title: A targeted systemic delivery platform of therapeutic modified mRNA and modRNA-derived antibodies for precision triple negative breast cancer treatment.

status: Public on Dec 31 2023

city: New York

first: Lior

last: Zangi

address: 1470 Madison Ave

department: Cardiovascular Research Institute

country: USA

institute: Icahn School of Medicine at Mount Sinai

type: Expression profiling by high throughput sequencing

summary: modified mRNA (modRNA) showed high efficacy and safety when used for COVID-19 mRNA vaccines. Upon vaccination, any cell receiving modRNA contributed to efficient expression of antigens resulting in robust immune response. However, in most disease settings it is crucial to restrict translation of therapeutic genes to clinically relevant cells. Here, we designed a breast cancer-Specific modRNA Translation system (bcSMRTs) for enriched gene expression in tumors after systemic delivery with lipid nanoparticles (LNP). Intravenous delivery of bcSMRTs led to a 114-fold increase in tumor-specific signal and a 383-fold decrease in other organs compared to regular modRNA. For therapeutic targeting, we designed modRNA-derived antibodies (modRNabs) in which host cells serve as a bioreactor to produce anti-checkpoint inhibitor antibodies such as anti-cytotoxic T lymphocyte antigen-4 (αCTLA-4). Our results show that αCTLA-4 modRNab inhibited tumor growth by 37% while bcSMRTs carrying Pip4K2c (Phosphatidylinositol-5-phosphate 4-kinase, type II, gamma) gene did so by 25%. Importantly, combining the two reduced tumor size by 75% and reorganized the immune cell landscape in a poorly immunogenic 4T1 model of breast cancer. The modular platform we created to evaluate and screen gene-based treatments in a breast cancer model can easily be adjusted to other types of cancer.

overall_design: The 4T1 breast cancer cell line (ATCC, #CRL-2539) was cultured in RPMI (Gibco, #72400-047) supplemented with 10% FBS and pen-strep. Cells were transfected with either Luc or Pip4K2c modRNA using Lipofectamine2000 (Invitrogen, #11668027) and collected 48h post transfection. RNA was isolated using Quick-RNA MiniPrep kit (Zymo Research, #R1055). n=2 in three independent experiments.

first: Magdalena

middle: M

last: Żak

first: Jimeen

last: Yoo

first: Alberto

last: Utrero-Rico

first: Wencke

last: Walter

first: Ann

middle: A

last: Kurian

first: Gayatri

last: Mainkar

first: Matthew

last: Adjmi

first: Daniel

middle: L

last: Ojalvo

first: Torsten

last: Haferlach

first: Jordi

last: Ochando

first: Patrick

last: Soon-Shiong

first: Filip

middle: K

last: Swirski


title: The Role of Histone H3 Leucine 126 as the Axial Copper Ligand

city: Los Angeles

first: Siavash

middle: K.

last: Kurdistani

state: CA

address: 615 Charles Young Dr. South

department: Department of Biological Chemistry

institute: David Geffen School of Medicine at UCLA

summary: The copper reductase activity of histone H3 suggests the presence of yet-to-be-discovered characteristics within the protein. Here, we investigated the function of leucine 126 (H3L126), which serves as the axial ligand for copper binding. Typically found as a methionine or leucine in copper binding proteins, the axial ligand influences the reduction potential of the bound ion, thereby modulating the capability of a protein to conduct electrons. Mutation of H3L126 to methionine (H3L126M) increased the enzymatic activity of yeast nucleosomes and intracellular Cu1+ levels, leading to improved copper-dependent activities including mitochondrial respiration and growth in oxidative media with low copper. H3L126 to histidine (H3L126H) mutation decreased nucleosome’s enzymatic activity and resulted in opposite phenotypes in vivo. Our findings demonstrate the role of H3L126 in fine-tuning the copper reductase activity of nucleosomes and underscore the utility of nucleosome enzymatic activity as a novel paradigm to uncover previously unnoticed features of histones.

overall_design: mRNA profiles of yeast with the histone H3 L126M and L126H mutations grown in fermentative and oxidative media

first: Chen

last: Cheng

first: Nataliya

middle: P

last: Tod


title: Profiling alterations of the metabolomic and transcriptomic characteristics and the therapeutic mechanism of Psoraleae Fructus in treating kidney-yang deficiency syndrome rats

city: Zhengzhou

first: Ming-Liang

last: Zhang

state: Henan Province

address: No. 19, Renmin Road

country: China

institute: The First Affiliated Hospital of Henan U

summary: Kidney-yang deficiency syndrome (KYDS) is a metabolic disease caused by neuroendocrine disorders often accompanied by abnormal liver function. Psoraleae Fructus (BGZ) is widely used to treat KYDS in China, but it is unclear whether BGZ plays a therapeutic role in regulating liver function. Organ index, ALT, AST, and HE staining were used to evaluate the protective effect of BGZ on KYDS in rats, and transcriptomics and metabolomics were employed to screen for potential biomarkers. The results showed that BGZ treatment significantly decreased the levels of ALT and AST, and ameliorated liver pathological damage in KYDS rats. 92 differentially expressed genes (DEGs) and 20 metabolites were significantly disturbed by BGZ in KYDS rats. Integrated analysis of metabolites and DEGs revealed that neuroactive ligand-receptor interaction, cAMP pathway, calcium signaling pathway, and cytokine-cytokine receptor interaction may be the main mechanism of BGZ treatment, and the key targets of the cAMP pathway were confirmed by ELISA and RT-qPCR. In conclusion, the cAMP pathway may be the partial mechanism by which BGZ exerts protective effects on KYDS, and the study results also lay the foundation for more in-depth mechanistic studies and drug-targeted therapy of KYDS in the future.

overall_design: The rats were randomly divided into four separate groups (N=5), which were administered with 0.5% sodium carboxymethylcellulose (CMC-Na) (CON group); BGZ_L powder, 0.9 g/kg (BGZ_L group, BGZ_L); hydrocortisone, 25 mg/kg (KYDS group); BGZ_L powder (0.9 g/kg) and hydrocortisone (25 mg/kg) (KYDS+BGZ_L group).

first: Jin-Fa

last: Tang

first: Xiao-He

last: Xiao

first: Xu

last: Zhao


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [Islet 2]

city: Bar Harbor

first: Gary

last: Churchill

state: Maine

address: 600 Main St

institute: The Jackson Laboratory

summary: Genetic and lifestyle factors greatly impact the development of metabolic diseases including Type 2 Diabetes (T2D). It is an ongoing challenge to determine how these factors and their interplay specifically contribute to risk of T2D. Mouse models allow precise control of environment and genetic replication, and mouse strains fed an unhealthy diet show variable signs of metabolic dysfunction ranging from overt diabetes to diet-induced obesity to complete resistance. When fed a high-fat high-sugar (HFHS) diet, NZO/HlLtJ (NZO) mice become severely obese and many become diabetic, C57BL/6J (B6J) mice develop obesity but seldom overt diabetes, and CAST/EiJ (CAST) mice are resistant to obesity and glucose intolerance. We present deep molecular and metabolic profiling of these three genetically diverse mouse strains fed control (low fat, no sugar) and HFHS diets to define inherited aspects of metabolism that may impact diabetes risk. Transcriptomic analysis of eight tissues revealed significant tissue-specific molecular variability underpinning the metabolic differences across strains. The most distinct diet responses were observed in adipose and pancreas. In adipose tissue, differences in immunometabolism, lipid metabolism, and oxidative phosphorylation pathways parallel the susceptibility to obesity and diabetes across strains.  In pancreatic islets, there was inflammation associated with HFHS diet in NZO mice that is expected to contribute to beta cell dysfunction. Taken together, physiological and molecular profiling of these genetically diverse mouse strains provides a foundation for deeper understanding the molecular basis of individual differences in susceptibility to metabolic diseases.

overall_design: Gene expression profiling analysis of RNA-seq data for male and female C57BL/6J, NZO/HlLtJ, and CAST/EiJ animals fed either a high fat, high sugar diet or control diet.

first: Candice

middle: N

last: Baker

first: Jeffery

last: Harder


title: Genome-wide analysis of gene expression in postnatal hippocampus of Neil1 and Neil2-deficient mice after hypoxia ischemia (HI)

city: Trondheim

first: Magnar

last: Bjørås

address: Erling Skjalgssonsgate 1

department: Department of Clinical and Molecular Medicine (IKOM)

country: Norway

institute: Faculty of Medicine and Health Sciences,NTNU

summary: NEIL 1-3 DNA glycosylases initiate the base excision repair pathway by removing oxidized bases from the DNA. NEIL1 and NEIL3 have been shown to protect the brain from ischemic stroke-induced injury in adult and perinatal mice, respectively. To assess the role of NEIL1 and NEIL2 in newborn mice, we used the Levine model of hypoxic-ischemic encephalopathy (HIE), modified for use in perinatal mice. We found that NEIL1 deficiency increased sensitivity to cerebral ischemia in newborn mice. In contrast, NEIL2 deficiency rendered the mice more resistant to hypoxia-ischemia. Importantly, no effect was seen in mice expressing base excision activity-deficient NEIL proteins and the global levels of the oxidative DNA lesion 5-hydroxycytosine, which is a substrate for the NEIL enzymes, did not differ significantly between the genotypes. Transcriptome analysis of NEIL1- and NEIL2-deficient hippocampus revealed changes in Neil2-deficient hippocampus that favour cell survival and limit brain injury after HI.  Our data suggest a role of NEIL2 in regulating the early transcriptional stress response, critical for neuronal cell death, after brain injury. This function seems to be independent of the base excision activity of the proteins.  The protective effect of NEIL2 deficiency makes NEIL2 a potential therapeutic target in treatment of perinatal HIE.

overall_design: Postnatal day 10 mice deficient for the DNA glycosylases Neil1 and Neil2 were subjected to HI for 3h and 6h, respectively. The hippocampus from the contralateral- and ipsilateral side was collected from two replicates of each genotype and time point and RNA isolated for transcriptome profiling.


title: Effect of agarooligosaccharide on gene expression of Ruminococcus gnavus

city: Toyoake

first: Tadashi

last: Fujii

state: Aichi

address: 1-98 Dengakugakubo Kutsukake-cho

department: School of Medicine, Gastroenterology and Hepatology

country: Japan

institute: FUJITA HEALTH UNIVERSITY

summary: We performed a transcriptome analysis of Ruminococcus gnavus with and without 0.1% (w/w) agarooligosaccharide exposure to validate the mechanism of growth inhibition.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for Ruminococcus gnavus with and without 5% (w/w) agarooligosaccharide exposure

first: Koji

last: Karasawa

first: Ikuya

last: Shirai

first: Kohei

last: Funasaka

first: Yoshiki

last: Hirooka

first: Takumi

last: Tochio


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [testis]


title: CD146 as a potent target for anti-vascular therapies in lung cancer brain metastasis

city: Dalian

first: Wenzhe

last: Duan

address: Shahekou Zone, Zhongshan Road 467

institute: Second hospital of Dalian Medical University

summary: To investigate the function of CD146 in the lung cancer brain metastasis cells, we established PC9-BrM3 cells in which CD146 has been knocked down by shRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of  PC9-BrM3 cells with or without AKR1B10 knockdown.

first: Wenwen

last: Liu

first: Shengkai

last: Xia

first: Qi

last: Wang


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [Skeletal muscle]


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [Hypothalamus]


title: Differentially expressed genes and functional categories in biopsy, peripheral blood and urine from kidney transplant patients with acute and chronic rejection

city: Medellín

first: Carlos

last: Carmona

address: Cl. 62 #52-59, La Candelaria, Medellín

department: Inmunología Celular e Inmunogenética

country: Colombia

institute: Universidad de Antioquia

summary: Kidney transplantation is the treatment of choice for patients with end-stage chronic kidney disease (ESKD). Despite the usefulness of transplantation as replacement therapy, long-term graft survival represents a major challenge for transplant immunology. Although nowadays there has been an advance in understanding immunological mechanisms mediating rejection, and the improvement of immunomodulation therapies, there are still underlying molecular processes marking an important variability among patients, and presumably influencing allograft rejection. With our analysis we explored differences in gene expression by Next Generation Sequencing implementing RNA-Seq in biopsies, blood and urine from kidney transplant patients with acute and chronic rejection. For this, we performed an intra-outcome analysis simultaneously in acute and chronic rejection, with which we sought: 1. To identify differences in gene expression between peripheral blood vs renal tissue and peripheral blood vs urine in acute rejection and chronic rejection; 2. To identify the level of agreement in gene expression between renal tissue and urine in acute rejection and chronic rejection and 3. To identify genes and biological processes associated with acute rejection and chronic rejection that could be potentially detected in blood, and simultaneously in urine and biopsy in acute rejection and in chronic rejection.

overall_design:
Kidney transplant patients diagnosed with either acute and chronic rejection were recruited, and blood, biopsy, and urine samples were obtained. RNA was obtained from each sample applying standard protocols and under nuclease-free conditions. RNA was sequenced and raw data was analyzed to obtain the table of raw counts, from which differential expression analyzes were performed. Comparisons were made separately for acute rejection and chronic rejection, using blood libraries as a baseline. This allowed the identification of DEGs in biopsy and in urine in relation to peripheral blood.
*** Raw sequencing data are not provided (cannot be recovered). ***

first: Cristiam

last: Àlvarez

first: Marlon

last: Castrillón

first: Gustavo

last: Zuluaga

first: Jhon

middle: F

last: Nieto

first: Luis

last: Arias


title: METTL14-mediated N6-methyladenosine modification of Col17a1/Itgα6/Itgβ4 governs epidermal homeostasis [MeRIP-seq]

city: Shanghai

first: Qirui

state: Shanghai

address: 639 Zhi Zao Ju Road

department: Department of Plastic and Reconstructive Surgery

institute: Shanghai Ninth People’s Hospital, Shanghai Jiao Tong University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: To elucidate the role of METTL14-mediated m6A modification in epidermal development, we conditionally knocked out the m6A methyltransferase METTL14 in mouse epidermal keratinocytes. We then performed MeRIP-seq analysis of epidermal keratinosis from P0 control mice (K14Cre,Mettl14F/+).

overall_design: We performed MeRIP-seq analysis of epidermal keratinosis from P0 control mice (K14Cre,Mettl14F/+).

first: Renpeng

last: Zhou

first: Siyi

last: Zeng

first: Yimin

last: Liang

first: Danru


title: Unveiling the Role of EGFL7 in Cervical Cancer: Polymorphisms, Expression, and Biological Function

city: Kunming

first: Weipeng

state: Yunnan

address: Jiao ling road

department: Institute of Medical Biology

institute: Chinese Academy of Medical Sciences

summary: Prior investigations have delineated the multifarious roles of EGFL7 within various cancer contexts. Nevertheless, the precise involvement of EGFL7 in the realm of human cervical carcinoma remains unclear. In this study, we investigated the relationship between EGFL7 polymorphisms and cervical cancer susceptibility in the Han Chinese population. Concurrently, we have scrutinized the expression patterns of EGFL7 in both the neoplastic cervical tissues and the cell lines HeLa and C33A. Furthermore, we explored the potential biological functions that EGFL7 may assume in the tumorigenesis of cervical cancer. Our findings manifest that the single nucleotide polymorphism rs9411260, ensconced within the transcriptional regulatory domain of EGFL7, is associated with cervical cancer risk in a Han Chinese population. Additionally, the mRNA expression of EGFL7 within cervical carcinoma tissues and the HeLa and C33A cell lines exhibits a marked reduction when compared with their adjacent normal counterparts and ECT1/E6E7 cells. Manipulation of EGFL7 expression precipitates alterations in the adhesion and migratory ability of cervical cancer cells. This investigation endows us with novel insights into the pathogenesis of cervical cancer.

overall_design: Total RNA was extracted from 6 samples, including three negative control samples and three samples with EGFL7 overexpression. We then performed gene expression profiling analysis using data obtained from RNAseg of these samples.

first: Zhixin

last: Niu

first: Li

last: Shi

first: Yufeng

last: Yao


title: Pathophysiological features of disease in a large animal model of COPD

city: Berwick

first: Habtamu

middle: Biyazen

last: Derseh

state: VIC

address: 100 Clyde Rd

country: Australia

institute: Federation University

summary: Background: Chronic obstructive pulmonary disease (COPD) is a serious chronic disease of the airways that affects many people worldwide and have limited treatment options. While small animal models provide a platform for therapeutic investigations into COPD, their deficiencies continue to impede clinical translation. Alternatively, as a large animal model, sheep have a respiratory system anatomically and physiologically similar to that of humans, encouraging their use in airway disease research. The aim of this study was to better understand disease pathology in a large animal (sheep) experimental model of COPD. Methods: COPD was induced in sheep following lung exposure to porcine elastase (PE) and repeated weekly lung exposures to lipopolysaccharide (LPS) over a period of 8 weeks. Bronchoalveolar fluid and blood samples were collected for immune analyses. Lung function was assessed and lung tissues were collected for histopathology and RNA sequencing. Results: Lung neutrophil levels were elevated in response to repeated airway exposure to PE/LPS, accompanied by a significant decline in ventilation over time. Histological evidence of COPD-like disease changes included chronic inflammation with increased airway and tissue inflammation scores, together with significantly larger airway wall area measures, increased connective tissue deposition and dysregulated gene expression. Conclusions: These studies demonstrate sustained chronic airway inflammation and pathophysiological lung changes in a sheep model of COPD, providing many similarities to that seen in COPD patients. This work opens a pathway for future translational studies using this unique large animal model of COPD, which will serve to bridge the gap between smaller animal models and humans.

overall_design: Total RNA samples from Saline- and Porcine Elastase/LPS-exposed lung lobes sheep (n=7 in triplicate)  sequenced after quality control analysis

middle: B

first: David

last: Piedrafita

first: Andrew

last: Davies

first: Jibriil

last: Ibrahim

first: Natasha

last: Herrmann

first: Paris

last: Papagianis

first: Sarah

last: Preston

first: Els

last: Meeusen

first: Robert

middle: J

last: Bischof


title: Functional exploration of novel glycoside hydrolases in Fervidibacter sacchari PD1T

city: Las Vegas

first: Nancy

last: Nou

state: NV

address: 4505 S Maryland Parkway

department: School of Life Sciences

institute: University of Nevada, Las Vegas

summary: Few aerobic hyperthermophiles degrade polysaccharides. We describe the genome-enabled enrichment and isolation of an aerobic hyperthermophile, Fervidibacter sacchari, which was originally ascribed to candidate phylum Fervidibacteria. F. sacchari uses polysaccharides and monosaccharides as sole carbon sources from 65-87.5 °C, and its genome encodes 117 glycoside hydrolases (GHs) spanning 49 GH families, including 31 homologs of understudied GH109, GH177, and GH179 domains. Here, we analyzed the transcriptomes of F. sacchari cells grown on eight different sole carbon and energy sources (beta-glucan, chondroitin sulfate, corn stover, gellan gum, locust bean gum, starch, xanthan gum, and xyloglucan) to link glycoside hydrolase substrate to function, as well as identify potential regulatory mechanisms. These data will provide preliminary characterization of novel carbohydrate-active enzymes at high temperatures.

overall_design: To investigate differential expression of F. sacchari glycoside hydrolases, we grew, in triplicate, cells in media each containing one of eight different carbon sources (beta-glucan, chondroitin sulfate, corn stover, gellan gum, locust bean gum, starch, xanthan gum, and xyloglucan) to mid-exponential phase. Using RNA-seq, we identify highest expressed transcripts as well as most distinct transcriptomes based on carbon source during growth.

first: Cale

middle: O

last: Seymour

first: Brian

last: Hedlund

first: Miranda

last: Harmon-Smith


title: METTL14-mediated N6-methyladenosine modification of Col17a1/Itgα6/Itgβ4 governs epidermal homeostasis [Ribo-Seq]

first: Qirui

last: Wang

summary: To elucidate the role of METTL14-mediated m6A modification in epidermal development, we conditionally knocked out the m6A methyltransferase METTL14 in mouse epidermal keratinocytes. We then performed ribosome-profiling analysis of epidermal keratinosis from P0 control mice (K14Cre,Mettl14F/+) and cKO mice (K14CreMettl14F/F).

overall_design: We performed ribosome-profiling analysis of epidermal keratinosis from P0 control mice (K14Cre,Mettl14F/+) and cKO mice (K14CreMettl14F/F).

first: Renpeng

last: Zhou

first: Siyi

last: Zeng

first: Yimin

last: Liang

first: Danru


title: Gene expresion profiling of two distnict splenic marginal zone B cell subpopulations, CD80high and CD80low MZ B cells

city: Suwon

first: Sujin

last: Lee

address: Seoburo 2066

department: Immunology

country: South Korea

institute: Sungkyunkwan Univ

summary: Marginal zone (MZ) B cells are innate-like B cells that not only rapidly secrete antibodies (Abs) against blood-borne pathogens but also serve Ab-independent functions such as antigen presentation and immune regulation, which may reflect their heterogeneity. Here, we discovered a subpopulation of MZ B cells that expressed higher levels of CD80, but not CD86, in naïve mice. CD80high MZ B cells revealed higher Ab-producing, proliferative, and IL-10-secreting capacities than CD80low MZ B cells. Notably, the CD80high MZ B cells survived 2 Gy whole-body irradiation, whereas CD80low MZ B cells were preferentially depleted by the irradiation and repleted in a month after the irradiation. The CD80high MZ B cells expressed higher levels of genes involved in proliferation, plasma cell differentiation, antioxidant response, and immune regulation. The CD80high MZ B cells contained autoreactive BCRs reactive to double-stranded DNA or type II collagen. Next-generation sequencing revealed more immunoglobulin heavy chains with a shorter complementarity-determining region 3 and no N-nucleotides in the CD80high MZ B cells than in CD80low MZ B cells. In summary, MZ B cells can be divided into two populations differing in CD80 expression, Ab-productive capacity, radioresistance, and B cell receptor repertoire, which may have different homeostatic functions.

overall_design: Splenic marginal zone (MZ) B cells are heterogeneous. We defined two distinct subpopulations of MZ B cells, CD80high and CD80low MZ B cells. To address transcriptional properties, we analyzed B cell receptor repertoire and gene expression of CD80high and CD80low MZ B cells.


title: MoS2 Reshapes the Tumor Microenvironment to Promote Tumor Cell Ferroptosis

city: Shenzhen

first: Dan

last: Shi

address: Xueyuan Avenue 1098

institute: Shenzhen University General Hospital

summary: MoS2 has found application in various biomedical fields, such as bioimaging and drug delivery. Nonetheless, utilizing MoS2 for anti-tumor therapy remains challenging, especially tumor immunotherapy. Macrophages, pivotal constituents of the tumor microenvironment, play a crucial role in driving tumor progression and chemoresistance. Modulating macrophages to reshape this microenvironment stands as a promising avenue for effective tumor treatment. In this study, we unveil a mechanism by which MoS2 induces the metamorphosis of macrophages from an M0 to an M1 phenotype, thus altering the tumor microenvironment. This transformation triggers pathways associated with inflammation within M1-type macrophages, leading to an upsurge in the expression of inflammatory molecules like IL1β. Macrophages activated by MoS2 exhibit a propensity to impede tumor cell proliferation. Through comprehensive RNA-sequencing analysis, we noted that MoS2 induces a greater enrichment of differentially expressed genes in the cytokine release pathway within macrophages. The excessive secretion of IL1β by MoS2-activated macrophages emerges as a pivotal catalyst, heightening ROS levels and decreasing GSH levels within tumor cells, ultimately culminating in ferroptosis. Therefore, we suggest MoS2 effectively reshapes the tumor microenvironment by steering macrophages toward releasing inflammatory molecules. The MoS2-triggered activation of macrophages, inducing the secretion of IL1β, emerges as a potent trigger for ferroptosis within tumor cells. Consequently, MoS2 holds substantial promise as an efficacious strategy for anti-tumor immunotherapy, achieved through the polarization of macrophages.

overall_design: ng analysis of RNA-seq data for Raw264.7 treated with MoS2


title: Inhalable textile microplastic fibers impair airway epithelial differentiation

city: Groningen

first: Barbro

last: Melgert

address: Antonius Deusinglaan 1

department: Molecular Pharmacology

country: Netherlands

institute: University of Groningen

summary:
Rationale
Microplastics are a pressing global concern and inhalation of microplastic fibers has been associated with interstitial and bronchial inflammation in flock workers. However, how microplastic fibers affect the lungs is unknown.
Objectives
Our aim was to assess the effects of 12x31 µm nylon 6,6 (nylon) and 15x52 µm polyethylene terephthalate (polyester) textile microplastic fibers on lung epithelial growth and differentiation.
Methods
We used human and murine alveolar and airway-type organoids as well as air-liquid interface cultures derived from primary lung epithelial progenitor cells and incubated these with either nylon or polyester fibers or nylon leachate. In addition, mice received one dose of nylon fibers or nylon leachate and 7 days later organoid-forming capacity of isolated epithelial cells was investigated.
Results
We observed that nylon microfibers, more than polyester, inhibited developing airway organoids and not established ones. This effect was mediated by components leaching from nylon. Epithelial cells isolated from mice exposed to nylon fibers or leachate, also formed fewer airway organoids, suggesting long-lasting effects of nylon components on epithelial cells. Part of these effects were recapitulated in human air-liquid interface cultures. Transcriptome analysis revealed upregulation of Hoxa5 post-exposure to nylon fibers. Inhibiting Hoxa5 protein during nylon exposure restored airway organoid formation, confirming Hoxa5's pivotal role in the effects of nylon.
Conclusions
These results suggest that components leaching from nylon 6,6 may especially harm developing airways and/or airways undergoing repair and we strongly encourage to characterize both hazard of and exposure to microplastic fibers in more detail.

overall_design: To investigate effects of nylon 6,6 fiber exposure on murine lung organoids. These lung organoid cultures consist of lung epithelial cells and CCL206 fibroblasts and were exposed to nothing (control), 12000, or 30000 12x31 um nylon 6,6 fibers in 6-well plates for 7 days. After 7 days epithelial cells were isolated from fibroblasts using anti-Epcam coated beads and the epithelial fraction was analyzed separately from the fiboblast fraction.

first: Shan

middle: S

last: Song

first: Gwenda

last: Vasse


title: Evaluation of anti-tumorigenic effects of anti-Lipocalin2 (anti-LCN2) monoclonal antibody against human cervical cancer xenografts in athymic nude mice

city: Bangalore

first: Nehanjali

last: Dwivedi

state: Karnataka

address: MSCTR, 8th floor A block

country: India

institute: MSCTR

summary: This study investigated the impact of an anti-LCN2 monoclonal antibody on STR-authenticated HeLa cells using a xenograft model in athymic nude mice. Treatment of tumors with anti-LCN2 antibody resulted in 39 – 60% reduction in tumor volume. RNA extracted from the tumors post-treatment was sequenced and aligned to human and mouse genome separately. Differential expression analysis of human mapped overexpressed genes in treated tumor revealed suppression of pro-tumorigenic TNF- and IL17 signalling pathways, whereas the corresponding mouse-mapped genes indicated pathways including activation of T-cells and T-cell mediated killing in treated tumors.  M2 mouse macrophage markers showed a decline under treatment signifying tumor regression. This observed T-cell activation and debilitation of M2 mouse macrophages by anti-LCN2 underlies its potential as an immune sensitizer that can potentially devour tumor cells through T-cell mediated cytotoxicity.

overall_design: Cultured HeLa cells (5 X 106) were injected subcutaneously into the dorsal flanks of NCr transgenic male nude mice. Mice were maintained under sterile and controlled conditions. Once tumors grew to about 100 mm3 in volume, they were injected with 100 µg anti-LCN2 antibody every alternate day directly into the tumor with PBS as the vehicle control in no treatment group. Animals were sacrificed when the tumor grew ~ 2000 mm3, after 2 weeks of treatment. RNA was isolated from the tumors (with and without treatment) and was subjected to sequencing on a NovaSeq 6000 (illumina) platform using 2 x 150 bp chemistry. Sequence reads were filtered for quality using Trimmomatic and filtered reads were separated based on mapping to human (GRCh38) and mouse (GRCm39) reference assembly using FastQ Screen. Separated reads were aligned to respective genome using STAR pipeline and differentially expressed genes were determined using edgeR.

first: Manjula

last: Das

first: Sujan

last: Dhar


title: Transcriptome Sequencing of Neo-2/15 stimulated CAR-NK cells

first: Jianhua

last: Luo

address: 800 Xiangyin Road

institute: National Key Laboratory of Immunology & Inflammation, Institute of Immunology

summary: We performed transcriptome sequencing on Neo-2/15 stimulated CAR NK cells,to shed light on the function and phenotype changes of CAR-NK cells stimulated by IL-2 and Neo-2/15.

overall_design: CAR NK cells stimulated with Neo-2/15 or IL-2, collect CAR NK cells and conduct the transcriptome analysis

first: Luo

last: Jianhua


title: Activation of glucocorticoid receptor signaling inhibits KSHV-induced inflammation and tumorigenesis

city: Pittsburgh

first: Luping

last: Chen

state: PA

address: 5117 Centre Avenue

institute: University of Pittsburgh

summary: The hallmark of Kaposi’s sarcoma (KS), the most common cancer in HIV-infected patients caused by Kaposi’s sarcoma-associated herpesvirus (KSHV) infection, is hyperinflammation. However, the role of inflammation and the mechanism of induction of inflammation in KSHV-induced cancer remain unclear. In a previous high-throughput screening against KSHV-induced oncogenesis, over half of the identified candidates were anti-inflammatory agents. Among them, dexamethasone, a common anti-inflammatory corticosteroid, functions through binding to and activating glucocorticoid receptor (GR). In this study, we examined the mechanism mediating KSHV-induced inflammation. We found that numerous inflammatory pathways were activated in KSHV-transformed cells. Particularly, the interleukin-1 alpha (IL-1α) and IL-1 receptor antagonist (IL-1Ra) from the IL-1 family, implicated in a wide variety of inflammatory diseases, were the most induced and suppressed cytokines in KSHV-transformed KMM cells compared to the matched primary MM cells, respectively. By using reverse genetics, we showed that KSHV-encoded miRNAs mediated IL-1α induction while both miRNAs and vFLIP mediated IL-1Ra suppression. Furthermore, the GR signaling was inhibited in KSHV-transformed cells, which was mediated by vFLIP and vCyclin. Importantly, dexamethasone treatment inhibited cell proliferation, and colony formation in softagar of KMM cells but had a minimal effect on MM cells. Consequently, dexamethasone suppressed the initiation and growth of KS-like KMM tumors in mice. Mechanistically, dexamethasone suppressed IL-1α expression but induced IL-1Ra expression. Treatment with recombinant IL-1α protein was sufficient to rescue the inhibitory effect of dexamethasone while overexpression of IL-1Ra alone caused a weak growth inhibition of KMM cells. Furthermore, dexamethasone induced IκBα expression resulting in the inhibition of the classical and alternative NF-kB pathways and IL-1α expression. Taken together, these results revealed the important role of IL-1 signaling pathway in KSHV-induced inflammation and oncogenesis, which can be inhibited by dexamethasone-activated GR signaling. This study determined the mechanism of inflammation in KSHV-induced oncogenesis and identified IL-1-mediated inflammation as a potential therapeutic target for KSHV-induced malignancies.

overall_design: To delineate the mechanism of dexamethasone inhibition of proliferation of KSHV-transformed cells, we performed mRNA-seq on both MM and KMM cells treated with 0.1 µM dexamethasone for 0, 2 and 4 days.

first: Ling

last: Ding

first: Xian

first: Yufei

last: Huang

first: Shou-Jiang

last: Gao


title: Edf1 control multiciliated ependymel cell associated genes expression

city: Wuhan

first: Haochen

last: Jiang

address: No.9. BoXue Road, economic development District

institute: Jianghan university

summary: The development and differentiation of Multiciliated ependymal cells  are crucial for brain development, with defects leading to conditions such as congenital hydrocephalus. The differentiation of MCCs depends on a unique transcriptional program. Our study shows that Edf1, previously implicated as a transcriptional co-factor, is consistently expressed during MCC development and positively regulates key genes involved in multiciliogenesis and physiological functions.

overall_design: To investigate the genes dependent on Edf1 during the development of multiciliated ependymal cells, we created Edf1 knockout (ko) mice using the CRISPR/CAS9 system. The isolated Radial Glial Cells (RGCs) were induced to differentiate into multiciliated ependymal cells. After six days of induction, we conducted an RNA-seq analysis. Each genotype included three biological replicates.

first: Mengting

last: Hua

first: Mei

first: Zhangfeng

last: Hu


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [liver]

first: Gary

last: Churchill

summary: Genetic and lifestyle factors greatly impact the development of metabolic diseases including Type 2 Diabetes (T2D). It is an ongoing challenge to determine how these factors and their interplay specifically contribute to risk of T2D. Mouse models allow precise control of environment and genetic replication, and mouse strains fed an unhealthy diet show variable signs of metabolic dysfunction ranging from overt diabetes to diet-induced obesity to complete resistance. When fed a high-fat high-sugar (HFHS) diet, NZO/HlLtJ (NZO) mice become severely obese and many become diabetic, C57BL/6J (B6J) mice develop obesity but seldom overt diabetes, and CAST/EiJ (CAST) mice are resistant to obesity and glucose intolerance. We present deep molecular and metabolic profiling of these three genetically diverse mouse strains fed control (low fat, no sugar) and HFHS diets to define inherited aspects of metabolism that may impact diabetes risk. Transcriptomic analysis of eight tissues revealed significant tissue-specific molecular variability underpinning the metabolic differences across strains. The most distinct diet responses were observed in adipose and pancreas. In adipose tissue, differences in immunometabolism, lipid metabolism, and oxidative phosphorylation pathways parallel the susceptibility to obesity and diabetes across strains.  In pancreatic islets, there was inflammation associated with HFHS diet in NZO mice that is expected to contribute to beta cell dysfunction. Taken together, physiological and molecular profiling of these genetically diverse mouse strains provides a foundation for deeper understanding the molecular basis of individual differences in susceptibility to metabolic diseases.

overall_design: : Gene expression profiling analysis of RNA-seq data for male and female C57BL/6J, NZO/HlLtJ, and CAST/EiJ animals fed either a high fat, high sugar diet or control diet.

first: Candice

last: Baker

first: Jeffery

last: Harder


title: METTL14-mediated N6-methyladenosine modification of Col17a1/Itgα6/Itgβ4 governs epidermal homeostasis [RNA-Seq]

first: Qirui

last: Wang

summary: To elucidate the role of METTL14-mediated m6A modification in epidermal development, we conditionally knocked out the m6A methyltransferase METTL14 in mouse epidermal keratinocytes. We then performed RNA-seq analysis of epidermal keratinosis from P0 control mice (K14Cre,Mettl14F/+) and cKO mice (K14CreMettl14F/F).

overall_design: We performed RNA-seq analysis of epidermal keratinosis from P0 control mice (K14Cre,Mettl14F/+) and cKO mice (K14CreMettl14F/F).

first: Renpeng

last: Zhou

first: Siyi

last: Zeng

first: Yimin

last: Liang

first: Danru


title: Genome-wide gene expression profile of human DIPG cell lines (ONC201 treatment)

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

summary: To study the effect of ONC201 treatment on DIPG-VII, DIPG-IV, and DIPG-XIII cell lines, we treated cell lines and performed RNA-Seq analysis.

overall_design: mRNA profiles of human DIPG cell lines (ONC201 treatment).

first: Jyothishmathi

last: Swaminathan

first: Shinji

last: Maegawa

first: Lin

last: Xu

first: Vidya

last: Gopalakrishnan


title: Regulation of the three-dimensional chromatin organization by transposable elements in pig spleen

city: Yangzhou

first: yu

middle: zhuo

last: li

state: 江苏省

address: No. 88, daxuenanlu Road

department: veterinary

institute: Yangzhou University

summary: We performed in situ Hi-C experiments to determine the 3D chromatin organization in pig spleen

overall_design: In situ Hi-C data are generated for pig spleen with two biological replicates

first: Yuzhuo

last: Li

first: Hairui

last: Fan

first: Weiyun

last: Qin

first: Wenbin

last: Bao

first: Ming-an

last: Sun


title: Effect of DUSP6 overexpression or knockdown on gene expression in AML12 cells

city: Beijing

first: Xiangyang

address: No.5 Yiheyuan Road, Haidian District

department: College of Life Sciences

institute: Peking University

summary: DUSP6 plays important roles in MAPK signaling pathway, but whether and how it is involved in liver funciton remains to be explored. Here, we performed RNA-seq analyses in AML12 cells where DUSP6 is disrupted. We overexpressed GFP-DUSP6 or GFP in AML12 cells, and tested the effects of  DUSP6 increase on gene expression in AML12 cells. Meanwhile, we knocked down DUSP6 in AML12 cells and tested the effects of  DUSP6 decrease on gene expression in AML12 cells. Taken together, we analyzed the changes of gene expression mediated by DUSP6, which provides new insights for the function of DUSP6 in liver

overall_design: We transiently overexpressed GFP-DUSP6 or GFP in AML12 cells by lipo2000, and 24 hours later harvested cells for RNA-seq analyses. Meanwhile, we transfected AML12 cells with DUSP6-specific siRNA or negative-control (NC) siRNA by lipo2000, and 48 hours later harvested cells for RNA-seq analyses. Each group contains three samples.


title: Whole kidney transcriptome of the rat after 3 days water restriction

city: Bristol

first: Benjamin

middle: Thomas

last: Gillard

address: Dorothy Hodgkin Building

department: Bristol Medical School

country: United Kingdom

institute: University of Bristol

summary: The aim of this study is to find genes with differential expression in the kidney when the organism has reduced water intake. Animals either had access to water ad libitum or had no access to water for 3 days. The whole kidney was sequenced to gain a comprehensive view of renal gene expression. Differentially expressed genes may be involved in the renal response to dehydration. This dataset is useful to compare to other whole kidney transcriptome datasets to find conserved gene expression responses.

overall_design: The whole kidney transcriptome of the rat was elucidated using RNAseq. Kidneys were dissected from rats belonging to either the control group (water ad libitum) or the dehydration group (3 days water restriction). Gene expression was compared across the groups to find osmoregulatory genes.

middle: T

first: Fernando

last: Alvira Iraizoz

first: Panjiao

last: Lin

first: Michael

last: Greenwood

first: David

last: Murphy


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [Ovary]

city: Bar Harbor

first: Gary

last: Churchill

address: 600 Main St

institute: The Jackson Laboratory

overall_design: Gene expression profiling analysis of RNA-seq data for male and female C57BL/6J, NZO/HlLtJ, and CAST/EiJ animals fed either a high fat, high sugar diet or control diet.

first: Candice

last: Baker

first: Jeffery

last: Harder


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [Heart]


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models

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

overall_design: Refer to individual Series


title: Multi-omic study of genome-edited human colonoids reveal patterns of microRNA regulation specific to different colorectal cancer mutation profiles

city: Ithaca

first: Praveen

last: Sethupathy

state: NY

address: Cornell University College of Veterinary Medicine, Box 17

department: Biomedical Science

institute: Cornell University

type: Non-coding RNA profiling by high throughput sequencing

summary: Colorectal cancer (CRC) is the third most diagnosed cancer and the second leading cause of cancer-related death worldwide Unique combinations of mutations can affect responsiveness to specific therapeutics. This can be, at least in part, due to mutation-specific alterations in gene regulatory mechanisms. To better understand how unique combinations of mutations affect gene regulation, we generated small RNA-seq, length extension chromatin run-on-seq (leChRO-seq), and RNA-seq  data from APC (A-mutant), APC/KRAS (AK-mutant), APC/KRAS/TP53 mutant (AKP-mutant), and iGFP control human colonic organoids. From these analyses, we found that our colonic organoid models demonstrate mutation-specific patterns of miRNA transcription, miRNA expression and transcriptional regulatory element actvitiy. Furthermore, we defined 10 patterns of miRNA expression across  organoid models. We highlighted one group of miRNAs that exhibited a unique downregulation of expression in AKP-mutant organoids (including miR-34a-5p and miR-10a-5p). Analysis of miRNA transcription revealed that most changes in miRNA expression are correlated with changes in miRNA transcription. Analysis of leChRO-seq data revealed that transcriptional regulatory elements upregulated in AKP-mutant colonic organoids have an enrichment of predicted binding sites for oncogenic transcription factors.

overall_design: Genetically modfieid colonic organoid (termed colonoid) models were generated using a dox-inducible CRISPR system. smRNA-seq data was generated for APC+dox mutant (A-mutant; n=3), APC/KRAS+dox mutant (AK-mutant; n=4), APC/KRAS/TP53+dox mutant (AKP-mutant; n=2), iGFP+dox (iGFP_dox; n=4), iGFP-dox (iGFP_noDox; n=4). Length extension chromatin run-on sequencing (leChRO-seq) data was generated for A-mutant (n=2), AK-mutant (n=2), AKP-mutant (n=2), iGFP_dox (n=2), and iGFP_noDox (n=2). RNA-seq data was generated for iGFP_dox (n=4) and AKP-mutant (n=3).

first: Jonathan

middle: W

last: Villanueva


title: Setdb1-loss induces type-I interferons and immune clearance of melanoma

city: New Haven

first: Meaghan

last: McGeary

state: CT

address: 300 Cedar St.

department: Immunobiology

institute: Yale School of Medicine


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [Dorsal Vagal Complex]

middle: M


title: Rational design of cyanobacteria aptamer sensitizes prostate cancer to hormone therapy

city: LOS ANGELES

first: Carlos

middle: David

last: Cruz-Hernandez

state: CALIFORNIA

address: 8700 Beverly Blvd #2900A

department: SOCC

institute: Cedars Sinai

summary: We performed RNA-seq to investigate gene expression changes in prostate cancer cells  treated with L-Gln and 56 mer Gln aptamer

overall_design: RNA-seq was performed in C4-2B and 22RV1 cells with biological triplicates under various conditions (56 mer 50 nM and L-Gln 2 mM).

first: Neil

middle: A

last: Bhowmick

middle: D


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [kidney]


title: Setdb1-loss induces type-I interferons and immune clearance of melanoma (RNA-Seq)

summary: Despite recent advances in the treatment of melanoma, many patients with metastatic disease still succumb to their disease. To identify tumor-intrinsic modulators of immunity to melanoma, we performed a whole-genome CRISPR screen in melanoma and identified multiple components of the HUSH complex, including Setdb1, as hits. We found that loss of Setdb1 leads to increased immunogenicity and complete tumor clearance in a CD8+ T-cell dependent manner. Mechanistically, loss of Setdb1 causes de-repression of endogenous retroviruses (ERVs) in melanoma cells and triggers tumor-cell intrinsic type-I interferon signaling, upregulation of MHC-I expression, and increased CD8+ T-cell infiltration. Furthermore, spontaneous immune clearance observed in Setdb1-/- tumors results in subsequent protection from other ERV-expressing tumor lines, supporting the functional anti-tumor role of ERV-specific CD8+ T-cells found in the Setdb1-/- microenvironment. Blocking the type-I interferon receptor in mice grafted with Setdb1-/- tumors decreases immunogenicity by decreasing MHC-I expression, leading to decreased T-cell infiltration and increased melanoma growth comparable to Setdb1wt tumors. Together, these results indicate a critical role for Setdb1 and type-I interferons in generating an inflamed tumor microenvironment, and potentiating tumor-cell intrinsic immunogenicity in melanoma. This study further emphasizes regulators of ERV expression and type-I interferon expression as potential therapeutic targets for augmenting anti-cancer immune responses.

overall_design: 1x10^6 cells were plated in complete media and incubate in culture for 24 hours to allow them to adhere. Cells were then treated with PBS or antibodies for 72 hours (with treated media replaced every 36 hours), then harvested for sequencing. 1x10^6 cells were pelleted, and RNA isolated using RNeasy kit, supplemented with QIAshredder and DNase treatment (Qiagen).

middle: K

first: William

last: Damsky

first: Andrew

last: Daniels

first: Eric

last: Song

first: Goran

last: Micevic

first: Clotilde

last: Huet-Calderwood

first: Huda

last: Lou

first: Sateja

last: Paradkar

first: Susan

last: Kaech

last: Calderwood

middle: E

last: Turk

first: Akiko

last: Iwasaki

first: Marcus

last: Bosenberg


title: Setdb1-loss induces type-I interferons and immune clearance of melanoma (scRNA-Seq)

overall_design: 3 tumors per condition were harvested, dissociated to single cell suspensions and tagged using HTO TotalSeq tags then pooled across condition. Samples were stained with antibodies to CD45, CD3e, CD8, Fixable Live/Dead Aqua (Life Tech), and sorted using BD FACS Aria, then pooled in the following ratios: CD45- (25%); CD45+ CD3- (25%); CD8+ (50%). 5000 cells per sample were loaded onto the 10X Chromium Library.

first: David

first: Benjamin


title: Pair bonding and disruption impact lung transcriptome in monogamous Peromyscus californicus

city: COLUMBIA

first: HAO

last: JI

state: SC

address: 715 SUMTER ST CLS RM 109

department: College of Pharmacy

institute: University of South Carolina

summary:
To investigate  the effects of bonding experiences on the transcriptome of monogamous P. californicus in the lungs.
Our results indicated that the lung transcriptomes of Peromyscus californicus are altered in a manner that depends on pair bonding. Pathways affected include hypoxia response and heart development.

overall_design: Comparative gene expression profiling analysis of RNA-Seq data. RNA was isolated from bonded, bond-disrupted, and virgin lung tissues.

first: Hippokratis

last: Kiaris

first: Asieh

last: Naderi

first: Hao

last: Ji


title: UBR7 an E3 ligase targets Sp110 via modulating IFN beta signalling in HBV-induced hepatic carcinoma

first: madavan

last: vasudevan

address: Kasturi Nagar

institute: Theomics International Private Limited

summary: UBR7 is an E3 ubiquitin ligase. We identified that Sp110 is a novel substrate for UBR7 which promotes HBV persistence.  UBR7 ubiquitinates Sp110 which leads to downregulation of type I interferon response pathway genes. Our study reports that UBR7 ubiquitinates Sp110 thereby promoting viral persistence and HBV- induced HCC.

overall_design: RNA seq of UBR7 knockdown in HBV 1.3mer treated HepG2 cells.

first: Chandrima

last: Das

first: Madavan

last: Vasudevan


title: mRNA expression quantitative Analysis of MV4-11 cell lines treated with JOA compared with control

city: Weifang

first: Liuya

last: Wei

address: 7166 number, Baotong West Street

institute: Weifang Medical University

summary: The goals of this study are toevaluate the mRNA expressions of genes in  MV4-11 cell lines treated with JOA

overall_design: There are 6 samples for MV4-11 cell line ( control and JOA-treated)

first: X

last: Li

first: L


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [Islets 1]

first: Gary

last: Churchill

first: Candice

middle: N

last: Baker

first: Jeffery

last: Harder


title: Priming of tomato mother plants using chemical elicitors linked to whole genome DNA methylation.

city: Wageningen

first: Marie

last: Duhamel

address: Droevendaalsesteeg 1

department: Plant Science Group

institute: Wageningen University & Research

summary: Inbred parental lines of two cultivars (cv Moneyberg and cv Bolstar Granda) of the model crop tomato were primed (induced for resistance) during four different moments in their development, i.e. once in the vegetative phase (time window 1), once in the generative phase at early flowering (time window 2), multiple times in the generative phase during flowering (time window 3), and once during ripening of the first fruit bunch (time window 4). The primers were ß-aminobutyric acid (BABA), 2,6-dichloroisonicotinic acid (INA), methyljasmonate (MeJA), and water as control; they were selected for their ability to induce different plant resistance pathways. After collecting seed batches from these plants we here look at the effect of priming the tomato plants with those different chemicals on the plant genome methylation level.

overall_design: Seeds from the same seed batch than the daughterplants displaying an improved resilience against pathogens were selected for DNA extraction : for Moneyberg, seeds from motherplants treated with BABA and Ina at time window 2 and treated with MeJa at time window 3, as well as seeds from control plants, for Bolstar: seeds from motherplants treated with BaBa and Ina at time window 2 as well as seeds from control plants.As a result, 48 seed samples were selected from the seed batches coming from 6 plants per treatments for the Bolstar cultivar and for the Moneyberg cultivar. 10 seeds per sample were pooled for each extraction. The extracted 48 DNA samples were sent to IGA technology to perform a whole genome bisulfite sequencing. A technical replicate was made for each sample resulting in 90 libraries. The libraries were prepared at the sequencing company. Sequencing was performed on a NovaSeq 6000 system generating 2*150bp paired end reads aiming for 10time coverage. Resulting sequences were obtained in fastq format.

first: Luc

last: van den Beld


title: Lung Tissue Exosome-Mediated Delivery of ceRNA Networks as a Novel Mechanism for Sepsis-induced Acute Lung Inflammation (lncRNA-Seq)

city: jiangxi

first: wei

last: deng

state: China

address: 17 Yongwai Zhengjie, Donghu District, Nanchang City, Jiangxi Province, China

institute: Department of Critical Care Medicine, First Affiliated Hospital of Nanchang University

summary: Acute lung injury (ALI) is associated with a high mortality rate; however, the underlying molecular mechanisms are poorly understood. The purpose of this study was to investigate the expression profile and related networks of long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and mRNAs in lung tissue exosomes obtained from sepsis-induced ALI. A mouse model of sepsis was established using the cecal ligation and puncture method. RNA sequencing was performed using lung tissue exosomes obtained from mice in the sham and CLP groups. Hematoxylin-eosin staining, western blotting, immunofluorescence, quantitative real-time polymerase chain reaction, and nanoparticle tracking analysis were performed to identify relevant phenotypes, and bioinformatic algorithms were used to evaluate competitive endogenous RNA (ceRNA) networks.Thirty lncRNA-miRNA-mRNA interactions were identified, including two upregulated lncRNAs, 30 upregulated miRNAs, and two downregulated miRNAs. Based on the expression levels of DEmRNAs, DELncRNAs, and DEmiRNAs, 30 ceRNA networks were constructed. This study revealed, for the first time, biomarkers of lung tissue exosome RNA and the related networks of lncRNA in sepsis-induced ALI. We revealed a novel molecular mechanism of sepsis-induced ALI, which may support the diagnosis and treatment of sepsis-induced ALI.

overall_design: Lung exosomes were extracted from sham operation group and sepsis model mice group for RNA sequencing

first: Wei

last: Deng

first: Fen

last: Liu


title: RNA-sequencing data of porcine alveolar macrophages exposed to probiotic bacteria

city: Frederiksberg C

first: Andrew

last: Williams

address: Dyrlægevej 100

country: Denmark

institute: University of Copenhagen

summary: Macrophages were treated with either Bacillus sp. Enterococcus sp., Poly I:C, or Poly I:C combined with either of the two bacteria

overall_design: Macrophages were obtained from the lungs of healthy pigs (Danish Landrace-Yorkshire) and exposed ex vivo to the various treatments.

middle: R


title: Effect of depletion of SLC1A5 on gene expression in T98G glioma cell line.

city: Xi'an

first: Liying

last: Han

state: Shaanxi Province

address: Xinsi Road No.1

institute: Tangdu Hospital

summary: To investigate the function of SLC1A5 in glioma cells, we establishedT98G cell line in which SLC1A5 has been knocked down by shRNA.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq.

first: Jinpeng

last: Zhou

first: Leiyang


title: Transcriptome and metabolic survey disclose the mode of action of static and dynamic low oxygen postharvest storage strategies to prevent the onset of superficial scald disorder in fruit of ‘Granny Smith’ apple cultivar

city: San Michele all'Adige

first: Fabrizio

last: Costa

state: N/A = Not Applicable

address: Via Mach 1

department: Center Agriculture Food Environment

country: Italy

institute: University of Trento

summary: To preserve quality feature and ensuring availability of fresh fruit on the market, apples need to be stored. The low temperature applied during storage, beside avoiding important fruit loss, can also promote the development of serious chilling injury type of disorder, such as superficial scald. One of the strategies largely employed to prevent the development of this phenomenon is the control of the storage atmosphere, by lowering down the concentration of oxygen. In this work, a multifaceted survey was carried out to investigate the variation in transcriptome together with three categories of metabolites (phenolics, lipids and volatile organic compounds, VOCs) in fruit of ‘Granny Smith’ apple cultivar stored in both static and dynamic hypoxia condition for 5 and 7 months, respectively. The global transcriptome survey identified a core set of differentially expressed genes in three main functional groups, revealing as the duration of storage had an important effect in the coordination of gene expression. The effect of the storage time was furthermore highlighted by the DEG-network analysis that identified a distinct number and type of transcriptomic hubs. Samples characterized by the development of superficial scald were distinguished by a higher concentration of chlorogenic acid and a higher expression of PAL and PPO in a time specific fashion. The prevention of this phenomenon was instead related to distinctive re-programming events, involving the accumulation of specific antioxidant types of metabolites, very long chain fatty acids and the expression of genes coordinating an hypoxia acclimation process, such as RAP2-like and PCO.

overall_design: RNA-Seq analysis of apple peel. In total 36 samples have been assessed (6 samples: RA, RA_SL, DCA, DCA_SL, ULO, ULO_SL; x 2 times: T1 and T2; 3 replicates /sample; 6 samples x 2 times x 3 replicates: 36)

first: Francesca

last: Populin

first: Lorenzo

last: Vittani

first: Angelo

last: Zanella

first: Stefan

last: Stuerz

first: Ilaria

last: Folie

first: Iulia

last: Komhenko

first: Franco

last: Biasioli

first: Matthias

last: Scholz

first: Domenico

last: Masuero

first: Urska

last: Vrhovsek

first: Nicola

last: Busatto


title: Lung Tissue Exosome-Mediated Delivery of ceRNA Networks as a Novel Mechanism for Sepsis-induced Acute Lung Inflammation (miRNA-Seq)

first: wei

last: deng

first: Wei

last: Deng

first: Fen


title: Comprehensive analysis of Bulk RNA-seq and Single-nuclei RNA-seq reveals the origin of high-grade serous “ovarian” carcinoma [bulk RNA-seq]

city: Yiwu

first: keren

last: cheng

state: Zhejiang

address: 1575 chouzhou bei road

department: School of Medicine

institute: Zhejiang University

summary: High grade serous ovarian cancer (HGSOC) is characterized by late stage, rapid progression, easy drug resistance, high mortality and recurrence rate. Tubal secretory cells have always been considered as the origin cells of HGSOC, due to the high heterogeneity of the latter, the type and mechanism of cell origin is poorly confirmed. Combined with single-nuclei RNA sequencing (snRNA-seq) and Bulk tissue transcriptome sequencing, we expounded the composition of epithelial cell subgroups of fallopian tubes and HGSOCs.

overall_design: Bulk RNA sequencing of fallopian tubes (isthmus, ampulla, fimbriae), epithelial ovarian cancer, and ovary.

first: Keren

last: Cheng

last: Yan


title: In vitro generation of long-lived human Plasma Cells II

city: York

first: Matthew

middle: Anthony

last: Care

state: North Yorkshire

address: Wentworth Way

department: Department of Biology

institute: The University of York

summary: Gene expression profiling of B-cells from a model differentiation series: from Naïve B-cells, through a proliferative plasmablast stage to long-lived antibody secreting plasma cells.

overall_design: B-cells were isolated from the peripheral blood of three adult donors and differentiated in vitro (see individual samples for culture conditions)

first: Mario

last: Cocco

first: Reuben

last: Tooze


title: DNA double-strand breaks regulate the cleavage-independent release of Rec8-cohesin during yeast meiosis

city: Suita

first: Masaru

last: Ito

state: Osaka

address: Yamadaoka 3-2

institute: Osaka University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: The mitotic cohesin complex necessary for sister chromatid cohesion and chromatin loop formation shows local and global association to chromosomes in response to DNA double-strand breaks (DSBs). Here, by genome-wide binding analysis of the meiotic cohesin with Rec8 as a kleisin, we found that Rec8 shows dynamic localization from middle to late meiotic prophase I with cleavage-independent global dissociation along chromosomes, driven by meiotic DSB formation. Each Rec8 binding site on the chromosome axis follows distinct dynamics with dissociation and association. Centromeres also showed reduced Rec8 binding in late prophase I relative to mid-prophase I, implying chromosome remodeling of the regions. Rec8 dissociation profile per chromosome is largely correlated with meiotic DSB density. Indeed, the spo11 mutant deficient in meiotic DSB formation did not show the cleavage-independent dissociation of Rec8 in late meiotic prophase I. These suggest the presence of a regulatory pathway for global Rec8-cohesin dynamics in response to meiotic DSBs.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for meiotic cohesin Rec8 in budding yeast S. cerevisiae

first: Akira

last: Shinohara

first: Kiran

last: Challa

first: Ghanim

last: V Fajish

first: Sagar

last: Salim

first: Ajith

last: V Pankajam

first: Yurika

last: Fujita

first: Koodali

last: T Nishant


title: Genotype-by-diet interactions determine susceptibility and resistance in T2D mouse models [adipose]

first: Gary

last: Churchill

state: Maine

summary: Genetic and lifestyle factors greatly impact the development of metabolic diseases including Type 2 Diabetes (T2D). It is an ongoing challenge to determine how these factors and their interplay specifically contribute to risk of T2D. Mouse models allow precise control of environment and genetic replication, and mouse strains fed an unhealthy diet show variable signs of metabolic dysfunction ranging from overt diabetes to diet-induced obesity to complete resistance. When fed a high-fat high-sugar (HFHS) diet, NZO/HlLtJ (NZO) mice become severely obese and many become diabetic, C57BL/6J (B6J) mice develop obesity but seldom overt diabetes, and CAST/EiJ (CAST) mice are resistant to obesity and glucose intolerance. We present deep molecular and metabolic profiling of these three genetically diverse mouse strains fed control (low fat, no sugar) and HFHS diets to define inherited aspects of metabolism that may impact diabetes risk. Transcriptomic analysis of eight tissues revealed significant tissue-specific molecular variability underpinning the metabolic differences across strains. The most distinct diet responses were observed in adipose and pancreas. In adipose tissue, differences in immunometabolism, lipid metabolism, and oxidative phosphorylation pathways parallel the susceptibility to obesity and diabetes across strains.  In pancreatic islets, there was inflammation associated with HFHS diet in NZO mice that is expected to contribute to beta cell dysfunction. Taken together, physiological and molecular profiling of these genetically diverse mouse strains provides a foundation for deeper understanding the molecular basis of individual differences in susceptibility to metabolic diseases.

overall_design: Gene expression profiling analysis of RNA-seq data for male and female C57BL/6J, NZO/HlLtJ, and CAST/EiJ animals fed either a high fat, high sugar diet or control diet.

first: Candice

last: Baker

first: Jeffery

last: Harder


title: Sepsis-Associated Coagulation and Inflammation are Differentially Regulated in Renal Microvascular Beds

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

overall_design: Refer to individual Series


title: Genome-wide effects of Karanjin on gene expression in T47D breast cancer cells

city: Guwahati

first: Anil

middle: Mukund

last: Limaye

state: Assam

address: IIT Guwahati

department: Department of Biosciences and Bioengineering

institute: Indian Institute of Technology Guwahati

summary: Application of next generation sequencing technology (RNA-seq) to identify genes modulated by Karanjin in T47D cells

overall_design: T47D cells were treated with 10 µM Karanjin or vehicle (DMSO) for 24 h.

first: Gaurav

last: Bhatt


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

city: Buffalo

first: Jianmin

last: Wang

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,
meanwhile, the other part of recipients are infected with LCMV,

first: Fengyin

last: Li

first: Hai-hui

last: Xue


title: Streptococcus pneumoniae endopeptidase O (PepO) induces trained immunity to defend the host against numerous pathogen infections

city: Chongqing

first: Xuemei

last: Zhang

address: No. 1, Medical College Road, Yuzhong District, Chongqing

institute: Chongqing Medical University

summary: Antibiotic resistance and the pandemic of infectious diseases pose major hazards to human health. As a novel anti-infection strategy, trained immunity has a promising future. Recombinant Streptococcus pneumoniae Endopeptidase O (rPepO) is a novel trained immunity inducer that is a highly effective broad-spectrum anti-infective molecule. Here, we demonstrate that rPepO training induces a protective effect by improving the function of several immune cells. rPepO trains macrophages in the periphery to improve their immunological response. In addition, macrophage-derived complement C3 stimulates B lymphocytes to bolster the host's initial line of defense. While trained-macrophage-derived G-CSF changes the host's hematopoiesis and promotes central trained immunity. The "trained" label is found on freshly differentiated mononuclear macrophages, which also possess significantly enhanced anti-infective properties. Consequently, our research reveals that rPepO can induce peripheral and central trained immunity and possesses broad-spectrum and durable antimicrobial characteristics.

overall_design: Peritoneal cells in 4 groups: negative control,  negative control with S.a restimulation, rPepO training, and rPepO training with S.a restimulation.  Three samples were analyzed in each group.

first: Wenlong

last: Xu


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

city: Shenyang,

first: Jia

middle: Ran

state: Liaoning

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

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

first: Jing

middle: Y

first: Ting

first: Pin

first: Yong

last: Liu

middle: X

last: Pan

first: Li

middle: J

last: Pang

first: Xiao

last: Lv


title: Intrinsic innate immunostimulation by small circRNA vaccines [BMDCs]

city: Richmond

first: Guizhi

last: Zhu

state: VA

address: 410 N 12th St

institute: Virginia Commonwealth University

summary: Various RNAs have been shown to elicit innate immunity by activating endosomal PRRs such as Toll-like receptors 3/7/8 (TLR3/7/8), and cytosolic PRRs (e.g., retinoic acid-inducible gene I (RIG-I), melanoma differentiation-associated protein 5 (MDA5)). Such innate immunity provides cytokines and co-stimulation signals that are essential for adaptive immunomodulation.

overall_design: We further employed RNA-seq genome-wide transcriptome analysis for the comprehensive understanding of the immunomodulation mechanisms by small circRNA vaccines in BMDCs or tumor tissues.

first: Yu

first: Jinze

first: Katarzyna

last: Tyc


title: Liver organoids generated from individuals carrying PiZZ variant of alpha-1-antitrypsin contain high lipid content

city: Madrid

first: Beatriz

last: Martinez-Delgado

address: Carretera Majadahonda-Pozuelo Km 2

department: Molecular Genetic Unit

country: Spain

institute: ISCIII/IIER

summary:
We generated hepatic organoids from MZ and ZZ patients with the aim to investigate their lipid status
To discover genes related to lipid metabolism likely involved in lipid deposits.

overall_design: Comparative gene expression analysis of RNA-seq data of hepatic organoids derived from alpha-1 antitrypsin deficiency

first: Sara

last: Pérez-Luz

first: Gema

last: Gómez-Mariano

last: Martínez-Delgado


title: BET inhibition abrogates global transcription via repressing m6A writer complex

city: Xia Men

last: Lu

address: Xiang'an south road

institute: Xiamen university

summary:
To characterize the role of m6A modification in mediating BRD4-dependent biological functions, we established METTL3 reconstituting cells and treated with JQ1
BRD4 directs gene transcription through diverse mechanisms. Here, we specifically focused on BETi-dependent transcriptome or chestrated by m6A-mediated regulation. To this end, we first need to identify bona fide m6A-dependent transcripts via rescue experiments in METTL3-knockdown cells by adding back wild-type METTL3 or METTL3-CD mutant (a catalytically inactive form of METTL3)

overall_design: RNA-seq was perform to illustrate potential targets regulated by BEi/m6A

first: Lichao

last: Peng

first: Jiancheng

last: Ding

first: Han

last: You


title: Gastric cancer cells exploit FABP5 via the PD-L1/TNF/IL-17 signaling axis

city: JiNan

first: Shu

last: Zhang

address: 440 Jiyan Road

department: Department of Gastroenterology, Shandong Cancer Hospital and Institute

institute: Shandong First Medical University and Shandong Academy of Medical Sciences

summary: Background: Gastric cancer (GC) is the second most lethal cancer globally and is associated with   poor prognosis. Fatty acid-binding proteins (FABPs) can regulate the biological properties of   carcinoma cells. FABP5 is overexpressed in many types of cancers; however, the role and mechanism   of FABP5 in GC are still unclear.   Aim: In this study, we aimed to evaluate the clinical and biological function of FABP5 in GC.  Methods: We assessed FABP5 expression using immunohistochemical analysis of 79 GC patients   and evaluated its biological functions following in vitro and in vivo ectopic expression. FABP5 targets   relevant to GC progression were determined using RNA sequencing (RNA-seq) analyses.  Results: Elevated FABP5 expression was closely related to poor outcomes, and ectopic expression of   FABP5 promoted GC cell proliferation, invasion, migration, and carcinogenicity, suggesting its   potential tumor-promoting role in GC. Additionally, RNA-seq analysis indicated that FABP5   activates immune-related pathways, including cytokine–cytokine receptor-interaction pathways,   interleukin-17 signaling, and tumor necrosis factor signaling, suggesting an important rationale for the   possible development of therapies combining FABP5-targeted drugs with immunotherapeutics.  Conclusion: These findings highlight the biological mechanisms and clinical implications of FABP5   in GC and suggest its potential as an adverse prognostic factor and/or therapeutic target.

overall_design: To detect the influence of FABP5 overexpression on GC activity in vivo, we subcutaneously   implanted BGC-823 cells overexpressing FABP5 into the shoulders of BALB/c mice.To identify the targets of FABP5 relevant to GC progression, we performed RNA-seq analysis using tissue obtained from the murine xenograft model.

first: Qiu

last: Mei-qing

first: Zhang

last: Shu

first: Wang

last: Hui-jun


title: Extrachromosomal circular DNAs are ubiquitous in mouse hearts and function as enhancers to promote chromosomal transcription [RNA-seq]

city: Xi’an

first: Banjun

last: Ruan

address: 169 Changle West Road

institute: Air Force Medical University

summary: To exaimine the transcription levels among embryonic, neonatal and adult mouse heart tissues, we performed the whole transcriptome sequencing.

overall_design: The transcription levels in different developmental stages of mouse heart tissues (embryonic, neonatal and adult) were determined.

first: Ling

last: Tao

first: Shan

last: Wang


title: Extrachromosomal circular DNAs are ubiquitous in mouse hearts and function as enhancers to promote chromosomal transcription [Circle-seq]

summary: To systematically analyzed the genome-wide characterization of potential eccDNAs in mouse heart tissues, we peformed Circle-seq in embryonic, neonatal and adult mouse heart tissues.

overall_design: EccDNA expression profiling was analyzed to determine what extent eccDNAs occur in different developmental stages of mouse heart tissues (embryonic, neonatal and adult).


title: Effect of Saikosaponin A on hepatocellular carcinoma cells

city: Quzhou

first: Si-wei

address: No.100 Minjiang Road

institute: Quzhou people's hospital

summary: Clarifying the molecular mechanism of Saikosaponin A against hepatocellular carcinoma.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for DMSO-treated and Saikosaponin A (20 μM) treated HepG2 cells

first: Tian

last: Lan


title: MiR-29ab regulates intestinal stem cell fate through fatty-acid-oxidation-related energy metabolism [after irradiation]

city: Beijing

first: Yao

address: No. 17, Tsinghua East Rd, Haidian District, Beijing

institute: Yao Lu, a student from China Agricultural University

summary:
To investigate the mechanism of miR-29ab in regulation of intestinal stem cells and partipation in epithelium post-injury regeneration, we established miR-29ab1-/- mice and applied irradiation to damage stem cell.
We then performed gene expression profiling analysis using data obtained from RNA-seq of intestinal crypts from WT and miR-29ab1-/- mice 3 day after irradiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and miR-29ab1-/- mice post irradiation.

first: Huiyuan

last: Guo

first: Yingying

last: Lin


title: MiR-29ab regulates intestinal stem cell fate through fatty-acid-oxidation-related energy metabolism

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


title: MiR-29ab regulates intestinal stem cell fate through fatty-acid-oxidation-related energy metabolism [before irradiation]

summary:
To investigate the mechanism of miR-29ab in regulation of intestinal stem cells and partipation in epithelium post-injury regeneration, we established miR-29ab1-/- mice and applied irradiation to damage stem cell.
We then performed gene expression profiling analysis using data obtained from RNA-seq of intestinal crypts from WT and miR-29ab1-/- mice before and after irradiation.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for WT and miR-29ab1-/- mice.


title: Physiological replication of the glomerulus using a triple culture microphysiological system.

city: Waltham

first: Seyedramin

last: Pajoumshariati

state: MA

address: 35 Gatehouse Dr

institute: AstraZeneca

summary:
to compare the incremental advances that each cell type brings to the phenotype of the others in the glomerulus we compared TGCs (triculture), BGCs (co-culture), and plate cultures (monocultures)
The function of the glomerulus depends on complex cell-cell/matrix interactions and replication of this in vitro would aid biological understanding in both health and disease. Previous models have not fully reflected all cell types and interactions present. We report here the development of a microphysiological system which contains all resident renal cell types in an anatomically relevant manner. We demonstrate functionally appropriate retention of albumin in the system along with providing a detailed transcriptomic analysis of the contributing biology of each cell type. The important role of mesangial cells is shown in promoting the health and maturity of the other cell types. AdditionallyAdditionally, we demonstrate that glomerular cells in simple 2D culture exhibit a state more reflective of human disease than previously recognised. This in vitro model will expand our capability to investigate glomerular biology in a more translatable manner by the inclusion of the important mesangial cell compartment.

overall_design: The five main glomerulus chip groups of this study are mature (podocytes) and immature (IM cells) tri-culture chips, biculture chips (only GECs and podocytes) and control IM seeded chips. In addition we have 3 main monoculture groups of endothelial cells, mesangial cells, and podocytes

first: Ramin

first: Lorna

last: Ewart

first: Raymond

last: Luc

first: Samantha

last: Peel

first: Heather

last: Weber

first: Bramasta

last: Nugraha

first: Pernille

last: Hansen

first: Ville

last: Kujala

first: Julie

last: Williams


title: RNAPII ChIP-Sequencing of A.thaliana tfiis mutant lines under heat stress conditions

city: Regensburg

first: Simon

last: Obermeyer

address: Universitätsstraße 31

country: Germany

institute: University Regensburg

summary: RNAPII ChIP Sequencing in Col-0 and tfiis mutant lines to elucidate the role of TFIIS during RNAPII mediated transcription

overall_design: Comparative ChIP-Sequencing using antibodies directed against S2P-modified (Ser2-phosphorylated heptapeptides of the carboxy-terminal domain of NRPB1) RNAPII (abcam, ab5095) in Col-0 and tfiis-1 under control conditions and heat shock conditions in biological triplicates


title: m6A modification in DP and iNKT cells

first: Shuyang

last: Yu

address: 2 Yuanmingyuan West Road

department: College of Biological Sciences

institute: China Agricultural University

summary: Invariant natural killer T (iNKT) cells are a specific innate-like counterpart of T lymphocytes, which response to lipid-based antigens and provide a functional bridge between the innate and adaptive immunity. The physiological role of m6A modification involved in NK cells differentiation remains unclear. We found that N6-Methyladenosine (m6A) methyltransferase METTL3 is intrinsically required for iNKT cell development and function in an m6A-dependent manner. To investigate the molecular mechanisms, m6A-LACE-seq was performed using iNKT cells and Merip-seq was performed using DP cells in thymocytes isolated from WT and KO mice to investigate the regulatory network.

overall_design: thymocytes iNKT cells (7AAD-CD1d-Tet+TCRβ+) and DP cells (7AAD-CD1d-Tet-CD4+CD8+) purified by FACS sorting


title: N6-Methyladenosine (m6A) methyltransferase METTL3 and iNKT cell development and function

overall_design: Refer to individual Series


title: Regulation of iNKT cell development and function by METTL3

summary: Invariant natural killer T (iNKT) cells are a specific innate-like counterpart of T lymphocytes, which response to lipid-based antigens and provide a functional bridge between the innate and adaptive immunity. The physiological role of m6A modification involved in NK cells differentiation remains unclear. We found that N6-Methyladenosine (m6A) methyltransferase METTL3 is intrinsically required for iNKT cell development and function in an m6A-dependent manner. To investigate the molecular mechanisms, RNA-seq was performed using iNKT cells in thymocytes isolated from WT and KO mice to investigate the regulatory network.

overall_design: thymocytes iNKT cells (7AAD-CD1d-Tet+TCRβ+) purified by FACS sorting


title: Autosomal recessive PIK3CD deficiency

city: Doha

first: nico

last: marr

email: nico_marr@outlook.com, tkhan@sidra.org

address: AL RAYYAN

department: Research

country: Qatar

institute: Sidra Medicine

summary: We studied a case with suspected PIK3CD deficiency with a homozygous mutation in the patient in PIK3CD (c.1340-1 G>A). All other family members were tested and defined as carriers of the same mutation and are clinically healthy. The literature states that there is an AD but also an AR form of the disease  (Immunodeficiency 14 A and B, respectively) linked to the gene. The clinical phenotype of the patient fits very well the description as LOF she suffers from severe, recurrent infections since infancy and has low overall IgG levels.

overall_design: We studied a case with suspected PIK3CD deficiency with a homozygous mutation in the patient in PIK3CD (c.1340-1 G>A).  Whole peripheral blood was preserved in Tempus solution and RNA was extracted according to the standard protocol.

first: Salim

last: Bougarn

first: Taushif

last: Khan

first: Manar

last: Ata

first: Fatima

last: Al-Ali

first: Mohammed

last: Toufiq

first: Evonne

last: Chin-Smith

first: Randa

last: Al Yafie

first: Mehdi

last: Adeli

first: Nico

last: Marr

first: Andrea

last: Guennoun


title: Clonally expanded CD38hi cytotoxic CD8 T cells define the T cell infiltrate in checkpoint inhibitor-associated arthritis

city: Boston

first: Deepak

last: Rao

address: 60 Fenwood Road

department: Division of Rheumatology, Inflammation, and Immunity

institute: Brigham and Women's Hospital

summary: Immune checkpoint inhibitor (ICI) therapies have improved outcomes for advanced malignancies by activating T cell responses, yet often also elicit harmful autoimmune reactions. The T cell mechanisms mediating these iatrogenic autoimmune events remain unclear. Here we focused on ICI-induced inflammatory arthritis (ICI-arthritis), which can clinically present indistinguishable from rheumatoid arthritis (RA). Compared to autoimmune RA and psoriatic arthritis (PsA), we found ICI-arthritis joints contained an expanded CD38hiCD127- CD8 T cell subset that displays cytotoxic, effector, and interferon (IFN) response signatures. Synovial T cells exposed to Type I IFN, more so than IFN-γ, induced the CD38hi cytotoxic phenotype. Single cell transcriptomic and T cell repertoire (TCR) analyses indicated the abundant CD38hi CD8 T cells resulted from local proliferation of a limited number of clones. The CD38hi phenotype was distinct from dysfunctional T cells and clonally most related to a TCF7+ memory population. Comparing CD8 T cells from both knees in a patient demonstrated considerable sharing of the CD38hi expanded TCR clonotypes. Further, expanded TCR clonotypes from the joints were detected in the circulation, and together with higher frequencies of circulating CD38hi CD8 T cells, represent potential biomarkers for irAEs. These results define a distinct CD8 T cell subset in humans that is activated by ICI therapy and mediates tissue-specific autoimmunity.

overall_design:
We sorted the CD38-CD127+PD-1int, CD38-CD127+PD-1-, CD38-CD127-PD-1intKLRG1+, PD-1hi and CD38hiCD127-PD-1int populations of CD8+ T cells from synovial fluid mononuclear cells of donors with checkpoint inhibitor-induced arthritis (CI), rheumatoid arthritis (RA), or psoriatic arthritis (PsA) to gene expression profiling using data obtained from RNA-seq.
Please note that RNA-Seq raw data is to be made available through dbGaP (controlled access) due to patient privacy concerns.

first: Runci

last: Wang

first: Anvita

last: Singaraju

first: Kathryne

last: Marks

first: Lorein

last: Shakib

first: Garrett

last: Dunlap

first: Amy

last: Cunningham-Bussel

first: Stinne

last: Greisen

first: Lin

last: Chen

first: Aidan

last: Tirpack

first: Miriam

last: Fein

first: Derrick

last: Todd

first: Lindsey

last: MacFarlane

first: Susan

last: Goodman

first: Edward

middle: F

last: DiCarlo

first: Elena

last: Massarotti

first: Jeffrey

last: Sparks

first: Ole-Petter

last: Hamnvik

first: Le

last: Min

first: A

middle: H

last: Jonsson

first: Michael

last: Brenner

first: Karmela

last: Chan

first: Anne

last: Bass

first: Laura

middle: T

last: Donlin


title: Nasal and blood transcriptomic pathways underpinning the clinical response to grass pollen immunotherapy (nasal)

city: Seattle

first: Naresh

last: Doni Jayavelu

state: WA

address: 1201 9th AVE

department: Systems Immunology/Bioinformatics

institute: Benaroya Research Institute at Virginia Mason

summary: The Gauging Response in Allergic Rhinitis to Sublingual and Subcutaneous Immunotherapy (GRASS) study was a randomized, double-blind, placebo-controlled trial of individuals with timothy grass allergy who received 2 years of placebo, subcutaneous (SCIT), or sublingual immunotherapy (SLIT) and were followed for a total of 3 years. Here we utilized longitudinal transcriptomic profiling of nasal brush and peripheral blood mononuclear cell (PBMC) samples after allergen provocation collected in the GRASS study to uncover airway and systemic expression pathways mediating responsiveness to immunotherapy.

overall_design: Nasal brush samples were collected 9 hours (+/- 2 hours) after nasal allergen challengen with timothy grass pollen allergen in grass allergic subjects and non-allergic controls. In grass allergic subjects samples were collected at 4 timepoints, prior to initation of grass immunotherapy (visit -2), 1 year after starting immunotherapy (visit 107), 2 years after starting immunotherapy (visit 207), and 1 year after stopping immunotherapy (visit 307; 3 years after visit -2).

first: Matthew

middle: C

last: Altman

first: Richard

middle: M

last: Segnitz

last: Jayavelu

first: Stephen

last: Durham


title: Nasal and blood transcriptomic pathways underpinning the clinical response to grass pollen immunotherapy (PBMC)

overall_design: Peripheral blood mononuclear cell samples were collected immediately before and 6-7 hours after nasal allergen challengen with timothy grass pollen allergen in grass allergic subjects and non-allergic controls. In grass allergic subjects samples were collected at 4 timepoints, prior to initation of grass immunotherapy (visit -2), 1 year after starting immunotherapy (visit 107), 2 years after starting immunotherapy (visit 207), and 1 year after stopping immunotherapy (visit 307; 3 years after visit -2).

middle: D


title: Characterization of in vitro cultured alveolar macrophages (AM) transcriptomes following DON treatment

city: Rochester

first: Min

last: Wang

state: MN

address: 200 1st ST SW

department: Pulmonary and Critical Care Medicine

institute: Mayo Clinic

summary: To identify molecular characteristics of WT AM with or without DON stimulation in vitro, we isolated RNA from AMs with various treatments and examined by bulk RNA-seq. We found a large number of gene profiles were altered following DON treatment in WT AMs, suggesting that DON treatment altered the balance of proliferative versus inflammatory genes in AMs, and glutamine metabolism is important in regulating AM self-renewal ability.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for AM following DON treatment

first: Chaofan

last: Li

first: Jie

last: Sun


title: Nasal and blood transcriptomic pathways underpinning the clinical response to grass pollen immunotherapy


title: Loss of BAF (mSWI/SNF) Chromatin-remodeling ATPase Brg1 causes multiple malformations of cortical development in mice

city: jinan

first: Yecheng

last: Jin

address: No.44 West Wenhua Road

institute: Shandong university

summary: Mutations in genes encoding subunits of the BAF (BRG1/BRM-associated factor) complex cause various neurodevelopmental diseases. However, the underlying pathophysiology remains largely unknown. Here, we analyzed the function of Brg1, a core ATPase of BAF complexes, in the developing cerebral cortex. Loss of Brg1 causes several morphological defects resembling human malformations of cortical development (MCDs), including microcephaly, cortical dysplasia, cobblestone lissencephaly, and periventricular heterotopia. We demonstrated that neural progenitor cell (NPC) renewal, neuronal differentiation, neuronal migration, apoptotic cell death, pial basement membrane, and apical junctional complexes, which are associated with MCD formation, were impaired after Brg1 deletion. Furthermore, transcriptome profiling indicated that a large number of genes were deregulated. The deregulated genes were closely related to MCD formation, and most of these genes were bound by Brg1. Cumulatively, our study indicates an essential role of Brg1 in cortical development and provides a new possible pathogenesis underlying Brg1-based BAF complex-related neurodevelopmental disorders.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and Brg1 cKO cerebral cortex.

first: Qiji

last: Liu

first: Jiangang

last: Gao


title: Gene expression profile of RA FLSs with or without ALKBH5 knockdown

city: Guangzhou

first: Yu

last: Kuang

state: Guangdong

address: 58 Zhongshan 2nd Road, Yuexiu District

department: Rheumatology and Immunology

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

summary: To investigate how ALKBH5 modulates RA FLSs functions, we conducted RNA sequencing of RA FLSs. The data were analyzed for differential expression with a nominal P<0.05. Through analysis of the input RNA-seq data, we identified significantly expressed 1956 genes(FC≥1.2).

overall_design: Three biological replicates from human RA FLSs infected with scramble or ALKBH5 shRNA lentivirus

first: Ruiru

first: Jingnan


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

city: ADELAIDE UNIVERSITY

first: Geraldine

last: Laven-Law

state: South Australia

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

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: RNA-seq (poly-A) in MDA-MB-453 cells

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

middle: E

last: Hickey


title: Single-cell full-length RNA-sequencing of MCF7 and BT-474 cells using down-scaled Smart-seq2

city: Freiburg i. Br.

first: Csaba

last: Jeney

state: Baden-Württemberg

address: Georges-Köhler-Allee 103

department: Department for Microsystems Engineering

institute: University of Freiburg

summary: We report single-cell RNA-sequencing data of wild type, breast cancer cells MCF7 and BT-474. Single cells were isolated using the F.SIGHT single cell dispenser. cNDA synthesis and library preparation were down-scaled to 1/10 of original reaction volumes. By comparative UMAP clustering we could show that our MCF7-cluster exactly overlapped with sequencing data from GSE151334. Data was analyzed using three common alignment tools: salmon, kallisto and STAR. DE analysis was performed with inputs from each aligner. We proved the overexpression of ErbB2 in BT-474 compared to MCF7 in all cases.

overall_design: After single cell isolation of MCF7 and BT-474 cells with the F.SIGHT, cDNA synthesis (Smart-seq2) and library preparation (Nextera XT) were performed at 1/10 of original reaction volumes.

first: Lange

last: Tobias

first: Jeney

last: Ábris

last: Csaba


title: Dietary fatty acids interact with gut microbiota and TLR4 to promote colitis and colorectal tumorigenesis

city: Camperdown

first: RENHUA

last: SONG

state: NSW

address: Charles Perkins Centre - D17, Level 4 West. The University of Sydney Johns Hopkins Drive

institute: Centenary Institute

summary: We show that oxidized LA, rather than LA itself,exacerbates colitis via Toll-like receptor 4 (TLR4)- and gut microbiota-dependent mechanisms.Administration of a diet containing oxidized LA, at low human-consumption levels, increases the severity of colitis and exacerbates the development of colorectal tumorigenesis in mice.

overall_design: To prepare “un-oxidized corn oil”, freshly opened commercial samples of corn oil were purified by column chromatography.

first: Guodong

last: Zhang

first: Weicang

last: Wang

first: Yuxin

first: Eric

middle: A

last: Decker


title: Genome-wide maps of m6a state in  RA FLSs with or without ALKBH5 knockdown.

first: Yu

last: Kuang

summary: To investigate how ALKBH5 modulates RA FLSs functions, we conducted m6A sequencing (MeRIP-seq) of RA FLSs. Consistent with previous studies, in both scramble controls and ALKBH5 knockdown cells, m6A modifications were highly enriched within the GGAC motif. m6A peaks are located mainly in the protein-coding region (CDS) and 3’ untranslated region (3’ UTR) of mRNA transcripts

overall_design: Input group and IP group cantain three biological replicates, respectively,  from human RA FLSs infected with scramble or ALKBH5 shRNA lentivirus.

first: Ruiru

last: Li

first: Jingnan