title: Infiltrating Monocytes Drive Cardiac Dysfunction in a Cardiomyocyte-Restricted Model of SARS-CoV-2 Infection

city: Saint Louis

first: Kory

last: Lavine

state: Missouri

address: 660 S. Euclid Ave

department: Internal Medicine - Cardiology

institute: Washington University School of Medicine

summary: Cardiovascular manifestations of COVID-19 include myocardial injury, heart failure, and myocarditis and are associated with long-term disability and mortality. SARS-CoV-2 RNA and antigens are found in the myocardium of COVID-19 patients, and human cardiomyocytes are susceptible to infection in cell or organoid cultures. While these observations raise the possibility that cardiomyocyte infection may contribute to the cardiac sequelae of COVID-19, a causal relationship between cardiomyocyte infection and myocardial dysfunction and pathology has not been established. Here, we generated a mouse model of cardiomyocyte-restricted infection by selectively expressing human angiotensin converting enzyme 2 (hACE2), the SARS-CoV-2 receptor, in cardiomyocytes. Inoculation of Myh6-Cre Rosa26LSL-hAce2 mice with SARS-CoV-2 resulted in viral replication within the heart, accumulation of macrophages, and moderate left ventricular (LV) systolic dysfunction. Cardiac pathology in this model was transient and resolved with viral clearance. Blockade of monocyte trafficking reduced myocardial viral replication and macrophage accumulation and suppressed the development of LV systolic dysfunction. These findings establish a mouse of model of SARS-CoV-2 cardiomyocyte infection that recapitulates features of cardiac dysfunctions of COVID-19 and suggests that both replication and resultant innate immune responses contribute to pathology

overall_design: bulk RNAseq of murine hearts at 3 days post inoculation from naïve ctrl mice [MYH6-Cre (-) Rosa-LSL-hACE2 (+/-)], SARS-CoV-2 inoculated ctrl mice [MYH6-Cre (-) Rosa-LSL-hACE2 (+/-)] and SARS-CoV-2 inoculated hACE2-KI mice [MYH6-Cre (+) Rosa-LSL-hACE2 (+/-)]

first: Oleksandr

last: Dmytrenko

first: Attila

last: Kovacs

first: Markus

last: Cicka

first: Meizi

last: Liu

first: Andrea

last: Bredemeyer

first: Matthias

last: Mack

first: Michael

last: Diamond

middle: J


title: β-glucan alleviates infective intestinal inflammation via activating Th17 cells in a teleost fish

status: Public on Dec 31 2023

city: Shanghai

first: dahai

last: Yang

address: No.130, Meilong Road, Xuhui District

country: China

institute: East China University of Science and Technology

type: Expression profiling by high throughput sequencing

summary: We established a bacteria infective intestinal inflammation in turbot (Scophthalmus maximus). And found that β-glucan could significantly alleviate the phenotype of turbot intestinal inflammation. We performed single cell transcriptome analysis to study bacteria infective intestinal inflammation and the effects of β-glucan. Furthermore, we revealed that β-glucan through activates Th17 cells to alleviate intestinal inflammation in turbot.

first: Jin

first: Shu

last: Cui

first: Zhuang

last: Wang

first: Yuanxing

last: Zhang

first: Qin

first: Dahai


title: Hexamethylene Amiloride synergizes with Venetoclax to induce lysosome-dependent cell death in acute myeloid leukemia

city: Guangzhou

first: Kexiu

last: Huang

address: 613W Huangpu Rd

institute: jinan university

summary: Tumors maintain an alkaline intracellular environment to enable rapid growth. The proton exporter NHE1 participates in maintenance of this pH gradient. However, whether targeting NHE1 could inhibit the growth of tumor cells remains unknown. Here, we report that the NHE1 inhibitor Hexamethylene amiloride (HA) efficiently suppresses the growth of AML cell lines. Moreover, HA combined with venetoclax synergized to efficiently inhibit the growth of AML cells. Interestingly, lysosomes are the main contributors to the synergism of HA and venetoclax in inhibiting AML cells. Most importantly, the combination of HA and venetoclax also had prominent anti-leukemia effects in both xenograft models and bone marrow samples from AML patients. In summary, our results provide evidence that the NHE1 inhibitor HA or its combination with venetoclax efficiently inhibits the growth of AML in vitro and in vivo.

overall_design: For RNA-seq analysis, MV4-11 cells were treated in triplicate with DMSO, 0.1 µM venetoclax, 10 µM HA, or combo (0.1 µM Venetocalx plus 10 µM HA) for 48 h.A total of 12 samples were sequenced using the Illumina NovaSeq 6000 platform.

first: Xinya

last: Jiang

first: Juan

last: Du

first: Hui

last: Zeng


title: The role of PCD-related circRNA/miRNA/mRNA regulatory network in the HF with AF

city: Taiyuan

first: Ziyang

last: Li

address: 56 South Xinjian Street

institute: Shanxi Medical University

summary: Background: Atrial fibrillation (AF), a critical health and economic issue is common in patients with heart failure (HF). Meanwhile, HF is a leading complication of nonvalvular atrial fibrillation (NVAF), and the presence of both conditions is associated with worsen outcomes. Accumulating evidence has indicated that messenger RNA (mRNA), microRNA (miRNA) and circular RNA (circRNA) play vital roles in the occurrence and progression of HF and AF. However, the underlying molecular mechanism of HF with AF remains elusive. We aimed to investigate the role of circRNA/miRNA/mRNA regulatory network in HF with AF through High-throughput sequencing and bioinformatics analysis. Methods: Peripheral blood mononuclear cells (PBMCs) were obtained from 4 patients who had heart failure with atrial fibrillation (HF /AF group) and 4 matched healthy subjects. RNA sequencing was performed to get circRNAs and mRNAs. miRNAs were obtained through miRanda and HMDD databases. qRT-PCR was used to verify our data. R software was employed for Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. The PPI network was completed using STRING. Immune infiltration analysis was performed using cibersort method. The ceRNA network of circRNA/miRNA/mRNA was constructed by Cytoscape.  Results: Differential expression analysis showed that circRNAs (137 upregulated and 31 downregulated) and mRNAs (534 upregulated and 255 downregulated) were considered as significantly different between HF with AF group and control group. Immune infiltration analysis demonstrated that macrophages were obviously upregulated and mast cells were significantly downregulated in PBMCs of the HF/AF group. GO and KEGG analyses showed that HF with AF-related mRNAs were abundant in the pathway of programmed cell death (PCD) and myocardial remodeling. So we confirm that hsa_circ_0047870/hsa-miR-34a-5p/SMPD1, hsa_circ_0127340/hsa-miR-192-3p/FBXW5, hsa_circ_0002484/hsa-miR-26b-3p/PYCARD, hsa_circ_0047870/hsa-miR-20b-3p/HTRA2 and hsa_circ_0004027/hsa-miR-26a-5p/HIF1A ceRNA axes could promote the development of HF with AF through the PCD-related pathway.  Conclusions: We suggested that the imbalance of immune cell composition in PBMCs may play an initial role in the progression of HF with AF. The PCD-related ceRNA regulatory network may be the potential therapeutic target in the occurrence and progression of HF with AF. The circRNAs could serve as novel diagnostic markers.

first: Wenli

last: Ren

first: Min

last: Guo


title: Differential activation states of direct pathway striatal output neurons associated with the development of L-DOPA-induced dyskinesia I

city: Birmingham

first: David

last: Figge

state: AL

address: 1719 6th Ave. S, CIRC 520

department: Neurology

country: USA

institute: University of Alabama-Birmingham

summary: L-DOPA-induced dyskinesia (LID) is a debilitating motor side effect arising from chronic dopamine replacement therapy with L-DOPA for the treatment of Parkinson disease (PD). We found repeated L-DOPA exposure induces unique transcriptional behavior in striatal neurons that is associated with the development of dyskinetic behaviors. These results suggest the development of a long-term neuronal engram underlying the persistence of LID .

overall_design: Nuclei from 3-4 dorsal striata pooled per sample, and sorted for Live Nuclei  on a BD FACsAria. Sorted nuclei were loaded onto the 10X Chromium 303 platform (10X genomics), and libraries were constructed using the Single Cell 3′ 304 Reagent Kit V2 according to the manufacturer’s instructions. Two biological replicates for each group were processed separately.

first: Karen

middle: E

last: Jaunarajs


title: Gene expression data from muscle-invasive bladder cancer samples II

city: Bangor

first: Tim

last: Smith

address: Dean Street

department: School of Computer Science and Engineering

country: United Kingdom

institute: University of Bangor

summary:
Gene signatures based on the median expression of a preselected set of genes can provide prognostic and treatment outcome prediction and so be valuable clinically.
Different health care services use different gene expression platforms to derive gene expression data. Here we have derived gene expression data using a microarray platform.

overall_design: RNA extracted from FFPE blocks from patients with muscle-invasive bladder cancer and full transcriptome analysis on Clariom S microarray platform.

middle: D

first: Brian

last: Lane

first: Elisabet

last: More

first: Nuradh

last: Joseph

first: Hitesh

last: Mistry

first: J

last: Irlam-Jones

first: Kimberley

last: Reeves

first: Peter

last: Hoskin

first: Ananya

last: Choudhury

first: Catharine

middle: L

last: West

first: Yee

middle: P

last: Song

first: Mark

last: Reardon

first: Syud

middle: A

last: Hussain

first: Helen

last: Denley

first: Emma

last: Hall

first: Nicolas

last: James

first: Robert

last: Huddart

first: Nuria

last: Porta


title: Decoding the gene promoters binding with BRD3 in LPS-primed THP1 monocytes

city: Changsha

first: Nian

last: Wang

state: Hunan

address: No.110 Xiangya Road

institute: Central south university

type: Genome binding/occupancy profiling by high throughput sequencing

summary: To screen the genes regulated by BRD3 in the THP1 monocytes induced by LPS, THP1 monocytes were treated by LPS for 1 hour in the presence or absence of OTX015

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for BRD3 in  the THP1 monocytes after LPS stimulation

first: Daolin

last: Tang


title: Structure-guided design of a selective inhibitor of the methyltransferase KMT9 with cellular activity

city: Freiburg

first: Eric

last: Metzger

address: Breisacherstr. 66

country: Germany

institute: Uniklinik-Freiburg

summary: Inhibition of epigenetic regulators by small molecules is an attractive strategy for cancer treatment. Recently, we characterised the role of lysine methyltransferase 9 (KMT9) in prostate, lung, and colon cancer. Our observation that the enzymatic activity was required for tumour cell proliferation identified KMT9 an attractive therapeutic target. Here, we report the development of the first-in-class, potent and selective KMT9 inhibitor (compound 4, KMI169) through structure-based drug design. KMI169 functions as a bi-substrate inhibitor targeting the SAM and substrate binding pockets of KMT9 and exhibits high potency, selectivity, and cellular target engagement. KMT9 inhibition selectively downregulates target genes involved in transcription and cell cycle regulation and impairs proliferation of tumours cells including castration- and enzalutamide-resistant prostate cancer cells. Together, KMI169 represents a valuable tool to probe cellular KMT9 functions and paves the way for the development of clinical inhibitors as therapeutic options to treat malignancies such as therapy-resistant prostate cancer.

overall_design: PC-3M prostate tumour cells were cultured 4 days in presence of DMSO, 360 nM of the KMT9 inhibitor KMI169, or 360 nM of the negative Ctrl compound KMI169 Ctrl prior to analyse the transcriptome.

first: Roland

last: Schüle

first: Sheng

first: Dominica

last: Willmann


title: Assessment of miRNA expression levels in an HCM mouse model containing R719W mutation in Myh6 gene

status: Public on Jan 03 2024

city: London

first: Seda

last: Eminaga

address: Westminster Bridge Road, St Thomas's Hospital

department: Cardiovascular Division

institute: King's College London

type: Non-coding RNA profiling by high throughput sequencing

summary: We compared the expression levels of miRNAs in left ventricular heart tissue from HCM vs WT mice, using gene expression profiling data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Cyclosporin(CsA)-treated WT (n=3) and HCM mutant mice (n=3).

first: Danos

last: Christodolou


title: FMR1 bound transcripts in mouse fetal oocytes

city: San Francisco

first: Diana

last: Laird

state: CA

address: 35 Medical Center Way

institute: UCSF

summary: Investigating FMR1 bound transcripts in fetal mouse ovaries through RNA Immunoprecipitation Sequencing (RIP-seq)

overall_design: Input samples are whole mouse E16.5 ovary from Fmr1 KO (samples_1-3) and WT littermate (samples_4-6); RIP samples are RNA Immunoprecipitation Sequencing (RIP-seq) from Fmr1 KO E16.5 ovary (samples_1-3) and WT E16.5 ovary (samples_4-6).

first: Suping

last: Peng

first: Jing

last: Li

first: Jocelyn

last: Crawford


title: Multiplexed transcriptional profiling to Dermatophagoides House Dust Mites allergens in human epithelium cells

city: Taichung city

first: Yu-Fan

last: Liu

address: No.110. Sec 1, Jianguo N. Rd.

department: Biomedical sciences

country: Taiwan

institute: Chung Shan Medical University

summary: Allergic asthma, a chronic disease-causing inflammation in the airways, is a significant public health concern. Our research team discovered that more than 80% of allergic children in central Taiwan were sensitized to various house dust mites (HDMs). This investigation focuses on how the crude extracts of HDMs affect human epithelium BEAS-2B cells to understand the early fundamental mechanisms for preventing allergic diseases. Therefore, RNA-seq analysis revealed that three Dermatophagoides HDMs allergens activate a common Toll-like receptor signaling pathway in human epithelial cells within a 4-hour treatment. During this process, the nuclear transcription factor NF-κB translocated into the cell nucleus within 30 minutes of allergen stimulation, triggering the expression of pro-inflammatory genes such as IL-6 and IL-8 over 4 hours. Additionally, treating the cells with specific Dermatophagoides microceras (Der m) allergens, there was an upregulation of genes in regulating type 1 diabetes mellitus signaling pathways, mediating IL-12A inflammation. Moreover, an increase in gene sets related to cilia function and the microtubule cytoskeleton in human epithelial cells following treatment combined with Der m allergens and Dexamethasone. Furthermore, OMICs analysis investigates the effects of HDMs allergenic stimulation on the human epidermal cells. This process aims to enhance our understanding of the cellular molecular mechanisms underlying potential targets and bioactive substances in precision medicine for treating asthma caused by HDMs allergens.

overall_design: To investigate the fundamental mechanism underlying the impact of crude extracts from HDMs on BEAS-2B cells, we treated the cells with specific Dermatophagoides HDMs allaergens. We subsequently conducted gene expression profiling analysis by utilizing RNA-seq data obtained from the cells at two time points, 4hr and 24hr post-stimluation. Eventually, comparative gene expression profiling analysis of RNA-seq data for BEAS-2 was perfomed.


title: Identification of circRNA expression profiles and functional networks in parotid gland of type 2 diabetes mouse

city: Beijing

first: Yan

last: Huang

address: No.22 ,Zhongguancun South Avenue, Haidian District

institute: Peking University School and Hospital of Stomatology

summary:
To identify Circular RNA and mRNA expression profile in the parotid gland of mouse with type 2 diabetes, and predict the potential role of differently expressed circular RNA in the dysfunction of diabetic parotid gland
Four 16-week-old male leptin receptor-deficient db/db mice weighting 40-55 g (a model of spontaneous type 2 DM) and age-matched db/m mice weighting 25-30 g were purchased from Changzhou Cavens Laboratory Animal Ltd. After anesthesia with an intraperitoneal injection of 1% pentobarbital sodium solution at 0.5 g/kg, the fresh PG samples were extracted and frozen with liquid nitrogen for 1-2 min, then stored at ‑80°C.

overall_design: Guang-Yan,Yu

first: Ruo-Lan

last: Xiang


title: Stanniocalcin-1 mediates aortic valve calcification via promoting osteochondrogenic differentiation from valve interstitial cells

city: Toon

first: Koh-ichi

last: Nakashiro

state: Ehime

address: 454 Shitsukawa

department: Oral and Maxillofacial Surgery

country: Japan

institute: Ehime University Graduate School of Medicine

summary:
Although calcific aortic valve stenosis (CAVS) is the most prevalent valvular heart disease, the molecular mechanisms underlying aortic valve calcification remain unknown. Here, we found a significant elevation in stanniocalcin-1 (STC1) expression in the valve interstitial cells (VICs) of calcific aortic valves by combined analysis of our comprehensive gene expression data and microarray datasets reported previously. Immunohistochemical staining showed that STC1 was located around the calcific area in the aortic valves of patients with CAVS. In vitro experiments using inhibitors and siRNA targeting osteoblast differentiation signaling revealed that activation of the Akt/STC1 axis was essential for runt-related transcription factor 2 (RUNX2) induction in the VICs. RNA sequencing and bioinformatics analysis of STC1-knocked down VICs in osteoblast differentiation medium resulted in silencing of the induction of osteoarthritis signaling-related genes, including RUNX2 and COL10A1. STC1 depletion in the murine CAVS model improved aortic valve dysfunction with high peak velocity and valve thickening and suppressed the appearance of osteochondrocytes. STC1-deficient mice also exhibited complete calcification abolishment, although partial valve thickening by aortic valve injury was observed. Our findings suggest that STC1 may be a critical factor in determining valve calcification and a novel target for preventing the transition to severe CAVS with calcification.
We analyzed the gene expression profiles of the valve interstitial cells (VICs) isolated from noncalcific and calcific areas in calcific aortic valve stenosis (CAVS) donors using a gene microarray.

overall_design: We compared the gene expression profiles of the valve interstitial cells (VICs) isolated from noncalcific and calcific areas in three calcific aortic valve stenosis (CAVS) donors with calcification.


title: Identification of unique and distinct regulators of Tfh cells elicited by different stimulations [ATAC-seq]

city: Buffalo

first: Jianmin

state: NY

address: Elm and Carlton Streets

department: Bioinformatics and Biostatistics

institute: Roswell Park Comprehensive Cancer Center

summary: To investigate/identify other factors that is commonly or distinctively required for Tfh cells generated under different conditions.

overall_design:
We then adoptively transfer SMARTA cells (CD45.2+) into CD45.1 mice, part of recipients are immunized with protein, and on day 5 (peak response), isolate Tfh and non Tfh cells from draining lymph nodes
meanwhile, The other part of recipients are infected with LCMV, and on day 5 (not peak response, but the Tfh and non-Tfh cell fate are committed), isolate Tfh and non-Tfh cells from the spleen by cell sorting.

first: Fengyin

first: Hai-Hui

last: Xue


title: DNA methylation of Relapsed/Refractory AML

city: Los Angeles

first: Gangning

last: Liang

address: 1441 Biggy street

department: Urology

institute: USC Keck school of medicine

type: Methylation profiling by genome tiling array

summary: Genome wide DNA methylation profiling of blood and bone marrow of Pediatric Patients with Relapsed/Refractory Acute Myeloid Leukemia. The Illumina Infinium EPIC Human DNA methylation Beadchip was used to obtain DNA methylation profiles across over 860,000 CpGs.

overall_design: Bisulphite converted DNA from the 4 samples were hybridised to the Illumina Infinium EPIC Human Methylation Beadchip.

first: Hong-Tao


title: gene expression profiling

city: luzhou

address: No. 25 Taiping Street

institute: The Affiliated Hospital of Southwest Medical University

summary: A number of homeobox genes have been found to be implicated in the development of various cancers. Here, we investigated the role of engrailed 2 (EN2), a member of the homeobox gene superfamily, in non-small cell lung cancer

overall_design: EN2 overexpression PC9 cell lines and their vector control cell lines were analyzed. EN2 overexpression A549 cell lines and their vector control cell lines were analyzed. Each cell line had two replicates.

first: Jie

last: Jiang

first: Xiaoyan

last: Wang

first: Yong

last: Cao

first: Li

first: Xueqin

last: Song

first: Fang

first: Mingying

first: Minglan

last: Yu

first: Feng

last: Chen

first: Haisu

last: Wan


title: The soil emergence-related transcription factor PIF3 regulates root penetration by interacting with the receptor kinase FER

first: Fan

last: Xu

address: N.O. 52 Tianma street

institute: Hunan University

summary: The cotyledons of etiolated seedlings from terrestrial flowering plants must emerge from the soil surface, while roots must penetrate the soil to ensure plant survival. We show here that the soil emergence related transcription factor PHYTOCHROME-INTERACTING FACTOR 3 (PIF3) regulates root penetration via transducing external signals perceived by the receptor kinase FERONIA (FER) in Arabidopsis thaliana. The loss of FER function in the fer-4 mutant resulted in a severe defect in root penetration into hard soil or medium. Single-cell RNA-seq profiling of roots revealed a distinct cell clustering pattern, especially for root cap cells, and revealed PIF3 as a putative FER-regulated transcription factor. Biochemical, imaging, and genetic experiments confirmed that PIF3 is required for root soil penetration. Moreover, FER interacted with and stabilized PIF3, which then modulated the expression of mechanosensitive ion channels and the sloughing of outer cells in the root cap. We propose a novel mechanism of soil penetration by plant roots.

overall_design: Col-0 mock, Col-0 RALF1, fer-4 mock  and fer-4 RALF1; each group has three replicates; 12 samples in total.

first: Yingbin


title: Identification of unique and distinct regulators of Tfh cells elicited by different stimulations

first: Jianmin

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

overall_design: Refer to individual Series


title: Gene expression profile at single cell level of leukocytes from the liver and spleen after CBL0137 treatment in mice bearing 4T1 tumor

first: Minhyung

last: Kim

address: Elm&Carlton Streets

summary: We used single cell RNA sequencing (scRNA-seq) to analyze the tumor microenviromental changes in the liver and spleen 5 days after different doses of CBL0137 injection.

overall_design: Leukocytes were isolated from the liver and spleen using a density gradient medium and anlyzed by scRNA-seq


title: Epigenomic profiling of SETX in meiotic germ cells by ChIP-seq

city: Bunkyo-ku

first: Yasuhiro

last: Fujiwara

address: 1-1-1 Yayoi

department: IQB

institute: The University of Tokyo

summary: SETX is a DNA/RNA helicase that resolves R-loop, and lack of SETX in germ cells causes meiotic arrest. To investigate roles of SETX in transcription during meiosis, we perfomred ChIP-seq of SETX using antibodies.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for SETX.

first: Yuki

last: Okada

first: Kouhei

last: Saito


title: Effect of Setx depletion on gene expression in the testis during the first-wave of spermatogenesis

summary: To investigate the transcriptome of testicular cells in both control  and Setx-KO mice (spcar3 mice).

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and Setx-KO testicular cells.

first: MaryAnn

last: Handel


title: Epigenomic profiling of SETX and Rloops in meiotic germ cells by CUT&Tag

summary: SETX is a DNA/RNA helicase that resolves R-loop, and lack of SETX in germ cells causes meiotic arrest. To investigate roles of SETX in transcription during meiosis, we perfomred CUT&Tag of SETX and R-loops using antibodies against them.

overall_design: CUT&Tag for SETX and R-loop in pachytene spermatocytes.


title: Trancriptomic profiles of Nicotinamide riboside kinase-2 in ischemic heart

city: Sharjah

first: Hezlin

last: Marzook

state: Sharjah

address: University city

department: Sharjah Institute of Medical Research

country: United Arab Emirates

institute: University of Sharjah

summary: Transcriptomic profiles of in the ischemic NRK-2 KO hearts to identify the novel dysregulated genes/pathways

overall_design: Expression profiling by high throughput sequencing

first: Firdos

last: Ahmad


title: single cell RNA-seq and Visium data of human spinal cord

city: BeiJing

first: hao

last: dong

address: Datun Rd

institute: ibp

summary: The spinal cord is the critical part of the central nervous system. We performed scRNA-seq and Visum spatial RNA-seq to decipher the development of human spinal cord in the embryonic stage. Together, we reveal the dynamics of neural lineage and glial lineage during the development of human spinal cord.

overall_design: We peformed scRNA-seq on 10 time points and 3 segments as well as 10x visium spatial transcitome on 4 time points.

first: Ying

middle: C

last: Shi

first: Hao

last: Dong


title: Transcriptomic insights into the deconstruction of lignocellulosic biomass by Beauveria bassiana

city: Johannesburg

first: Wai Yin

last: Chan

state: Gauteng

address: 1 Modderfontein Road, Sandringham,

country: South Africa

institute: National Institute for Communicable Disease

summary: This study was aimed at highlighting the endophytic to the saprophytic adaptive plasticity of B. bassiana. Thus the objective was to elucidate and compare the transcriptome of B. bassiana  the fungi under endophytic, saprophytic and basal conditions.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for B. bassiana under three different simulated trophic conditions.

first: Ayodeji

last: Amobonye

first: Prashant

last: Bhagwat

first: Nonsikelelo

last: Mthethwa

first: Stanford

last: Kwenda

first: Arshad

last: Ismaili

first: Mushal

last: Ali

first: Sheena

last: Kumari

first: Suren

last: Singh

first: Santhosh

last: Pillai


title: E-7386 IS NOT A SPECIFIC CBP/β-CATENIN ANTAGONIST

city: Duarte

first: Ching

last: Ouyang

address: 1500 E. Duarte Rd.

institute: City of Hope National Medical Center

summary: Our data show that E-7386 which has been reported to be a “first-in-class orally active CBP/beta-catenin modulator” anticancer agent, unfortunately by multiple criteria does not appear to be a bona fide CBP/β-catenin selective

overall_design: Comparative gene expression profiling analysis of RNA-seq data for SW480 treated with different CBP/β-catenin antagonists (ICG-001, C82, and E7386).

first: Michael

last: Kahn


title: Expression data from T47D/S2 (control) and T47D/TR-2 (tamoxifen-resistant) cell lines

city: Seoul

first: Mi-Ock

last: Lee

address: 1 Gwanak-ro, Gwanak-gu

department: College of Pharmarcy

country: South Korea

institute: Seoul National University

summary:
Basal expression profiling was performed to understand molecualr pathways specifically altered in tamoxifen-resistant cells.
Tamoxifen is the most accepted targeted agent for treating patients with estrogen receptor (ER)-positive breast cancer (BC), but its efficacy has been limited due to drug resistance, manifested as disease recurrence and eventually death. Metabolic reprogramming of lipids has recently been recognized as a new mode of therapeutic resistance in various cancers. Therefore, we investigated previously unrecognized perturbations in lipid metabolism in tamoxifen-resistant BC by conducting comprehensive metabolomics and transcriptomics analysis.

overall_design: T47D/S2 control cells and T47D/TR-2 tamoxifen-resistant cells were maintained in RPMI 1640 (pheno red-free) medium + 2% FBS + glutamax + insulin. T47D/TR-2 cells were maintained with 1 μM tamoxifen. Both cells were subjected for microarray analysis in duplicates, using Affymetrix gene profiling.

first: Sewon

last: Hwang


title: Transcriptome sequencing of lncRNAs, circRNAs, miRNAs, mRNAs and interaction network constructing in acute exacerbation of idiopathic pulmonary fibrosis [microarray]

city: Shenyang,

first: Jia

middle: Ran

last: Wang

state: Liaoning

address: No. 79 Chongshan East Road, Huanggu District,

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

summary: Background: Acute exacerbation of idiopathic pulmonary fibrosis (AE-IPF) is the most common cause of acute respiratory deterioration and death in IPF patients, with an elusive etiology and pathogenesis. Roles of noncoding RNAs in AE-IPF have been proposed, however, it was rare to find studies have systematically investigated the crosstalk among various transcripts until now. The construction of RNA functional networks such as lncRNA-miRNA-mRNA and circRNA-miRNA-mRNA interaction networks could therefore facilitate our understanding of RNA interactions in AE-IPF. The study aimed to identify the expression differences of RNA transcripts in RNA sequencing from AE-IPF patients and stable IPF (S-IPF), and further to construct the potential RNA networks.  Methods: Five AE-IPF patients and five S-IPF were recruited in this study to perform RNA sequencing and miRNA sequencing. The differentially expression profiles of lncRNAs, circRNAs, miRNAs and mRNAs between AE-IPF and S-IPF patients were identified for further analyses. Gene Oncology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of were performed. The competing endogenous RNAs (ceRNAs) network of lncRNA/circRNA-miRNA-mRNA was constructed, and the core regulatory molecules in the ceRNA network were analyzed.  Results: A total of 69 lncRNAs, 150 circRNAs, 27 miRNAs and 56 mRNAs were differentially expressed between AE-IPF and S-IPF. GO and KEGG analysis show that differentially expression mRNAs are significantly associated with tight junction and Hepatitis C, etc. In the ceRNA network, all nodes are directly or indirectly involved in the progression of AE-IPF. 1 lncRNAs, 6 circRNAs, 1 miRNAs, and 5 mRNAs constituted a hsa-miR-150-5p core sub-network. Based on the analysis of ceRNA sub-network, NR_120628/hsa-miR-150-5p/E2F3 and has-circ-0053515/hsa-miR-150-5p/E2F3 were considered to be the key ceRNA axis.  Conclusions: In conclusion, this study reveals NR_120628/hsa-miR-150-5p/E2F3 and has-circ-0053515/hsa-miR-150-5p/E2F3 may be the key ceRNA axis in the regulation of AE-IPF, providing clues for future studies on their roles for AE-IPF. Our findings will help to explore the pathological mechanism of AE-IPF from a transcriptomic perspective and provide enlightenment for the biomarker and therapeutic targets of AE-IPF.

overall_design: This study complied with the Declaration of Helsinki and was approved by the Ethics Committee of the Affiliated Hospital of Liaoning University of Traditional Chinese Medicine with the approval number 20200055FS(KT)-028-02. All participants provided written informed consent prior to research participation.  Ten participants (5 patients with AE-IPF and 5 patients with IPF) were recruited from the Affiliated Hospital of Liaoning University of Traditional Chinese Medicine (Shenyang, China) as the sequencing cohort. All the subjects aged between 45 to 80 years old. The diagnosis of AE-IPF was comfirmed by clinical symptoms of significant exacerbation of acute dyspneachest within a month and high resolution computed tomography of new GGO and/or consolidation shadows in both lungs on the background of UIP type changes. All AE-IPF patients met the international working group criteria for AE-IPF. The diagnosis of IPF was mainly according to UIP of HRCT which mentioned by the ATS/ERS/JRS/ALAT criteria for IPF [1]. Individuals with other respiratory or rheumatic immune diseases were all excluded from the study.  Fresh peripheral whole blood samples (4-8mL) were drawn from each subject and centrifuged to get plasma. Samples were frozen on liquid nitrogen and then all frozen samples were transported in frozen conditions using dry ice.

first: Ning

middle: Z

last: Zang

middle: R

first: Jing

middle: Y

first: Ting

middle: T

last: Li

first: Pin

first: Yong

middle: M

last: Liu

middle: X

last: Pan

first: Li

last: Pang

first: Xiao

last: Lv


title: Matched analysis of detailed peripheral blood and tumor immune microenvironment profiles in bladder cancer

city: Lebanon

first: Ji-Qing

last: Chen

state: New Hampshire

address: 1 Medical Center Drive, Williamson level 6

department: Epidemiology

institute: Dartmouth College

summary: Background: Bladder cancer and therapy responses hinge on immune profiles in the tumor microenvironment (TME) and blood, yet studies linking tumor-infiltrating immune cells to peripheral immune profiles are limited. Methods: DNA methylation cytometry quantified TME and matched peripheral blood immune cell proportions. With tumor immune profile data as the input, subjects were grouped by immune infiltration status and consensus clustering. Results: Immune hot and cold groups had different immune compositions in the TME but not in circulating blood. Two clusters of patients identified with consensus clustering had different immune compositions not only in the TME but also in blood. Conclusions: Detailed immune profiling via methylation cytometry reveals the significance of understanding tumor and systemic immune relationships in cancer patients.

overall_design: Bisulphite converted DNA from tumor tissue and matched white blood cells from 88 bladder cancer patients, were hybridised to the Illumina Infinium HumanMethylationEPIC Beadchip v1.0_B4

first: Brock

last: Christensen

first: Lucas

last: Salas

first: Margaret

last: Karagas

first: John

middle: K

last: Wiencke

first: Devin

last: Koestler

first: Annette

last: Molinaro

first: Angeline

middle: S

last: Andrew

last: Seigne

first: Karl

last: Kelsey


title: circRNA vaccines

city: Richmond

first: Guizhi

last: Zhu

state: VA

address: 410 N 12th St

institute: Virginia Commonwealth University


title: Potential involvement of KANK1 haploinsufficiency in centrosome aberrations

city: Fukuoka

first: Ikumi

last: Imamura

address: 2-3-1 Matsukadai Higashi-ku

department: Life sience

institute: Kyushu sangyo university

summary: KANK1 was found as a tumor suppressor gene based on frequent deletions in renal cell carcinoma and the inhibitory activity of tumor cell proliferation. Previously, we reported that knockdown of KANK1 induced centrosomal amplification, leading to abnormal cell division, through the hyperactivation of RhoA small GTPase. Here, we explored to the effect of loss of function of KANK1 through CRISPR/Cas9-based genome editing to knockout the gene. After several rounds of genome editing, however, there were no cell lines with complete loss of KANK1, and it was found that less the wild-type KANK1 dosage was, greater the number of cells with abnormal numbers of centrosomes and the rates of cell-doubling times and apoptosis were, suggesting the involvement of KANK1 haploinsufficiency in centrosome aberrations. RNA-sequencing analysis of the cells with reduced dosages of functional KANK1 revealed potential involvement of other cell proliferation-related genes, such as EGR1, MDGA2 and BMP3, which were reported to show haploinsufficiency when they function. Thus, haploinsufficiency of KANK1 may contribute to centrosome aberrations through the network of haploinsufficiency-related genes.

overall_design: KANK1 partial knockout (partial KANK1-KO) cells were generated using the CRISPR/Cas9 system using guide RNA (gRNA) located immediate downstream of the first ATG. The duplex DNA with the sequences of 5'-TGACACCGGTGAGTTCAGAAGG-3', corresponding to the gRNA part, and its complementary 5'-CCTTCTGAACTCACCCGGGTGTCA-3', was incorporated into the pGuide-it-ZsGreen1 vector (Takara Bio, Shiga, Japan) to express Cas9 protein and gRNA. To introduce the vector into cells, 1.0 × 10^6 cells were pre-seeded and cultured at 37°C for 24 hr, and after the vector (1.2 μg) was introduced into the cells using a Lipofectamine 3000 Transfection kit (Thermo Fisher Scientific), the cells were cultured for 3 days.

first: Ryoiti

last: Kiyama


title: Genome-wide analysis of distribution of RNA Helicase Maleless (MLE) in Drosophila Melanogaster early female embryo, before (0-2 Hr) and after (2-4 Hr) maternal to zygotic transition (MZT)

city: Providence

first: Erica

last: Larschan

state: RI

address: Sidney Frank Hall 367, 185 Meeting Street

department: MCB

institute: Brown University

summary: Transcription factor CLAMP associates with RNA helicase, Maleless MLE as part of Male-specific MSL complex in males, which regulates dosage compensation in males. Both CLAMP and MLE are maternally deposited proteins (protein expression detectd in 0- Hr embryo, before zygotic genome activation) and MLE is also a conserved component of spliceosome. Moreover, CLAMP too associates with many other RNA binding protein compoments of spliceosomes. Both these proteins  are well expressed in females, but apart from that might influence splicing in females, not much is known if they have any female-specific function. Furthermore, whether they regulate each other's function in females is not known as well, especially before zygotic genome activation starts, in a pre-MZT embryo (0-2 Hr Embryo). Therefore,  we performed CutnRun assay to detrmine  MLE binding sites on chromatin in female embryos before (0-2 Hr) and after MZT (2-4 Hr). And then identify, in absence of maternal CLAMP, whether there is change is distribution of control MLE female peaks. We identified regions on chromatin where MLE binds during 0-2 Hr pre-MZT and 2-4 Hr post-MZT embryonic stages in females. CLAMP unlike to males do not affect MLE distribution on chromatin in females.

overall_design: Female embryos with maternal CLAMP (control, MTD-GAL4>GFPRNAi mothers) at two time points-1)0-2 Hr pre-MZT and 2) 2-4 Hr post-MZT and depleted maternal CLAMP (experimental, MTD-GAL4>CLAMPRNAi mothers) at one time points-1)0-2 Hr pre-MZT collected. Embryos were sexed using the meiotic drive system that produces sperm with  only X chromosomes (Reider et al 2017), resulting in progeny of only female genotypes. Using anti-MLE antibody the DNA fragments bound to MLE protein captured using Cut and Run protocol (Uyehara and McKay 2019) and DNA libraries made. Pair-end sequencing of DNA libraries in a Hi-seq illumina platform. Multiple batches of crosses were set and embryos collected from multiple timed egg-layings used to make DNA libraries.

first: Mukulika

last: Ray

first: Joseph

last: Anguilera


title: circRNA sequence authenticity in live cells

summary: Exogenous RNA, such as circRNA, could be edited by endogenous editors, such as C-to-U editor activation-induced deaminase and apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like (AID/APOBEC), and A-to-I editor Adenosine deaminases acting on RNA (ADAR) (I: inosine, recognized as G). Editing of circRNA may interfere with IRES and Kozak sequence to initiate antigen translation, and may alter antigen products or mutate stop codons.

overall_design: Using circRNA sequencing (circRNA-seq) followed by bioinformatic circRNA mapping, we monitored the sequence integrity of circRNA-SIINFEKL after transfection in live mouse bone marrow dendritic cells (BMDCs) for 24 h.

first: Yu

last: Zhang

first: Jinze

last: Liu

first: Katarzyna

last: Tyc


title: Newcastle disease virus activates methylation-related enzymes to reprogram m6A Methylation in infected cells

city: wuhan

first: Weifeng

last: Yuan

state: hubei

address: hubei province wuhan wuchang

institute: Wuhan University

summary:
To investigate the  role of m6A modification during Newcastle disease virus (NDV) infection
We then performed gene expression profiling analysis using data obtained from RNA-seq and MeRIP-seq of NDV infected CEF cells  and normal cells.

overall_design: Comparative gene and m6A expression profiling analysis of RNA-seq data  and MeRIP-seq data of NDV infected CEF cells  and normal cells.

first: Yuechi

last: Hou


title: Identifying differential binding of transcription factor CLAMP on chromatin in S2 (male) and Kc (female) emmbryonic cell lines

summary: CLAMP is a maternally deposited transcription factor binding to GA-rich genomic region. It recruits male-specific MSL (Male sex-lethal) complex on male X-chromosome that regulates dosage compensation in males, and competes with other GA-binding proteins like GAF, acting both synergistically as well as antagonistically in a context dependent manner. Considering CLAMP's male specific role in dosage compensation but ubiquitous expression in both males and females, what regulates differential binding of CLAMP is still unknown. Furthermore, ChiP-seq analysis has being long used to study protein-DNA interactions, however, since it uses physical force to shear DNA after protein capture, it is prone to both false negative and false positive peaks being called. To minimise these discrepancies, a recent CutnRun MNase based technique have being developed (Heinkoff Lab) which captures the DNA fragments bound to protein of interest. Due to higher accuracy in identifying the size and sequence of the protein bound DNA region, one can also identify monomeric or multimeric protein binding on the chromatin. We have used this technique to identify differential and shared CLAMP binding sites in male and female cells. We also compared CLAMP DNA binding peaks with CLAMP RNA binding peaks (iCLIP data) in male and female cells to understand sex-biased co-transcriptional RNA processing mechanism.

overall_design: rabbit anti-CLAMP was used to immunoprecipitate CLAMP bound DNA fragments from non-UV crosslinked, unfixed male (S2) and female (Kc) cell lines. 3 replicates  each for males and females were run, however, during later stages one female sample was dropped due to insufficient starting material. Rabbit IGG was used as control, one for each male and female cell line sample.

first: Pranav

last: Mahableshwarkar

first: Ashley

last: Conard


title: m6A methylome in JQ1 treatment and control in MDA-MB-231 cells.

city: Xia Men

first: Xiao

last: Lu

address: Xiang'an south road

institute: Xiamen university

summary: We report the application of MeRIP sequencing technology for high-throughput profiling of m6A methylome in breast cancer cells. Comparison of m6A methylome between control and BETi-treated cells revealed the following findings: 1) Significant global alteration of methylation sites due to BETi-treatment (herein defined as BETi-m6A signature).  2) Gene Ontology (GO) analysis of the differential meRIP-seq candidates enriched pathways involved in chromatin modification, RNA splicing and pathways regulating cell fate , reflecting a critical role of m6A in diverse biological processes.

overall_design: Examination of different m6A modification levels and gene expressions in JQ1 treatment and control in MDA-MB-231 cells.

first: Lichao

last: Peng

first: Jiancheng

last: Ding

first: Han

last: You


title: Programmed Death Ligand 1 in Tumor Margins with Implications of Regulation by Interferon Gamma, and a Novel Immuno-Oncologic Transcriptional Signature for Malignant Transformation

city: Baltimore

first: Rania

middle: Hassan

last: Younis

state: MD

address: 650 W Batimore St

department: Oncology and Diagnostic Sciences

institute: University of Maryland School of Dentistry

summary: Basic analysis of 5 pairs of tumor margin and invasive OSCC tumor tissue using basic nsolver analysis showed, PD-L1 and IFN-γ 6 gene signature to be higher in morphologically normal epithelial tumor margin than in dysplastic tumor margin, yet the invasive OSCC area was the highest in PD-L1 and IFN-γ 6 gene signature. It also demosntrates 38 significant Immuno oncologic gene signature for maligant transformation relative to tumor margins.

overall_design: Under an Institutional Review Board (IRB) approved protocol and patient consent whole excision tumor tissues were collected prospectively at the University of Maryland School of Medicine (UMSOM) under (HP-00073603),  and retrospectively under (IRB HP-00088284).Five tumors were mapped for tumor margins and invasive area of OSCC for RNA extraction using nCounter Human Pan Cancer IO-360  nanoString Technology .

middle: H

first: Manar

last: Elnaggar

first: Vasileios

last: Theofilou


city: Taichung

first: Shih-Chieh

last: Hung

address: No.6, Hsueh-Shih Road., North Dist.

department: Drug Development Center, Institute of New Drug Development

institute: China Medical University

summary: Krueppel-like factor 1 (KLF1) is one of the key transcriptional regulators associated with tumor immunity. However, the importance of LEPR lineage cells in CAF development and the regulatory role of the KLF1 transcription factor in CRC CAF function remain to be elucidated.

overall_design: Lepr-cre; Tomato cells were sorted from bone marrow flush and then carry out CUT & RUN ChIP-seq to compare the difference between WT and KLF1-KO mice.

first: Yu-Ting

last: Yen


title: PD-L1 ubiquitination by MIB2 enables its translocation to the plasma membrane for tumor immune evasion

city: Houston

first: xinfang

last: yu

state: TX

address: one baylor plaza alkek building N720

institute: BAYLOR COLLEGE OF MEDICINE

summary: Programmed death-ligand 1 (PD-L1), a critical immune checkpoint ligand, is a transmembrane protein synthesized in the endoplasmic reticulum of tumor cells and transported to the plasma membrane to interact with programmed death 1 (PD-1) expressed on T cell surface. This interaction delivers co-inhibitory signals to T cells, thereby suppressing their function and evading antitumor immunity. Most companion or complementary diagnostic devices for PD-L1 expression levels in tumor cells used in the clinic or clinical trials require membranous staining. However, the mechanism driving PD-L1 translocation to the plasma membrane after de novo synthesis is poorly understood. Herein, we showed that mind bomb homolog 2 (MIB2) is required for PD-L1 transportation from the trans-Golgi network (TGN) to the plasma membrane of cancer cells. MIB2 deficiency leaded to fewer PD-L1 proteins on the tumor cell surface and promotes antitumor immunity in mice.We performed a single-cell RNA sequencing (scRNA-seq) of B16-F10 tumors from C57BL/6 syngeneic mice. Knockdown of MIB2 resulted in an increase in the percentage of CD8+ CTLs (approximately 5-fold) and CD4+/CD8+ effector/activated T cells (approximately 2-fold), indicating that MIB2 downregulation enhanced the antitumor immune activity centered on CD8+ CTLs and changed their transcriptional profile. Our findings demonstrate that non-proteolytic ubiquitination of PD-L1 by MIB2 is required for its transportation to the plasma membrane and tumor cells' immune evasion.

overall_design: scRNA-seq

first: Wei

last: Li

first: Xinfang

last: Yu

first: Yong


title: Sex differences in NK cells mediated by the X-linked epigenetic regulator UTX

city: Los Angeles

first: Joey

middle: Han Tang

address: 615 Charles E. Young Dr S

institute: UCLA

summary: Sexually dimorphic immune responses are evident by increased susceptibility of males to viral infections. Interestingly, our results indicate that while males possess more natural killer (NK) cells, they display impaired effector function. These differences are attributed to lower male expression of X-linked UTX, an epigenetic regulator which escapes X-inactivation in females. NK cell-specific heterozygous deletion of UTX in females recapitulated male NK cell phenotypes of increased NK cells and defective effector function. Notably, mice with NK cell-intrinsic UTX deficiency show increased lethality to mouse cytomegalovirus. Integrative UTX CUT&Tag, ATAC-seq and RNA-seq analysis revealed a critical role for UTX in regulating the chromatin landscape and expression at gene loci involved in NK cell homeostasis and effector function. Collectively, these data implicate UTX as a molecular determinant of sex differences in NK cell homeostasis and effector function and suggest enhancing UTX as a strategy to boost endogenous NK effector responses.

overall_design: CUT&Tag followed by Illumina sequencing

first: Mandy

middle: I

last: Cheng

first: Luke

last: Riggan

first: Bryan

last: Chen

first: Rana

last: Yakhshi Tafti

first: Scott

last: Chin

first: Feiyang

last: Ma

first: Matteo

last: Pellegrini

first: Haley

last: Hrncir

first: Arthur

last: Arnold

first: Timothy

middle: E

last: O'Sullivan

first: Maureen

last: Su


title: SIRT6 overexpression predicts high risk of metastasis and relapse in Delta16HER2-positive breast cancer [ChIP-seq]

city: PADOVA

first: GIUSEPPE

last: PERSICO

state: PD

address: VIA UGO BASSI 58/B

country: Italy

institute: UNIVERSITA' DI PADOVA

summary: We investigate the impact of SIRT6-overexpression (SIRT6-OE) in the breast cancer mouse model Delta16HER2. After an initial delay in the tumor onset, starting form 20 weeks of age, SIRT6-OE induces a more aggressive phenotype of Delta16HER2 tumors, promoting the formation of more tumors and metastases with respect to controls. SIRT6 can regulate gene expression and chromatin integrity via deacetylation of H3K9ac. Therefore, to gain mechanistic insights, we performed H3K9ac ChIP-seq and RNA-seq on tumors from Delta16HER2/SIRT6-OE and Delta16HER2 mice, harvested at 20 weeks of age.

overall_design: We analyzed the H3K9ac histone modification in the chromatin from 3 Delta16HER2/SIRT6-OE and 2 Delta16HER2 tumors resected from mice at 20 weeks of age.

first: Cristina

last: Andreani

first: Caterina

last: Bartolacci

first: Giuseppe

last: Persico

first: Francesca

last: Casciaro

first: Stefano

last: Amatori

first: Mirco

last: Fanelli

first: Marco

last: Giorgio

last: Galié

first: Daniele

last: Tomassoni

first: Junbiao

last: Wang

first: Roberto

last: Coppari

first: Augusto

last: Amici

last: Marchini


title: Hypothalamus-specific NSCs derived from human brain organoids ameliorate age-associated dysfunction upon transplantation into aged mouse hypothalamus [human]

first: Yanuar

middle: Alan

last: Sulistio

address: Wangsimni-ro 222

department: Biomedical Science

institute: Hanyang University

summary: The hypothalamus is the brain region that regulates systemic body metabolism and multiple functions in other brain regions. In adult mice, the hypothalamus harbors neural stem/precursor cell (NSC)-like cells. Along with the dysregulation of body metabolism and physiology that occurs during aging, the NSC population in the hypothalamus declines with age. Here, we introduce a novel protocol that yields scalable and storable hypothalamus-specific NSCs (htNSCs) from hypothalamus-like organoids derived from human pluripotent stem cells (hPSCs). Implanting htNSCs into the medio-basal hypothalami of aged mice conspicuously ameliorated age-related declines in metabolic fitness, physical capacity, and cognitive function and produced corresponding histologic changes in various body tissues. Single transcriptome and immunohistochemical analyses of the grafted hypothalamic tissues showed that the anti-aging effects were attained by correcting glial NF-κB, TNFα, and NLRP3 inflammasome pathways. Collectively, our findings support the potential of anti- or healthy aging therapies that target htNSCs and hypothalamic inflammation.

overall_design: scRNAseq transcriptome survey of hPSC-derived hypothalamus organoid terminally differentiated for 70 days

first: Kelvin

last: Pieknell

first: Sang-Hun

last: Lee


title: DNA methylation profile of Prostate Cancer cell lines

city: Alcala de Henares

first: Santiago

last: Ropero

state: Madrid

address: Medical School

department: Department of System Biology

country: Spain

institute: University of Alcala

summary: Genome wide DNA methylation profiling of androgen-sensitive and –refractory prostate cancer cells. The Illumina Infinium HumanMethylation450 Beadchip was used to obtain DNA methylation profiles across approximately 480.000 CpGs in Prostate cancer cell lines showing different sensitivity to hormonal treatments. Samples included the androgen receptor negative cell lines PC3 and DU145, the androgen sensitive cell line LNCaP and the LNCaP abl cell line expressing androgen receptor but refractory prostate cancer cell line to hormonal treatments.

overall_design: Bisulphite converted DNA from the samples were hybridised to the Infinium HumanMethylation450 Beadchip

first: María

middle: J

last: Orea


title: Hypothalamus-specific NSCs derived from human brain organoids ameliorate age-associated dysfunction upon transplantation into aged mouse hypothalamus [mouse]

overall_design: snRNAseq transcriptomics of aging (~18 mo) mice hypothalamus transplanted with hPSC-derived hypothalamus stem cell vs control

middle: A


title: Identification of cross-species preserved cis-regulatory elements containing type 2 diabetes GWAS variants (pcHiC)

city: Bar Harbor

first: Kristen

last: O'Connell

state: ME

address: 600 Main St

institute: The Jackson Laboratory

summary: Non-coding regions of the genome contain cis-regulatory elements (CREs) that govern transcriptional activity critical for development and physiologic functions of major metabolic tissues, such as islets, adipose, liver, and skeletal muscle. Moreover, they contain the majority of genetic variants associated with risk of type 2 diabetes and quantitative alterations in related metabolic phenotypes. Here, we defined comprehensive, representative CRE maps of these major metabolic tissues in mice of both sexes using ATAC and pcHiC data and incorporating genetic variation of the 8 major Collaborative Cross founders and diet-response. Cross-species comparison of these representative maps with those from corresponding human tissues revealed conservation and functional preservation of ~28% of CREs in one or more major metabolic tissues. Importantly, this included an average of 700 (1.8%) cross-species concordant peaks that harbored genetic variants associated with T2D and related metabolic traits, including variants in the CAMK1D/CDC123, C2CD4A/B, and ADCY5 loci. Germline knock-out of the cross-species concordant CRE in ADCY5 yielded mice with impaired fasting glucose, demonstrating the importance of these functionally preserved CREs to glucose homeostasis and genetic risk of type 2 diabetes and progression. Together, the creation and cross-species comparison of comprehensive CRE maps in major metabolic tissues provides a critical resource for variant-to-function studies of type 2 diabetes and an array of related metabolic and cardiovascular traits and demonstrates the power of these mapping strategies to identify conserved metabolic cis-regulatory networks and enable data-driven creation of new preclinical models of diabetes and related metabolic diseases.    Sample preparation:    Promotor capture libraries were constructed via the following method. Crosslinked cells were lysed, digested with DpnII, ends filled in using biotin-14-dATP followed by overnight proximity ligation.  Ligated samples underwent crosslink reversal, DNA extraction with proteinase K, and biotin removal from unligated fragments.  DNA was fragmented to 500-600 bp, column purified, and biotinylated fragments pulled down. Biotinylated fragments were converted into Illumina compatible libraries using the SureSelect XT HS2 DNA System and a custom SureSelect probe set (design ID S3346176) (Agilent Technologies) according to the manufacture’s protocol with the following exception:  pre-capture PCR was performed as four 50 ul reactions that were recombined during clean-up. The quality and concentration of the libraries were assessed using the High Sensitivity D5000 ScreenTape (Agilent Technologies) and Qubit dsDNA HS Assay (ThermoFisher), respectively, according to the manufacturers’ instructions. Libraries were sequenced 150 bp paired end on an Illumina NovaSeq 6000.

overall_design: The total target bait design resulted in 125,187 in silico targeted fragments. In initial analysis testing, we found that the full capture array resulted in too little coverage per fragment. Therefore, to increase the coverage per fragment we binned all in silico digest fragments and targeted fragments into 5kb virtual bins with the ‘makeBins.R’ script from the Chicago package [PMID: 27306882] with the ‘--include_baits’ flag. The binned files were passed the ‘makeDesignFiles_py3.py’ script from the Chicago package with ‘6-cutter suggested settings’ per suggestions in Freire-Pritchett, et al. 1. Binned fragments and design files were used in all downstream analysis.     pcHiC data for three strains (C57BL/6J, NZO/HlLtJ, and CAST/EiJ) from, islet, liver, and adipose tissues were processed in the following way. Reads were quality trimmed with AGeNT Trim (https://www.agilent.com/en/product/next-generation-sequencing/hybridization-based-next-generation-sequencing-ngs/ngs-software/agent-232879). Trimmed reads were processed with the HiCUP pipeline [PMID: 26835000]. Following the HiCUP filter step, mapped, hicup_filter alignments were demultiplex with UMI aware AGeNT Locatit. On target ‘captured.bam’ files were then generated for demultiplex alignments with `HiCUP_Capture` a tool from the HiCUP pipeline. On target captured BAMs files were converted to Chicago format with ‘bam2chicago_V02.sh’ using the 5kb binned fragments and target baitmap as inputs 2. The resulting ‘chinput’ files were process with Chicago via the ‘runChicago.R’ script with suggested 6-base-cutter settings. Processed resulting output with ‘fitDistCurve.R’ with the flag ‘-t -5’ to obtain adjusted p-value weight settings relative to our data. The ‘chinput’ were then reprocessed with ‘runChicago.R’ with final settings from the re-weighting analysis. Due to difficulty associated with harvesting tissue, Islet and adipose samples yielded low per sample coverage. Therefore, to maintain consistency across all tissues on target alignments were pooled by strain and pooled data were used in the downstream Chicago analysis.     1 Freire-Pritchett, P. et al. Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools. Nat Protoc 16, 4144-4176 (2021). https://doi.org:10.1038/s41596-021-00567-5  2 Cairns, J. et al. CHiCAGO: robust detection of DNA looping interactions in Capture Hi-C data. Genome Biol 17, 127 (2016). https://doi.org:10.1186/s13059-016-0992-2

first: Michael

middle: W

last: Lloyd

first: Anuj

last: Srivastava

first: Candice

middle: N

last: Baker

first: Sai

last: Lek

first: Isabela

last: Gerdes Gyuricza

first: Jake

last: Emerson

first: Mary

last: Barter

first: Harianto

last: Tjong

first: Heidi

last: Munger

first: Rahul

last: Maurya

first: William

last: Schott

first: Anita

last: Adams

first: Margaret

last: Gaca

first: Chew

last: Ngan

first: Chia-Lin

last: Wei

first: Madeleine

last: Braun

first: Alan

middle: D

last: Attie

first: Mark

middle: P

last: Keller

middle: L

last: Stitzel

first: Gary

last: Churchill


title: Spatial transcriptomic studies of the colon from a wildtype mouse

city: San Diego

first: Wendy

last: Huang

address: 9500 Gilman Drive #0651

department: Cellular and Molecular Medicine

institute: University of California San Diego

summary: Transcriptomic analysis of the colon from a wildtype 8 week old female mice in C57BL6 background. In particular, we characterized the expression of genes encoding known receptors for  Regenerating islet-derived proteins (REG3III) among the different colonic intestinal epithelial cell subsets under steady state. Colonic DCLK1+ tuft cell-containing spots had the highest expression levels of genes encoding various REG3III receptors.

overall_design: One entire colon tissue was obtained from a steady state female 8wk-old wildtype mouse.

first: Juan

last: Hernandez


title: Single cell RNA-seq of Nutlin3a-Induced Senescent mouse embryonic fibroblasts with or without expressing OSKM

city: Minato City, Tokyo

first: Teh-Wei

last: Wang

address: 4 Chome-6-1 Shirokanedai

institute: IMSUT

summary:
Purpose: Use scRNA-seq to determine the trajectories of transcriptomes during partial reprogramming of nutlin-3a senescent MEFs.
Methods: MEFs were isolated from p16-CreERT2/rtTA3-mKate2/TRE-OSKM-mCherry mice. After the senescence induction through RO3306 and nutlin-3a, treatments with 4-OHT for 9 days and doxycycline for 12 days were performed to induce OSKM expression. The doxycycline treated MEFs and untreated MEFs were collected by trypsinization and directly used for scRNA library preparation through droplet system.

overall_design: Examining  differentially expressed genes and identifing transposable elements within quiescent and nutlin3a-induced senescent pulmonary fibroblasts

first: Xiangyang

last: Liu

first: Zhaoyi

first: Makoto

last: Nakanishi


title: SIRT6 overexpression predicts high risk of metastasis and relapse in Delta16HER2-positive breast cancer

first: GIUSEPPE

last: PERSICO

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

overall_design: Refer to individual Series


title: BRD4 ChIP-seq in JQ1 treatment and control in MDA-MB-231 cells.

first: Xiao

last: Lu

summary: Aberrant expression of m6A writer complex has been reported across human cancers, resulting in abnormal m6A epitranscriptome that drives tumorigenesis. But the regulatory mechanism remains unknown. Here, we identified an unappreciated interplay between the histone acetyl-lysine reader BRD4 and the m6A methyltransferase complex (MTC) across human cancers. BRD4 directly stimulates transcript expression of seven MTC subunits, allowing the maintenance of nuclear METTL3/METTL14 abundance and the formation of functional writer complex to catalyze m6A modification.

overall_design: ChIP-seq performed in this study was designed to uncover the role of BRD4-mediated regulation of gene transcription.

first: Lichao

last: Peng

first: Jiancheng

last: Ding

first: Han

last: You


title: Role of H3K4me1 and H3K27ac histone marks in aging Drosophila

city: Singapore

first: Ching Thong

last: Choo

address: 1 Research Link

country: Singapore

institute: Temasek Life Sciences Laboratory

summary: Temporal and spatial gene expression patterns are regulated by enhancer-specific histone modifications H3K4me1 and H3K27ac. To better understand age-dependent alteration of these enhancer marks, we analysed their genome-wide profiles and compared against changes in gene expression in the head tissues harvested from young Day 10 and D50 male Drosophila. The genome-wide binding patterns of H3K4me1 and H3K27ac remain highly similar (>85%) during ageing with marginally higher signals for both marks in older Day 50 flies. Signals were significantly higher in Day 50 flies near the transcription start sites for H3K4me1 whereas for H3K27ac, signals were significantly higher in Day 50 flies globally. Interestingly, analysis using MACS bdgdiff identified “x” H3K4me1 and “y” H3K27ac differential peaks that correlated with distinct sets of age-dependent differential expressed genes (DEG). Most of the H3K4me1 differential peaks (percentage of x) are located within the gene body of DEGs that are associated with RNA and metabolic processes. On the other hand, majority of differential H3K27ac peaks (percentage of y) are located 5 kb upstream of TSS of DEG enriched for various immune responses. Our results suggest that while both enhancer marks do not undergo significant global reconfiguration during aging, they are likely to be involved in activating independent sets of genes through distinct transcription activators.

overall_design: ChIP-sequencing of Drosophila heads isolated at day 10 and 50 of adult life.

first: Ching-Thong

first: Zhen-Kai

last: Ngian

first: Swarnaseetha

last: Adusumalli

first: Wei‐Qi

last: Lin

first: Chin-Tong

last: Ong


title: Hypothalamus-specific NSCs derived from human brain organoids ameliorate age-associated dysfunction upon transplantation into aged mouse hypothalamus

city: Seoul

first: Yanuar

last: Sulistio

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: Transcrptome Analysis Reveals Cesium Interferes with ABA perception and Stimulates Expression of Thiamine Biosynthesis Genes

city: Yokohama

first: Wen Dee

state: Kanagawa

address: 1-7-22 Suehiro-cho

institute: CSRS RIKEN

summary: Cesium (Cs) is known to exert toxicity in plants by competition and interference with the transport of potassium (K). However, the precise mechanism of how Cs mediates its damaging effect is still unclear. To identify putative genes that are functionally involved in this response, RNA-seq was conducted on Arabidopsis roots grown in low K and Cs medium conditions. Comparison of both stress condition reveals Cs alters ABA signaling during seed germination and induced expression of thiamine biosnynthesis genes.

overall_design: Comparative gene expression analysis of Arabidopis root exposed to two stress condition, low potassium and cesium treatment.

first: Wen-Dee

first: Makita

last: Yuko

first: Matsui

last: Minami

first: Ryoung

last: Shin


title: Enhancer Cis Elements Instruct Promoter-Enhancer Interaction, Promoter-Enhancer Insulation and Compartmental Segregation

city: La Jolla

first: Hanbin

address: 9500 Gilman Drive, NSB 5108

institute: UCSD

summary: Enhancers harbor instructions encoded for the interactions between cis-elements and transcription factors to orchestrate lineage specific gene programs. Here we developed a modified method for chromosome conformation capture (3C), named MID Hi-C, to reveal how in mouse embryonic stem cells differential cooperation of enhancers and the chromatin remodeler BAF, as instructed by the underlying transcription factor motifs, modulate enhancer-promoter communication. We show that BAF-dependent enhancers permit genomic interactions beyond enhancer boundaries. BAF-dependent enhancers do not dictate genomic interactions within enhancer-promoter loop domains but rather act to instruct remote enhancer-promoter communication. In contrast, BAF-independent enhancers interact with promoter regions within tightly insulated enhancer-promoter loop domains that are marked by promoter and enhancer boundary elements. In addition, enhancer activeness modulated by BAF enforces compartment segregation. Based on these observations, we propose that enhancer cis elements instruct with great precision BAF-induced enhancer-promoter communication and compartmental segregation.

overall_design: We benchmarked the qualities of MID Hi-C data against published in situ Hi-C and Micro-C data on mouse embryonic stem cells (mESCs). Then, using ATAC-seq and our newly-developed MID Hi-C, we investigated changes in chromatin accessibilities and chromatin interactions during BRG1 degradation in mESCs.

first: Paula

last: Pham

last: Han

first: Jiajing

last: Zhou

first: Wenqi

last: Wang

first: Ken

last: Cho

first: Cornelis

last: Murre


title: PRPF8 controls alternative splicing of PIRH2 to modulate the p53 pathway and survival of human embryonic stem cells

city: Shanghai

first: Yiyang

last: Sun

state: Shanghai

address: 320 Yueyang Road

institute: Shanghai Institute of Nutrition and Health

summary: To investigate the function of PRPF8 in survial in hESCs, we established hESC cell lines H9 in which PRPF8 has been knocked down by siRNA.We then performed gene expression profiling analysis and alternative splicing analysis using data obtained from RNA-seq of 4 different cells at two time points.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for NT cells and P8i-3 cells. Alternative splicing analysis of RNA-seq data for NT cells and P8i-3 cells.

first: Zhuoqing

last: Fang

first: Dingyu

last: Liu

first: Min

last: Shao


title: Identification of cross-species preserved cis-regulatory elements containing type 2 diabetes GWAS variants

first: Kristen

last: O'Connell

summary: Non-coding regions of the genome contain cis-regulatory elements (CREs) that govern transcriptional activity critical for development and physiologic functions of major metabolic tissues, such as islets, adipose, liver, and skeletal muscle. Moreover, they contain the majority of genetic variants associated with risk of type 2 diabetes and quantitative alterations in related metabolic phenotypes. Here, we defined comprehensive, representative CRE maps of these major metabolic tissues in mice of both sexes using ATAC-seq and incorporating genetic variation of the 8 major Collaborative Cross founders and diet-response. Cross-species comparison of these representative maps with those from corresponding human tissues revealed conservation and functional preservation of ~28% of CREs in one or more major metabolic tissues. Importantly, this included an average of 700 (1.8%) cross-species concordant peaks that harbored genetic variants associated with T2D and related metabolic traits, including variants in the CAMK1D/CDC123, C2CD4A/B, and ADCY5 loci. Germline knock-out of the cross-species concordant CRE in ADCY5 yielded mice with impaired fasting glucose, demonstrating the importance of these functionally preserved CREs to glucose homeostasis and genetic risk of type 2 diabetes and progression. Together, the creation and cross-species comparison of comprehensive CRE maps in major metabolic tissues provides a critical resource for variant-to-function studies of type 2 diabetes and an array of related metabolic and cardiovascular traits and demonstrates the power of these mapping strategies to identify conserved metabolic cis-regulatory networks and enable data-driven creation of new preclinical models of diabetes and related metabolic diseases.    Sample preparation:    ATAC-seq libraries were prepared from adipose, liver, muscle, and islets as described in [Corces et al., 2016 (Nature Genetics) with slight modifications. Adipose, liver, and muscle samples were dissociated into single cell suspensions using MACS Miltenyi Biotec Adipose Tissue (130-105-808), Liver (130-105-807), and Skeletal Muscle (130-098-305) Dissociation Kits. Dissociated cells were counted and 50,000 cells were resuspended in freezing media (10% DMSO, 50% FBS, 40% RPMI) and frozen at -80°C until cells were thawed and washed in cold PBS, and incubated in ATAC lysis buffer. Islets were isolated from total pancreas as described in [Simonett et al., 2021 (JCI)], and 50 islets were rested overnight in RPMI in 37°C incubator. The following day islets were washed in cold PBS, incubated in ATAC lysis buffer, and triturated with 25-gauge needle and centrifuged to generate a crude nuclei pellet, and washed in ATAC lysis buffer. Prepared nuclei from all tissues were transposed using the Tagment DNA TDE1 Enzyme and Buffer kit (Illumina) with the addition of 0.01% digitonin (1x TDE for liver, muscle; 2x TDE for adipose). Transposed DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo Research), amplified with 11 cycles of PCR, and cleaned using KAPA Pure Beads (Roche). All ATAC-seq libraries were sequenced at 2 x 100 bp using Illumina NovaSeq 6000.    1. Corces M.R., Buenrostro J.D., Wu B., Greenside P.G., Chan S.M., Koenig J.L., Snyder M.P., Pritchard J.K., Kundaje A., Greenleaf W.J. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet. 2016;48:1193–1203.  https://www.nature.com/articles/ng.3646      2. Simonett S.P., Shin S., Herring J.A., Bacher R., Smith L.A., Dong C., Rabaglia M.E., Stapleton D.S., Schueler K.L., Choi J., Bernstein M.N., Turkewitz D.R., Perez-Cervantes C., Spaeth J., Stein R., Tessem J.S., Kendziorski C., Keleş S., Moskowitz I.P., Keller M.P., Attie A.D. Identification of direct transcriptional targets of NFATC2 that promote beta-cell proliferation. J Clin Invest. 2021;131(21):e144833. https://doi.org/10.1172/JCI144833.

overall_design: 386 ATAC-seq profiles were generated from three biological replicates each of adipose, skeletal muscle, pancreatic islets, and liver tissues harvested from male or female mice for each of eight diversity outbred mouse founder strains (A/J, C57Bl6/J , 129S1/SvlmJ, NOD/ShiLtJ, NZO/HlLtJ, CAST/EiJ, PWK/PhJ, and WSB/EiJ), fed 44% fat + fiber or 10% fat + fiber diets. ATAC-seq libraries were prepared from adipose, liver, muscle, and islets as described in [Corces et al., 2016 (Nature Genetics) with slight modifications. Adipose, liver, and muscle samples were dissociated into single cell suspensions using MACS Miltenyi Biotec Adipose Tissue (130-105-808), Liver (130-105-807), and Skeletal Muscle (130-098-305) Dissociation Kits. Dissociated cells were counted and 50,000 cells were resuspended in freezing media (10% DMSO, 50% FBS, 40% RPMI) and frozen at -80°C until cells were thawed and washed in cold PBS, and incubated in ATAC lysis buffer. Islets were isolated from total pancreas as described in [Simonett et al., 2021 (JCI)], and 50 islets were rested overnight in RPMI in 37°C incubator. The following day islets were washed in cold PBS, incubated in ATAC lysis buffer, and triturated with 25-gauge needle and centrifuged to generate a crude nuclei pellet, and washed in ATAC lysis buffer. Prepared nuclei from all tissues were transposed using the Tagment DNA TDE1 Enzyme and Buffer kit (Illumina) with the addition of 0.01% digitonin (1x TDE for liver, muscle; 2x TDE for adipose). Transposed DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo Research), amplified with 11 cycles of PCR, and cleaned using KAPA Pure Beads (Roche). All ATAC-seq libraries were sequenced at 2 x 100 bp using Illumina NovaSeq 6000.  1. Corces M.R., Buenrostro J.D., Wu B., Greenside P.G., Chan S.M., Koenig J.L., Snyder M.P., Pritchard J.K., Kundaje A., Greenleaf W.J. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat. Genet. 2016;48:1193–1203.  https://www.nature.com/articles/ng.3646  2. Simonett S.P., Shin S., Herring J.A., Bacher R., Smith L.A., Dong C., Rabaglia M.E., Stapleton D.S., Schueler K.L., Choi J., Bernstein M.N., Turkewitz D.R., Perez-Cervantes C., Spaeth J., Stein R., Tessem J.S., Kendziorski C., Keleş S., Moskowitz I.P., Keller M.P., Attie A.D. Identification of direct transcriptional targets of NFATC2 that promote beta-cell proliferation. J Clin Invest. 2021;131(21):e144833. https://doi.org/10.1172/JCI144833.

first: Michael

last: Lloyd

first: Anuj

last: Srivastava

first: Candice

last: Baker

first: Sai

last: Lek

first: Isabela

middle: G

last: Gyuricza

first: Jake

last: Emerson

first: Mary

last: Barter

first: Harianto

last: Tjong

first: Heidi

last: Munger

first: Rahul

last: Maurya

first: William

last: Schott

first: Anita

last: Adams

first: Margaret

last: Gaca

first: Chew

middle: Y

last: Ngan

first: Chia-Lin

last: Wei

first: Madeleine

last: Braun

first: Alan

last: Attie

first: Mark

last: Keller

last: Stitzel

first: Gary

last: Churchill


title: The FOXP3+ pro-inflammatory T cell: A Potential Therapeutic Target in Crohn’s Disease

city: Rochester

first: Asha

last: Nair

address: 200 1ST ST SW

institute: Mayo Clinic

summary: The incidence of inflammatory bowel disease, including Crohn’s disease (CD), continues to increase worldwide, however, the contribution of CD4+ cell populations remains to be elucidated. Emerging evidence suggested increased infiltration of potentially dysfunctional FOXP3+ regulatory T (Treg) cells in inflammatory lesions. In this study, we aimed to provide an in-depth transcriptional assessment of CD4+ cells driving chronic ileal inflammation. For this purpose, ileal biopsies were isolated from five CD patients as well as six healthy individuals and CD4+ cells were purified for subsequent single cell RNA-sequencing (scRNA-seq).  Our data revealed the presence of five distinct Treg subpopulations and that Tregs isolated from healthy control subjects represent the origin of pseudotemporal development into inflammation-associated subtypes. These pro-inflammatory Tregs isolated from CD patients displayed a unique responsiveness to TNFα signaling resulting in the upregulation of Treg-specific genes induced in Crohn’s (TRICs). We were able to establish an in vitro model of these pro-inflammatory FOXP3-positive cells which displayed an upregulation of TRICs, impaired suppressive activity as well as an elevated cytokine response in a novel organoid co-culture system. Intriguingly, based on our scRNA-seq data, an in silico drug prediction tool identified the histone deacetylase (HDAC) inhibitor (HDACi) Vorinostat as a putative regulator of the gene expression patterns from CD Tregs compared to control Tregs. Indeed, Vorinostat treatment resulted in a normalization of gene expression patterns and rescued the suppressive function of FOXP3-positive cells in vitro. Together, we provide insight into the role of CD4+ cells in CD lesions and have demonstrate a pathophysiologic role for TNFα-exposed Treg cells, underlying transcriptome-wide changes as well as potential novel therapeutic approaches.  The incidence of inflammatory bowel disease, including Crohn’s disease (CD), continues to increase worldwide, however, the contribution of CD4+ cell populations remains to be elucidated. Emerging evidence suggested increased infiltration of potentially dysfunctional FOXP3+ regulatory T (Treg) cells in inflammatory lesions. In this study, we aimed to provide an in-depth transcriptional assessment of CD4+ cells driving chronic ileal inflammation. For this purpose, ileal biopsies were isolated from five CD patients as well as six healthy individuals and CD4+ cells were purified for subsequent single cell RNA-sequencing (scRNA-seq).  Our data revealed the presence of five distinct Treg subpopulations and that Tregs isolated from healthy control subjects represent the origin of pseudotemporal development into inflammation-associated subtypes. These pro-inflammatory Tregs isolated from CD patients displayed a unique responsiveness to TNFα signaling resulting in the upregulation of Treg-specific genes induced in Crohn’s (TRICs). We were able to establish an in vitro model of these pro-inflammatory FOXP3-positive cells which displayed an upregulation of TRICs, impaired suppressive activity as well as an elevated cytokine response in a novel organoid co-culture system. Intriguingly, based on our scRNA-seq data, an in silico drug prediction tool identified the histone deacetylase (HDAC) inhibitor (HDACi) Vorinostat as a putative regulator of the gene expression patterns from CD Tregs compared to control Tregs. Indeed, Vorinostat treatment resulted in a normalization of gene expression patterns and rescued the suppressive function of FOXP3-positive cells in vitro. Together, we provide insight into the role of CD4+ cells in CD lesions and have demonstrate a pathophysiologic role for TNFα-exposed Treg cells, underlying transcriptome-wide changes as well as potential novel therapeutic approaches.

overall_design: Single cell RNA-sequencing on ileal biopsies extracted from healthy controls and Crohn's disease patients.

first: Robyn

last: Kosinsky

first: Michelle

middle: M

last: Gonzalez

first: Dominik

last: Saul

first: Luísa

last: Leite Barros

middle: R

last: Sagstetter

first: Yaroslav

last: Fedyshyn

first: Zhifu

last: Sun

first: Feda

last: Hamdan

first: Hunter

last: Gibbons

first: Brooke

last: Druliner

first: Steven

last: Johnsen

last: Faubion


title: AP-2β activates enhancers that define mammary hormone sensing cell identity [ChIP-Seq]

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

address: Adelaide Health & Med Sci Bldg, Corner George St & North Terrace

country: Australia

institute: The University of Adelaide

summary: The Activating Protein 2β transcription factor (TFAP2B; AP-2β) is a marker for both lobular and molecular apocrine/HER2-E breast cancers, despite these tumours having very different  prognoses. We show that simultaneous expression of both AP-2β and the estrogen receptor (ESR1, ER) marks well differentiated, low proliferation cells that are characteristic of luminal A lobular tumours, but loss of ER expression occurs when the tumour cells progress to molecular apocrine tumours. To discover potential explanations for this behaviour we performed chromatin immunoprecipitation sequencing (ChIP-seq) for AP-2β, AR, GATA3, FOXA1 and H3K27 acetylation in ER-negative MDA-MB-453 breast cancer cells. We find that all four transcription factors frequently bind to the same enhancers and that these enhancers are more likely to be active when AP-2β is present. Molecular apocrine genes are significantly more likely to have enhancers bound to all four transcription factors flanked by H3K27 acetylation. When AP-2β binds separately from the other factors, it binds close to the transcription start site, where it shows very high enrichment for H3K27 acetylation. AP-2 family proteins activate transcription by recruiting CITED proteins and p300/CBP. Since AR, FOXA1 and GATA3 are themselves able to recruit histone acetyl-transferases, we infer that AP-2β regulates the activity of those histone acetyl-transferases. We propose that this broad fundamental role in transcription explains the contradictory functions, both oncogenic and tumour suppressing, that have been assigned to AP-2 family members in previous studies on cancer.

overall_design: AP-2β, AR, and FOXA1 ChIP-seq in MDA-MB-453 cells after 4 h treatment with DHT

first: E

last: Mustafa

first: L

last: Hosseinzadeh

first: G

first: Z

last: Kikhtyak

first: K

last: Chia

first: J

last: Winter

first: R

last: Iggo

first: A

last: Dwyer

first: S

last: Pederson

last: Carroll

first: W

last: Tilley

first: T

last: Hickey


title: Transcriptomic Regulation of Apical Periodontitis by Nociceptors

city: San Antonio

first: Yidong

last: Chen

state: Texas

address: 8403 Floyd Curl Drive, MSC 7784

department: Population Health Sciences

institute: UT Health Science Center at San Antonio

summary: Apical periodontitis (AP) is a painful inflammatory disease resulting from tooth infection that affects millions worldwide with a marked impact on quality of life and is accompanied by bone loss surrounding the affected tooth. There is growing evidence that the nociceptive fibers densely innervating teeth regulate the disease progression, in addition to their sensorial function. We hypothesized that nociceptors regulate the transcriptomic profile of the periapical osteolytic lesion in a mouse model of AP. Male control (Nav1.8 cre+/-) and nociceptor-ablated (Nav1.8cre+/- DTAlox+/-) mice were generated and underwent pulp exposure procedures on all 4 first molars and at 8 weeks of age. At either 0, 7, or 14 days after pulp exposure, periapical tissues were dissected from mice (n=3-4/strain/time point). Total RNA was extracted from the pooled periapical lesions from each animal and submitted for total RNA sequencing and bioinformatic analysis. We found that pulp exposure triggers the differential expression of hundreds of genes within the periapical lesion over the course of infection with marked differences between in both control and mice with nociception ablation. Importantly, at 14 days post pulp-exposure, 422 genes were differentially expressed between nociceptor-ablated and control mice with greater enrichment of biological processes related to inflammation, specifically immune cell chemotaxis and migration, compared to control mice. Among these inflammatory markers, TNFα, IL-1α, and IL-1β, that are known to play a crucial role in AP were significantly upregulated in nociceptor-ablated mice. In conclusion, nociceptor-ablation regulates the transcriptomic profile of periapical lesions in a mouse model of AP, shifting the gene expression profile to a greater enrichment of inflammatory genes, suggesting nociceptors play a role in the kinetics of the immune response. This newly uncovered neuro-immune axis and its mechanisms in AP can potentially be an important therapeutic target for the treatment of this prevalent disease.

overall_design: 3-4 male mice (~8 weeks old) were used from each strain (Nav1.8cre+ [control] and Nav1.8cre+/DTA+ [nociceptor-ablated]) at each time point (Day 0, Day 7, and Day 14), 20 samples total.

first: Anibal

last: Diogenes

first: Katherine

middle: V

last: Lillis

first: Zhao

last: Lai


title: Transcriptome comparison of Arabidopsis thaliana dark-grown B-GATA double mutant gnc gnl, and the transgenic line GNLox, in different sucrose conditions

city: Freising

first: Jan

last: Sala

address: Emil-Ramann-Str. 8

department: Plant Systems Biology

institute: Technical University of Munich

summary: To investigate the role of LLM-domain B-GATAs in starch metabolism we performed gene expression profiling analysis of RNA-seq data, obtained with Illumina technologies. B-GATA double mutant gnc gnl and the transgenic line overexpressing GNL were grown in dark conditions to avoid interference from photosynthesis or other light-dependent processes affecting sugar and starch biosynthesis.

overall_design: Transcriptome comparison including three replicate measurements of three biological samples.

first: Claus

last: Schwechheimer


title: 99-MiDeTe

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

summary: We studied microRNA expression levels from serum of postmenopausal women with osteoporosis by investigating the anti-osteoporotic treatment denosumab for a period of 2 years in a longitudinal study. Serum RNA was extracted and subject to small RNA sequencing on an Illumina HiSeqV4 SR50 using 50bp, single end reads. After mapping against GRCh38.p12 provided by Ensembl and miRBase v22.1 differential expression analysis was undertaken with edgeRv3.28 using a quasi-likelihood negative binomial generalized log-linear model. We identified a panel of altered small non-coding RNAs between 3 different time points for all patients.

overall_design: Examination of small non-coding RNAs in serum samples of postmenopausal women from 3 different time points under anti-osteoporostic treatment denosumab using pairwise comparisons.

first: David

last: Carro Vázquez

first: Zora

last: Messner

first: Matthias

last: Hackl

first: Roland

last: Kocijan


title: Spatial transcriptomics analysis of wild type, 5XFAD mice, 5XFAD mice treated with either vehicle or human neural stem cells (hNSC)

city: Ann Arbor

first: Mohamed

last: Noureldein

address: 109 Zina Pitcher Place

department: Neurology

institute: University of Michigan

summary: Spatial transcriptomics analysis was performed to detect differential gene expression in brain sections of of wild type, 5XFAD mice (model of Alzheimer's Disease), 5XFAD mice treated with either vehicle or human neural stem cells (hNSC)

overall_design: Brains were sectioned from wild type, 5XFAD mice, 5XFAD mice treated with either vehicle or human neural stem cells (hNSC) at 41 weeks of age and subjected to 10X Visium spatial transcriptomics to get gene expression information.

first: Lisa

last: McGinley

first: Kevin

first: Eva

last: Feldman


title: Genotyping of Malignant Pleural Mesothelioma primary cell lines by SNP array

city: Paris

first: Sandrine

last: Imbeaud

address: 15 rue de l'Ecole de Médecine

department: INSERM UMRS1138-EQUIPE 28, Sorbonne Université-Inserm-Université de Paris

country: France

institute: Centre de Recherche des Cordeliers

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

summary:
SNP array data from 45 cell lines of Malignant Pleural Mesothelioma were used to explore recurrent copy number alterations.
This study was part of Cartes d'Identité des Tumeurs (CIT) project from the french Ligue Nationale Contre le Cancer.

overall_design: 45 primary cell lines of Malignant Pleural Mesothelioma were analyzed with Illumina HumanOmniExpress-24 v1.0 BeadChip SNP arrays.

first: Yuna

last: Blum

first: Clément

last: Meiller

first: Aurélien

last: de Reyniès

first: Didier

last: Jean


title: RNA-seq of Wild type (WT) tomato (Solanum lycopersicum, cultivar Ailsa Craig) and NAC-NOR CRISPR mutant (slnor, AC background)

city: Shenzhen

first: yujing

last: lin

address: No. 1088 Xueyuan Avenue, Nanshan District, Shenzhen City, Guangdong Province

institute: Southern University of Science and Technology

summary: Using RNA-seq to study the transcription level of genes in WT and slnor mutant

first: Ying

last: Gao

first: Yujing

last: Lin

first: Min

last: Xu

first: Hanxiao

last: Bian

first: Chi

last: Zhang

first: Jingyu

last: Wang

first: Hanqing

first: Yaping

first: Qingfeng

last: Niu

first: Jinhua

last: Zuo

first: Da-Qi

last: Fu

first: Yu

last: Pan

first: Kunsong

last: Chen

first: Harry

last: Klee

first: Zhaobo

last: Lang

first: Bo


title: SIRT6 overexpression predicts high risk of metastasis and relapse in Delta16HER2-positive breast cancer [RNA-seq]

city: PADOVA

first: GIUSEPPE

last: PERSICO

address: VIA UGO BASSI 58/B

institute: UNIVERSITA' DI PADOVA

summary: We investigate the impact of SIRT6-overexpression (SIRT6-OE) in the breast cancer mouse model Delta16HER2. After an initial delay in the tumor onset, starting form 20 weeks of age, SIRT6-OE induces a more aggressive phenotype of Delta16HER2 tumors, promoting the formation of more tumors and metastases with respect to controls. SIRT6 can regulate gene expression and chromatin integrity via deacetylation of H3K9ac. Therefore, to gain mechanistic insights, we performed H3K9ac ChIP-seq and RNA-seq on tumors from Delta16HER2/SIRT6-OE and Delta16HER2 mice, harvested at 20 weeks of age.

overall_design: We analyzed the total RNA from 2 Delta16HER2/SIRT6-OE and 2 Delta16HER2 tumors resected from mice at 20 weeks of age

first: Cristina

last: Andreani

first: Caterina

last: Bartolacci

first: Giuseppe

last: Persico

first: Francesca

last: Casciaro

first: Stefano

last: Amatori

first: Mirco

last: Fanelli

first: Marco

last: Giorgio

last: Galié

first: Daniele

last: Tomassoni

first: Junbiao

first: Roberto

last: Coppari

first: Augusto

last: Amici

last: Marchini


title: Heterogeneity in antigen presenting cells to infection revealed by single cell RNAseq

city: Ede

first: Alphonsus

middle: Chinedu

last: Ugwu

state: osun state

address: redeemers' university ede osun state

department: Biological Sciences

country: Nigeria

institute: Africa Centre of Excellence for Genomics of Infectious Disease (ACEGID), Redeemer’s 6 University, Ede, Osun State, Nigeria

summary: Antigen presenting cells (APC) play a central role in the host immune response to pathogen invasion by triggering early innate responses and facilitating the subsequent adaptive immune system for effective control and clearance of the infection. Accordingly, APC critically impact the outcome of an immune response. In vitro bone marrow (BM) derived APC facilitate studies aimed at dissecting their biology and function. BM derived cell cultures differentiated with granulocyte-macrophage colony stimulating factor (GM-CSF) consists of a heterogeneous mix of both dendritic cells (DC) and macrophages (MØ). Here we addressed the question of the impact of heterogeneous APC populations in their response to RNA viruses using the well characterised lymphocytic choriomeningitis virus (LCMV) infection model of BMDC populations. We compared LCMV infection and treatment with the dsRNA mimic poly (I:C)) to characterise the response of different subsets of BMDC using single cell transcriptomic analysis. Our results identified differences in the transcriptional response of BM derived APC to LCMV and poly (I:C). BM-DC were more effective at antigen presentation to T cells, whereas BM-MØ were efficient cytokine producers.

overall_design: Sorted CD11c+MHC class II+ bone marrow derived cell populations (dendritic cells [BMDC], macrophages [BM-M], double negative cells [DN]) were infected with LCMV clone 13 expressing GFP or stimulated with 100 µg poly (I:C)/ml  , as previously described for 12hr and 48hr for single cell (from the 12 h culture) sorting into customised BD WTA single cell encoding plates for RNA extraction and reverse transcription (primary infection) according to manufacturer’s instructions (PN 910000014 Rev. 03). Furthermore, a subset of infected cells (from the 48 h culture) were stimulated with 100 µg poly (I:C)/ml and incubated for another 6hr before single cell sorting into BD WTA single cell encoding plate as previously described (two plates per BM group). In the primary infection, a cell was considered to be infected if there was at least one GFP sequence read count. Differential gene expression was measured between infected and uninfected cells in each subset (Adjusted p-value less than 0.05). In the secondary stimulation with poly (I:C) gene expression was compared between infected cells alone and infected cells plus stimulation among the three BM groups. Selected antiviral ISGs and other genes from a curated database (http://www.informatics.jax.org/vocab/gene_ontology/GO:0002532) were compared between the three BM derived cells (CCL5, CD40, CD86, CXCL10, DDX58, GBP2, IFIT1,IFIT2, IFIT3, IFITM3, IL1b, IL6, IRF7, ISG15, ISG20, MX1, OASL1, OASL2, PML, RSAD2).

first: Chinedu

first: Barbara

last: Blacklaws

first: Paul

last: Tonks

first: Julien

last: Bauer

first: Juan

middle: C

last: De La Torre

first: Jonathan

last: Heeney


title: Double-stranded RNA triggers a distinct integrated stress response in the early embryo [cas9 tol2]

status: Public on Jan 01 2024

city: Qingdao

first: tong

last: lu

address: 72, binghai rd

institute: ShanDong University

summary: Gene functional study and the emerging mRNA therapy technology heavily rely on in vitro transcribed (IVT) mRNA, but the double-stranded RNA (dsRNA) by-product generated during IVT is often recognized by cells as a marker of virus replication, leading to the integrated stress response (ISR).The biological effects of dsRNA in undifferentiated cells differ significantly from those of differentiated counterparts.Here, we found that dsRNA triggered an unprecedented ISR in zebrafish early embryos, leading to developmental delay, severe cell necrosis, and lethal malformations.Mechanistically, dsRNA stimulation caused a PKR-eIF2α independent global translation inhibition and a burst of p53 signaling. In turn, p53 activated Interferon Stimulated Genes (ISGs) and other defense-related genes in the absence of the IFN system. Unexpectedly, p53 does not promote cell death; instead, it plays a protective role in weakening the damage of translation repression by compromising protein turnover via enhanced ISGylation.This study thus unveils a distinct ISR upon dsRNA stimulation, which may help perform faithful gene overexpression in early embryos and shed light on the strategies of undifferentiated cells against RNA virus infection.

overall_design:
To investigate the impact of the dsRNA-induced stress response, we compared the transcriptomes between uninjected and dsRNA-containing mRNA-injected zebrafish embryos at 6 hpf
Comparative gene expression profiling analysis of RNA-seq data for WT uninjected embryos and its injected cas9 or tol2 mRNA embryos

first: Tong

last: Lu

first: Ming

last: Shao


title: Small non-coding RNAs in extracellular vesicles derived from equine synovial fluid and plasma in a model of equine osteoarthritis

first: Andreas

last: Diendorfer

summary: We studied extracellular vesicles (EVs) from plasma and synovial fluid in an in vivo model of equine osteoarthritis by investigating longitudinal samples. EVs were isolated using size exclusion chromatography from plasma and synovial fluid of four horses subjected to an osteochondral fragment model of osteoarthritis at 0, 10, 35, 42, 49, 56, 63 days with relevant controls.EV RNA was extracted and subject to small RNA sequencing on an Illumina NovaSeq SP using 100bp, single end reads. After mapping against EquCab.3.0 and miRBase v22.1 differential expression analysis was undertaken with edgeRv3.28 using a quasi-likelihood negative binomial generalized log-linear model. We identified a panel of altered small non-coding RNAs.

overall_design: Examination of small non-coding RNAs in longitudianl samples of extracellular vesiscles derived form biofluids in a model of equine osteoarthritis using pairwise comparisons.

first: Mandy

last: Peffers

first: James

last: Anderson

first: Matthias

last: Hackl


title: BRCA1 and ELK-1 regulate Neural Progenitor Cell Fate in the Optic Tectum in response to Visual Experience in Xenopus laevis tadpoles

first: Caroline

last: McKeown

state: CA

address: 10550 N. Torrey Pines Rd., DNC-216

department: Dorris Neuroscience Center

institute: The Scripps Research Institute

summary: To identify regulators of activity-dependent neural progenitor cell fate, we used RNA-Seq to profile the transcriptomes of proliferating neural progenitor cells and newly-differentiated immature neurons. We identified six DE transcription factors which are predicted to regulate the majority of the other DE transcripts. We investigated the effect of BRCA1 and ELK-1 on activity-regulated neurogenesis in the tadpole visual system and found that knockdown of either BRCA1 or ELK-1 altered the fates of neural progenitor cells, and furthermore that the effects of visual experience on neurogenesis depend on BRCA1 expression, while the effects of visual experience on neuronal differentiation depend on ELK-1 expression. These studies provide insight into the potential mechanisms by which neural activity affects neural progenitor cell fate.

overall_design: Comparison of mRNA profiles in the X. laevis optic tectum at stages 46 between neural progenitor-enriched and immature neuron-enriched populations

first: Lin-Chien

last: Huang

first: Haiyan

last: He

first: Aaron

last: Ta

first: Hollis

middle: T

last: Cline


title: Stem tranascriptome of sweet sorghum variety ICSA38

city: New Delhi

first: Manoj

middle: K.

last: Sharma

state: Delhi

country: India

institute: Jawaharlal Nehru University

summary: We report transcriptome profiling from three developing stages of  middle internode in  sweet sorghum. Samples were harvested at Booting, milky stages and physiological maturity.

overall_design: Examination of 2 different stages of middle internode  development in sweet Sorghum variety ICSA38

first: Neeraj

last: Kumar

first: A

last: Umakanth

first: Rita

middle: K