title: The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PAT-seq]

summary: Epithelial-mesenchymal transition (EMT) plays important roles in tumour progression and is orchestrated by dynamic changes in gene expression. While it is well established that post-transcriptional regulation plays a significant role in EMT, the extent of alternative polyadenylation (APA) during EMT has not yet been explored. Using 3’ end anchored RNA sequencing, we mapped the alternative polyadenylation landscape (APA) following TGF-β-mediated induction of EMT in human mammary epithelial cells and found APA generally causes 3’UTR lengthening during this cell state transition. Investigation of potential mediators of APA indicated the RNA-binding protein Quaking (QKI), a splicing factor induced during EMT, regulates a small subset of events including the length of its own transcript. Analysis of QKI CLIP-seq data identified the binding of QKI within 3’UTRs was enriched near cleavage and polyadenylation sites. Following QKI knockdown, APA of many transcripts are altered to produce predominantly shorter 3’UTRs associated with reduced gene expression. These findings reveal the changes in APA that occur during EMT and identify a potential role for QKI in this process.

overall_design: The Poly(A)-Test RNA-seq, or PAT-seq approach, was applied to total RNA isolated from HMLE, mesHMLE and mesHMLE (QKI knockdown) to determine gene expression and alternative polyadenylation. Total RNA was isolated and processed as previously published by Harrison et al 2015.

first: Daniel

middle: P

last: Neumann

first: Caroline

last: Phillips

first: Paul

last: Harrison

first: Traude

last: Beilharz

first: Gregory

last: Goodall

first: Philip


title: The landscape of alternative polyadenylation during EMT and its regulation by the RNA-binding protein Quaking [PANQKI_HITS-CLIP]

status: Public on Dec 21 2023

city: Adelaide

first: Katherine

middle: Anne

last: Pillman

state: SA

address: North Terrace

department: Centre for Cancer Biology

country: Australia

institute: Adelaide University

overall_design: HITS-CLIP was performed on endogenous QKI from using antibodies specific to the QKI-5 isoform (QKI5-Be & QKI5-NM) or all QKI isoforms (panQKI).

first: B

middle: K

last: Dredge

first: Andrew

middle: G

last: Bert

middle: A

middle: J

last: Gregory


title: NFKB2 mediates colorectal cancer cell immune escape and metastasis in a STAT2/PD-L1-dependent manner

city: shanghai

first: Zhang

last: JIwei

address: 1200 Cai Lun Road

country: China

institute: Shanghai University of Traditional Chinese Medicine

type: Expression profiling by high throughput sequencing

summary: This study systematically analyzed the molecular mechanism and function of nuclear factor kappa B subunit 2 (NFKB2) in colorectal cancer (CRC) to investigate the potential of NFKB2 as a therapeutic target for CRCTo investigate the potential of NFKB2 as a therapeutic target for colorectal cancer (CRC), we conducted a systematic analysis of the molecular mechanism and function of NFKB2 in CRC. VariousA range of experimental techniques, including RNA sequencing, proteome chip assays, and small molecule analysis, were used to obtaingain a deeper understanding of the regulation of NFKB2 in CRC. TheOur results revealed that NFKB2 was upregulated in a significant proportion of patients with advanced hepatic metastasismetastases of CRC. NFKB2 played an importanta role in promoting tumor growth through CD8+ T cell exhaustion. MoreoverAdditionally, NFKB2 directly interacted with signal transducer and activator of transcription 2 (STAT2)STAT2, leading to increased phosphorylation of STAT2 and the upregulation of programmed death ligand 1 (PD-L1)PD-L1 expression. Applying aThe application of a small molecule inhibitor of NFKB2 (Rg5) led to a reduction in PD-L1 expression and improved response to programmed death-1 (PD-1)PD-1 blockade-based immunotherapy. In conclusion,These findings suggest that the facilitated NFKB2-STAT2/PD-L1 axis may suppresses immune surveillance in CRC and targeting NFKB2 maycould enhance the efficacy of immunotherapeutic strategies. Our resultsThis study provides novel insights into the molecular mechanisms underlying the contribution of NFKB2 in CRC immune escape. However, our findings requireand further validation of these findings in a clinical trial is needed to establish NFKB2 inhibition as a therapeutic strategy for CRC patients.

overall_design: Transcriptomic profiles of MC38 tumors in C57 mouse model with (3 samples) or without (3 smaples) NFKB2 overexpression

first: Jiwei

last: Zhang

first: Fen

last: Ma

first: Yang

last: Li

first: Yidi

last: Sun

first: Zhengtao

last: Wang


title: ATAC-seq to profile the chromatin accessibility in T-cell blasts from individuals with an AIOLOS E82K and Q402X mutation and healthy controls

city: Bethesda

first: Julie

middle: E

last: Niemela

state: MD

address: 10 Center Dr.

department: Dept. of Lab. Medicine

country: USA

institute: NIH Clinical center

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ATAC-seq was performed for T-cell blasts for the following study groups: healthy controls (HC, n=6) and patients with AIOLOS E82K (n=6) and Q402X (n=1). ATAC-Seq was performed using the Active Motif ATAC-Seq Kit following the manufacturer’s protocol and sequenced using the Illumina NextSeq 2000 with 42-bp paired end reads. Using Basepair bioinformatics tools and pipelines (https://www.basepairtech.com/), reads were aligned using Bowtie2, and peaks were called with MACS2 and annotated using Homer. Differential testing, annotation, and visualization were performed using R (v.4.3.1) and the following Bioconductor R packages (https://bioconductor.org/): DESeq2 (v.1.40.2), DiffBind (v.3.10.1), ChIPQC (v.1.36.1), ChIPseeker (v.1.36.0), clusterProfiler (v.4.8.2), and goseq (v.1.52.0).

overall_design: ATAC-seq profiling for T-cell blasts from individuals with an AIOLOS E82K and Q402X mutation and healthy controls

first: S

middle: D

last: Rosenzweig

first: H

middle: S

last: Kuehn

first: J

last: Stoddard


title: Development of a benzarone derivative as targeted therapy for SHH-medulloblastoma

city: Boston

first: Rosalind

last: Segal

state: MA

address: 360 Longwood Ave.

department: Cancer Biology

institute: Dana-Farber Cancer Institute

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

overall_design: Refer to individual Series


title: Effect of depletion of ALKBH5 on transcriptional landscape in human neutrophils during bacterial infection

city: Beijing

last: Liu

address: Dongdan Santiao 5

department: Immunology

institute: Peking Union Medical College&Chinese Academy of Medical Sciences

summary: By performing RNA-seq analysis on ALKBH5-deficient (ALKBH5-/-, KO) and Wild-type (WT) dHL-60 human neutrophils infected with Escherichia coli, we want to investigate the effect of ALKBH5 on transcriptional landscape of human neutrophils during bacterial infection. Then, we performed gene expression profiling and Gene Ontology enrichment analysis of the significantly differentially expressed genes using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for ALKBH5-deficient and WT human neutrophils infected with Escherichia coli.


title: Unstable EBV latency drives inflammation in multiple sclerosis patient derived spontaneous B cells [RNA-Seq]

city: Philadelphia

first: Priyankara

last: Wickramasinghe

state: PA

address: 3601 Spruce Street

department: Bioinformatics

institute: The Wistar Institute

summary: Epidemiological studies have demonstrated that Epstein-Barr virus (EBV) is a known  etiologic risk factor, and perhaps prerequisite, for the development of MS. EBV establishes life-long latent infection in a subpopulation of memory B cells. Although the role of memory B cells in the pathobiology of MS is well established, studies characterizing EBV-associated mechanisms of B cell inflammation and disease pathogenesis in EBV (+) B cells from MS patients are limited. Accordingly, we analyzed spontaneous lymphoblastoid cell lines (SLCLs) from multiple sclerosis patients and healthy controls to study host-virus interactions in B cells, in the context of an individual’s endogenous EBV.  We identify differences in EBV gene expression and regulation of both viral and cellular genes in SLCLs. Our data suggest that EBV latency is dysregulated in MS SLCLs with increased lytic gene expression observed in MS patient B cells, especially those generated from samples obtained during “active” disease. Moreover, we show increased inflammatory gene expression and cytokine production in MS patient SLCLs and demonstrate that tenofovir alafenamide, an antiviral that targets EBV replication, decreases EBV viral loads, EBV lytic gene expression, and EBV-mediated inflammation in both SLCLs and in a mixed lymphocyte assay. Collectively, these data suggest that dysregulation of EBV latency in MS drives a pro-inflammatory, pathogenic phenotype in memory B cells and that this response can be attenuated by suppressing EBV lytic activation. This study provides further support for the development of antiviral agents that target EBV-infection for use in MS.

overall_design: RNA-seq and WGS of spontaneous LCL derived from healthy donors and MS in active and stable state

first: Samantha

last: Soldan

first: Paul

last: Lieberman


title: Sensory nerve regulates progenitor cells via FGF-ETV5/PTCH1-Hh axis during  tooth root morphogenesis

city: Los Angeles

first: Fei

last: Pei

state: CA

address: 2250 Alcazar St

institute: USC

summary: The goal of this study is to investigate the role of nerve in tooth root morphogenesis

overall_design:
Methods: mRNA profiles of control and Fgfr2 mutant mice were generated by deep sequencing, in triplicate, using NextSeq500 High Output. The quality of RNA samples was determined using an Agilent 2100 Bioanalyzer.
Methods: single-cell RNAseq were obtained from trigemial ganglion of mice at PN3.5


title: RNA-seq data of nasopharyngeal carcinoma (NPC) in non-endemic areas

city: Milan

first: Loris

last: De Cecco

address: via Venezian 1

country: Italy

institute: IRCSS Istituto Nazionale Tumori

summary: Epstein-Barr virus (EBV) related nasopharyngeal carcinoma (NPC) is an epithelial malignancy with higher incidence in Asian endemic area (EA) than in non-endemic area (NEA), where frequency is below 1/105/year. The causes of such difference are unclear and might be related to viral, environmental (e.g. diet) and genomic factors. We aimed at dissecting the gene expression (GE) and microenvironment landscape in NPC leading to the identification of molecular subtypes explaining the differences between EA and NEA.

overall_design: FFPE tumor tissue of 50 Italian EBV related NPC patients were collected at initial diagnosis. RNASeq was carried out by QuantSeq 3' mRNA-Seq (Lexogen). Tumor microenvironment and biological characteristics of EA and NEA cases were evaluated by xCell, and Gene Set Enrichment analyses, while the association with radiosensitivity was assessed with a specific signature.  By unsupervised clustering analysis, four molecular clusters (cl 1,2,3,4) were disclosed in EA. All clusters were predicted in NEA with the exclusion of cl4.   Cl4 and cl3 exhibited a high RadioSensitivity Index (RSI) suggesting that patients classified in these clusters are more resistant than patients included in cl2 and cl1 (p=5.9e-05). To our knowledge this is the first in-deep molecular comparison between EA and NEA NPC.


title: Local IL-4 signaling within bone marrow drives pathogenic myelopoiesis in lung cancer

status: Public on Dec 20 2023

city: New York

first: MATTHEW

middle: Dae-Young

last: PARK

state: NY

address: 50 East 98th Street, 6A-1

institute: Icahn School of Medicine at Mount Sinai

summary: Myeloid cells, in particular monocytes and macrophages, are well-described to suppress the antitumor immune response. However, the molecular mechanisms controlling immunosuppressive myeloid cell states are ill- defined, hampering the development of myeloid-targeted therapies for cancer1,2. Here, we transcriptionally profiled over 500,000 tumor infiltrating leukocytes in non-small cell lung cancer (NSCLC) patients and in the KrasG12DTp53-/- (KP) murine lung adenocarcinoma model. In both species, the Type 2 cytokine IL-4 was predicted to be the primary driver of tumor infiltrating monocyte-derived macrophage (mo-mac) phenotype, despite the fact that lung tumors were largely devoid of IL-4 producing cells. Using a panel of conditional knockout mice, we found that only deletion of IL-4Ra within early myeloid progenitors in bone marrow (BM) reduced lung tumor burden, while deletion of this receptor in downstream mature myeloid cells had no effect. Detailed transcriptional analysis followed by mechanistic studies in vivo revealed an essential role for local BM IL-4 signaling in reprograming myelopoiesis in cancer. Mechanistically, basophils and eosinophils within BM upregulated IL4 production upon sensing distal tumor cues; local BM IL-4 acted on granulocyte-monocyte progenitors to transcriptionally program the development of immunosuppressive myeloid cells, which then homed to the tumor and promoted tumor growth. Consequentially, specific depletion of basophils, which were enriched in BM but absent from the tumor, profoundly reduced tumor burden and normalized myelopoiesis in experimental lung tumors. Prompted by these results, we designed and initiated the first clinical trial of dupilumab, a humanized IL- 4Ra blocking antibody commonly used for atopic disease, given in conjunction with PD-(L)1 blockade in relapsed/refractory NSCLC patients who had progressed on standard chemoimmunotherapy combinations. Consistent with our preclinical mouse data, dupilumab drove a reduction in circulating monocytes. This was coupled with an expansion of circulating and tumor-infiltrating CD8 T cells. Notably, one out of the six patients who enrolled in Phase 1b of this trial exhibited significant decrease in his tumor burden after two months of dupilumab treatment, and the clinical response deepened further to a near complete response even after cessation of dupilumab, suggestive of successful reprogramming of the antitumor response. Collectively, our study defines a role for IL-4 signaling in lung tumor progression, identifies a central axis controlling immunosuppressive myelopoiesis in cancer, and highlights a novel combination therapy for immune checkpoint blockade in humans.

overall_design: For all mouse scRNA-seq analyses, three mice were analyzed per condition. For scRNA-seq of KP tumor bearing Il4ra+/+ and Il4ra-flox Ms4a3-CRE lungs, T cells and myeloid cells were separately sorted and barcoded with 10x Cellplex oligos before being encapsulated using the 10X Chromium 3’ v3 chemistry kit according to manufacturer’s instructions. Cells sorted from the same genotype were barcoded and pooled into individual lanes. A total of 12,000 cells were loaded per lane from each condition. For scRNA-seq of bone marrow of naïve, tumor- bearing and IL-4c treated mice, bone marrow myeloid cells and were sorted for sequencing. Due to their abundance in bone marrow, neutrophils were separately sorted and then recombined back with the above cells at a 1:10 ratio. Sorting strategies for all sequencing experiments can be found in Extended Data Fig. 8a and Extended Data Fig. 8b. Cells sorted from the same genotype were barcoded and pooled into individual lanes. A total of 12,000 cells were loaded per lane from each condition. All sequencing libraries were prepared per manufacturer instructions. After stringent cDNA and sequencing library quality control with the CybrGreen qPCR library quantification assay, samples were sequenced at a depth of 100 million reads per library with a 75-cycle kit on an Illumina Nextseq 550.

first: Nelson

middle: M

last: LaMarche

first: Matthew

last: Park

first: Samarth

last: Hegde

first: Miriam

last: Merad


title: Multi-cellular phenotypic dynamics during the progression of breast tumors

city: Stockholm

first: Jean

last: Hausser

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institutet

summary: In cancer, improving diagnostics and therapeutic interventions can benefit from understanding the cellular and phenotypic heterogeneity of the tumor microenvironment (TME). In recent years, the TME has been profiled at an unprecedented level of detail by performing single-cell RNA sequencing (scRNAseq) on patient samples. However, from patient samples, studying the temporal dynamics of the TME has been challenging. Characterizing the temporal dynamics of the TME is critical to understand how inter-tumor heterogeneity is organized into a temporally ordered sequence of causes and consequences in cellular events. Here we survey the temporal dynamics of the TME by performing longitudinal scRNAseq on mouse breast tumors at different progression time points. We find multicellular phenotypic dynamics that follow one out of three possible temporal patterns: stable colonization, wave-like, or progressive increase. In particular, IFN-responsive cancer cells, GzmB+ cytotoxic T cells, as well as macrophages of a phagocytic phenotype, progressively increase as tumors progress. These findings establish the single-cell types and phenotypes in a progressing breast tumor, and determine when these players enter and leave the TME. This single-cell dataset could serve to position clinical samples where timing is unknown on a temporal axis of progression, and suggest optimal timing for different therapies.

overall_design: Clustering and comparative gene expression analysis on duplicate tumor samples from allograft model originally derived from a MMTV-PyMT GEMM of breast cancer in immunocompetent mice.

first: Louise

last: Gsell

first: Spencer

last: Watson

first: Iva

last: Sutevski

first: Matteo

last: Massara

first: Klara

last: Soukup

first: Antony

last: Cougnoux

first: Johanna

last: Joyce


title: Effect of depletion of ALKBH5 on transcriptional landscape in bone marrow neutrophils from septic mice

first: Yang

last: Liu

summary: By performing RNA-seq analysis on bone marrow neutrophils from the Alkbh5-deficient mice and Wild-type littermates undergoing CLP-induced sepsis, we want to investigate the effect of ALKBH5 on transcriptional landscape of mouse bone marrow neutrophils during bacterial infection. Then, we performed gene expression profiling and Gene Ontology enrichment analysis of the significantly differentially expressed genes using data obtained from RNA-seq.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for bone marrow neutrophils from Alkbh5-deficient mice (Alkbh5-/-, KO) and Wild-type littermates (WT) at 12h after CLP.


title: Gene expression profiling in EORTC 90111 study, a  window of opportunity trial with afatinib in HNSCC

summary: In the EORTC 90111, open-label, randomised, multicentre, phase II trial, patients were treated with afatinib for 14 days (day 15 until day 1) before surgery (day 0). Tumour biopsies, 2-[fluorine-18]-fluoro-2-deoxy-d-glucose positron emission tomography (18-FDG PET) and magnetic resonance imaging (MRI) were performed at diagnosis and just before surgery. The main aim of the study was to identify predictive biomarkers among treatment-naive patients in this curative setting.

overall_design: Eligible patients had to have a new histological diagnosis of HNSCC of the oral cavity, oropharynx, hypopharynx or larynx and be selected for primary curative surgery. Thirty-eight  samples corresponding to paired pre- and post-treatment specimens belonging to 19 cases were profile for gene expression.  The primary tumor needs to be ≥ 2 cm in their largest diameter measured bidimensionally by imaging done within two weeks prior to randomization. The primary outcome was the reduction in the tumor uptake volume as assessed by FDG-PET. The response to therapy was expressed as a continuous trait representing the change in SUVmax between the pre- and post-treatment as: ΔSUV = (SUVmax post – SUVmax pre)/SUVmax pre.


title: ALKBH5

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: CircRNA expression-profiling to predict prognosis in locoregionally advanced nasopharyngeal carcinoma

city: Guangzhou

first: Yingqin

last: Li

state: Guangdong

address: Room 927, Building 2, No. 651 Road Dong Feng East

institute: Sun Yat-sen University Cancer Center

summary: CircRNAs serve as prognostic biomarkers in various types of cancer. We aimed to identify a circRNA signature for individual relapse risk assessment in patients with locoregionally advanced nasopharyngeal carcinoma (LA-NPC).

overall_design: Using Agilent SurePrint G3 Custom GE 4x180K Microarray, we profiled the circRNA expression in tissues between 5 normal nasopharyngeal tissues and 25 NPC tissues, among which 8 tissues from patients with recurence and distant metastasis after radical treatment.

first: Y

middle: L

last: Liang

first: J

last: Ma

first: N

middle: Q


title: TDP-43 is a genome-wide DNA-binding protein and regulator of snRNA expression

city: Shanghai

first: Xiang

last: Yu

state: Shanghai

address: 800 DongChuan

institute: Shanghai Jiao Tong University

summary: TAR DNA-binding protein 43 (TDP-43) is the major protein component of neuronal inclusions characterizing the adult-onset neurodegenerative diseases amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration with ubiquitinated inclusions (FTLD-TDP). Whereas TDP-43 was originally identified as a DNA-binding protein that bound the HIV-1 trans-activation response (TAR) DNA element, recent work elucidating its role in neurodegenerative disease pathogenesis has largely focused on TDP-43’s role as an RNA-binding protein. Here, we demonstrate that in human cells, TDP-43 binds DNA genome-wide, with strong enrichment at small nuclear RNA (snRNA) genes. Moreover, TDP-43 binding to snRNA genes is not dependent on RNA, and the snRNA products of TDP-43-bound sites are incorporated into Smith antigen-containing snRNPs. Furthermore, TDP-43 knockdown increases expression of bound snRNA genes, supporting a role for TDP-43 in the negative regulation of snRNA biogenesis. Finally, ALS-associated missense mutations in the gene encoding TDP-43, TARDBP, reduce binding to snRNA genes. Together, our data suggest that the DNA-binding role of TDP-43 is important in health and in disease, and aberrant TDP-43 binding to snRNA gene loci may alter splicing function in ALS and FTLD-TDP.

overall_design: TDP-43 ChIP-seq in HEK293 cells. Input, three independent TDP-43 ChIP replicates, negative control TDP-43 ChIP in the context of TDP-43 knockdown.

first: Pierce

last: Nathanson

first: Jordan

middle: T

last: Mak

first: Shawn

middle: W

last: Foley

first: Travis

last: Unger

first: Brian

last: Gregory

first: Alice

last: Chen-Plotkin


title: Mars2 deficiency in mouse leads to activation of the type I interferon response

first: Sander

last: Houten

address: 1425 Madison Avenue, Box 1498

department: Genetics and Genomic Sciences

summary: Recessive single-nucleotide mutations in MARS2 are causative for a mitochondrial translation deficiency disorder with a primary phenotype including developmental delay, sensorineural hearing loss, and hypotonia. We generated a mouse model of MARS2 deficiency by introduction of the p.R135W mutation, the sequence homolog of the human p.R142W mutation.

overall_design: 6 samples from gastrocnemius muscle (3 WT and 3 Mars2R135W/R135W) and 6 samples from liver (3 WT and 3 Mars2R135W/R135W) were analyzed.

first: Bryn

last: Webb

first: Carmen

last: Argmann


title: Antipsychotic Drug Trifluoperazine as a Potential Therapeutic Agent against Nasopharyngeal Carcinoma

city: Taipei

first: MingYing

last: Lan

address: No.201, Sec. 2, Shipai Rd., Beitou District

department: Department of Otolaryngology-Head and Neck Surgery

country: Taiwan

institute: Taipei Veterans General Hospital, Taipei, Taiwan

summary: Trifluoperazine (TFP), a typical antipsychotic primarily used for treating schizophrenia, exhibits anticancer effect on several types of cancer in recent years. Nevertheless, the effect of TFP on na-sopharyngeal carcinoma (NPC) is still unknown. In this study, we aimed to evaluate if TFP can be the potential therapeutic agent against NPC and to identify its underlying molecular mechanisms. We used four NPC cell lines, namely TW01, TW03, TW04, and BM, to assess the anticancer effects of TFP using cytotoxicity, wound healing, colony formation, and cell invasion assays. RNA se-quencing combined with Ingenuity Pathways Analysis was performed to identify the mechanism by which TFP influences NPC cells. Our data revealed that TFP decreased NPC cell viability in a dose-dependent manner. The invasion and migration of NPC cells were inhibited by TFP. RNA sequencing showed several anticancer molecular mechanisms after TFP administration. It is promising that the antipsychotic drug TFP can be used as a potential therapeutic regimen in NPC treatment in the future.

overall_design: Total RNA from NPC cells administered with or without TFP for 72 hours was ex-tracted using the RNeasy Mini Kit (Qiagen, Hilden, Germany) in accordance with the manufacturer’s protocol. RNA was subjected to RNA-Seq analysis on a Novaseq 6000 in-strument by Biotools Co., Ltd.

first: Chien-Fu

last: Yeh

first: Wen-Ya

last: Lee

first: Ting-Han

first: Yen-Bin

last: Hsu

first: Ming-Chin

first: Ming-Ying


title: Induction of Local Immunosuppression in Allogenic Cell Transplantation by Cell-type-specific Expression of PD-L1 and CTLA4Ig

first: Baoyang

last: Hu

state: Select State/Province

address: Beichenxilu

department: State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology

summary: Immune rejection has long hindered allogenic cell transplantation therapy. Current genetic modification approaches, including direct targeting of major histocompatibility complex or constitutive expression of immune inhibitory molecules, exhibit drawbacks such as severe adverse effects or an elevated risk of tumorigenesis. To overcome these limitations, we propose an innovative approach aimed at inducing cell-type-specific immune tolerance in differentiated cells. By engineering human embryonic stem cells, we enable the exclusive production of immune inhibitory molecules, PD-L1/CTLA4Ig, within differentiated cells following lineage commitment. Leveraging this approach, we have successfully generated hepatocyte-like cells expressing PD-L1 and CTLA4Ig, which effectively induced local immunotolerance. This strategy was evaluated in a humanized mouse model designed to mimic human immune system. Our results demonstrate robust and selective induction of immunotolerance specific to hepatocytes, thereby improving graft survival without tumor formation. This precise immune tolerance strategy holds promise for advancing the development of stem cell-based therapeutics in regenerative medicine.

overall_design: wild-type hPSC, ALB-PD-L1/CTLA4Ig hPSC, AAV-PD-L1/CTLA4Ig derived MHLCs were collected, and the total RNA was extracted by Trizol. RNA samples were shipped to the ANOROAD GENOME for analysis as a service. The DNBs were loaded into the patterned nanoarrays and pair-end reads of 150 bp were read through on the MGI platform for the following data analysis study. For this step, the MGI platform combines the DNA nanoball-based nanoarrays and stepwise sequencing using PE150 Method.

first: Wenliang

last: Zhu


title: RNA-seq and ATAC-seq profiling of mouse Sox2+ dental epithelial stem cell [RNA-seq]

city: Iowa City

first: HUOJUN

last: CAO

state: IA

address: 801 Newton Road

institute: University of Iowa

summary: While multiple human postnatal dental mesenchymal stem cell has been isolated, so far there is no available source of human dental epithelial stem cell (DESC) after permanent teeth were formed. Currently, we known very little of DESC. We generate transcriptome (RNA-seq) and epigenome (ATAC-seq) profiles of mouse DESC and comprehensively identify putative key transcription factor of DESC based on its molecular profiles.

overall_design: We utilize a mouse line Sox2-GFP, in which GFP expression is driven by endogenous promoter of Sox2, to isolate mouse DESCs. Labial cervical loop (LaCL) region of P2 mouse lower incisors were dissected and kept in ice cold DMEM. Collagenase and Neutral Protease mixture were used to dissociate tissue to single cells. Sox2 positive and Sox2 negative cells were sorted with FACS. Smart-seq2 protocol were used to generate RNA-seq libraries. The improved ATAC-seq protocol (Omni-ATAC) were used to generate ATAC-seq libraries.

first: Fan

last: Shao

first: Huojun

last: Cao


title: Transcriptome profile of MafB-cKO Sertoli cells. [2]

city: Nagoya

first: Hossam

middle: Hassan

last: Shawki

state: Aichi

address: Mizuho Ward, Ōtachō, 3-chōme−1

department: Comparative and Experimental medicine

country: Japan

institute: Nagoya City University

summary: MafB is a transcription factor acts as an important regulator of the development and differentiation of various organs and tissues. MafB is expressed in sertoli, leydig, and germ cells in adult mice testis. However, analysis of MafB cKO mice testis showed that MAFB is required for the initiation of the first spermatogenic wave but not the subsequent waves. We examined the transcriptome profile of MafB-cKO Sertoli cells during the first spermatogenic wave. Results of the down-regulated genes revealed that some genes are direct targets of MAFB since the presence of MARE sites in their promoters. Thus, they are candidates of maintaining MAFB function in sertoli cells.

overall_design: Examination of 2 samples (cKO and Control). Each sample contains RNA mixed from 3 mice. Paired-end RNA sequencing was performed with NextSeq500 sequencer (Illumina).

middle: H

first: Satoru

last: Takahashi


title: Global gene expression analysis of CD14+ monocytes and CD4+ effector memory T cells before and during fingolimod treatment

city: Zurich

first: Hubert

last: Rehrauer

address: Winterthurerstr. 190

department: FGCZ

country: Switzerland

institute: ETH Zurich / University of Zurich

summary: Treatment of multiple sclerosis (MS) patients with sphingosine-1-phosphate receptor agonist fingolimod (FTY) increases for unknown reasons the risk for symptomatic reactivation of alpha-herpesviruses, in particular of varicella zoster virus (VZV), but not of other co-infecting herpesviruses (e.g. human cytomegalovirus (HCMV). To elucidate this specific signal in adverse events, we systematically assessed changes in global and herpesvirus-specific immune responses and signatures in MS patients before and during FTY therapy. In addition to phenotypical and functional changes, we thought to identify FTY-induced modifications on the gene expression level, which might add to perturbations in antiviral immune responses. Therefore, gene expression of CD4+ EM T cells and CD14+ monocytes were analyzed.  These two subsets, CD4+ EM T cells and CD14+ monocytes, were isolated from PBMC of six female RRMS patients collected before (V0) and after 9 months of FTY therapy (V9) for RNA sequencing (RNASeq). Comparison of gene expression profiles of monocytes between V0 and V9 revealed 226 down- and 38 upregulated genes. Gene ontology categories and pathway analysis detected most significant alterations for genes involved in immune response, defense against viruses as well as type-1 interferon signaling pathways. Next, we compared gene expression profiles of CD4+ EM T cells collected at V0 and V9 of FTY therapy and found 314 down- and 219 upregulated genes. The most significantly modified pathways were involved in immune responses, including NK cell chemotaxis, cytotoxicity and antiviral responses. In summary, gene expression analysis of monocytes suggests that HCMV might be more susceptible to reactivation during FTY treatment because of FTY-induced modifications of immune control pathways important for HCMV latency. However, increased cytolytic potential of CD4+ EM T cells and expansion of HCMV-specific CD4+ T cells might counteract synthesis or release of viral particles and prevent viremia.

overall_design: RNA of CD14+ monocytes and effector memory T cells collected from PBMC of six female RRMS patients before and nine month during Fingolimod therapy was isolated and sequenced.

first: Fabienne

last: Largey

first: Ivan

last: Jelcic

first: Adam

last: Czaplinksi

first: Riccarda

last: Capaul

first: Mireia

last: Sospedra

first: Roland

last: Martin

first: Ilijas


title: Role of AP-2a/AP-2b transcription factors in the adult epidermis.

city: Charlestown

first: Alexander

last: Marneros

address: 13th Street

institute: Massachusetts General Hospital

summary: To investigate the effects of inactivation of the transcription factors AP-2a and/or AP-2b in the adult mouse skin.

overall_design: Comparative expression analysis of total RNA by RNA-Seq. Epidermal sheets from mouse skin were used for RNA isolation. Epidermis from 3-week-old or 6-months-old experimental mouse groups were used for RNA isolation.


title: RNA-seq and ATAC-seq profiling of mouse Sox2+ dental epithelial stem cell [ATAC-seq]


title: RFX6 facilitates aerobic glycolysis-mediated growth and metastasis of hepatocellular carcinoma through targeting PGAM1 [RNA-Seq]

first: Zhiyu

last: Qiu

address: 651 Dongfeng East Road

summary: Background: Hepatocellular carcinoma (HCC) cells undergo reprogramming of glucose metabolism to support uncontrolled proliferation, of which the intrinsic mechanism still merits further investigation. Although regulatory factor X6 (RFX6) is aberrantly expressed in different cancers, its precise role in cancer development remains ambiguous.   Methods: Microarrays of HCC tissues were employed to investigate the expression of RFX6 in tumor and adjacent non-neoplastic tissues. Functional assays were employed to explore the role of RFX6 in HCC development. Chromatin immunoprecipitation (ChIP), untargeted metabolome profiling, and sequencing were performed to identify potential downstream genes and pathways regulated by RFX6. Metabolic assays were employed to investigate the effect of RFX6 on glycolysis in HCC cells. Bioinformatics databases were used to validate the above findings. Results: HCC tissues exhibited elevated expression of RFX6. High RFX6 expression represented as an independent hazard factor correlated to poor prognosis in patients with HCC. RFX6 deficiency inhibited HCC development in vitro and in vivo, while its overexpression exerted opposite functions. Mechanistically, RFX6 bound to the promoter area of PGAM1 and upregulated its expression. The increased PGAM1 protein levels enhanced glycolysis and further promoted the development of HCC.  Conclusions: RFX6 acted as a novel driver for HCC development by promoting aerobic glycolysis, disclosing the potential of the RFX6-PGAM1 axis for therapeutic targeting.

overall_design: To investigate the functions of RFX6 in HCC cells, we established Hep3B cell line in which RFX6 has been knocked out by sgRNA

first: Chenwei

last: Wang

first: Yunfei

last: Yuan

first: Binkui

last: Li


title: RFX6 facilitates aerobic glycolysis-mediated growth and metastasis of hepatocellular carcinoma through targeting PGAM1 [ChIP-Seq]

overall_design: To investigate the functions of RFX6 in HCC cells, ChIP followed by next-generation sequencing analysis (ChIP-seq) was performed to identify unique peaks from RFX6-overexpressing MHCC-97H cells.


title: Drosophila zinc finger proteins CG9609, AEF1 and CG10543 are colocalized with SAGA, SWI/SNF and ORC complexes on gene promoters and involved in transcription regulation

city: Moscow

first: Aleksey

last: Krasnov

address: Vavilova 34/5

country: Russia

institute: Institute of Gene Biology RAS

summary: We purified the DUB module of the Drosophila SAGA complex and found that a number of zinc proteins interact with it, including CG9609, Aef1 and CG10543. A genome-wide study showed that CG9609, Aef1 and CG10543 proteins are localized predominantly on the promoters of active genes. The binding sites of these proteins colocalize with the SAGA, dSWI/SNF and ORC complexes. It has been shown that CG9609, Aef1 and CG10543 proteins are involved in transcription regulation.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-Seq) for zinc finger proteins CG9609, Aef1 and CG10543 in Drosophila S2 cells.

middle: N


title: Cooperation between ASTER-dependent nonvesicular transport and NPC1L1 facilitates dietary cholesterol uptake

city: Dallas

first: Lara

last: Bideyan

state: TX

address: 5323 Harry Hines Blvd., MC: 9077 Y6.314

department: Internal Medicine

institute: UT Southwestern

summary: Intestinal cholesterol absorption is an important determinant of systemic cholesterol homeostasis.  Niemann-Pick C1 Like 1 (NPC1L1), the target of the drug ezetimibe, is a critical player in dietary cholesterol uptake.  But how cholesterol moves within the cell downstream of NPC1L1 is unknown.  Here we show that the nonvesicular sterol transporters Aster-B and -C cooperate with NPC1L1 to deliver dietary cholesterol from the gut lumen to the enterocyte ER for chylomicron packaging.    Aster proteins are recruited to the enterocyte plasma membrane (PM) in response to NPC1L1-dependent cholesterol accumulation.   Mice lacking Asters in intestine have impaired cholesterol absorption, and reduced plasma cholesterol.  NanoSIMS imaging and tracer studies reveal delayed lipid trafficking into chylomicrons in Aster-deficient enterocytes.  Interestingly, in addition to potently blocking NPC1L1, ezetimibe is also a low-affinity inhibitor of Aster-B and -C but not -A, and the structure of the Aster-C-ezetimibe complex reveals the basis for this selectivity.  Our findings support a model in which NPC1L1 enriches dietary cholesterol at the apical PM, and ASTERs subsequently traffic this cholesterol to the ER.  The findings identify the enterocyte Aster pathway as potential target for treatment of hypercholesterolemia.    Alessandra Ferrari, PhD

overall_design: RNA-Seq of distal jejunum from WT and Aster-B/C global knock out mice fed with a low cholesterol diet with or without ezetimibe

first: Alessandra

last: Ferrari

first: Peter

last: Tontonoz


title: Intermitochondrial cement (IMC) harbors piRNA biogenesis machinery and exonuclease domain-containing proteins EXD1 and EXD2 in mouse spermatocytes

city: Gneveva

first: Ramesh

last: Pillai

address: 30, Quai Ernest-Ansermet

department: Department of Molecular Biology

institute: University of Geneva

summary: Germ granules are large cytoplasmic ribonucleoprotein complexes that emerge in the germline to participate in RNA regulation. The two most prominent germ granules are the intermitochondrial cement (IMC) in meiotic spermatocytes and the chromatoid body (CB) in haploid round spermatids, both functionally linked to the PIWI-interacting RNA (piRNA) pathway. In this study, we clarified the IMC function by identifying proteins that form complexes with a well-known IMC protein PIWIL2/MILI in the mouse testis. The PIWIL2 interactome included several proteins with known functions in piRNA biogenesis. We further characterized the expression and localization of two of the identified proteins, Exonuclease 3′–5′ domain-containing proteins EXD1 and EXD2, and confirmed their localization to the IMC. We showed that EXD2 interacts with PIWIL2, and that the mutation of Exd2 exonuclease domain in mice induces misregulation of piRNA levels originating from specific pachytene piRNA clusters, but does not disrupt male fertility. Altogether, this study highlights the central role of the IMC as a platform for piRNA biogenesis, and suggests that EXD1 and EXD2 function in the IMC-mediated RNA regulation in postnatal male germ cells.

overall_design: Small and long RNA-sequencing was used to analyze the effect of deletion of 3' end of exon 2 of the mouse Exd2 gene (Exd2∆) on piRNA biogenesis. Two biological replicas of  Exd2∆ and control Exd2+/+ mice were used.

first: Opeyemi

last: Olotu

first: Mark

last: Dowling

first: David

last: Homolka

first: Tiina

last: Lehtiniemi

first: Matteo

last: Da Ros

first: Magdalena

last: Wojtas

first: Noora

last: Kotaja


title: Construct a ceRNA regulatory network to explore potential pathogenesis and therapy options of human hepatocellular carcinoma

city: nantong

first: zhaolian

last: bian

address: No. 60, Middle Qingnian Road

institute: Nantong Third People's Hospital, Affiliated Nantong Hospital 3 of Nantong University

summary: The human circRNA profiles of Hepatocellular carcinoma are rarely reported.   Surgically removed human HCC tissues and matched normal liver tissues (5cm away from tumor) were collected to make an Agilent microarray.

overall_design:
Five paired of human HCC tissues and normal controls were collected. All patients have no radiotherapy or chemotherapy before surgery. None of these five patients have distant metastasis.
It provides new markers and therapeutic targets for the diagnosis and treatment of hcc


title: RFX6 facilitates aerobic glycolysis-mediated growth and metastasis of hepatocellular carcinoma through targeting PGAM1

first: Zhiyu

last: Qiu

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

overall_design: Refer to individual Series


title: Gene expression in liver of HCC and CHC patients

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

summary: In order to compare age depenpdence of mRNA between HCC and CHC patients, we measured gene expression by microarray.

overall_design: 24 liver samples are taken from HCC and CHC patients with various ages and gender.

first: Y-h

first: Yoshiki

last: Murakami


title: Single-cell RNA sequencing reveals roles of fibroblasts during intestinal injury and repair in rats with severe acute pancreatitis

city: Jinan

first: Shulei

last: Zhao

state: China

address: Department of Gastroenterology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, 324 Jingwu Weiqi Rd, Jinan 250021, China.

department: Gastroenterology

summary: We used single-cell sequencing to explore the molecular mechanisms of intestinal injury and treatment by analyzing changes in cellular heterogeneity and composition in rat ileal tissue during injury and treatment processes.

overall_design: We constructed a rat model of severe acute pancreatitis (SAP) and evaluated treatment with an injected of monoacylglycerol lipase (MAGL) inhibitor (JZL184) solution using three experimental groups: healthy male Sprague-Dawley (SD) rats injected with vehicle (CON), male SD SAP model rats injected with vehicle (SAP), and male SAP rats injected with JZL184. We obtained and prepared a single-cell suspension of ileal tissue of each rat for single-cell transcriptome sequencing.

first: Jing

last: Wang

first: Hongwei

last: Xu

first: Changqin


title: Effect of GDNF-Gel/HA-Mg nerve conduit on gene expression during peripheral nerve regeneration

city: Xi’an

first: Yuanqing

last: Cai

state: Shaanxi

address: No.157, Xiwu Road

institute: The Second Affiliated Hospital of Xi’an Jiaotong University

summary: In this study, glial cell line-derived neurotrophic factor (GDNF)- Gelatin methacryloyl (Gel)/hydroxylapatite (HA)-Mg nerve conduit was developed. the conduit was implanted in sciatic nerve defect model in SD rats to explore its role in repairing peripheral nerve defects. Regenerated nerve tissues from GDNF-Gel/HA-Mg group and negative control group were collected for RNA-seq, aiming to explore the potential molecular mechanism of GDNF-Gel/HA-Mg in peripheral nerve regeneration.

overall_design: To investigate the potential molecular mechanism of GDNF-Gel/HA-Mg in peripheral nerve regeneration, GDNF-Gel/HA-Mg was implanted in SD rats, the regenerated nerves were collected  for RNA-seq.The control group (NC group) received no treatment and  the wounds were closed directly, the regenerated nerves from NG group were used as controls.


title: Multiomic spatial landscape of innate immune cells at human central nervous system borders

city: Freiburg

first: Roman

last: Sankowski

address: Breisacher Str. 64

department: Institute of Neuropathology

country: Germany

institute: University of Freiburg Medical Center

summary: The innate immune system of the human central nervous system (CNS) is highly diverse already during homeostasis. Several immune cell populations such as macrophages that are frequent in the brain parenchyma (microglia) and less numerous at the brain interfaces as CNS-associated macrophages (CAMs) constitute the local immune compartment. Due to their scantiness and particular location, little is known about the presence of temporally and spatially restricted CAM subclasses during development, health and perturbation. Here, we combined several high-dimensional technologies, such as single-cell RNA-sequencing, time-of-flight mass cytometry and single-cell spatial transcriptomics with fate mapping and advanced immunohistochemistry to comprehensively characterize the immune system at human CNS interfaces. We also provide a comprehensive analysis of resident and engrafted myeloid cells in the brains of individuals with peripheral blood stem cell transplantation, revealing remarkable dynamics. These approaches enabled us to identify a previously unappreciated spectrum of transcriptional classes of human CAMs and to decipher their turnover with circulating cells. CAM signatures profoundly changed during ontogeny and pathology. Our results highlight myeloid diversity at the interfaces of the human CNS with the periphery and provide new insights into the human brain’s immune system.

overall_design:
Single-cell RNA sequencing using 10x and Cel-Seq2 was conducted on cell suspensions and after nuclei extraction from fresh frozen sections or formalin-fixed formalin embedded tissues. A part of the single cell analyses was multilexed and analyzed using CITE-Seq. The raw fastq files can be found in the access controlled European genome phenome Archive under the accession number EGAS50000000030 https://ega-archive.org/studies/EGAS50000000030.
NOTE FROM SUBMITTER: The raw fastq filese can be found in the access controlled European genome phenome Archive account associated with the study.

first: Marco

last: Prinz


title: Maternal CXCR4 deletion results in placental defects and pregnancy loss mediated by immune dysregulation

city: New Haven

first: Richard

last: Flavell

state: CT

address: 300 Cedar Street

institute: Yale University

summary: The pregnant decidua is infiltrated by many immune cells which are thought to originate in the bone marrow (BM) promoting pregnancy. CXCR4 is a key regulator of the development of NK cells and dendritic cells, both of which play an important role in early placental development and immune tolerance at the maternal-fetal interface. However, the role of CXCR4 in pregnancy is not well understood. To generate tamoxifen-inducible CXCR4 knockout mice, we used the Cre/LoxP tamoxifen-inducible system. For animal experiments, Cre+/CXCR4fl/fl mice and their Cre-/CXCR4fl/fl littermates were used. After tamoxifen treatment, we refer to Cre-/CXCR4fl/wt mice as WT (wild type), and Cre+/CXCR4fl/null mice as CXCR4 KO (knockout). For adoptive bone marrow transplant (BMT) experiments, BMT was performed from either WT GFP transgenic male donor mice into WT or CXCR4 KO females, or from CXCR4 KO male donors into CXCR4 KO females as negative control. Collectively, our study found an important role for maternal CXCR4 expression in immune cell function, placental development and pregnancy maintenance.

overall_design: Female wild type mice (8-10 weeks old) underwent bone marrow transplantation from GFP-expressing transgenic wild type male donors following 5-fluorouracil-based submyeloablation. After timed mating, uterine implantation sites were collected on E10.5. Implantation sites were dissected to remove embryonic and placental parts. The uterine tissues were finely minced and subjected to enzymatic digestion to obtain single cell suspensions. scRNA-seq was performed using droplet microfluidics (10x Chromium). Libraries were created with Single Cell 3′ Library kit V2 according to the manufacturer’s protocol, and sequenced on Illumina HISeq 4000 instrument.

first: Tal

last: Reshef


title: Homeostatic, repertoire and transcriptional relationships between colon T regulatory cell subsets

city: Boston

first: CBDM

last: Lab

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

summary: Foxp3+ regulatory T cells (Tregs) in the colon are key to promoting peaceful co-existence with symbiotic microbes. Differentiated in either thymic or peripheral locations, and modulated by microbes and other cellular influencers, colonic Treg subsets have been identified through key transcription factors (TF; Helios, Rorg, Gata3, cMaf), but their inter-relationships are unclear. Here, we perform genomic analysis of colonic lamina propria Tregs with conditional KOs of each of these TFs to better understand how each TF contributes to colonic Treg identity and function.

overall_design: Mouse CD4+ regulatory Tregs from WT or Treg-specific conditional TF KO (Gata3, Ikzf2, cMaf, Rorc) littermate control mice were isolated from colonic lamina propria by FACS for scATAC-seq using 10x Genomics.

first: Deepshika

last: Ramanan

first: Kaitavjeet

last: Chowdhary

first: Christophe

last: Benoist


title: Composition of colonic microbes in mice deficient in intestinal Treg subsets

summary: Regulatory T cells (Tregs) are immune cells that play a crucial role in maintaining tolerance to harmless antigens, including commensal microbes. In the intestine, Tregs can be classified into subsets based on their expression of transcription factors Helios, Rorg, Gata3 and cMaf. The exact functions of the intestinal Treg subsets and their role in maintaining tolerance to intestinal microbes is not fully understood. Here, we generated conditional knockout mice of each Treg subset and profiled the composition of their intestinal microbiota by performing 16S rRNA sequencing of stool from conditional knockouts and matched littermate controls.

overall_design: Each condtional knockout strain and its paired control littermate (sex-matched) were selected from experimental batches of mice used for immune profiling spanning 3 years. Stool samples were collected from 6-8 week old mice.

first: Diane

last: Mathis


title: Highly dynamic inflammatory and excitability transcriptional profiles in hippocampal CA1 following status epilepticus

city: Bonn

first: Ashley

last: van Waardenberg

address: Venusberg-Campus 1

institute: i-Synapse

summary: Transient brain insults including status epilepticus (SE) can initiate a process termed ‘epileptogenesis’ that results in chronic temporal lobe epilepsy (TLE). As a consequence, the entire tri-synaptic circuit of the hippocampus is fundamentally impaired. A key role in epileptogenesis has been attributed to the CA1 region as the last relay station in the hippocampal circuit and as site of aberrant plasticity, e.g. mediated by acquired channelopathies. The transcriptional profiles of the distinct hippocampal neurons are highly dynamic during epileptogenesis. Here, we aimed to elucidate the early SE-elicited mRNA signature changes and the respective upstream regulatory cascades in CA1. RNA sequencing of CA1 was performed in the mouse pilocarpine-induced SE model at multiple time points ranging from 6 to 72 hours after the initial insult. Bioinformatics was used to decipher altered gene expression, signalling cascades and their corresponding cell type profiles. Robust transcriptomic changes were detected at 6h after SE and at subsequent time points during early epileptogenesis. Major differentially expressed mRNAs encoded primarily immediate early and excitability-related gene products, as well as genes encoding immune signalling factors.

overall_design: RNA sequencing of CA1 hippocampus sections was performed in the mouse pilocarpine-induced SE model at multiple time points ranging from 6 to 72 hours after the initial insult.

first: Daniel

last: Galvis Montes

first: Karen

last: van Loo

first: Rainer

last: Surges

first: Susanne

last: Schoch

first: Albert

last: Becker

first: Julika

last: Pitsch


title: Activation of GPER1 in macrophage ameliorates UUO-induced renal fibrosis

city: Shanghai

first: Xiangchen

last: Gu

address: 110 Ganhe Rd, Hongkou  Distrcit

department: Department of Nephrology

institute: Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine

summary: Numerous studies have proven the critical role of macrophages in the renal fibrosis process. Notably, G Protein-coupled Estrogen Receptor 1 (GPER1), a novel estrogen receptor, has been shown to play a ubiquitous role in the regulation of macrophage activities and proinflammatory pathways. However, the precise role of GPER1 in macrophage-mediated renal fibrosis is unknown.  In this study, we aimed to investigate the function of macrophage GPER1 in the UUO-induced renal fibrosis model. Compared to vehicle-treated ovariectomized (OVX) female and male UUO models, we observed that G-1 (GPER1 agonist)-treated OVX female and male UUO mice had fewer renal fibrotic lesions and less M1 and M2 macrophage infiltration in the kidney tissues. Conversely, Gper1 deletion in male UUO mice accelerated renal fibrosis and increased inflammation. In vitro studies also revealed that GPER1 activation reduced M0 macrophage polarization towards M1 and M2 phenotypes. The RNA sequencing analysis and immunoblotting indicated that GPER1 activation was primarily involved in downregulating immune pathways activation and inactivating MAPK pathways.   Tubular epithelial cells co-cultured with G1-pretreated M1 macrophages exhibited fewer injuries and immune activation. In addition, fibroblasts co-cultured with G1-pretreated M2 macrophages showed downregulated extracellular matrix expression.  Overall, this is the first study to demonstrate the effect of GPER1 on macrophage-mediated renal fibrosis via inhibition of M1 and M2 macrophage polarization. These findings indicate that GPER1 may be a promising therapeutic target for the treatment of renal fibrosis.

overall_design: To invsetigate the role of GPER1 activation in macrophage,  bone marrow macrophages were isolated and differntiated into M0 macrophages. Then M0 were polarized into M1 or M2 phenotype macrophages stimulated with LPS/INF or IL4, with or without treatment of  GPER1 agonist.  Further, primary tubular epithelial cells or fibroblast  were co-cultured with M1 or M2 macrophages pretreated with G-1 or DMSO. Then the RNA sequencing was performed on Macrophage control, macrophage treated with LPS/INF, macrophages treated with G-1, macrophages treated with G-1 and LPS/INF,  macrophages treated with IL-4, macrophages treated wtih G-1 and IL-4. Tubular epithelial cells co-cultured with LPS/INF treated macrophages and Tubular epithelial cells co-cultured with G-1 and LPS/IFN treated macrophages.

first: Lin

last: Xie

first: Ye

last: Cheng


title: Expression data of  C. elegans JK1466 strain treated with tryptophan-derived betaxanthins

city: Murcia

first: Fernando

last: Gandía-Herrero

state: Murcia

address: Universidad de Murcia, Campus Espinardo - Edificio Veterinaria

department: Biochemistry and Moleular Biology

country: Spain

institute: University of Murcia

summary:
Effects of tryptophan derived-betaxanthins in C. elegans  Jk1466 strain gene expression is studied.
Microarrays were used to detail the global programme of gene expression underlying the lifespan extension and identified distinct classes of up/down-regulated genes in animal treated with tryptophan-derived betaxanthins

overall_design: C. elegans young adults treated with tryptophan-derived betaxanthins from L1 stage were selected  for RNA extraction and hybridization on Affymetrix microarray chips.

first: P

last: Henarejos-Escudero

first: M

last: Lopez-Andreo

first: F

middle: F

last: Méndez-García

first: S

last: Hernandez-Garcia

last: Martinez-Rodriguez

last: Gandia-Herrero


title: Human monocytes exposed to SARS-CoV-2 display features of trained immunity producing high levels of CXCL10 upon restimulation

city: Bilthoven

first: Jelena

last: Cvetkovic

address: Antonie van Leewenhoeklaan 9

department: Centre for Infectious Disease Control

country: Netherlands

institute: RIVM

summary: The capacity of innate immune cells to build immunological memory after a first encounter with certain pathogens or vaccines that allow them to respond stronger to reinfection is referred to as “trained immunity”. Despite few studies highlighting an important role for trained immunity in protection during COVID-19 infection or vaccination, no study so far has shown whether SARS-CoV-2 can train innate immune cells to respond stronger to a second stimuli. The aim of this study was to investigate whether this virus can induce trained immunity in human monocytes. To this purpose we used monocytes from healthy donors and exposed them to inactivated (i) SARS -CoV-2 for 24 hours followed by a resting period of several days in medium only and restimulation on day 6. On day 6, to evaluate the effects of iSARS-CoV-2 training on monocyte gene expression,  transcriptomic analysis of human monocytes, before or 3h after LPS stimulation, was done. Our data provide the transcriptional profile of untrained and trained monocytes with iSARS-CoV-2.

overall_design: The transcriptomic profile of iSARS-CoV-2 trained and untrained monocytes prior and post-secondary LPS stimulation was investigated. Comparisons were made for four groups namely, untrained monocytes in medium only (Unt-Med); untrained monocytes stimulated with LPS on day 6 (Unt-LPS); trained monocytes with iSARS-CoV-2 without LPS stimulation on day 6 (Trn_S-Med) and iSARS-CoV-2-trained monocytes stimulated with LPS on day 6 (Trn_S-LPS).

first: Alberto

last: Miranda-Bedate

first: Elena

last: Pinelli


title: Role of KCTD1/KCTD15 in the skin

first: Alexander

last: Marneros

summary: To investigate the effects of inactivation of Kctd15 and Kctd1/Kctd15 in mouse skin.

overall_design: Comparative expression analysis of total RNA by RNA-Seq. Whole skin of P4 WT and littermate K14Cre+Kctd1fl/flKctd15fl/fl mice were used for RNA isolation. Epidermis from 3-week-old K14Cre+Kctd15fl/fl and K14Cre+Kctd1fl/flKctd15fl/fl mice was used for RNA isolation.


title: FoxP3-mediated blockage of ryanodine receptor 2 is the molecular basis for the contact-based suppression by regulatory T cells

city: Calgary

first: Shuang

last: Geng

address: 2500 University Dr NW

country: Canada

institute: University of Calgary

summary: The suppression mechanism of regulatory T cells (Tregs) is an intensely investigated topic.  As our focus has shifted towards a model centered on indirect inhibition of dendritic cells, a universally applicable effector mechanism controlled by the transcription factor forkhead box P3 (FoxP3) expression has not been found.  Here, we report that FoxP3 blocks the transcription of ER Ca2+-release channel ryanodine receptor 2 (RyR2).  Reduced RyR2 shuts down basal Ca2+ oscillation in Tregs, which reduces m-Calpain activities that is needed for T cells to disengage from DCs, suggesting a persistent blockage of DC antigen presentation.  RyR2 deficiency renders the CD4+ T cell pool to become immune suppressive, and behave in the same manner as FoxP3+ Tregs in viral infection, asthma, hypersensitivity, colitis and tumor development.  In the absence of FoxP3, RyR2-deficient CD4+ T cells (CKO) rescue the systemic autoimmunity associated with Scurfy mice.  Therefore, FoxP3-mediated Ca2+ signaling inhibition may be a central effector mechanism of Treg immune suppression.

overall_design: We examined chromatin structure using ATAC-seq in 4 cell types  (Treg, RyR2 CKO Treg, Tconv, RyR2 CKO Tconv) with or without anti-CD3/anti-CD28 stimulation.


title: Augmented Drug Resistance of Osteosarcoma Cells within Decalcified Bone Matrix Scaffold: the role of Glutamine Metabolism

first: Lei

last: Cui

address: No. 50 Chifeng Road, Siping Street, Yangpu District, Shanghai

institute: Tongji university

summary: Due to the lack of a precise in vitro model that can mimic the nature microenvironment in osteosarcoma, the understanding of its resistance to chemical drugs remains limited. Here, we report a novel three-dimensional model of osteosarcoma constructed by seeding tumor cells (MG-63 and MNNG/HOS Cl #5) within in demineralized bone matrix scaffolds. Demineralized bone matrix scaffolds retain the original components of the natural bone matrix (hydroxyapatite and collagen type I), and possess good biocompatibility allowing osteosarcoma cells to proliferate and aggregate into clusters within the pores. Growing within the scaffold conferred elevated resistance to doxorubicin on MG-63 and MNNG/HOS Cl #5 cell lines as compared with two-dimensional cultures. Transcriptomic analysis showed an increased enrichment for drug resistance genes along with enhanced glutamine metabolism in osteosarcoma cells in demineralized bone matrix scaffolds. Inhibition of glutamine metabolism resulted a decrease in drug resistance of osteosarcoma, which could be restored by α-ketoglutarate supplementation. Overall, our study suggests that microenvironmental cues in demineralized bone matrix scaffolds can enhance osteosarcoma drug responses and that targeting glutamine metabolism may be a strategy for treating osteosarcoma drug resistance.

overall_design: To investigate the differences between OS cells cultured in 3D and 2D environment at whole transcriptional level, we performed transcriptome RNA sequencing (RNA-seq) of MING/HOS(HOS) cells at day7 after cell seeding.

first: Jiaxin

last: Ren


title: Transcriptomic analysis of engineered myometrial tissues with varied tissue architecture and matrix rigidity

city: Los Angeles

first: Megan

last: McCain

address: 1042 Downey Way

department: Biomedical Engineering

institute: University of Southern California

summary: We report the use of RNA-seq for transcriptional analysis of engineered myometrial tissues cultured on hydrogels with varied matrix rigidity and tissue alignment.

overall_design: mRNA profiles of engineered myometrial tissues on representative healthy (13 kPa - aligned) and fibrotic (90 kPa - isotropic) substrates

first: Antonina

middle: P

last: Maxey

first: Jaya

last: Travis


title: SRPX2 promotes cancer cell proliferation and migration of thyroid cancer

city: Bengbu

first: Jiajun

last: Wu

state: None Selected

address: 浙江省杭州市拱墅区朝晖街道上塘路158号浙江省人民医院

institute: Bengbu Medical College

summary:
We found that SRPX2 expression level was higher in thyroid tumors, and greater SRPX2 expression was closely related with a higher tumor grade and poorer clinical prognosis.
SRPX2 promotes the development of papillary thyroid cancer (PTC) by promoting cell proliferation and migration

overall_design: Comparative gene expression profiling analysis of RNA-seq data for TPC1 cells and its knockdown derivatives (si-SRPX2).

first: Haiwei

last: Guo

first: Haibo

last: Zhang


title: CAR gene delivery by T-cell targeted lentiviral vectors is enhanced by rapamycin induced reduction of antiviral mechanisms

city: Langen

first: Christian

middle: J.

last: Buchholz

state: Hessen

address: Paul-Ehrlich-Strasse 51-59

institute: Paul Ehrlich Institut

summary: Lentiviral vectors (LV) have become the dominant tool for stable gene transfer into lymphocytes including chimeric antigen receptor (CAR) gene delivery to T cells, a major breakthrough in cancer therapy. Yet, room for improvement remains, especially for the latest LV generations delivering genes selectively into T cell subtypes, a key requirement for in vivo CAR T cell generation. Towards improving gene transfer rates with these vectors, we conducted whole transcriptome analyses on human T lymphocytes after exposure to CAR-encoding conventional vector VSV-LV, and vectors targeted to CD8+ (CD8-LV) or CD4+ T cells (CD4-LV). Genes related to quiescence and antiviral restriction were found to be upregulated in CAR-negative cells exposed to all types of LVs. Down-modulation of various antiviral restriction factors including the interferon-induced transmembrane proteins (IFITMs) was achieved with rapamycin as verified by mass spectrometry (LC-MS). Strikingly, rapamycin enhanced transduction by up to 7-fold for CD8-LV and CD4-LV without compromising CAR T cell activities, but did not improve VSV-LV. When administered to humanized mice, CD8-LV resulted in higher rates of GFP gene delivery as well as faster in vivo CAR T cell generation and tumor control. The data favors multi-omics approaches for improvements in gene delivery.

overall_design: scRNA-seq analysis of lentiviral vector generated CAR T cells

first: Filippos

last: Charitidis

first: Elham

last: Adabi

first: Naphang

last: Ho

first: Angela

last: Braun

first: Ciara

last: Tierney

first: Lisa

last: Strasser

first: Frederick

middle: B

last: Thalheimer

first: Liam

last: Childs

first: Jonathan

last: Bones

first: Colin

last: Clarke


title: GSC23 shG12 vs shCTL

city: La Jolla

first: Olga

last: Chaim

address: 9500 Gilman Drive

department: Department of Pharmacology

institute: University of California, San Diego

summary: To investigate GNA12 role in GBM patient tumor samples. We knocked down GNA12 using knockdown by shRNA.

overall_design: RNA-seq from tumor samples (4 mice tumors for biological replicates in each group)

first: Joan

last: Heller Brown


title: Nuclear translocation of PTH receptor hijacks thyroid hormone signaling for bone mass regulation [ChIP-Seq]

city: changsha

first: Jian xi

last: Zhu

state: -- Select state --

address: XiangYa hospital

department: Department of Orthopaedics

institute: Xiangya Hospital, Central South University

summary: After preliminary verification of physical interaction between PTH1R and THR, we next performed chromatin co-immunoprecipitation sequencing (ChIP -seq) to detect the overlapping downstream promoters genome-widely between PTH1R and THR.

overall_design: Chromatin immunoprecipitation DNA-sequencing (ChIP-seq) for PTH1R and THR in MC3T3-E1 cells.

first: Tailai

last: He

first: Yihe

last: Hu

first: Bin

first: Xiangmin

last: Chen

first: Yong

first: Jianxi


title: Nuclear translocation of PTH receptor hijacks thyroid hormone signaling for bone mass regulation [RNA-seq]

summary: After demonstrating that the bone-forming ability of mice is altered by blocking PTH1R entry into the nucleus, We performed RNA-seq on BMSCs from Pth1rΔNLS individuals and wild-type individuals to explore the mechanism behind this phenomenon.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for BMSCs solated from heterozygotes and wild-type individuals of Pth1rΔNLS mice

last: Guo


title: Ageing in space: microgravity triggers ferroptosis and accelerates senescence in osteoblastic cells

city: Liege

first: Nancy

last: Garbacki

address: avenue Hippocrate 13

country: Belgium

institute: University of Liege

summary: To understand the cellular and molecular mechanisms allowing MG63 osteoblastic cells to perceive, transduce and react to microgravity environment.

overall_design: RNAseq was used to compare MG63 cells cultured in microgravity on the ISS to MG63 cells cultured on the ISS in a “1 g centrifuge” (used as the most appropriate control).

first: Alain

last: Colige

first: Betty

last: Nusgens

first: Jérôme

last: Willems

first: Christophe

last: Deroanne


title: Epitranscriptome analysis of NAD-capped RNA by spike-in-based normalization and prediction of chronological age

first: Dean

last: Li

address: Haike Road 100

institute: Chinese Academy of Science

summary: The hub metabolite, nicotinamide adenine dinucleotide (NAD), can be used as an initiating nucleotide in RNA synthesis to result in NAD-capped RNAs (NAD-RNA). We investigated the dynamics of NAD-modified epitranscriptome during human normal aging.

overall_design: A total of two independent cohorts were recruited: the discovery cohort (17 females and 18 males) aged 23-67 years and the validation cohort (14 females and 12 males) aged 23-67 years. Peripheral blood mononuclear cells (PBMCs) were isolated from blood drawn from participants, and used for NAD-RNA profilings. Combined, we subjected 10 μg total RNAs from human PBMCs mixed with 40 μg total RNAs from Drosophila, 0.1 ng spike-in 2 RNAs, and 0.1 ng spike-in 3 RNAs to NAD-RNA sequencing, followed by enONE computational analysis of NAD-RNA profiles.

last: Liu


title: RNA-seq analysis of MEK or ERK1/2 inhibitor treatment in uveal melanoma cell lines.

city: Philadelphia

first: Andrew

last: Aplin

state: PA

address: 233 South 10th St.

institute: Thomas Jefferson University

summary: Activating GNAQ/GNA11 are present in majority of uveal melanomas resulting in downstream activation of the MAPK pathway. To elucidate changes in the transcriptome after MEK or ERK1/2 inhibition, we performed RNA sequencing on two UM cell lines. Differential analysis revealed that MARK3 expression was not altered but STK10 expression was reduced.

overall_design: RNA was obtained from PDX4 and UM004 after drug treatment for 24 hours in uveal melanoma cell lines.

first: Usman

last: Baqai

first: Timothy

middle: J

last: Purwin

first: Anna

last: Han


title: Ribosome biogenesis controls suture mesenchymal stem cell fate via selective regulation of complement pathway in to prevent craniosynostosis

first: Supawadee

last: Jariyasakulroj

address: Alcazar street

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

overall_design: Refer to individual Series


title: WCRC-25: A novel luminal Invasive Lobular Carcinoma cell line model

city: Pittsburgh

first: Kai

last: Ding

address: 204 Craft Ave

institute: University of Pittsburgh

summary: Breast cancer is categorized by the molecular and histologic presentation of the tumor; with the major histologic subtypes observed in patients being No Special Type (NST; commonly known as Invasive Ductal Carcinoma, IDC) and Invasive Lobular Carcinoma (ILC). ILC are characterized by growth in a single file discohesive manner with stromal infiltration attributed to their hallmark loss of E-cadherin (CDH1). The Cancer Cell Line Encyclopedia (CCLE) currently only lists three ILC cell lines; emphasizing the need to expand the inventory of models available to researchers. Here we report the successful establishment and characterization of a novel ILC cell line, WCRC-25, from a metastatic pleural effusion from a postmenopausal Caucasian woman with metastatic ILC. WCRC-25 is an ER-negative luminal epithelial ILC cell line with both luminal and Her2-like features. It exhibits anchorage independent growth and haptotactic migration towards Collagen I. Sequencing revealed a CDH1 Q706* truncating mutation in WCRC-25, together with mutations in FOXA1, CTCF, BRCA2 and TP53 which were also seen in a series of metastatic lesions from the patient. Copy number analyses revealed amplification and deletion of genes frequently altered in ILC while optical gene mapping (Bionano) revealed novel structural rearrangements. RNA-seq analysis comparing the primary tumor, metastases and the cell line revealed signatures for cell cycle progression and receptor tyrosine kinase signaling. To assess targetability, we treated WCRC-25 with AZD5363 and Alpelisib confirming WCRC-25 as susceptible to PI3K/Akt signaling inhibition as predicted by our RNA sequencing analysis. In conclusion, we report WCRC-25 as a novel ILC cell line with much promise as a valuable research tool to advance our understanding of ILC and its therapeutic vulnerabilities.

overall_design: RNA sequencing analysis of multifocal metastases from the same patient and patient-derived cell line models.

first: Steffi

last: Oesterreich

first: Adrian

middle: V

last: Lee

first: Jennifer

last: Atkinson

first: Ashuvinee

last: Elangovan

first: Emily

middle: A

last: Bossart


title: Ribosome biogenesis controls suture mesenchymal stem cell fate via selective regulation of complement pathway in to prevent craniosynostosis  [RNA-seq]

summary: Suture mesenchymal stem cell (MSC) drives calvarial suture development, homeostasis, and regeneration. Its loss leads to craniosynostosis, a prevailing craniofacial disorder characterized by premature suture closure. Ribosome biogenesis, historically thought to be a static house-keeping process, is now known to have tissue-specific roles. However, the functional specificity of ribosome biogenesis in suture MSCs remains largely unexplored, hampering development of therapeutic strategies for craniofacial tissue regeneration. We genetically perturb ribosome biogenesis using Snord118, a small nucleolar RNA (snoRNA) required for ribosomal RNA (rRNA) maturation. MSC specific conditional knockout (cKO) of Snord118 in mice leads to p53 activation, cell death, mesenchymal and MSC loss, impaired osteogenic and osteoclastic activity, resulting in suture growth and craniosynostosis defects. Using our newly established human induced pluripotent stem cell (iPSC)-derived MSCs combined with ribosome profiling, we found that SNORD118deficiency in MSCs causes global translation dysregulations and downregulation of complement pathway, a part of innate immune system with selective but poorly characterized physiological functions in craniofacial tissue homeostasis. Overall, ribosome biogenesis controls suture MSC fate via selective regulation of complement pathway.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MSCs and its snord118 mutant heterozygote. Experiments were performed in two biological duplicates.

first: Jianfu

last: Chen


title: Ribosome biogenesis controls suture mesenchymal stem cell fate via selective regulation ofcomplement pathway in to prevent craniosynostosis [Ribo-seq]

overall_design: We performed ribosome profiling in MSCs and its snord118 mutant heterozygote. Experiments were performed in two biological duplicates.


title: Next generation sequencing analysis of ginseng transcriptomes in response to Botrytis cinerea △BcSpd1 treatment

city: Changchun

first: Shouan

address: Xi-An-Da Road 5333

institute: Jilin University

summary: Next generation sequencing (NGS) was performed to identify genes changed in ginseng upon Botrytis cinerea △BcSpd1 treatment. The goal of the work is to find interesting genes involved in ginseng in response to fungi induction. The object is to reveal the molecular mechanism of ginseng defense induced by Botrytis cinerea △BcSpd1 .

overall_design: mRNA profiling of ginseng in response to Botrytis cinerea △BcSpd1 treatmet.


title: FAM13B knockdown in iCMs

city: Cleveland

first: Han

last: Sun

state: OH

address: 9500 Euclid Ave

department: QHS

institute: Cleveland Clinic

summary: Common human genetic variation near the FAM13B gene are associated with atrial fibrillation as well as with the expression level of FAM13B mRNA in human left atrial appendage tissues.  To determine the effects of FAM13B gene expression in human cardiomyocytes derived from induced pluripotent stem cells (iCMs from iCell Cardiomyocytes), we used siRNA targeted against FAM13B to knockdown its gene expression (KD) or an siRNA with a scrambled sequence (SCR). Total RNA was prepared from biological triplicate plates of cells and subjected to bulk RNAseq.  100-bp paired-end sequencing was performed on the Illumina HiSeq 2000.  The sequence reads were mapped to the human genome using the STAR aligner (version 2.3.0) to derive a digital count of the expression of genes, which were defined using the Ensembl gene catalog (version 69). Genes were filtered to ensure a CPM (counts per million) > 5 in at least 2 samples, resulting in 11,017 genes. Differential expression analyses of FAM13B KD versus control SCR siRNA in iCMs was performed using the limma-voom approach with false discovery rate control.

overall_design: 3 biological replicates each for FAM13B KD and scrambled siRNA control

first: Greg

last: Tchou

first: Shamone

last: Gore-Panter

first: John

last: Barnard

first: Jonathan

middle: D

last: Smith


title: Effects of siRNA depletion on gene expression during C2C12 skeletal muscle differentiation initiation

city: Haverford

first: Amy

last: Cooke

address: 370 Lancaster Ave

department: Biology

institute: Haverford College

summary: In humans, skeletal muscles comprise nearly 40% of total body mass, which is maintained throughout adulthood by a balance of muscle protein synthesis and breakdown. Cellular amino acid (AA) levels are critical for these processes, and mammalian cells contain transporter proteins that import AAs to maintain homeostasis. Until recently, the control of transporter regulation has largely been studied at the transcriptional and post-translational levels; however, our recent work demonstrates that the RNA-binding protein YBX3 is critical to intracellular sustain AA in human cells. Here we report that YBX3 post-transcriptionally controls the levels of specific AA transporter messenger (m)RNAs in skeletal muscle cells, which impacts the intracellular levels transported by these proteins. Further, we find that reduction of YBX3 protein reduces proliferation during skeletal muscle differentiation, and that YBX3 expression increases substantially during skeletal muscle differentiation, which is independent to changes in itsmRNA levels. Taken together, our findings suggest that YBX3 regulates AA transport in skeletal muscle cells and that its expression is critical to maintain skeletal muscle cell proliferation during differentiation.

overall_design: To identify genes whose expression is controlled by YBX3, we used high-throughput RNA sequencing (RNAseq) in C2C12 mouse skeletal muscle cells depleted of YBX3 by small interfering RNA (siRNA).  We assessed changes in transcripts levels in myoblasts before (proliferating) and one day after differentiation initiation (differentiating), which allowed for cells to be harvested concurrently at 48 hours post siRNA transfection.

first: William

last: Vostrejs

first: Silina

last: Awad

last: Skipper


title: Spatial gene regulatory network of miRNA165a in Shoot apical meristem of Arabidopsis

city: Mohali

first: Hasthi

last: Ram

address: Sector 81

department: Agriculture biotechnology

country: India

institute: NABI (National Agri-Food Biotechnology Institute)


title: RNA-Seq analysis of HCT-8 cells infected with BCoV and/or Cparvum

city: Ås

first: Alejandro

last: Jimenez Melendez

address: Elizabeth Stephansens vei 15

department: PARAFAG

country: Norway

institute: NMBU

summary: Among the causative agents of neonatal diarrhea in calves, two of the most prevalent are bovine coronavirus (BCoV) and Cryptosporidium parvum. Although several studies indicate that co-infections between the two pathogens are associated with greater symptom severity, the host-pathogen interplay remains to be further investigated. The main objective of the present work was to investigate the modulation of the transcriptome of HCT-8 cells during single or co-exposures to BCoV and C. parvum by means of RNA-Seq.

overall_design: HCT-8 cells were  inoculated with  (1) BCoV (2) C. parvum (3) BCoV and C. parvum and, for all set ups, harvested at two time points (24 and 72 h post infection). Non-exposed cells were harvested at the same time point. After RNA extraction, the samples were subjected to RNA-Seq

last: Jimenez-Melendez

first: Ruchika

last: Shakya

first: Turhan

last: Markussen

first: Lucy

last: Robertson

first: Mette

last: Myrmel

first: Shokouh

last: Makvandi-Nejad


title: Apobec1 and acute kidney injury

city: West Haven

first: Xiaojia

last: Guo

state: Connecticut

address: Rm 7-188, Building 2, 950 Campbell Ave

institute: Yale University School of Medicine

summary:
Kidney tissues from a cisplatin-induced acute kidney injury mouse model of global Apobec1 knockout mice compared with wild type mice. 6 months old male mice examined.
We used microarrays to identify genes that are differentially expressed during acute kidney injury in the absence of apobec1 compared with wild type mice.

overall_design: WT and Apobec1 KO mice were injected with saline as control or cisplatin for 3 days,  kidneys were collected and RNA were extracted for microarray study


title: miRNA expression in the extracellular vescle (EV) fraction

city: Koto-ku

first: Fumio

last: Maeda

state: Tokyo

department: Cellular and Molecular Biotechnology Research Institute

institute: National Institute of Advanced Industrial Science and Technology

type: Non-coding RNA profiling by high throughput sequencing

summary:
To developed the mothod for obtaining miRNA information in cells non-destructively,  we aimed to produce EVs encapsulating miRNA-binding protein fragments that actively incorporate miRNAs into EVs.
We then performed gene expression profiling analysis using data obtained from RNA-seq of control cells and cells co-expressing EV-inducing protein and miRNA binding protein.

overall_design: Gene expression profiling analysis of RNA-seq data for HEK293T control cells and cells co-transfected with the EV-inducing protein (EPN-01) and the miRNA binding protein fragment (Flag-MID-PIWI-Vpr

first: Shungo

last: Adachi

first: Tohru

last: Natsume


title: Transcriptomic analysis of REVOLUTA and mir165a cell-types of Arabidopsis shoot apical meristem

summary: Dorso-ventral (DV) patterning at the Shoot Apical meristem (SAM) is essential for organogenesis in Arabidopsis. Dorsal and ventral gene expressed domains are separated by boundaries from where the new organ initiation starts. Here by using cell-types specific transcriptomics approach, we have identified dorsal, ventral and boundary specific genes in SAM.

overall_design: 6 different cell-types, and 4 biological replicates for each cell-type were collected through FACS, and used for RNA-Seq analysis. The corresponding position for each cell-type is as following: BFPYFP- Epidermal Rev expressing cells, BFPGFP- epidermal miRNA165a expressing cells, BFP- Epidermal cells not expressing REV and mir165a, YFP-subepidermal cells expressing REV, GFP-subepidermal cells expressing miRNA165a, Allneg-Cells not expressing any marker.

first: Marcus

last: Heisler


title: Nuclear translocation of PTH receptor hijacks thyroid hormone signaling for bone mass regulation

first: Jian xi

last: Zhu


title: mRNA profiling of schwann cells cultured with monocytes derived macrophages and PDAC cell lines supernants-induced tumor-associated macrophages (TAMs)

city: Guangzhou

first: Leyi

last: Huang

state: Guangdong

address: 107 Yan Jiang West Road, Guangzhou, P.R. China

institute: Sun Yat-sen University

summary: Tumor associated macrophages(TAMs) have been demonstrated to promote tumor progression and perineural invasion in PDAC, however the underlying machanism of TAMs interacting with Schwann cells is still unclear. We found the gene expression of Schwann cell is different from TAMs-induced Schwann cells by comparing mRNA profiling.

overall_design: mRNA profile of schwann cells, which are co-cultured with monocytes derived macrophages(MDMs) or 3 kinds of PDAC-induced TAMs

first: Bin

last: Zhang

first: Xiaofeng


title: Effect of KO of CCND1, ORAOV1, or miR548K in FaDu cancer cell lines or oral keratinocytes

city: San Francisco

first: Celine

middle: Ismay

last: Mahieu

state: California

address: 513 Parnassus Ave, HSE 740

department: Otolaryngology | Head and Neck Surgery

institute: University of California San Francisco

summary:
To investigate the function of CCND1/CCND2/ORAOV1/miR548K in 11q13-amplified cancer cells or non cancerous keratinocytes, we established respective KO cells through CRISPR-Cas9.
We performed gene expression profiling analysis using data obtained from RNA-seq upon target KO in either FaDu cells or TP53/CDKN2A k.o. oral keratinocytes

overall_design: Comparative gene expression profiling analysis of RNA-seq data for FaDu and TP53/CDKN2A KO oral keratinocytes KO derivatives (CCND1, CCND2, ORAOV1, miR548K, compared to 11q13-noncoding to control for copy number cuts).

middle: I

first: Aaron

last: Tward


title: The role of S100A9 in brain metastesis in EGFR-mutant lung cancer

city: New York

first: Swarnali

last: Acharyya

state: NY

address: 1130 ST NICHOLAS AVE, HERBERT IRVING COMP CANCER, Room 401A,

department: Pathology and Cell Biology

institute: Columbia University

summary: Metastatic relapse from treatment failure has been a formidable challenge to finding a cure for EGFR-mutant lung cancer. Metastasis to the brain is a severe complication for 45% of patients with EGFR-mutant lung cancer that drastically reduces their quality of life and survival. Here, we demonstrate that genetic inhibition of S100A9, ALDH1A1, RAR, or pharmacological inhibition of the RA pathway using pan-RAR inhibitors significantly reduces brain relapse from osimertinib-refractory cancer cells. Our study has therefore revealed a novel S100A9-ALDH1A1-RA signaling axis in the EGFR-mutant lung cancer cells that drives osimertinib-refractory metastatic brain relapse and identified a potential vulnerability in lung cancer cells that can be therapeutically targeted to prolong progression-free survival in EGFR-mutant lung cancer patients.

overall_design: RNA-seq of brain metatstatic derivatives of PC9 and H1650 cell lines.

first: Anup

middle: K

last: Biswas

first: Wanchao

last: Ma

first: Aidan

last: Quinn


title: RNA-Seq analysis after overexpression of AtmiR165a and LHG4 in Arabidopsis Shoot Apical Meristem

first: Hasthi

last: Ram

summary: Results from experiments done on knock-down of adaxial class III HD ZIP genes, using overexpression of miR165a, in shoot meristem show that Class III HD-ZIP genes act generally to repress the formation of new growth axes where they are expressed. This study explored the genes directly regualted by miRNAs as well as indirectly regulated by class III HD-ZIPs.

overall_design: Comparative gene expression profiling analysis of RNA-seq data Arabidopsis shoot apical meristem (SAM) of ap1cal mutant plants and ap1cal mutant plants expressing AtmiR165a under the Ubiquitin10 promoter.


title: A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas [scRNA-seq]

status: Public on Dec 19 2023

first: Rohit

last: Chandwani

address: 413 East 69th St, BRB 1360G

department: Surgery

institute: Weill Cornell Medicine

summary: Inflammation is essential to the disruption of tissue homeostasis and can destabilize the identity of lineage-committed epithelial cells. Here, we employ lineage-traced mouse models, single-cell transcriptomic and chromatin analyses, and CUT&TAG to identify an epigenetic memory of inflammatory injury in the pancreatic acinar cell compartment. Despite resolution of pancreatitis, our data show that acinar cells fail to return to their molecular baseline, with retention of elevated chromatin accessibility and H3K4me1 at metaplasia genes, such that memory represents an incomplete cell fate decision. In vivo, we find this epigenetic memory controls lineage plasticity, with diminished metaplasia in response to a second insult but increased tumorigenesis with an oncogenic Kras mutation. The lowered threshold for oncogenic transformation, in turn, can be restored by blockade of MAPK signaling. Together, we define the chromatin dynamics, molecular encoding, and recall of a prolonged epigenetic memory of inflammatory injury that impacts future responses but remains reversible.

overall_design: Single cell suspensions were prepared from pancreata and stained with DAPI. ~300k DAPI(-) cells were sorted and collected via FACS. ~300k DAPI(-) tdTomato(+) cells were sorted and collected via FACS. ~300k DAPI(-) & ~300k DAPI(-) tdTomato(+) were combined into a single tube.

first: David

last: Falvo


title: mRNA profiling of monocytes derived macrophages and PDAC cell lines supernants-induced tumor-associated macrophages (TAMs)

summary: Tumor associated macrophages have been demonstrated to promote tumor progression, but the mechanism is still unclear. We found the gene expression of monocytes derived macrophages is different from TAMs by comparing mRNA profiling.

overall_design: mRNA profile of monocytes derived macrophages treated with complete medium and those treated with 3 kinds of tumor supernant

last: Guo


title: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and NELL-1(+/6R) Mouse Hippocampus Transcriptomes

city: Los Angeles

first: Zhong

last: Zheng

address: 675 Charles E Young Dr, South

institute: UCLA

summary: The goal of this study is to profile and compare the hippocampus transcriptomes of wild type (WT) and NELL-1(+/6R) mice to gain insight on their neurological function.

overall_design: Hippocampus tissues were isolated from 3-month-old adult WT and NELL-1(+/6R) mice. Total RNA was isolated using Qiagen Rneasy Lipd Tissue Mini Kit. NGS was conducted on Illumina HiSeq3000 as single read at 1 x 50 read length.

first: Chenshuang

last: Li


title: A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas [CUT&Tag]

overall_design: Characterization of bulk histone PTMs via CUT&Tag of lineage-traced acinar and acinar-derived cells treated with caerulein (or saline as control) following 2 days or 12 weeks of recovery.


title: Iron scavenging and suppression of collagen cross-linking underlie antifibrotic effects of carnosine in the heart with obesity

city: Iowa City

first: Ethan

last: Anderson

state: Iowa

address: 180 South Grand Ave, CPB 548

department: Pharmaceutical Sciences and Experimental Therapeutics

institute: University of Iowa - College of Pharmacy

summary: Oral consumption of histidyl dipeptides such as l-carnosine has been suggested to promote cardiometabolic health, although therapeutic mechanisms remain incompletely understood. We recently reported that oral consumption of a carnosine analog suppressed markers of fibrosis in liver of obese mice, but whether antifibrotic effects of carnosine extend to the heart is not known, nor are the mechanisms by which carnosine is acting. Here, we investigated whether oral carnosine was able to mitigate the adverse cardiac remodeling associated with diet induced obesity in a mouse model of enhanced lipid peroxidation (i.e., glutathione peroxidase 4 deficient mice, GPx4+/−), a model which mimics many of the pathophysiological aspects of metabolic syndrome and T2 diabetes in humans. Wild-type (WT) and GPx4+/− male mice were randomly fed a standard (CNTL) or high fat high sucrose diet (HFHS) for 16 weeks. Seven weeks after starting the diet, a subset of the HFHS mice received carnosine (80 mM) in their drinking water for duration of the study. Carnosine treatment led to a moderate improvement in glycemic control in WT and GPx4+/− mice on HFHS diet, although insulin sensitivity was largely unchanged. Interestingly, while our transcriptomic analysis revealed that carnosine therapy had no significant impact on global gene expression in the heart, carnosine substantially upregulated cardiac GPx4 expression in both WT and GPx4+/− mice on HFHS diet. Carnosine also significantly reduced protein carbonyls and iron levels in myocardial tissue from both genotypes on HFHS diet. Importantly, we observed a robust antifibrotic effect of carnosine therapy in hearts from mice on HFHS diet, which further in vitro experiments suggest is due to carnosine’s ability to suppress collagen-cross-linking. Collectively, this study reveals antifibrotic potential of carnosine in the heart with obesity and illustrates key mechanisms by which it may be acting.

overall_design: At 8-10 weeks of age, male GPx4+/- and WT littermates  were randomly assigned to either normal chow diet (CNTL, D20122207, Research Diets, Inc) or high fat high sucrose diet (HFHS), D09071704, Research Diets, Inc) for 16 weeks. Seven weeks after starting the diet, a subgroup of the mice on HFHS diet in both genotypes was started on 80mM carnosine supplemented in their drinking water and the diet intervention was continued. Diets were matched for protein and macronutrients except that the HFHS diet is comprised of lard-based fat (35.5% daily kcal) and cholesterol (1.5% daily kcal), plus sucrose (38% daily kcal), compared with the CNTL diet with low fat (6% daily kcal), and starch-based carbohydrates (~75% daily kcal). HFHS diet and water were refreshed every 3-4 days.  mRNA sequencing of total bulk RNA myocardial tissue was performed by the University of Iowa Genomics Division, using commercial protocols provided by vendors. Briefly, 500 ng of total RNA (DNAse-1 treated) was used to prepare sequencing libraries using the Illumina TruSeq stranded mRNA library preparation kit (Cat. #RS-122-2101, Illumina, Inc., San Diego, CA).  Final concentrations of the resulting indexed libraries were determined using the Fragment Analyzer (Agilent Technologies, Santa Clara, CA) and pooled equally for sequencing. Library pool concentration was determined using the Illumina Library Quantification Kit (KAPA Biosystems, Wilmington, MA) and sequenced on a SP flowcell of the Illumina NovaSeq 6000 genome sequencer using 150 bp paired-end SBS chemistry, at a read depth of ~ 35M reads per sample

first: Jared

last: McLendon

first: Islam

last: Berdaweel


title: Oxidation-reduction process of Arabidopsis thaliana roots induced by bisphenol compounds based on RNA-seq analysis

city: Taiyuan

first: Huifeng

last: Yue

state: Shanxi

address: Nanzhonghuandong Street

institute: Shanxi University

summary:
Bisphenol compounds (BPs) have various industrial uses and can enter the environment through various sources. To evaluate the ecotoxicity of BPs and identify potential gene candidates involved in the plant toxicity, Arabidopsis thaliana was exposed to bisphenol A (BPA), BPB, BPE, BPF, and BPS at a concentration of 1, 3, 10 mg/L for a duration of 14 days, and their growth status were monitored. At day 14, roots and leaves samples were collected for internal BPs exposure concentration detection, RNA-seq, and morphological observations. As shown in the results, exposure to BPs significantly disturbed root elongation, exhibiting a trend of stimulation at low concentration and inhibition at high concentration. Additionally, BPs exhibited pronounced generation of ROS, while none of the pollutants caused significant changes in root morphology. Internal exposure concentration analysis indicate that BPs tend to accumulate in the roots, with BPS exhibiting the highest level of accumulation. The results of RNA-seq indicate that shared 211 differently expressed genes (DEGs) of these 5 exposure groups are enriched in defense response, generation of precursor metabolites, response to organic substance, response to oxygen-containing, response to hormone, oxidation-reduction process and so on. Regarding unique DEGs in each group, BPS was mainly associated with the redox pathway, BPB primarily influenced seed germination, and in BPA, BPE and BPF were primarily involved in metabolic signaling pathways. Our results provide new insights for BPs induced adverse effects on Arabidopsis thaliana and suggest that the ecological risks associated with BPA alternatives cannot be ignored.
At 14 d, roots in 3 mg/kg BPA, BPB, BPE, BPF and BPS exposure groups and the control were collected for RNA-seq analysis.

overall_design: Comparative gene expression profiling analysis of RNA-seq data from roots (control group, BPA, BPB, BPE, BPF and BPS exposure group).

first: Xiaotong

last: Ji

first: Weiwei

last: Wang

first: Jiande

first: Liangpo

last: Liu


title: A reversible epigenetic memory of inflammatory injury controls lineage plasticity and tumor initiation in the mouse pancreas [scATAC-seq]

overall_design: Single cell suspensions were prepared from inflammation-resolved (or control) pancreata and stained with DAPI. ~300k DAPI(-) cells were sorted and collected via FACS. ~300k DAPI(-) tdTomato(+) cells were sorted and collected via FACS. ~300k DAPI(-) & ~300k DAPI(-) tdTomato(+) were combined into a single tube.