe-interactions.

overall_design: Root cell-layer response to infection by three fungi with different lifestyles

first: Wolfgang

last: Dröge-Laser

last: Fröschel


title: Microarray expression data of 18 pairs of small cell lung cancer (sclc) and tumor and adjacent lung tissues

city: Dallas

first: Ling

last: Cai

state: TX

address: 5323 Harry Hines Boulevard

institute: UT Southwestern Medical Center at Dallas

summary: Samples were collected from surgery resection

overall_design: 18 pairs of small cell lung cancer tumor and adjacent lung tissues were obtained from surgical resection. Gene expression profiling was performed by microarray.

first: Hongyu

last: Liu