title: S100A8/A9 induced by interaction with macrophages in esophageal squamous cell carcinoma promotes the migration and invasion of cancer cells via Akt and p38 MAPK pathways

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary:
Tumor-associated macrophages enhance the malignant phenotypes of esophageal squamous cell carcinoma (ESCC) cells. We have previously identified several factors associated with ESCC progression using an indirect co-culture assay between ESCC cells and macrophages. Here, we newly established a direct co-culture assay between ESCC cells and macrophages which is closer to the actual cancer microenvironment than an indirect co-culture assay. To investigate the gene expression changes by co-culture with macrophages, we performed cDNA microarray analysis between mono-cultured and co-cultured ESCC cells with macrophages. We found that the expression of S100 calcium binding protein A8 and A9 (S100A8 and S100A9) was enhanced in co-cultured ESCC cells with macrophages.
S100A8 and S100A9 commonly exist stable and function as a heterodimer (S100A8/A9). S100A8/A9 is widely known as an inflammation marker. It also contributes to the enhancement of malignant phenotypes in several cancers. S100A8/A9 enhances the migration and invasion of ESCC cells by activating Akt and p38 MAPK signaling pathways. The higher expression levels of S100A8/A9 were associated with poor prognosis in ESCC patients. These results suggest that S100A8/A9 contributes to the progression of ESCC.

overall_design: CD14 positive peripheral blood monocytes (PBMos) were selectively collected from healthy volunteers. Recombinant human macrophage colony stimulating factor (rhM-CSF) was added to induce M2 macrophages. We seeded ESCC cell line (TE-11) and direct co-cultured with the M2 macrophages. As a control, the same amount of TE-11 without macrophage was seeded and mono-cultured. We performed cDNA microarray analysis between mono-cultured TE-11 cells and co-cultured TE-11 cells with macrophages.

first: K

last: Tanigawa

first: Y

middle: I

last: Koma


title: Interspecies commensal interactions have nonlinear impacts on host immunity

status: Public on Dec 01 2021

city: New Haven

first: Tyler

last: Rice

state: CT

address: 10 Amistad St Rm 102

department: Immunobiology

country: USA

institute: Yale University

type: Expression profiling by high throughput sequencing

summary: The impacts of individual commensal microbes on immunity and disease can differ dramatically depending on the surrounding microbial context, yet the specific bacterial combinations that dictate divergent immunological outcomes in humans remain largely undefined. We isolated a novel Allobaculum strain from an inflammatory bowel disease (IBD) patient that elicited antigen-specific mucosal and systemic antibody responses at homeostasis and exacerbated colitis in gnotobiotic mice. Using human microbiota-associated mouse models, we uncovered an inverse correlation between Allobaculum and the taxonomically-divergent immunostimulatory species Akkermansia muciniphila, which was also reflected in human cohorts. Co-colonization with Allobaculum and A. muciniphila reprogrammed the immune responses evoked by each microbe on its own, ameliorated Allobaculum-induced colitis, and blunted A. muciniphila-induced T and B cell responses. These studies thus identify a reciprocal ‘epistatic’ interaction between unique immunostimulatory human gut bacteria and establish a generalizable framework to dissect the role of microbial context in strain-specific microbial effects on human disease.

overall_design: Female 6-week-old germ-free C57BL/6 mice were colonized with mock community bacteria (MC), MC+Allobaculum sp. 128, MC+A. muciniphila, or MC+Allobaculum sp. 128+A. muciniphila (n=3 mice/group) for 4 weeks, microbiotas were confirmed by 16S rRNA sequencing, then euthanized for harvest of mesenteric lymph nodes (MLN) and Peyer's patches (PP). Cells were gently isolated by digestion, stirring, and filtration, then normalized and pooled for 10X Genomics Chromium 5P V2 library preparation. Cellular transcriptomic responses were analyzed by single cell RNA sequencing.

middle: A

first: Agata

last: Bielecka

first: Mytien

middle: T

last: Nguyen

first: Connor

middle: E

last: Rosen

first: Deguang

last: Song

first: Nicole

middle: D

last: Sonnert

first: Yi

last: Yang

first: Yiyun

last: Cao

first: Jason

middle: R

last: Catanzaro

first: Anjelica

middle: L

last: Martin

first: Saleh

last: Rashed

first: Shana

last: Leopold

first: Liming

last: Hao

first: Varnica

last: Khetrapal

first: Xuezhu

last: Yu

first: David

last: van Dijk

first: Aaron

middle: M

last: Ring

first: Richard

last: Flavell

first: Marcel

last: de Zoete

first: Noah

middle: W

last: Palm


title: RNA-seq for fetus mice liver tissue of C57BL/6 mice and C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic mice.

city: Beijing

first: Guan

last: Guiwen

state: Beijing

address: 38 Xueyuan Road, Haidian District

country: China

institute: Peking University

summary: To investigate whether HBsAg intrauterine exposure affected the offspring's immune response against HBV and the relevant mechanism, the difference of fetal liver tissue transcriptome between the C57BL/6 mice and C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic mice was analyzed.

overall_design: The difference of fetal liver tissue transcriptome between the C57BL/6 mice and C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic mice was analyzed.

first: Jing

last: Ning

first: Guiwen

last: Guan

first: Fengmin

last: Lu

first: Xiangmei

last: Chen


title: The role of epithelial Progesterone Receptor Isoforms in embryo implantation

status: Public on Dec 02 2021

city: RTP

first: Franco

last: Demayo

state: NC

address: 111 TW Alexander Drive

institute: NIEHS

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies unique proteotypes associated with patient outcomes

status: Public on Nov 23 2021

city: Toronto

first: Ming-Sound

last: Tsao

state: Ontario

address: 101 College St

department: Princess Margaret Cancer Research

country: Canada

institute: University Health Network


title: The role of epithelial Progesterone Receptor Isoforms in embryo implantation  [RNAseq-Foxo1dd_LE]

summary: RNA-seq analysis of uterine luminal epithelium at D4.5 indicates that epithelial PGRA and PGRB shares conseved pathways. Constitutive epithelial PGRA and PGRB disrupts the embryo implantation both through the suppressed FOXO1 signaling by excluding FOXO1 from the nuclear at the uterine epithelium. There are three layers of regulation. Firstly, PGRA and PGRB diminishes Lif transcription in uterine glands by blocking ESR1 binding at the Lif promoter at D3.5 which is critical for the FOXO1 nuclear expression at D4.5 through LIF/pSTAT3/FOXO1. Secondly, PGRA and PGRB directly suppres Foxo1 transcription at the uterine epithelium probably through direct binding at Foxo1 promoter. Thirdly, PGRA and PGRB promotes the Sgk1 transcription, the kinases that phosphorylate FOXO1 to translocate it into cytoplasma for degradation.

overall_design: The uterine luminal epithelium were collected from Foxo1f/f and Pgrcre/+ Foxo1f/f mice at pregnancy day 4 by laser capture for RNA-seq analysis

first: Rong

last: Li

first: Tianyuan

last: Wang

first: Lecong

last: Zhou

first: San-Pin

last: Wu

first: Francesco

middle: J

last: DeMayo


title: Smart-seq for HBs-specific CD8+ T cells sorted from C57BL/6 mice and C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic mice liver

summary: Previous studies have paid more attention to hepatitis B e antigen (HBeAg) intrauterine exposure, however the effect of solely hepatitis B surface antigen (HBsAg) exposure on the immune response of offspring against hepatitis B virus (HBV) is still unclear. In this study, we investigated whether HBsAg intrauterine exposure affected the offspring's immune response against HBV and the relevant mechanism, which is important for the prevention of HBV mother-to-infant transmission.

overall_design: HBs-specific CD8+ T cells were sorted from C57BL/6 mice and C57BL/6-Tg (HBV Alb-1) Bri44 HBV transgenic mice liver, and the Smart-seq was used to compare the difference between two groups.


title: The role of epithelial Progesterone Receptor Isoforms in embryo implantation  [ChIPseq-PGR-H3K27AC]

overall_design: PgrcrePgrALsL/+ and PgrcrePgrBLsL/+ mice were ovariectomized for 2 weeks. And the whole uterus were collected for PGR ChIP-Seq after 1h progesterone treatment. Wildtype mouse were mated with stud males. The day the vaginal plug detected was defined as pregnant day 0.5. The uterus were collected at pregnant day 3.5 for H3K27AC ChIP-Seq.


title: Changes in histone modifications measured by CUT&RUN after recruitment of chromatin regulators to dual-gene synthetic reporters

status: Public on Nov 29 2021

city: Stanford

first: Sarah

last: Lensch

state: CA

address: 443 Via Ortega

department: Bioengineering

institute: Stanford University

summary: In mammalian cells, genes that are in close proximity are coupled transcriptionally: silencing or activating one gene can affect its neighbors. Changes in histone modifications can be involved in driving these transcriptional changes as certain modifications have been shown to spread through reader-writer feedback mechanisms. We investigate this process by recruiting repressive chromatin regulators (KRAB and HDAC4) to dual-gene synthetic reporters with different spacers between the two genes (no spacer- NS and 5kb lambda DNA - 5kb). We then look at changes in both active and repressive chromatin marks by CUT&RUN. We find that silencing by KRAB results in loss of the activating histone 3 lysine acetylation (H3Kac) and histone 3 lysine 4 trimethylation (H3K4me3) marks, as well as a strong increase in the repressive modification histone 3 lysine 9 trimethylation (H3K9me3) across the NS and 5kb reporters both in CHO-K1 and K562 cells. In K562 cells, we also see a larger enrichment of H3K9me3 spanning approximately 50-60 kb beyond the reporter.  Silencing by histone deacetylase HDAC4 of the upstream gene can also lead to downstream gene silencing. By CUT&RUN we observe a decrease in acetylation levels,  no change in H3K9me3, and a surprising increase in histone 3 lysine 27 trimethylation (H3K27me3) throughout the NS and 5kb reporters. H3K27me3 is associated with polycomb repressive complex 2 (PRC2) and has not been previously reported in direct association with HDAC4; however, our results reveal coordinated transcriptional silencing where removal of acetylation by HDAC4 indirectly led to H3K27me3 deposition, likely by PRC2. These data give insight into how chromatin modifications are associated with changes in expression in a synthetic reporter system.

sample_organism:
Homo sapiens
Cricetulus griseus

platform_organism:
Homo sapiens
Cricetulus griseus

overall_design: We use CUT&RUN (Cleavage Under Targets and Release Using Nuclease), an epigenomic profiling strategy to assess various histone modifications after recruitment of chromatin regulators (KRAB and HDAC4) by the addition of doxycycline (dox), which causes transcriptional repression of neighboring genes. We look at both activating (H3Kac, H3K4me3) and repressive marks (H3K9me3, H3K27me3) at our dual-fluorescent gene reporters (no spacer- NS and 5kb lambda DNA - 5kb) in K562 and CHO-K1 cells.

first: Connor

middle: H

last: Ludwig

first: Joydeb

last: Sinha

first: Lacra

last: Bintu


title: Decoupling of H2Aub and H3K27me3 in early mammalian development

status: Public on Nov 17 2021

city: Hangzhou

first: Li

last: Shen

state: Zhejiang Province

address: 866 Yuhangtang Road

institute: Life Sciences Institute, Zhejiang University

summary: Polycomb group (PcG) proteins play critical roles during development. H2Aub and H3K27me3 are deposited by Polycomb-repressive Complex 1 and 2 (PRC1/2) respectively, and largely overlap in the genome due to mutual recruitment of the two complexes. However, whether PRC1/H2Aub and PRC2/H3K27me3 also function independently remains elusive. Here we uncovered a large-scale decoupling of H2Aub and H3K27me3 in preimplantation mouse embryos, at both canonical PcG targets and broad distal domains. H2Aub represses future bivalent genes without H3K27me3 but does not contribute to maintenance of H3K27me3-dependent non-canonical imprinting. Our study thus revealed their distinct and independent functions in early mammalian development.

overall_design: Mouse gametes and embryos were selected for H2AK119ub1 ChIP-seq profiling.

first: Yezhang

last: Zhu

first: Jiali

last: Yu


title: Desmosterol suppresses inflammasome activation and protects against atherosclerosis II

first: Xinbo

last: Zhang

state: Connecticut

address: Rm320, 10 Amistad St

department: Comparative Medicine

summary: Cholesterol biosynthetic intermediates such as lanosterol and desmosterol are emergent immune regulators of macrophages in response to inflammatory stimuli or lipid overloading, respectively. However, the participation of these sterols in regulating macrophage functions in the physiological context of atherosclerosis, an inflammatory disease driven by the accumulation of cholesterol-laden macrophages in the artery wall, has remained elusive. Here we report that desmosterol, the most abundant cholesterol biosynthetic intermediate in human coronary artery lesions, plays an essential role during atherogenesis, serving as a key molecule integrating cholesterol homeostasis and immune responses in macrophages. Depletion of desmosterol in myeloid cells by overexpression of 3β-hydroxysterol Δ24-reductase (DHCR24), the enzyme that catalyzes conversion of desmosterol to cholesterol, promotes the progression of atherosclerosis. Single cell transcriptomics in isolated CD45+CD11b+ cells from atherosclerotic plaques demonstrate that depletion of desmosterol increases interferon (IFN) responses and attenuates the expression of anti-inflammatory macrophage markers. Lipidomic and transcriptomic analysis of in vivo macrophage foam cells demonstrate that desmosterol is a major endogenous liver X receptor (LXR) ligand involved in LXR/RXR activation and thus, macrophage foam cell formation. Decreased desmosterol accumulation in mitochondria promotes macrophage mito-ROS production and NLRP3-dependent inflammasome activation. Deficiency of NLRP3 or ASC rescues the increased inflammasome activity and atherogenesis observed in desmosterol-depleted macrophages. Altogether, these findings underscore the critical function of desmosterol in the atherosclerotic plaque to dampen inflammation, by integrating with macrophage cholesterol metabolism and inflammatory activation, and protecting from disease progression.

overall_design: RNA-seq of peritoneal macrophages (PMs) from WT or Dhcr24TG mice injected with PCSK9 adeno-associated virus (AAV8-Pcsk9) and fed on a chow diet (CD) or western diet (WD) for 16 weeks

first: Carlos

last: Fernández-Hernando


title: Transcriptional contribution of nuclear lamina protein emerin and BAF in Drosophila ovaries

city: Iowa City

first: Samuel

middle: Cole

last: Kitzman

state: IA

address: 3135E MERF

department: Biochemistry

institute: University of Iowa

summary: Nuclear lamina (NL) contributes to tissue homeostasis. In Drosophila, compromised NL blocks differentiation and causes loss of germline stem cells (GSCs) due to activation of the Chk2 checkpoint kinase. Checkpoint activation occurs upon loss of the NL protein Drosophila emerin or its partner Barrier-to-autointegration factor (BAF). As NL has long been thought to interact with specific genomic loci and regulate transcription, we examined transcriptional changes in emerin-/- and baf KD ovaries. We found thousands of genes are mis-regulated upon loss of emerin or BAF in GSCs. Remarkably, more than 90% of mis-regulated genes are shared between emerin-/- and baf KD. Finally, we show that transcriptional changes are downstream of Chk2 activation, as transcription are restored in chk2, emerin double mutant ovaries.

overall_design: Ovary mRNA profiles of newly eclosed wildtype, emerin mutant and bafKD Drosophila. G/PI and G/PK are the genotypes of the two emerin null flies. The G, PK, and PI alleles are emerin null, we used both backgrounds to control for background effects.

first: Tingting

last: Duan

middle: C

first: Pamela

last: Geyer


title: Transcriptome dataset of two different adipose tissues in gestational diabetes patients.

status: Public on Nov 18 2021

city: East Lansing

first: David

middle: Rodrigo

last: Salcedo-Tacuma

state: Mi

address: 567 Wilson road

department: Physiology

institute: Michigan State University

summary: Using next generation RNA sequencing (RNA-seq), this study evaluated the whole transcriptome of subcutaneous (SC) and omental (OM) adipose tissues from patients with gestational diabetes (GD) and healthy matching controls that were collected during cesarean delivery (C-section). Results show a strong separation of the transcriptomic profiles based on anatomical location and reveal specific RNA expression patterns unique to GD patients

overall_design: mRNA profile of 20 tissue patient samples from 2 different anatomical positions. 10 Patients with Diabetes Gestational and 10 controls. SUbcutaneous adipose biopsies and omental tissie biopsies were collected.

first: Leonardo

last: Bonilla

first: Maria

last: Geney

first: Jorge

last: Gonzalez

first: Sandra

last: Gutierrez

first: Miguel

last: Chirivi

first: G

last: Contreras


title: Intestinal epithelial GR in the regulation of intestinal inflammation and colon cancer

status: Public on Nov 15 2021

city: Durham

first: Jian-Liang

last: Li

address: 111 TW Alexander Dr

summary: The goal of this project is to investigate the role of glucocorticoids and their receptor, glucocorticoid receptor (GR), in intestinal stress response and tissue homeostasis. Using a mouse model with specific deletion of GR in intestinal epithelium (GR iKO mice), we recently discovered that intestinal epithelial GR deficiency deteriorates acute colitis while reducing chronic inflammation-associated colon cancer formation in mice. To understand the molecular mechanisms underlying these phenotypes, we examined colonic transcriptomes of Flox control and GR iKO mice treated with or without dextran sulfate sodium (DSS) for 7 days by microarray analysis.

overall_design: Total RNA were extracted from colon tissues of 4 pairs of regular Flox control and GR iKO mice and 3 pairs of Flox and GR iKO mice treated with 2.5% DSS in drinking water for 7 days.  Gene expression profiles were analyzed using Agilent Whole Mouse Genome 4x44 multiplex format oligo arrays (014868) (Agilent Technologies, Santa Clara, CA), following the Agilent 1-color microarray-based gene expression analysis protocol.

first: Xiaoling

first: Shuang

last: Tang


title: Single‐cell transcriptomics of LepR‐positive skeletal cells reveals heterogeneous stress‐dependent stem and progenitor pools

first: Li

last: Shen

summary: Leptin receptor (LepR)-positive cells are key components of the bone marrow hematopoietic microenvironment, and highly enrich skeletal stem and progenitor cells that maintain homeostasis of the adult skeleton. However, the heterogeneity and lineage hierarchy within this population has been elusive. Using genetic lineage tracing and single-cell RNA sequencing, we found that Lepr-Cre labels most bone marrow stromal cells and osteogenic lineage cells in adult long bones. Integrated analysis of Lepr-Cre-traced cells under homeostatic and stress conditions revealed dynamic changes of the adipogenic, osteogenic, and periosteal lineages. Importantly, we discovered a Notch3+ bone marrow sub-population that is slow-cycling and closely associated with the vasculatures, as well as key transcriptional networks promoting osteo-chondrogenic differentiation. We also identified a Sca-1+ periosteal sub-population with high clonogenic activity but limited osteo-chondrogenic potential. Together, we mapped the transcriptomic landscape of adult LepR+ stem and progenitor cells and uncovered cellular and molecular mechanisms underlying their maintenance and lineage specification.

overall_design: Single-cell transcriptomic profiling of Prrx1-Cre- and Lepr-Cre-traced stromal cells in steady state long bones from Prrx1-Cre;tdTomato;Col2.3-GFP and Lepr-Cre;tdTomato mice, respectively, as well as Lepr-Cre-traced stromal cells from Lepr-Cre;tdTomato mice under stress conditions such as aging, rosiglitazone feeding, irradiation and bone fracture. Bulk transcriptomic profiling of wild-type bone marrow stromal cells (BMSCs) cultured in 3D GelMA hydrogel alone, or 3D co-cultured with bone marrow endothelial cells (ECs).

first: Chunyang

last: Mo

first: Jingxin

last: Guo

first: Jiachen

last: Qin

first: Xiaoying

first: Yuxi

last: Sun

first: Hanjing

last: Wei

first: Dandan

last: Cao

first: Yiying

first: Chengchen

last: Zhao

first: Yanhong

last: Xiong

first: Yong

first: Yao

first: Rui

last: Yue


title: Trajectories of partial and full EMT of mammary tumor cells in the MMTV-PyMT mouse model

city: Basel

first: DBM Bioinformatics

last: Core Facility

state: BS

address: Hebelstrasse 20

department: Departement of Biomedicine

country: Switzerland

institute: University of Basel

summary: Epithelial-mesenchymal transition (EMT) is a multistep process of cell de-differentiation which confers carcinoma cells with a variety of malignant characteristics. Due to the transient and reversible nature of the process, cancer cells may transit between various stages of an EMT continuum, including epithelial, partial EMT or full EMT, and the actual status of cancer cells, the kinetics of cellular state transition in vivo and the consequences thereof have remained elusive. We have established tamoxifen inducible dual recombinase lineage tracing systems combined with live cell imaging and 5-cell RNA-sequencing analysis to track cancer cells undergoing a partial or a full EMT in the MMTV-PyMT mouse model of metastatic breast cancer. In primary tumours, cancer cells infrequently undergo an EMT, and most of these cells transition between epithelial and partial EMT states, but rarely undergo a full EMT. Consequently, cells that have ever undergone a partial EMT dynamically transit between various EMT states, and they contribute to lung metastasis and chemoresistance. In contrast, full EMT cells mostly retain a mesenchymal phenotype and stably reside in perivascular regions, but fail to colonize the lungs. However, full EMT cancer cells are enriched in recurrent tumors upon chemotherapy. Our findings suggest that cancer cells in various stages of the EMT continuum contribute differentially to hallmarks of breast cancer malignancy, such as cell migration, invasion, metastasis and chemoresistance.

overall_design: Partial and full EMT mammary tumor cells were sorted by flow cytometry from tumors of Tnc-CreERT2;MMTV-Flpo;RC::FrePe;MMTV-PyMT (Tnc-CreERT2) and Cdh2-CreERT2;MMTV-Flpo;RC::FrePe;/MMTV-PyMT (Cdh2-CreERT2) mice. The dual recombinase lineage tracing system allows to label all breast cancer cells as mCherry expressing cells (red). Upon tamoxifen administration cancer cells that have undergone either partial or full EMT switch to the expression of GFP (green). This red to green color switching is irreversible, which allows to trace all cancer cells that have ever undergone an EMT by the expression of GFP, even if they have reverted back to an epithelial state by undergoing a MET. In consequence, mCherry+ cells are breast cancer cells,  GFP+ cells are breast cancer cells that have ever undergone either partial or full EMT and double positive cells are cells undergoing an EMT (transtioning cells). Based on the expression of GFP or mCherry in combination with the epithelial marker EpCAM expression, 3 populations of mCherry+ cells (P5, P17 and P18), 4 populations of GFP+ cells (P15, P10, P16 and P9) and 1 population of doble positive cells (P22) were collected from Tnc-CreERT2 mice, and 3 populations of mCherry+ cells (P5, P17 and P18) and 1 population of GFP+ cells (P15) were collected from Cdh2-CreERT2 mice. mCherry populations, P05: mCherry+ EpCAM-, P17:  mCherry+ EpCAMhigh, P18: mCherryhigh EpCAMhigh. GFP populations, P15:GFP+ EpCAM-, P10:  GFP+ EpCAMlow, P16: GFP+ EpCAMmed and  P18: GFPhigh EpCAMmed. Double positive cells: P22: mCherry+ GFP+ EpCAMhigh

first: Nami

last: Sugiyama

first: Fabiana

last: Lüönd

first: Robert

last: Ivanek

first: Gerhard

last: Christofori


title: Topoisomerases I and II facilitate the translocation of condensin DC in C. elegans

status: Public on Nov 16 2021

city: New York

first: Ana

middle: Karina

last: Morao

state: New York

address: 29 Washington Place

department: Biology

institute: New York University

sample_organism:
Caenorhabditis briggsae
Caenorhabditis elegans


title: Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies unique proteotypes associated with patient outcomes [WG-DASL]

first: Ming-Sound

last: Tsao

summary: Non-small cell lung cancer (NSCLC) death rates exceed the next 3 prevalent cancers combined; however, most NSCLC tumors lack actionable mutations. Recent studies of NSCLC and other cancers revealed profound proteome remodelling with prognostic impact that is not fully predicted by DNA or RNA analyses. These revelations portend proteome-based cancer classification and treatment. This will require model systems that recapitulate tumor proteomes and phenotypes. A subset (~35%) of the most aggressive NSCLC can form a patient-derived xenograft (PDX). We generated 137 PDX models of aggressive NSCLC, which represent the histological, genome, transcriptome, and DNA methylation features and proteome remodelling of primary NSCLC. The models indicate 3 lung adenocarcinoma and 2 squamous cell carcinoma proteotypes that are associated with different patient outcomes, protein-phosphotyrosine profiles, candidate targets, and in adenocarcinoma, distinct stromal immune features. The PDX resource will foster proteome-directed stratification and development of new treatments for aggressive NSCLC.

overall_design: Total RNAs from xenografts were amplified by DASL or DirectHyb kit and hybridized to Illumina HumanHT-12 WG-DASL V4 beadchip or Illumina HT12v4 chip

first: Quan

last: Li


title: OsCOMT, encoding a caffeic acid O-methyltransferase in melatonin biosynthesis, increases grain yield through regulating leaf senescence and vascular patterning

status: Public on Nov 12 2021

city: Yangzhou

first: Liexiang

last: Huangfu

address: daxue road

institute: Yangzhou University

summary: Melatonin, a natural phytohormone present in most plants, plays multiple roles in plant growth and stress responses. Although melatonin biosynthesis-related genes have been suggested to possess diverse biological functions, their roles and functional mechanisms in regulating rice grain yield remain largely unexplored. Here, we revealed that a rice caffeic acid O-methyltransferase (OsCOMT) gene is involved in melatonin biosynthesis through in vitro and in vivo evidences. Transgenic assays show OsCOMT significantly delays leaf senescence at the grain filling stage, and then improves photosynthesis efficiency. Further experimental and transcriptomic data suggest that OsCOMT inhibits the degradation of chlorophyll and chloroplast, which in turn delay leaf senescence. Histological analysis also reveals the role of OsCOMT in the development of vascular bundle system in rice. The levels of melatonin and cytokinin were significantly increased in the culm of OsCOMT-overexpression plant relative to those of the wild-type (WT). In the OsCOMT-overexpression line, the cytokinin-biosynthesizing genes were up-regulated and the cytokinin-degrading genes were down-regulated, thereby increasing the cytokinin levels compared with the WT. Thus, OsCOMT-mediated vascular patterning may result from the crosstalk between melatonin and cytokinin. More importantly, OsCOMT significantly increased grain number and yield production of rice in various background, including Nipponbare (NIP) and Suken118 (SK118). Our findings show novel insights into melatonin-mediated leaf senescence and vascular patterning, and provide a new strategy to enhance rice yield production.

overall_design: A total of nine samples, including three genotypes. Each genotype was detected  at a time point with 3 replicates.


title: Transcriptomics following CRISPR KO of individual DUBs or inhibition of DUBs with small molecule inhibitors

status: Public on Nov 03 2021

city: Boston

first: Clemens

last: Hug

state: MA

address: 200 Longwood Avenue

department: Harvard Program in Therapeutic Science

institute: Harvard Medical School

summary:
CRISPR KO RNA-seq data: To generate knockouts, we used a commercially available arrayed CRISPR-Cas9 library targeting 81 out of ~100 DUBs and 13 additional proteins in the ubiquitin-proteasome system, including ubiquitin-like proteins; the library was constructed with four, pooled, guides per target. mRNA profiling was performed 96 hours after guide RNA transfection using a high-throughput, low-cost RNA-sequencing method (3’ Digital Gene Expression or 3’DGE-seq) in the MDAMB231 breast cancer cell line.
Inhibitor RNA-seq data: For the small molecule inhibitor signatures, MDAMB231 or MCF7 or MCF7 TP53 shRNA breast cancer cells were treated with a panel of DUB inhibitors for 24 hours, then 3'DGE-seq was used to perform the mRNA profiling.

overall_design: mRNA profiles following DUB KO or DUB inhibition with small molecule inhibitors

first: Laura

last: Doherty

first: Sarah

last: Boswell

middle: B

first: Caitlin

last: Mills

first: Sara

last: Buhrlage

first: Peter

last: Sorger


title: Maladaptive functional changes in alveolar fibroblasts due to perinatal hyperoxia impair epithelial differentiation

city: Cincinnati

first: John

middle: M.

last: Snowball

state: OH

address: 3333 Burnet Ave

department: Pulmonary Research

institute: Cincinnati Childrens Hospital

summary: PDGFRa+ matrix and myofibroblasts decrease and PDGFRa+ lipofibroblasts increase during hyperoxia injury at both a transcriptional and population level.

overall_design: MACS-sorted PDGFRa+ (CD140+) FBs from either RA or O2 PN4, PN7, and PN10 mouse lungs were prepared for bulk RNA-seq.

first: Matthew

last: Riccetti

first: Anne-Karina

last: Per


title: Baricitinib attenuates the proinflammatory phase1 of COVID-19 driven by lung-infiltrating monocytes

status: Public on Oct 30 2021

city: Atlanta

first: Diego

last: Moncada

state: Georgia

address: 201 Dowman Dr

department: Pediatrics

institute: Emory University

summary: COVID-19 patients are generally asymptomatic during initial SARS-CoV-2 replication, but may suffer severe immunopathology after the virus has receded and blood monocytes have infiltrated the airways. In the bronchoalveolar lavage fluid from patients with severe COVID-19, lung-infiltrating monocytes expressed high mRNA levels encoding inflammatory mediators, including CXCL8and IL-1ß, and contained SARS-CoV-2transcripts. To study this process in more depth, we developed a novel organotypic model whereby primary human blood monocytes are transmigrated across a differentiated human lung epithelium infected by SARS-CoV-2. Infiltrating monocytes acquiredSARS-CoV-2 from the epithelium and upregulated expression and secretion of inflammatory mediators includingCXCL8 and IL-1ß, mirroring in vivo data. The JAK1/2inhibitor baricitinib gained emergency use authorization by the FDA for the treatment of COVID-19 originally in combination with the antiviral remdesivir, and recently as a stand-alone treatment. To explore the mechanisms by which baricitinib alone or in combination with remdesivir may result in more favorable disease outcomes, we leveraged this model to characterize viral burden, gene expression and inflammatory mediator secretion by lung epithelial cells and infiltrating monocytes. As expected, remdesivir decreased viral burden in both the epithelium and monocytes, while baricitinib enhanced antiviral signaling and decreased specific inflammatory mediators in monocytes. Combined use of baricitinib and remdesivir enhanced the rate of virus clearance from SARS-CoV-2-positivemonocytes. Taken together, baricitinib enhances the antiviral state of monocytes infiltrating the COVID-19 lung, while decreasing the expression of inflammatory mediators, thus limiting the likelihood of a cytokine storm and ensuing acute respiratory distress syndrome (ARDS).

overall_design: To determine the relationship between airway epithelium, SARS-CoV-2 infection and airway monocytes we used an in vitro organotypic model to condition epithelial cells at air-liquid interface followed by infection with SARS-CoV-2 and transmgiration by primary blood monocytes.

first: Brian

last: Dobosh

last: Moncada Giraldo

first: Rabindra

last: Tirouvanziam


title: A humanized mouse model of COVID-19

status: Public on Nov 04 2021

first: Rihao

last: Qu

address: 300 George Street

institute: BBS Program, Yale University

summary: Mice with a human immune system (humanized mice), generated by transplantation of human hematopoietic stem and progenitor cells (HSPCs), serve as invaluable tools to study the development and function of the human immune system in vivo. By adapting recombinant adeno-associated virus (AAV)-driven gene therapy to deliver hACE2 to the lungs, which allows infection with SARS-CoV-2 of MISTRG6 mice engrafted with HPSCs, we created a humanized mouse model of COVID-19 that recapitulates the distribution and function of the human innate and adaptive immune system and is amenable to the mechanistic study of COVID-19 and its myriad of complications. MISTRG6 mouse model was engineered by a human/mouse homolog gene-replacement strategy to provide physiological factors with regard to quantity, location and time and enable essentially all classes of human HSPCs to develop in mice. MISTRG6 (acronym for genes replaced) mice encode humanized M-CSF (enabling monocytes and  tissue macrophage development), GM-CSF/IL-3 (to provide lung alveolar macrophages), SIRPa (establish macrophage tolerance to human cells), ThPO (hematopoiesis and platelets), and IL-6 (better engraftment allowing study of adult human patients and improved antigen-specific antibody responses as well as human IL-6 per se), in a Rag2/Gamma common chain deleted background. We evaluated the transcriptional landscape in uninfected and SARS-CoV-2 infected lungs of humanized mice at multiple time points (2, 4, 7, 14, 28 dpi).

overall_design: We  delivered AAV-hACE2 to lung tissues of immune-reconstituted MISTRG6 mice (MISTRG6-hACE2) that have been engrafted with human HSPCs. MISTRG6-hACE2 mice were then infected with SARS-CoV-2.  Lung tissues from infected and uninfected controls were collected. RNA isolated from homogenized lung tissue was used for whole tissue transcriptome analysis. Libraries were prepared with an Illumina rRNA depletion kit and sequenced on a NovaSeq.

first: Esen

last: Sefik

first: Richard

last: Flavell


title: PRMT7 knockdown in Jurkat-Cas9  and Molt-4 T-ALL cell line

status: Public on Oct 22 2021

city: Tampere

last: Oksa

address: Arvo Ylpön katu 34

department: Faculty of Medicine and Health Technology

country: Finland

institute: Tampere University

summary: T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematological malignancy with only few established prognostic biomarkers.In this study, we examined the expression of protein arginine methyltransferases across hematological malignancies and discovered high levels of PRMT7 mRNA in T-ALL, particularly in the mature subtypes of T-ALL. High PRMT7 was associated with decreased event-free and overall survival in two independent patient cohorts. Genetic deletion of PRMT7 by CRISPR-Cas9 significantly decreased the colony-forming capacity of the cells and negatively impacted cell viability. In the knockout cells, alterations were seen in the monomethyl arginine levels in proteins associated with RNA processing. These results suggest that PRMT7 plays an active role in T-ALL pathogenesis.

overall_design: mRNA expression profiler were generated from four different Jurkat Cas9 PRMT7 knockdown and two Molt-4 derived PRMT7 knockout cell lines, three replicates per cell line (knockdown made using CRISRP-Cas9 technology)

first: Olli

last: Lohi


title: RNA-seq of human CD8+ T cells treated with engineered IL-10 variants

status: Public on Oct 28 2021

first: Robert

last: Saxton

address: 279 Campus Drive, Beckman Center, Room B173

department: Department of Molecular & Cellular Physiology

summary: RNA-seq analysis of human CD8+ T cells treated with PBS, WT IL-10, super-10, or 10-DE.

overall_design: Human CD8+ T cells were MACS isolated from patient derived PBMC, and activated with anti-CD3/CD28 for three days. Cells were then cultured in the presence or absence of IL-10 variants for 24 hours.

first: K

last: Garcia


title: Integrative analysis of non-small cell lung cancer patient-derived xenografts identifies unique proteotypes associated with patient outcomes [HT12v4]

first: Ming-Sound

last: Tsao

first: Quan

last: Li


title: Next Generation Sequencing facilitates quantitative analysis  of spinal cord tissue to explore the mechanisms of hyperbaric oxygen treatment  alleviating the spinal cord inury

status: Public on Oct 08 2021

first: Xuehua

last: Liu

address: 8 Gongti South Road, Chaoyang District Beijing

department: Department of Hyperbaric Oxygen

institute: Beijing Chaoyang Hospital, Capital Medical University

summary:
Aims: To better understand the potential mechanisms of hyperbaric oxygen (HBO) treatment alleviating spinal cord injury (SCI).
Materials and methods: The SCI model was firstly built in mice, which were randomly divided into three groups: Sham (SH), SCI and HBO groups, followed by hind limb motor function evaluation. Then the spinal cord tissue samples were harvested for histological evaluation and genome-wide transcriptional analysis at 1 week after injury. Finally, some oxidative stress and cell death related differently expressed genes were selected to be analyzed followed by the functional analysis.
Results: HBO treatment significantly improved the recovery of hind limb motor function and decreased the histology score compared to the SCI group. In the genome-wide transcriptional analysis, a total of 76 common differently expressed gene among the three groups were obtained at 1 week after injury, which were enriched in functional pathway such as ferroptosis, calcium signaling pathway, serotonergic synapse, etc. Trends in expression of the six genes were consistent with transcriptional analysis.
Conclusions: Identified differentially expressed genes and related signaling pathways may be associated with HBO treatment alleviating second spinal cord injury. These results contribute to elucidate the mechanism of HBO in the treatment of SCI.

overall_design: Spinal cord mRNA profiles of sham, spinal cord injury and HBO treatment groups on the 7th day after SCI

first: Zhencheng

last: Sun

first: Fang

last: Liang

first: Jing

last: Yang

first: Qingjun

last: Su


title: Leaf transcriptome profiling of contrasting sugarcane genotypes for drought tolerance under field conditions

status: Public on Nov 05 2021

city: Ribeirão Preto

first: Danyel

last: Contiliani

address: Av. Bandeirantes, 3900

country: Brazil

institute: University of Sao Paulo

summary: Transcriptional profiling of sugarcane leaf (+1) was collected from drought-prone areas at 42 and 117 days after the last rainfall when plants were 6- and 9-month-old, respectively. Sample hybridization (non-irrigated treatment against irrigated control) was performed to monitor gene expression in a two-color Agilent custom microarray. Our goal was to investigate the effect of mild and severe water stress on the transcriptomes of drought-sensitive (IACSP97-7065) and -tolerant (IACSP94-2094) sugarcane genotypes.

overall_design: Two-condition experiment: irrigated (control) vs. non-irrigated at 42nd day after the last rainfall (mild water stress), irrigated (control) vs non-irrigated at 117th day after the last rainfall (severe water stress).

middle: F

first: João

last: Nebó Carlos de Oliveira

first: Larissa

last: Andrade

first: Rafael

last: Peixoto Júnior

first: Ricardo

last: Machado

first: Daniel

last: Nunes

middle: V

last: Ribeiro

first: Mariana

last: Belloti

first: Tiago

last: Pereira

first: Regina

last: de Matos Pires

first: Patrícia

last: Rezende

first: Gláucia

last: Souza

first: Marcos

last: Landell

first: Antonio

last: de Oliveira Figueira

first: Silvana

last: Creste


title: SPEN is required for Xist upregulation during initiation of X chromosome inactivation (RNA-seq)

status: Public on Sep 30 2021

city: Rotterdam

first: Beatrice

last: Tan

address: Dr. Molewaterplein 40

department: Developmental Biology

country: Netherlands

institute: Erasmus MC

summary: At initiation of X chromosome inactivation (XCI), Xist is monoallelically upregulated from the future inactive X (Xi) chromosome, overcoming repression by its antisense transcript Tsix. Xist recruits various chromatin remodelers, amongst them SPEN, which are involved in silencing of X-linked genes in cis and establishment of the Xi. Here, we show that SPEN plays an important role in the initiation of XCI. Spen null female mouse embryonic stem cells (ESCs) are defective in Xist upregulation upon differentiation. We find that Xist-mediated SPEN recruitment to the Xi chromosome happens very early in XCI, and that SPEN-mediated silencing of the Tsix promoter is required for Xist upregulation. Accordingly, failed Xist upregulation in Spen-/- ESCs can be rescued by concomitant removal of Tsix. These findings indicate that SPEN is not only required for the establishment of the Xi, but is also crucial in the initiation of the XCI process.

overall_design: We performed RNA-seq on wild type and Spen-KO mESCs at different time points of monolayer differentiation, treated or not with doxycycline to force Xist upregulation (two biological replicates per condition).

first: Teresa

last: Robert-Finestra

first: Wilfred

last: van IJcken

first: Joost

last: Gribnau


title: Transcriptomic profiling of human senescent cells in the setting of grape seed extract intervention

status: Public on Oct 04 2021

city: Shanghai

first: Yu

last: Sun

address: 320 Yueyang Rd, Life Sciences Building A #1508

department: Shanghai Institute of Nutrition and Health

institute: Chinese Academy of Sciences

summary: Aging and age-related pathologies can be delayed by specifically targeting the senescence-associated secretory phenotype (SASP), a hallmark feature of senescent cells. Achieving the goal using small molecule inhibitors would have a tremendous impact on the quality of lifespan and burden of age-related chronic diseases. We report the potential of grape seed extract (GSE), a naturally existing source of phytochemicals including terpenoids, carotenoids, and flavonoids, in targeting senescent cells via induction of programmed cell death. This study demonstrates the impact of GSE as a medicinal compound on the expression profile of senescent cells and provides a strong rationale for its future use in geriatric medicine.

overall_design: Examination of in vitro efficacy of GSE, a grape-derived product that has been used to maintain healthy condition through controlling inflammatory responses by decreasing the expression of inflammation-related factors, in modulating the expression profile of senescent cells and their survival.

first: Qixia

last: Xu


title: SPEN is required for Xist upregulation during initiation of X chromosome inactivation (ChIP-seq)

overall_design: We performed H3K27me3 ChIP-seq on wild type and Spen KO mESCs at different time points of monolayer differentiation (two biological replicates per condition).

first: Hegias

last: Mira-Bontenbal


title: Transcriptomics of an ectosymbiotic marine nematode

status: Public on Nov 11 2021

city: Vienna

first: Silvia

last: Bulgheresi

address: Djerassiplatz 1

department: Functional and Evolutionary Ecology

country: Austria

institute: University of Vienna

summary: Eukaryotes may experience oxygen deprivation under several physiological and pathological conditions. Because oxygen shortage leads to a reduction in cellular energy production, all the eukaryotes studied so far evolved ways to conserve energy via suppression of metabolism. However, the molecular physiology of animals that naturally and repeatedly experience anoxia is poorly studied. One such animal is the symbiotic marine nematode Laxus oneistus. This thrives, invariably coated by its sulfur-oxidizing bacterium Candidatus Thiosymbion oneisti, in anoxic sulfidic or hypoxic sand. Here, by applying transcriptomics and proteomics, we discovered that, irrespective of the oxygen concentration it is subjected to, this nematode is mostly and constitutively engaging in ubiquitination-mediated proteolysis, energy generation, oxidative stress response and immune response. Furthermore, by incubating L. oneistus under sulfidic anoxic or hypoxic conditions, we found that, under the first condition, the worm upregulated genes involved in ribosome biogenesis, proteolytic systems (autophagy and the ubiquitin-proteasome system), chaperones, detoxification and lectins. Degradation pathways were likely induced to recycle damaged cellular components (mitochondria) and misfolded proteins into nutrients, whereas lectins were likely expressed to promote the attachment of its anaerobic, thiotrophic symbiont. Besides, L. oneistus appeared to survive oxygen deprivation by using alternative electron carriers (rhodoquinone) and acceptors (fumarate) to rewire the electron transfer chain. On the other hand, under hypoxia, genes involved in costly processes (e.g., development, amino acid biosynthesis, feeding behaviour, mating) were upregulated. Intriguingly, the worm’s Toll-like innate immunity pathway and a number of immune effectors (e.g., Bacterial Permeability Increasing proteins, fungicides) were upregulated in the presence of oxygen.   In conclusion, we hypothesize that L. oneistus survives in anoxic sulfidic sand by overexpressing degradation processes, rewiring oxidative phosphorylation and by reinforcing its coat of bacterial sulfur-oxidizers. In the presence of oxygen, instead, it appears to exploit glycolysis to eat, mate and grow. Moreover, oxygen appears to affect L. oneistus immune system in such way, as to favor specific attachment of its anaerobic partner in anoxia and to produce broad-range antimicrobials when oxygen is present.

overall_design: rRNA-depleted total RNA was sequenced (RNA-Seq) of symbiotic nematodes (50 per sample) that were incubated for 24 h under 4 different conditions (oxic, hypoxic, anoxic, anoxic-sulfidic)

first: Gabriela

last: Paredes

first: Tobias

last: Viehboeck

first: Stephanie

last: Markert

first: Michaela

middle: A

last: Mausz

first: Yui

last: Sato

first: Marvin

last: Weinhold

first: Manuel

last: Liebeke

first: Lena

last: König


title: Uterine leiomyoma status in CCCA patients has no impact on the gene expression profile in the lesional scalp

status: Public on Sep 15 2021

city: Baltimore

first: Crystal

last: Aguh

state: Maryland

address: 1500 Orleans St, CRB II Suite 200

department: Dermatology

institute: Johns Hopkins School of Medicine

summary: Central centrifugal cicatricial alopecia (CCCA) has recently been associated with increased expression of genes implicated in fibroproliferative disorders (FPDs) in the affected scalp and higher prevalence of uterine leiomyomas (UL). We therefore sought to examine the effect of UL status on the gene expression profile of the lesional scalp in CCCA patients. Scalp biopsy was obtained from 16 patients with a confirmed diagnosis of CCCA between 2017 and 2020. Microarray analysis was used to identify differential gene expression between CCCA patients with and without a history of UL. Of the 20,000 genes analyzed, 23 of 25 genes with highest expression in CCCA patients with UL held no statistical significance. No genes previously implicated in FPDs were found among the upregulated transcripts. Of all genes analyzed, only 8 upregulated genes and zero downregulated genes had a fold change >2 in CCCA patients with UL compared to CCCA patients without UL. Our findings highlight similar gene expression patterns in the scalp of CCCA patients with and without a history of UL.

overall_design: We performed gene expression microarrays on sixteen tissue samples from the affected scalp in sixteen patients, eight with and eight without history of uterine leiomyomas

first: Taylor

last: Jamerson

first: C

last: Talbot Jr

first: Yemisi

last: Dina


title: 10X genomics single cell GEX and VDJ 5' sequencing of PBMC from Type 1 Diabetes patients treated with Treg therapy alone or plus low dose IL-2

status: Public on Sep 25 2021

city: San Francisco

first: Jeffrey

last: Bluestone

state: California

address: 513 Parnassus Ave

institute: UCSF

summary:
Background: A previous Phase I study showed that the infusion of autologous Treg cells expanded ex-vivo into recent onset Type 1 Diabetes (T1D) patients had an excellent safety profile, however, the majority of the infused Tregs could no longer be detected in the peripheral blood three months post-infusion (NCT01210664-Treg-T1D Trial). Interleukin-2 (IL-2) is a well-characterized cytokine that has been shown to enhance human Treg cell survival and expansion at low doses in vivo. Therefore, a Phase 1 study (NCT02772679-TILT trial) was conducted combining a single infusion of autologous polyclonal Tregs, expanded ex vivo, followed by one or two 5-day courses of recombinant human low dose IL-2 (ld-IL-2) at 0.3 x 10^6 to 1 x 10^6 units/dose. The infusions had an acceptable safety profile, but all 9 patients failed to maintain C-peptide production at pre-treatment levels.
Results: Single cell gene expression analysis revealed that the combination therapy led to a transient increase in the number of infused and endogenous Tregs but also resulted in a significant increase from baseline in a subset of activated NK, Mucosal-associated invariant T (MAIT) and clonal CD8+ T populations from populations

overall_design:
CD45+ cells were isolated by FACS, combined into 30 pools and sequenced into three distinct batches. The data from each time point of each patient’s sample was then deconvoluted using the Demuxlet computational package. The gene expression profile and TCR sequencing of more than 400,000 cells was analyzed
Each sequenced sample is a mix of several patients and timepoints.

first: Shen

last: Dong


title: Transcriptomic analysis of PD-L1 positive and negative hot lung adenocarcinomas identifies a different molecular immunogenic landscape

status: Public on Sep 27 2021

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

country: Germany

institute: University of Lübeck

summary: Lung cancer is a major global health problem, as it is the leading cause of cancer- related deaths worldwide. Non-small-cell lung cancer (NSCLC), the most common form, is a heterogeneous disease with adenocarcinoma and squamous cell carcinoma being the predominant subtypes.  Immune-inhibiting interaction of Programmed cell death-ligand 1 (PD-L1) with programmed cell death-protein 1 (PD-1) causes checkpoint mediated immune evasion and is, accordingly, an important therapeutic target in cancer. In NSCLC, improved understanding of PD-1/PD-L1 checkpoint blockade-responsive biology is warranted.  We aimed to identify the landscape of immune cell infiltration in primary lung adeno- carcinoma (LUAD) in the context of tumor PD-L1 expression and the extent of immune infiltration (“hot” vs. “cold” phenotype). Therefore, the study comprises LUAD cases (n=138) with “hot” and “cold” tumor immune phenotype and positive and negative tumor PD-L1 expression, respectively. Tumor samples were immunohistochemically analyzed for expression of PD-L1, CD4 and CD8 and further analyzed on transcriptomic level by Nanostring nCouter Pan Cancer Immune Profiling Panel. We detected significantly differentially expressed genes associated with PD-L1 positive and “hot” versus PD-L1 negative and “cold” phenotype.  The presented study illustrates novel aspects of PD-L1 regulation, with potential biological relevance, as well as relevance for immunotherapy response stratification.

overall_design: 144 lung adenocarcinomas were classified into four different groups, depending on their PD-L1 expression status determined by IHC and total immune infiltration determined by H&E. Cases with tumors expressing PD-L1 and high total immune cell infiltration were designated as PH (n=23), cases with tumors expressing PD-L1 and low total immune cell infiltration were designated as PC (n=7), cases with no PD-L1 expression and high total immune cell infiltration were designated as NH (n=53) and cases with no PD-L1 expression and low total immune cell infiltration were designated as NC (n=55).

first: Anke

last: Fähnrich

first: Jutta

last: Kirfel

first: Christiane

last: Kümpers

first: Mladen

last: Jokic

first: Sven

last: Perner


title: Single-cell sequencing of 12 months old zebrafish telencephalon

status: Public on Sep 23 2021

first: Caghan

last: Kizil

state: NY

institute: Columbia University Irving Medical Center

summary: Zebfrafish brains were injected with neutral cell tracking dye. Zebrafish telencephalon were dissociated and dye postive cells were sorted by FACS and single-cell sequencing performed from these cells.

overall_design: Single cell analyses of zebrafish telencephalon by 10X Genomics

first: Mehmet

middle: I

last: Cosacak


title: Effect of NF90-NF45 knock-down on whole gene expression in Beta-TC-6 cells, a pancreatic beta cell line

status: Public on Sep 28 2021

city: Nankoku

first: Shuji

last: Sakamoto

state: Kochi

address: Oko-cho, Kohasu

department: Science Research Center

institute: Kochi University

summary:
We found that knock down of NF90 and its binding factor, NF45, complex leads to retardation of growth in Beta-TC-6 cells, a pancreatic beta cell line.
To uncover molecular mechanisms for the growth retardation in Beta-TC-6 cells depleted of NF90-NF45, we performed comprehensive analysis of gene expression using microarray.

overall_design: RNAs were extracted from Beta-TC-6 cells depleted of either NF90-NF45 or a non-targeting control. The RNAs were hybridized with GeneChip Mouse Gene 2.1 ST Array Strip which is an Affymetrix microarray

first: Sylvia

last: Lai


title: LIN28 Promotes Nucleolar/Ribosomal Functions to Repress the 2C-like Transcriptional Program in Pluripotent Stem Cells [scRNA-seq]

city: Hangzhou

first: Hua

last: Yu

address: No.18 Shilongshan Road

institute: Westlake University

summary: LIN28 is an RNA binding protein with important roles in early embryo development by interaction with let-7 microRNA precursors or mRNAs in cytoplasm. Here, we showed novel roles of LIN28 within the nucleolus in cultured pluripotent stem cells (PSCs). We found Lin28 deficiency led to activation of the 2-cell (2C)-like transcriptional program and repression of the ES cell program. Mechanistically, LIN28 maintains a peri-nucleolar heterochromatin-residing complex to repress 2C activator Dux via association with NCL and TRIM28. Meanwhile, it promotes liquid-liquid phase separation (LLPS) of nucleolar proteins FBL and NCL to support nucleolar function through its RNA binding domains and intrinsic disordered regions. These findings elucidate novel roles for nucleolar LIN28 in coordinately regulating the ES/2C state homeostasis, and shed light on RNA binding protein-mediated nucleolar phase separation mechanisms in PSCs and early embryo development.

overall_design: Examination of gene expression in wide-type and Lin28 knockout ES cells in single-cell level.

first: Zhen

last: Sun


title: LIN28 Promotes Nucleolar Phase Separation to Regulate the ES/2C State Homeostasis in Pluripotent Stem Cells [CLIP-seq]

overall_design: Examination of LIN28 binding signal derived from CLIP-seq in ES cells.

first: Xiaohua

last: Shen


title: LIN28 Promotes Nucleolar Phase Separation to Regulate the ES/2C State Homeostasis in Pluripotent Stem Cells [Hi-C]

overall_design: Examination of the difference of chromatin high-order structure  in wild type ES cells and Lin28a-/- ES cells.


title: LIN28 Promotes Nucleolar/Ribosomal Functions and Phase Separation in Pluripotent Stem Cells

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

overall_design: Refer to individual Series


title: Genetic, metabolic, and molecular insights into the diverse outcomes of diet-induced obesity in mice

status: Public on Sep 07 2021

city: Lausanne

first: Jean-David

middle: Horacio

last: Morel

state: Vaud

address: Station 15

department: SV/IBI

institute: Ecole Ploytechnique Fédérale de Lausanne

summary: Overweight and obesity are increasingly common public health issues worldwide, leading to a wide range of diseases from metabolic syndrome to steatohepatitis and cardiovascular diseases.  While the increase in the prevalence of obesity is partly attributable to changes in lifestyle (i.e. increased sedentarity and changes in eating behaviour), the metabolic and clinical impacts of these obesogenic conditions varies between sexes and genetic backgrounds.  The conception of personalised treatments of obesity and its complications require a thorough understanding of the diversity of responses to conditions such as high-fat diet intake. By analysing nine genetically diverse mouse strains, we show that much like humans, mice respond to high-fat diet in a genetic- and sex-dependent manner.    Results:  Physiological and molecular responses to high-fat diet are associated with expression of genes involved in immunity and mitochondrial function. Finally, we find that mitochondrial function and supercomplex assembly may explain part of the diversity of physiological responses. By exploring the complex interactions between genetics and metabolic phenotypes via gene expression and molecular traits, we shed light on the importance of genetic background and sex in determining metabolic outcomes. In addition to providing the community with an extensive resource for optimizing future experiments, our work serves as an exemplary design for more generalizable translational studies.

overall_design: Design: This RNAseq dataset covers the response to HFD in the mouse liver of 9 mouse strains (PWK/PhJ, CAST/EiJ, WSB/EiJ, NZO/HlLt, JNOD/ShiLtJ, 129S1/SvImJ, A/J, DBA/2J, C57BL/6J). 6 female and 6 male animals from 9 inbred mouse strains were fed with either a chow diet (CD) or high-fat diet (HFD) from the age of 8 to 21 weeks and various metabolic and fitness phenotypes were measured. Eight of these strains are known as the founders of the Collaborative Cross (CC) and Diversity Outbred (DO) populations, with the addition of the DBA/2J strain.

first: Alexis

last: Bachmann

first: Maroun

last: Bou Sleiman

first: Johan

last: Auwerx


title: LIN28 Promotes Nucleolar/Ribosomal Functions to Repress the 2C-like Transcriptional Program in Pluripotent Stem Cells [RNA-seq]

overall_design: Examination of gene expression in wide-type and Lin28 knockout ES and iPS cells.


title: Extracellular Microenvironment in Patient-derived Hydrogel Organoids of Prostate Cancer Regulates Therapeutic Response

status: Public on Oct 01 2021

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

summary: Following treatment with androgen receptor (AR) pathway inhibitors, ~20% of prostate cancer patients progress by shedding their dependence on AR. These tumors undergo epigenetic reprogramming turning castration-resistant prostate cancer adenocarcinoma (CRPC-Adeno) into neuroendocrine prostate cancer (CRPC-NEPC). Currently, no targeted therapies are available for CRPC-NEPCs. A major hurdle in the development of new therapies and treatment of CRPC-NEPC is the lack of accurate models to test candidate treatments. Such models would ideally capture components of the tumor microenvironment (TME) factors, which likely regulate the phenotypic, genetic, and epigenetic underpinnings of this aggressive subset. The TME is a complex system comprised not only of malignant prostate cells but also stromal and inflammatory cells and a scaffold of extracellular matrix (ECM). ECM proteins are implicated in the survival and progression of cancer and development of chemoresistance, while are equally integral to the development of prostate cancer organoids. Here, using a combination of patient tumor proteomics and RNA sequencing, we define putative ECM cues that may guide the growth of prostate tumors in patients. Using this molecular information, we developed synthetic hydrogels that recapitulate the tumor ECM. Organoids cultured in the synthetic hydrogel niches demonstrate that ECM subtypes regulate the morphology, transcriptome, and epigenetics hallmarks of CRPC-Adeno and CRPC-NEPC. CRPC-NEPC organoid showed a differential response to small molecule inhibitors of epigenetic repressor EZH2 and Dopamine Receptor D2 (DRD2), the latter being a novel target in CRPC-NEPC when grown in tumor-specific ECM. Finally, in those synthetic ECM niches where drug resistance was observed in CRPC-NEPCs, cellular reprogramming by a synergistic combination of EZH2 inhibitors with DRD2 antagonists inhibited tumor growth. The synthetic platform can provide a more realistic prostate-specific microenvironment and subsequently enable the development of effective targeted therapeutics for prostate cancers.

overall_design: RNAseq for prostate cancer organoids from two patients (WCM1358 and WCM155), grown in 4 different types of matrices (Matrigel, REDV, GFOGER, RGD)

first: Ankur

last: Singh

first: Matt

last: Mosquera

first: Rohan

last: Bareja


title: LIN28 Promotes Nucleolar/Ribosomal Functions to Repress the 2C-like Transcriptional Program in Pluripotent Stem Cells [ATAC-seq]

overall_design: Examination of the difference of chromatin openness in mouse ES cells.


title: RNase III-CLASH of multi-drug resistant Staphylococcus aureus reveals a regulatory mRNA 3’UTR required for intermediate vancomycin resistance

status: Public on Sep 14 2021

city: Sydney

first: Jai

middle: Justin

last: Tree

state: NSW

address: Rm s110 Bldg F25, UNSW, Gate 11 Botany St

department: School of Biotechnology and Biomolecular Sciences

country: Australia

institute: University of New South Wales

summary: Treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections is dependant on the efficacy of last-line antibiotics like vancomycin. Vancomycin treatment failure is most commonly linked to the emergence of vancomycin-intermediate resistance in clincal isolates (termed VISA). These isolates have not acquired resistance genes but appear to accumulate a heterogenous collection of single nucleotide polymerisms that collectively alter the physiology of the cell to increase vancomycin tolerance. Cell wall thickening is common among VISA isolates and is thought to decrease vancomycin permeability. Changes in regulatory sRNA expression have been correlated with antibiotic stress responses in VISA isolates however the functions of the vast majority of these RNA regulators is unknown. Here we have used the endoribonuclease RNase III to capture RNA-RNA interactions using an RNA proximity-dependant ligation technique termed CLASH. RNase III-CLASH uncovered hundreds of sRNA-mRNA interactions in vivo allowing functional characterisation of many sRNAs for the first time. Surprisingly, we find that an mRNA encoding an unusually long 3’UTR (here termed vigR) functions as a regulatory ‘hub’ within our RNA-RNA interaction network. We demonstrate vigR promotes expression of the cell wall lytic transglycosylase encoded by isaA through a direct mRNA-mRNA interaction. Further, we find that the vigR mRNA 3’UTR is required for cell wall thickening and that deletion of the vigR 3’UTR re-sensitises VISA to vancomycin. Our results demonstrate the utility of RNase III-CLASH for identifying new regulatory RNA functions and indicate that S. aureus may use mRNA-mRNA interactions to co-ordinate gene expression much more widely than previously appreciated.

sample_organism: Staphylococcus aureus subsp. aureus str. JKD6008

sample_organism: Staphylococcus aureus subsp. aureus str. JKD6009

overall_design:
This series consists of four different  sequencing datasets: 1. RNase III-CLASH (RNA proximity-dependant ligation) data from S. aureus JKD6009, 2. dRNA-seq mapping of RNA 5' end,  3. Term-seq mapping of RNA 3' ends, and 4. Total RNA-sequencing data

Please note that the following update has been made on Jan 2022:
GSM4811620-GSM4811625 raw data files have been replaced (the submitters found that the strains used to generate these FASTQ files had a number of SNPs that might affect the data and generated new sequencing data from re-generated strains).
The previous 'd275v_WTv_DESeq2.xls' was replaced with '2021.03.16_MUTvsWT.DEseq2_combined_output.xlsx'
Three additional samples were included

first: Daniel

last: Mediati

first: Julia

last: Wong

first: Sylvania

last: Wu

first: Ignatius

last: Pang


title: Transcriptional Characterization of healthy cornea

status: Public on Sep 04 2021

city: Freiburg

first: Clemens

last: Lange

address: Kilianstraße 5

department: Klinik für Augenheilkunde

institute: Uniklinik Freiburg

overall_design: MACE RNA sequencing of 3 human healthy corneal specimens

first: Julian

last: Wolf


title: LIN28 Promotes Nucleolar/Ribosomal Functions to Repress the 2C-like Transcriptional Program in Pluripotent Stem Cells [ChIP-seq]

first: Hua

last: Yu

overall_design: Examination of histone modifications in wide-type and Lin28a/b double knockout iPS cells by ChIP-seq.

first: Zhen

last: Sun


title: Excessive Branched Chain Amino Acid Accumulation Creates an Unfavourable Myocardial Milieu that Inhibits the Cardioprotective Effects of Implanted Mesenchymal Stem Cells in Ischemic Heart Injury

status: Public on Sep 02 2021

city: Xi'an

first: Fuyang

last: Zhang

state: Shaanxi

address: 127 West Changle Rd

department: Cardiology

institute: Xijing hospital


title: The Human Eye Transcriptome Atlas: A Searchable Transcriptome Database for Healthy and Diseased Human Eye Tissue

status: Public on Sep 05 2021


title: circRNA and mRNA transcriptome of Human Daoy and HEPM cells in the context of Hedgehog signaling activation

status: Public on Oct 13 2021

city: Huddinge

first: Ani

last: Azatyan

state: Stockholm

address: Hälsovägen 7C

department: Biosciences and Nutrition

country: Sweden

institute: Karolinska Institutet

type: Non-coding RNA profiling by high throughput sequencing

summary: Circular RNAs have largely emerged as novel regulators of human biology, including brain function and cancer development. On the other hand, the Hedgehog pathway has established roles in regulating biological processes, including tumorigenesis. Here, the circular RNA transcriptome, in the context of Hedgehog signaling activation of medulloblastoma Daoy and human embryonic palatal mesenchyme HEPM cells, was determined.

overall_design: We have identified the circRNA transcriptome of two human cell lines, the SHH medulloblastoma Daoy and the embryonic palatal mesenchyme HEPM cells, in the context of Hedgehog signaling activation with the purified ligand SHH or the small molecule SAG. Total RNA from treated and untreated cells was divided into two fractions to enrich for either linear mRNAs (poly(A) selection) or circRNAs (ribosomal RNA depletion and RNase R treatment) and subjected to Illumina RNA-seq.

first: Peter

middle: G

last: Zaphiropoulos


title: Expression data of Clone 2A cells (Cl.2A) comparing the control cells with single knockouts of FMOD and SOX2 genes, as well as a double knockout of both FMOD and SOX2 genes.

city: Copenhagen

first: victor

last: oria

state: Zealand

address: Ole Maaløes Vej 5, 4th Floor

department: BRIC

country: Denmark

institute: University of Copenhagen

summary: We used microarrays to evaluate the transcriptomic differences in Cl.2A cells following CRISPR Cas9 knockout of FMOD, SOX2, and FMOD/SOX2 genes

overall_design: 3 replicates for each of the 4 samples giving a total of 12 samples total. Replicates labeled as follows: C1, C2, C3, F1, F2, F3, S1, S2, S3, SF1, SF2, and SF3.

first: Victor

last: Oria

first: Lucia

last: Jilaveanu


title: Role of RNA Helicase gene DDX41

status: Public on Sep 03 2021

city: Cincinnati

first: Kwangmin

last: Choi

state: Ohio

address: 333 Burnet Avenue

department: Experimental Hematology & Cancer Biology

institute: Cincinnati Children's Hospital Medical Center

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: PRC2 shields naive pluripotent cells from trophectoderm and mesoderm differentiation [RNA-seq]

status: Public on Aug 23 2021

city: Solna

first: Simon

last: Elsässer

address: Tomtebodavägen 23A

department: Medical Biochemistry and Biophysics

summary: The first lineage choice made in human embryo development separates trophectoderm from the inner cell mass, which proceeds to form the pluripotent epiblast and primitive endoderm. Trophectoderm on the other hand gives rise to the placenta. Naïve pluripotent stem cells are derived from the pluripotent epiblast of the blastocyst and offer possibilities to explore how lineage integrity is maintained. Here, we discover that Polycomb repressive complex 2 (PRC2) restricts an intrinsic capacity of naïve pluripotent stem cells to give rise to trophectoderm. Through quantitative epigenome profiling, we find that broad histone H3 lysine 27 trimethylation (H3K27me3) hypermethylation is a common feature of naïve pluripotency across species. We define a previously unappreciated, naïve-specific set of bivalent promoters, featuring PRC2-mediated H3K27me3 concomitant with H3K4me3. Naïve bivalency maintains key trophectoderm transcription factors in a transcriptionally poised state that is resolved to an active state upon depletion of H3K27me3 via inhibition of the enzymatic subunits of PRC2, EZH1/2. Conversely, primed human embryonic stem cells  cannot be driven towards trophectoderm development via PRC2 inhibition. While naïve and primed hESCs share the majority of bivalent promoters, PRC2 contributes to the repression of largely non-overlapping subsets of these promoters in each state, hence H3K27me3-mediated repression provides a highly adaptive mechanism to restrict lineage potential during early human development.

overall_design: RNA-Seq was performed in triplicates from naïve and primed female H9 human pluripotent embryonic stem cells (hESC). EZH2 was inhibited with EPZ-6438 for 7 days.

first: Banushree

last: Kumar

first: Carmen

last: Navarro

first: Nerges

last: Winblad

first: Fredrik

last: Lanner


title: Different miRNA expression between melanoma and nevus tissues

status: Public on Sep 01 2021

city: Xuzhou

first: Suwei

last: Dong

address: NO.32 Meijian RD

institute: The Second Affiliated Hospital of Xuzhou Medical University

summary: Total RNA were extracted from 5 primary melanoma and 5 nevus tissues, all of which were formalin-fixed and parrffin-embedded tissues.

overall_design: Compare the different miRNA expression between melanoma and nevus tissues

first: Dong

last: Suwei

first: Li

last: Zhen


title: Different gene expression between melanoma and nevus tissues

summary: Total RNA were extracted from 5 primary melanoma and 4 nevus tissues, all of which were formalin-fixed and parrffin-embedded tissues.

overall_design: Compare the different gene expression between melanoma and nevus tissues


title: PRC2 shields naive pluripotent cells from trophectoderm and mesoderm differentiation.


title: Single-cell RNA-seq of Drosophila neuroblast tumors induced by the knockdown of prospero, E(z) and trx

status: Public on Aug 31 2021

city: Marseille

first: Cédric

last: Maurange

address: Parc Scientifique de Luminy

department: Developmental Biology Institute of Marseille (IBDM)

country: France

institute: CNRS

summary: COMPASS and Polycomb complexes are antagonistic chromatin complexes that are frequently inactivated in cancers, but how their inactivation affects the cellular hierarchy, composition and growth of tumors is unclear. Such characteristics can be systematically investigated in Drosophila neuroblast tumors in which cooption of temporal patterning induces a developmental hierarchy that confers cancer stem cell (CSC) properties to a subset of neuroblasts retaining an early larval temporal identity. Here, using single-cell transcriptomics, we reveal that the trithorax/MLL1/2-COMPASS-like complex guides the developmental trajectory at the top of the tumor hierarchy. Consequently, trithorax inactivation drives larval-to-embryonic temporal reversion and the dramatic expansion of CSCs that remain locked in a spectrum of early temporal states. Surprisingly, this phenotype is amplified by concomitant inactivation of Polycomb Repressive Complex 2 genes, unleashing tumor growth. This study exemplifies how inactivation of specific COMPASS and Polycomb complexes cooperates to impair tumor hierarchies and induce CSC plasticity and heterogeneity.

overall_design: Droplet Based Single Cell RNA sequencing library were generated for a Drosophila melanogaster tissue using the 10x Genomics Chromium Platform and sequenced on the Illumina Nextseq 500

first: Cassandra

last: Gaultier


title: Expression Data from YUGEN8 parental cell line and its clonally related isogenic variants Clone 1A, Clone 2A, and Clone 2B hereby labeled as GEN, Cl.1A, Cl.2A, and Cl.2B respectively

summary: We used microarrays to evaluate the transcriptomic differences between the parental cell line and its clonally related isogenic variants

overall_design: 3 replicates for each of the 4 samples giving a total of 12 samples total. Replicates labeled as follows: 1A1, 1A2, 1A3, 2A1, 2A2, 2A3, 2B1, 2B2, 2B3, GEN1, GEN2, and GEN3.


title: Microarray analysis of Lin- ckit+ CD150+ CD48- hematopoietic stem cells (HSCs) after treatment of mice with LPS and IFNa.

status: Public on Aug 09 2021

city: Heidelberg

first: Yasmin

middle: Essam

last: Demerdash

state: Germany

address: Im Neunheimer Feld, 280

department: Inflammatory Stress in Stem Cells

institute: DKFZ

summary: Here we aim to dissect the complex nature of the acute systemic response of HSCs to lipopolysaccharide (LPS), mimicking a bacterial infection. Acute LPS challenge transiently induced proliferation of quiescent HSCs in vivo, without yet impairing HSC function. We hypothesized that the effect of LPS on HSCs is indirectly mediated via proinflammatory cytokines. Our results showed that Acute LPS exposure depends in part on IFN signaling to activate HSCs.

overall_design: Bone marrow (BM) was isolated from mice 18h post treatment of PBS (control), LPS or IFNa treatment. This experiment included 6 biological replicated per condition. BM cells were then subjected to lineage depletion followed by sorting of Lin- ckit+ CD150+ CD48- HSCs. The RNA was then isolated from the sorted cells and hybridized on Illumina chips.

first: M

last: Essers

first: S

last: Sujer

first: A

last: Kuck

first: U

middle: M

last: Demel

first: Y


title: Translation switch from initiation to elongation needs Not4 and Not5 collaboration

status: Public on Aug 18 2021

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

institute: University of Geneva

summary: Not4 and Not5 are crucial components of the Ccr4-Not complex with pivotal functions in mRNA metabolism. Both associate with ribosomes but mechanistic insights on their function remain elusive. Here we determine that Not5 and Not4 synchronously impact translation initiation and Not5 alone alters translation elongation. Deletion of Not5 causes elongation defects in a codon-dependent fashion, increasing and decreasing the ribosome dwelling occupancy at minor and major codons respectively. This enhanced difference in codon translation velocities alters translation globally and enables normally kinetically unfavorable processes such as nascent chain deubiquitination to take place. In turn this leads to abortive translation and favors protein aggregation. These findings highlight the global impact of Not4 and Not5 in controlling the programmed local speed of mRNA translation.

overall_design: Assessment of translation through ribosome footprinting, SILAC and tRNA abundance and charging levels

first: Olesya

last: Panasenko

first: Martine

last: Collart

first: Zoya

last: Ignatova

first: Zoltan

last: Villanyi

first: Marina

last: Zagatti

first: Christine

last: Polte


title: Transcript profiling of Candida albicans tor1 kinase mutants

status: Public on Aug 17 2021

city: Dublin

first: Gary

middle: P.

last: Moran

address: Lincoln Place

department: Dental Science

country: Ireland

institute: Trinity College Dublin

summary: This study analyses the effects of truncation of the gene encoding Tor1 kinase in Candida albicans. The study involves a mutant tetO-TOR1-Del381 which has the N terminal regulator HEAT repeats deleted compared to a full length tetO-TOR1 strain and a heterozygous TOR1/tor1 control. Cell were grown in vitro in YEPD broth at 30˚C. In shut off experiments, doxycycline (30 µg.ml) was added to cultures to shut off the tetO promoter and inhibit Tor1 expression.

overall_design: Study compares (i) Mutant  tetO-TOR1-Del381 versus and full length tetO-TOR1, (ii) tetO-TOR1-Del381 versus heterozygous TOR1/tor1 control in the presence of doxycycline (2h and 8) and (iii)  tetO-TOR1 heterozygous versus TOR1/tor1 control in the presence of doxycycline (2h and 8h). All experiments with four dye swaped replicates.

middle: P


title: Hormetic response and transcriptome profiling reveal the mechanism underlying metabolic and cuticular resistance to host-specific terpenoid defenses in an emerging insect pest, Pagiophloeus tsushimanus (coleoptera: curculionidae)

status: Public on Aug 21 2021

city: Nanjing

first: Shouyin

last: Li

state: Jiangsu

address: Nanjing, China

institute: Nanjing Forestry University

summary: The resistance mechanisms evolved by insects to overcome host-plant allelochemicals is a key consideration in pest management. Camphor oil (EO) and its main component (i.e D-camphor) form a specific terpenoid-defensive system in camphor trees, Cinnamomum camphora. However, an emerging insect pest, Pagiophloeus tsushimanus has recently caused serious damage to this intractable plant species, which is largely elusive. Here, we used feeding bioassays and RNA-seq to investigate the mechanism underlying the resistance of the beetle to host-specific terpenoid defenses. Firstly, a hormetic response in both larval weight and developmental time was observed in terpenoid-feeding individuals, which is a highly generalized dose-response phenomenon in toxicology whereas occurs infrequently in the context of insect-plant interactions. Then, comparative transcriptome analysis between terpenoid-feeding and control groups indicated that both CYP450s-mediated metabolic resistance and CPs-mediated cuticular resistance were jointly employed to cope with terpenoid-induced stress. In addition, a small portion of genes involved in glucose transport pathway were up-regulated at the low D-camphor dose, suggesting an extra intake of glucose used for larval growth may contribute to a hormetic response. These findings probably implied that the dual terpenoid-resistance mechanisms existing in this specialist is an essential precondition for hormetic response in larval growth, ultimately contributing to successfully colonize host camphor trees with impunity. Overall, our study will open new avenues for understanding the insect-plant coevolutionary adaptation and developing durable pest control strategies.

overall_design: mRNA profiles of larvae feeding on terperoid-infused diet and terperoid-free diet

first: Jingting

last: Wang

first: Cong

last: Chen

first: Hui


title: Spatial transcriptomics of human brain metastases

status: Public on Aug 04 2021

city: Houston

first: William

last: Hudson

state: TX

address: 1 Baylor Plaza

department: Molecular and Cellular Biology

institute: Baylor College of Medicine

summary: Spatial transcriptomics of six surgically-resected human brain metastasis samples

overall_design: After surgical resection, parts of six human brain metastases were embedded in OCT and frozen in a dry ice/2-methylbutane bath. 10 μM sections were placed on Visium gene expression slides which were stored at -80C until use. Slides were methanol fixed and stained with H&E and imaged at 10X on a Biotek Lionheart microscope. Tissues were permeabilized and libraries generated according to the manufacturer's protocols. Images for all samples are available in all_spatial_images.tar.gz.

middle: H


title: PRC2 shields naive pluripotent cells from trophectoderm and mesoderm differentiation [ChIP-seq]

first: Simon

middle: J

last: Elsässer

overall_design: MINUTE-ChIP was performed in triplicates from naïve and primed female H9 human pluripotent embryonic stem cells (hESC). EZH2 was inhibited with EPZ-6438 for 7 days.

first: Banushree

last: Kumar

first: Carmen

last: Navarro

first: John

last: Schell

first: Fredrik

last: Lanner


title: Disrupted Circadian Oscillations in Type 2 Diabetes are Linked to Altered Rhythmic Mitochondrial Metabolism in Skeletal Muscle

first: Ali

last: Altintas

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

institute: Copenhagen University

overall_design: Refer to individual Series


title: Disrupted Circadian Oscillations in Type 2 Diabetes are Linked to Altered Rhythmic Mitochondrial Metabolism in Skeletal Muscle [RNA-seq]

summary: Circadian rhythms are generated by an auto-regulatory feedback loop composed of transcriptional activators and repressors. Disruption of circadian rhythms contributes to Type 2 diabetes (T2D) pathogenesis. We elucidated whether altered circadian rhythmicity of clock genes is associated with metabolic dysfunction in T2D. Transcriptional cycling of core clock genes BMAL1, CLOCK, and PER3 was altered in skeletal muscle from individuals with T2D and this was coupled with reduced number and amplitude of cycling genes and disturbed circadian oxygen consumption. Inner-mitochondria associated genes were enriched for rhythmic peaks in NGT, but not T2D, and positively correlated with insulin sensitivity. ChIP-sequencing identified CLOCK and BMAL1 binding to inner-mitochondrial genes associated with insulin sensitivity, implicating regulation by the core clock. Inner-mitochondria disruption altered core-clock gene expression and free-radical production, phenomena that were restored by resveratrol treatment. We identify bi-directional communication between mitochondrial function and rhythmic gene expression, processes which are disturbed in diabetes.

overall_design: Skeletal muscle biopsies were obtained from men with either T2D or normal glucose tolerance (NGT). Primary myotubes cultures were prepared, synchronized and harvested every 6 hours over 42 hours and the transcriptome was analyzed by RNA-sequencing.

first: Brendan

last: Gabriel

last: Altıntaş

first: Laura

last: Sardon-Puig

first: Rhianna

middle: C

last: Laker

first: Romain

last: Barrès

first: Nicolas

last: Pillon

first: Anna

last: Krook

first: Juleen

last: Zierath


title: Comparison between calorie-restricted and time-restricted without calorie restriction

status: Public on Aug 16 2021

city: Madison

first: Heidi

middle: Hayang

last: Pak

state: WI

address: 2500 Overlook Terrace

department: Medicine

institute: University of Wisconsin-Madison

summary: Recently, it has been shown that fasting for a portion of each day has metabolic benefits, and promotes lifespan. These findings complicate the interpretation of rodent CR studies, which typically feed the animals only once per day; as they rapidly consume their food, such a regimen collaterally imposes fasting.

overall_design: Here, we addressed if fasting alone can recapitulate the response of a CR diet, without calorie restriction at the transcriptional level.

first: Dudley

last: Lamming


title: Single cell RNA-sequencing of human brain metastasis-infiltrating T cells

last: Hudson

summary: The goal of this study is to understand the biology of brain metastasis-infiltrating T cells.

overall_design:
Single cell suspensions were generated from surgically-resected metastatic brain tumors. For five patients (5, 14, 15, 16, and 17), tumor-infiltrating PD-1+ CD8 T cells were isolated by FACS from each patient, combined with patient-matched circulating naive CD8 T cells and subjected to scRNA-seq with VDJ sequencing. Hashing antibodies were used to distinguish naïve (Totalseq C0251) from tumor-infiltrating (Totalseq C0252) cells. Separate captures and sequencing libraries were generated for each patient. An additional scRNA-seq experiment was performed on pooled tumor-infiltrating total (CD4 + CD8) T cells from patient 16 (Totalseq C0251), patient 26 (Totalseq C0252), and patient 27 (Totalseq C0253). Circulating T cells were also sorted from a healthy donor and included with this experiment (Totalseq C0254). Cells were pooled, two captures were performed, and libraries were sequenced. In this latter experiment, cells were also stained with anti-CD8 Totalseq C0046, anti-CD4 Totalseq C0045, and anti-PD-1 biotin followed by streptavidin Totalseq C0961.
Please note that each processed data was generated from GEX, CITE-seq, and VDJ libraries, and is linked to the corresponding GEX sample records.


title: Global gene expression of pediatric acute myeloid leukemia

status: Public on Aug 01 2021

first: Charles

middle: Yang

last: Lin

department: Molecular and Human Genetics

summary: Somatic mutations are rare in pediatric AML (pAML), indicating alternate strategies are needed to identify new, pediatric AML-specific, druggable targets. We defined the enhancer landscape of 22 pAML patient samples and observed many known leukemia regulators are SE-associated in pAML. We confirmed that the expression of several of these SE-associated genes correlated with gene expression by RNA-Seq. The retinoic acid receptor alpha (RARA) gene was differentially regulated in our cohort and present in all cyto/molecular subtypes tested, totaling 64% of the pAML samples. RARA SE-positive pAML cell lines and samples had higher RARA mRNA levels than RARA SE-negative samples and also were specifically sensitive to the synthetic RARA agonist tamibarotene in vitro, with halted proliferation and upregulated retinoid target genes. Tamibarotene prolonged survival and suppressed the leukemia burden of a RARA SE-positive pAML patient-derived xenograft (PDX) mouse model compared to a RARA SE-negative PDX. These data demonstrate the utility of leveraging chromatin regulation to identify new dependencies in pediatric AML and specifically lay the preclinical foundation for a tamibarotene trial in children with relapsed/refractory AML.

overall_design: Global bulk RNA-sequencing of pediatric acute myeloid leukemia samples

first: Joanna

middle: S

last: Yi

middle: Y

first: Jost

last: Koren

first: Oscar

last: Sias-Garcia

first: Monika

middle: W

last: Perez

first: Woojun

middle: D

last: Park


title: Whole-transcriptome RNA sequencing of skin reveals innate immunity differences between wild-type and yellow mutant rainbow trout

city: Xining

first: Delin

last: Qi

address: No. 251, Ningda Road

institute: Qinghai university

summary: Rainbow trout (Oncorhynchus mykiss) is an important aquaculture fish species that is farmed worldwide, and it is also the most widely cultivated cold water fish in China. This species, a member of the salmonidae family, is an ideal model organism for studying the immune system in fish. Two phenotypes of rainbow trout are widely cultured; wild-type rainbow trout with black skin (WR_S) and yellow mutant rainbow trout with yellow skin (YR_S). Fish skin is an important immune organ, however, little is known about the differences in skin immunity between WR_S and YR_S in a natural flowing water pond aquaculture environment, and very few studies were conducted to investigate the ceRNA mechanism for fish skin.

overall_design: In the present study, whole-transcriptome sequencing was performed to uncover global molecular expression differences of skin immunity between WR_S and YR_S in a natural flowing water pond culture environment at both mRNAs and ncRNAs levels.

first: Jinqiang

last: Huang

first: Shenji

last: Wu


title: Genome-wide mapping of histone H3 lysine 27 acetylation in acute myeloid leukemia

summary: Somatic mutations are rare in pediatric AML (pAML), indicating alternate strategies are needed to identify new, pediatric AML-specific, druggable targets. We defined the enhancer landscape of 22 pAML patient samples and observed many known leukemia regulators are SE-associated in pAML. The retinoic acid receptor alpha (RARA) gene was differentially regulated in our cohort and present in all cyto/molecular subtypes tested, totaling 64% of the pAML samples. RARA SE-positive pAML cell lines and samples had higher RARA mRNA levels than RARA SE-negative samples and also were specifically sensitive to the synthetic RARA agonist tamibarotene in vitro, with halted proliferation and upregulated retinoid target genes. Tamibarotene prolonged survival and suppressed the leukemia burden of a RARA SE-positive pAML patient-derived xenograft (PDX) mouse model compared to a RARA SE-negative PDX. These data demonstrate the utility of leveraging chromatin regulation to identify new dependencies in pediatric AML and specifically lay the preclinical foundation for a tamibarotene trial in children with relapsed/refractory AML.

overall_design: H3K27ac ChIP-seq in untreated pediatric AML primary patient samples and cell lines

last: Vrabic Koren


title: Global RNA-sequencing of a pediatric AML primary sample treated with Tamibarotene or vehicle

summary: The purpose of this study was to assess the global transcriptional changes in a pediatric AML primary sample treated with Tamibarotene. This patient sample has a retinoic acid receptor alpha (RARA) super-enhancer, which is correlated with higher RARA mRNA levels and increased sensitivity to Tamibarotene in vitro and in vivo (Patient-derived xenograft mouse model).

overall_design: There were 4 replicates per treatment condition: Tamibarotene or DMSO (as a control) for the 1 patient sample


title: Asymmetric Synthesis of Flavanols via Cu-Catalyzed Kinetic Resolution of Chromenes and Their Anti-Inflammatory Activity

status: Public on Jul 30 2021

city: Hong Kong

first: Zihao

last: Wang

address: 224 Waterloo Road

department: School of Chinese Medicine

country: Hong Kong

institute: Hong Kong Baptist University

summary: We report a highly efficient kinetic resolution of chromenes for the first time via a Cu-catalyzed asymmetric hydroboration. This novel approach features simple one-pot synthesis of chiral flavan-3-ols containing two vicinal stereogenic centers via a highly efficient kinetic resolution pathway (s factor up to 1060, >99% ee for most substrates and products, exclusively trans products). In addition, the anti-inflammation effects of these diversified flavan-3-ols have been further studied by the in vitro experiments and RNA-sequencing (RNA-seq) analysis. The modified flavan-3-ol natural product derivatives showed inhibitory effects on the expression and secretion of pro-inflammation cytokines including IL-1β, IL-6 and TNF-α, as well as inhibiting the inflammation responses through downregulating the gene transcriptions closely related to IL-17 signaling pathway, PI3K-Akt signaling pathway and TNF signaling pathway, which suggest these newly synthesized compounds are potent lead compounds for treating inflammation diseases.

overall_design: mRNA profiles of RAW264.7

first: Qingjing

last: Yang

first: Jun

first: Zhaoxiang

last: Bian


title: Hypoxia inducible factors individually facilitate inflammatory myeloid metabolism and inefficient cardiac repair

status: Public on Jul 24 2021

city: Chicago

first: Connor

last: Lantz

state: IL

address: 303 E. Chicago Ave. Ward 4-075

institute: Northwestern University

summary: Following myocardial infarction, tissue ischemia leads to activation of hypoxia inducible factors. DeBerge et al. demonstrate that HIF-1a and HIF-2a activation in myeloid cells antagonizes cardiac repair pathways through cleavage of cardioprotective MerTK and suppression of anti-inflammatory mitochondrial metabolism, respectively.

overall_design: scRNAseq of 1 deidentified patient with ischemic cardiomypapthy

first: Matthew

last: DeBerge

first: Edward

middle: B

last: Thorp


title: Defining the Transcriptional Control of Pediatric AML Highlights RARA as a Super-Enhancer Regulated, Druggable Dependency

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


title: ARID1A loss derepresses human endogenous retrovirus-H to modulate BRD4-dependent transcription

status: Public on Jul 21 2021

city: Leiden

first: Jiale

last: Chen

address: Einsteinweg 55

institute: Leiden University

summary:
Purpose: The transposable elements (TEs) through evolutionary exaptation have become an integral part of human genome, offering ample regulatory sequences and shaping chromatin 3D architecture. While the functional impacts of TE-derived sequences on early embryogenesis are recognized, their role in malignancy has only started to emerge.
Results: Here we show that many TEs, especially the pluripotency-related endogenous retrovirus H (HERVH), are abnormally activated in colorectal cancer (CRC) samples. The transcriptional upregulation of HERVH is associated with mutations of several tumor suppressors including ARID1A. Knockout of ARID1A in CRC cells leads to increased accessibility at HERVH loci and enhanced transcription, which is dependent on ARID1B. Suppression of HERVH in CRC cells and patient-derived organoids impairs tumor growth. Mechanistically, HERVH transcripts colocalize with nuclear BRD4 foci, modulate their dynamics, and co-regulate many target genes.
Conclusions: Altogether, we uncover a critical role for ARID1A in restraining HERVH, which can promote tumorigenesis by stimulating BRD4-dependent transcription when ARID1A is mutated.

overall_design: mRNA profiles of HCT116 wild type (WT), HCT116 ARID1A Knockout(KO), and HCT116 ARID1A KO and HERVH knockdown(KD) cells.

first: Xiaoyun

last: Lei

first: Chunhong

last: Yu

first: Kai

last: Yuan


title: Cellular abundance shapes function in piRNA-guided genome defense

city: Bethesda

first: Pavol

last: Genzor

state: MD

address: 6720A Rockledge Drive, Suite 100

department: ACESO

institute: Henry M Jackson Foundation

summary: Abstract: Akin to an adaptive immune system, PIWI-interacting small RNAs (piRNAs) protect the integrity of germline genomes by silencing mobile genetic elements.  Precision of piRNA silencing is crucial, as failing to silence a single active transposon or wrongly silencing an essential gene threaten the survival of the species.  How piRNAs discriminate between self and nonself and adapt during evolution remains a central question in reproductive biology.  Target specificity is determined by basepairing complementarity and places the sequence of piRNAs at the heart of piRNA-guided self/nonself discrimination.  Here, we characterize millions of piRNA sequences in flies and mice in search for conserved patterns that determine the specificity of piRNA-guided silencing.  We identify two groups of piRNA sequences that differ in abundance, complexity and function.  The first group represents the top 1% most abundant sequences and drives piRNA-silencing in a reporter assay.  In contrast, the second group of sequences does not function in every cell, every individual or every generation.  These rare piRNAs establishes cell-to-cell polymorphism and present opportunity for adaptation to novel genomic invaders during evolution.  A model emerges that entrust a selected group of piRNA sequences to establish self/nonself discrimination for future generations, and another group to cultivate polymorphisms.

overall_design: Piwi-associated RNAs (piRNAs) were immunoprecipitated from fly ovarian somatic sheet cells (OSC), cloned using ten unique molecular identifiers (UMIs), and sequenced to large depth using next generation sequencing. The sequence identity and sequence abundance characteristics of individual piRNAs accross three biological replicates were then analyzed.

first: Parthena

last: Konstantinidou

first: Daniel

last: Stoyko

first: Amirhossein

last: Manzourolajdad

first: Celine

last: Marlin Andrews

first: Alexandra

middle: R

last: Elchert

first: Constantinos

last: Stathopoulos

first: Astrid

last: Haase