title: Effects of gene-by-environment interaction in light of differential susceptibility

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

overall_design: Refer to individual Series


title: Revealing the Grammar of Small RNA Secretion Using Interpretable Machine Learning

status: Public on Jan 27 2024

city: San Francisco

first: Hani

last: Goodarzi

state: CA

department: Biochemistry and Biophysics

country: USA

institute: UCSF

type: Non-coding RNA profiling by high throughput sequencing


title: CD38-directed, single-chain T cell-engager targets leukemia stem cells through IFNγ-induced CD38 expression

city: Duarte

first: Mariam

last: Murtadha

address: 1500 E. Duarte Rd

institute: City of Hope

type: Expression profiling by high throughput sequencing


title: Transcriptome-based identification of tumor-reactive and bystander CD8+ T cell receptor clonotypes in human pancreatic cancer

status: Public on Jan 26 2024

city: Heidelberg

first: Zibo

last: Meng

address: Im Neuenheimer Feld 280

country: Germany

institute: DKFZ

summary: Pancreatic ductal adenocarcinoma (PDAC) is generally refractory to immune checkpoint blockade, although patients with genetically unstable tumors can show modest therapeutic benefit. We previously demonstrated the presence of tumor-reactive CD8+ T cells in PDAC samples. Here, we charted the tumor-infiltrating T cell repertoire in PDAC by combining single-cell transcriptomics with functional testing of T cell receptors (TCRs) for reactivity against autologous tumor cells. On the basis of a comprehensive dataset including 93 tumor-reactive and 65 bystander TCR clonotypes, we delineated a gene signature that effectively distinguishes between these T cell subsets in PDAC, as well as in other tumor indications. This revealed a high frequency of tumor-reactive TCR clonotypes in three genetically unstable samples. In contrast, the T cell repertoire in six genetically stable PDAC tumors was largely dominated by bystander T cells. Nevertheless, multiple tumor-reactive TCRs were successfully identified in each of these samples, thereby providing a perspective for personalized immunotherapy in this treatment-resistant indication.

overall_design: Single-cell RNA-sequencing of fluorescence-activated cell sorting–purified CD45+CD3+ T cell fractions isolated from enzymatically dissociated tissue samples of nine primary resected pancreatic ductal adenocarcinoma tumor

first: Aaron

middle: R

last: Ehrenfried

first: Chin

middle: L

last: Tan

first: Laura

middle: K

last: Steffens

first: Hannes

last: Kehm

first: Stefan

last: Zens

first: Claudia

last: Lauenstein

first: Oliver

last: Strobel

first: Michael

last: Volkmar

first: Isabel

last: Poschke

first: Rienk

last: Offringa


title: Deep transcriptomics analysis reveals the development of postoperative ileus and the therapeutic effect of electroacupuncture

city: Beijing

first: shuang

middle: qing

last: wei

address: No. 11, Bei San Huan Dong Lu, Chaoyang District

country: China

institute: beijing university of chinese medcine

summary: Postoperative ileus (POI) often occurs and prolongs hospital stay, which costs expensive. Electroacupuncture (EA), as an appropriate non-pharmacotherapy supported by emerging clinical trials, the mechanism needs to be clarified. In this study, the intestinal manipulation (IM) method was used to establish the POI model, and EA was used to treat it. Sham surgery (SS), simple electrical stimulation (ES), and sham electroacupuncture (SEA) were introduced as control. Gastrointestinal transit and colonic transport were employed to evaluate interventions’ effects. RNA sequencing was then carried out using the intestine tissue of mice.

overall_design: Intestine mRNA profiles of C57BL/6 mice.

first: Qingshuang

last: Wei

first: Fan

last: Jiang

first: Jiangli

last: Wu

first: Zhigang

last: Li


title: CXCR4 overexpression in chronic lymphocytic leukemia associates with poorer prognosis: a prospective, single-center, observational study

city: Chengdu

first: xinran

last: xue

address: No. 37, Guoxue Xiang, Wuhou District, Chengdu

department: Department of Laboratory Medicine

institute: West China Hospital, Sichuan University

summary: Controversial data have been reported on the prognostic value of C-X-C motif chemokine receptor 4 (CXCR4) in chronic lymphocytic leukemia (CLL). This prospective, single-center, observational study aimed to evaluate the role of CXCR4 in the pathophysiology of CLL and its prognostic role. A total of 158 patients of CLL were enrolled, and CXCR4 expression on CLL cells was detected by flow cytometry (FCM) at initial diagnosis. The patients were divided into 2 groups according to the CXCR4 mean fluorescence intensity (MFI) median. Also, four patient specimens from the CXCR4low and CXCR4high groups were selected for whole transcriptome sequencing. The progression-free survival (PFS) of CLL patients in the CXCR4high group was significantly shorter than the CXCR4low group, with a median follow-up time of 27 months (log-rank P < 0.001). Moreover, CXCR4 overexpression (MFI > 3376) was an independent marker of poor PFS in CLL patients (P < 0.001). Analysis of whole transcriptome sequencing results revealed that CXCR4 plays an important role in the migration of CLL. Collectively, CXCR4 expression levels on leukemia cells can be detected rapidly by FCM. CXCR4 overexpression was significantly associated with poorer prognosis in CLL patients within a shorter follow-up time.

overall_design:
To better explore the potential pathogenic mechanism of CXCR4 in CLL, four specimens with the CXCR4low and CXCR4high groups respectively were selected for whole transcriptome sequencing.
Comparative gene expression profiling of RNA-seq data from CXCR4low group CLL cells and CXCR4high group CLL cells.

first: Xinran

last: Xue

first: Zhihao

last: Wen

first: Xin

last: Zhang

first: Ying

last: Yang

first: Yifei

first: Ruoxi

last: Liao

first: Qin

last: Zheng

first: Yang

last: Fu

first: Yu

last: Liu

first: Hongyan


title: gene expression profile of entire adult mouse invtervertebral disc

city: Stanford

first: Malachia

last: Hoover

address: 265 Campus Drive Room G3105

institute: Stanford University

summary: The intervertebral disc is a specialized fibrocartilage structure of the spinal column that is pivotal for spinal mobility and function. It is composed of 3 distinct anatomical components: the annulus fibrosus, nulceus pulposus and cartilage endplates. We used 10x single cell seq to identify the various cell components of the disc as well as discover novel cell populations and signaling networks.

overall_design: A lumbar disc was disscted from a young adult mouse (8 weeks old) and digested via collagenase. Cells were then counted (10k) and dead cells removed via Trypan blue staining and counting.


title: Transcriptomic profiling of HeLa cells treated with miR-744-5p and control-miR

city: Cologne

first: Konrad

middle: U.

last: Förstner

state: North Rhine-Westphalia

address: Gleueler Str. 60

department: Information Services

institute: ZB MED - Information Centre for Life Sciences

summary: To have a global picture of the targets of the mir-744-5p, we assessed transcriptome changes, by deep-sequencing, of HeLa cells transfected with this miRNA or a control miRNA (cel-miR-231).

overall_design: transcriptmic profiles of HeLa cells treated miR-744 and control-miR  were generated by deep sequencing, using Illumina HiSeq2000.

first: Ana

last: Eulalio

first: Claire

last: Maudet


title: Transcriptomical study on multipul pat mutants

city: Copenhagen

first: Morten

last: Petersen

address: Ole Maaløes Vej 5

country: Denmark

institute: University of Copenhagen

summary: The Arabidopsis genome encodes 3 PAT mRNA decapping factors: PAT1(AT1g79090), PATH1 (AT3g22270) and PATH2 (AT4g14990). We generated single, double and triple knockouts (KOs) of the three PATs by CRISPR/CAS9-mediated genome editing in the summ2-8 background to avoid immune activation. The 6 weeks-old soil-grown pat triple mutants exhibited markedly stunted growth compared to the other pat single or double mutants indicating functional redundancy of PATs in regulating plant development. To identify genes which affect different developmental programs regulated by PATs, we performed RNA-seq from plants of pat1-1path1-4path2-1summ2-8 and all single and double mutant combinations.

first: Zhangli

last: Zuo


title: Wnt/β-catenin-YAP axis may be involved in primary intraosseous carcinoma, NOS, arising from odontogenic keratocyst

city: Fukuoka

first: Kana

last: Hasegawa

state: Fukuoka

address: 3-1-1 Maidashi, Higashi-ku

country: Japan

institute: Kyushu University

summary: Odontogenic tumors (OGTs), which originate from cells of odontogenic apparatus and their remnants, are rare entities. Primary intraosseous carcinoma, NOS (PIOC), is one of the OGTs, but it is even rarer and has a worse prognosis. The characteristics of PIOC, especially in immunohistochemical features and its pathogenesis, remain unclear. We characterized a case of PIOC arising from the left mandible, in which histopathological findings showed a transition between the odontogenic keratocyst and the carcinoma. The tumorous lesion of this PIOC exhibited malignant potentials with an invasive growth of carcinoma cells into the bone tissue, an elevated Ki-67 index, and lower signal for CK13 and higher signal for CK17 compared with the non-tumor region, histopathologically and immunohistopathologically. Further immunohistochemical analyses demonstrated increased expression of ADP-ribosylation factor (ARF)-like 4c (ARL4C) (accompanying expression of β-catenin in the nucleus) and yes-associated protein (YAP) in the tumorous lesion. On the other hand, YAP was expressed and the expression of ARL4C was hardly detected in the non-tumor region. In addition, quantitative RT-PCR analysis using RNAs and dot blot analysis using genomic DNA showed the activation of Wnt/β-catenin signaling and epigenetic alterations, such as an increase of 5mC levels and a decrease of 5hmC levels, in the tumorous lesion. A DNA microarray and gene ontology analysis demonstrated that numerous gene expression variations and signal activation, including Notch signaling, were altered in non-tumor and tumor lesions within this PIOC. Experiments with the GSK-3 inhibitor revealed that β-catenin pathway increased not only mRNA levels of ankyrin repeat domain1 (ANKRD1) but also protein levels of YAP and TAZ in oral squamous cell carcinoma cell lines. These results suggested that further activation of YAP signaling by Wnt/β-catenin signaling may be associated with the development of PIOC arising from odontogenic keratocyst in which YAP signaling is activated.

overall_design: DNA microarray analysis was performed using RNAs extracted from the tumorous lesion and the non-tumor region of primary intraosseous carcinoma, NOS.

first: Yusuke

last: Nakako

first: Shinsuke

last: Fujii

first: Yukiko

last: Kami

first: Masafumi

last: Moriyama

first: Kari

middle: J

last: Kurppa

first: Kristiina

last: Heikinheimo

first: Kazunori

last: Yoshiura

first: Shintaro

last: Kawano

first: Tamotsu

last: Kiyoshima


title: WRN loss accelerates abnormal adipocyte metabolism in Werner Syndrome

city: Hong Kong

first: Wai- Yee

last: Chan

state: Hong Kong

address: Shatin

department: School of Biomedical Sciences

country: Hong Kong

institute: The Chinese University of Hong Kong

summary: Metabolic dysfunction is one of the main symptoms of Werner syndrome (WS); however, the underlying mechanisms remain unclear. Here, we report that loss of WRN accelerates adipogenesis at an early stage both in vitro (stem cells) and in vivo (zebrafish). Moreover, WRN depletion causes a transient upregulation of late-stage of adipocyte-specific genes at an early stage.

overall_design: RNA-sequencing (RNA-seq) for WRN in human mesenchymal stem cells (hMSCs).

first: Yuyao

last: Tian

first: Wai-Yee


title: TheArf‐GAPProteins AoAge1 and AoAge2 are Required for Mycelial Growth, Conidiation, Stress Responses, Trap Formation, and the Secondary Metabolism inthe Nematode-Trapping Fungus Arthrobotrys oligospora

city: kunming

first: le

last: 杨

state: 校内

address: cuihubeilu

institute: yunnan university

summary: ADP-ribosylation factors (Arfs) belong to the small GTPases superfamily and regulate mycelial development, endocytosis, and virulence in fungi. Nematode-trapping (NT) fungi can form unique infection structures (traps) to capture and kill free-living nematodes, thus play a potential role in the biocontrol of nematodes. Arthrobotrys oligospora is a representative species of the NT fungi. Here, the functions of two Arf-GAPs, Age1 (AoAge1) and Age2 (AoAge2) orthologue to S. cerevisiae were identified in A. oligospora by gene knockout and multi-phenotypic analysis. It was found that AoAge1 and AoAge2, especially AoAge2, play an important role in vegetative growth, conidiation, trap formation, DNA damage, endoplasmic reticulum stress, mitochondrial activity, endocytosis, heat shock stress, ROS level, and autophagy of A. oligospora. Importantly, our transcriptomic analysis (12 h) showed that nearly 62.7% of A. oligospora genes (11479) were directly or indirectly regulated by AoAge2, indicating that Arf-GAP plays a global role in the growth and development of A. oli gospora.  Revealed by transcriptomic analysis differentially upregulated genes in the absence of Aoage2 were involved in autophagy and carbohydrate, amino acid and sphingolipid metabolism while downregulated genes were involved in longevity regulating pathway and carbohydrate, amino acid and secondary metabolites biosynthesis. In addition, metabolomic analysis showed that many compounds were markedly reduction in ΔAoage2 mutants strain. Our results highlighted that AoAge1 and AoAge2 play a crucial role in the asexual growth, development, differentiation, and lifestyle transition, especially, AoAge2 is indispensable for conidiation and trap morphogenesis of A. oligospora. These results demonstrated crucial roles for AoAge1 and AoAge2 in the fungal growth, environmental adaption and pathogenicity, which provided insights into the function of Arf-GAPs in A. oligospora and other fungi.

overall_design: Mycelial samples of the WT and ΔAoage2 mutant strains were collected after trap formation induced by nematodes at different time points (0, 6, 12, and 24 h), and cDNA libraries of each sample were constructed and sequenced.

first: Le

last: Yang

first: Xuemei

last: Li

first: Yuxin

last: Ma

first: Meichen

last: Zhu

first: Keqing

last: Zhang

first: Jinkui


title: Upregulation of developmentally-downregulated miR-1247-5p promotes neuroprotection and axon regeneration in vivo

city: Farmington

first: Ephraim

middle: F

last: Trakhtenberg

state: CT

address: 263 Farmington Ave. RM L4005

department: Neuroscience

institute: University of Connecticut School of Medicine


title: In vivo multiplexed screen reveals a critical role of Keap1/Nrf2 pathway in small cell lung cancer [TUBAseq]

city: Houston

first: Pawel

middle: Karol

last: Mazur

state: TX

address: 1515 Holcombe Blvd.

institute: University of Texas MD Anderson Cancer Center

summary: Approximately 15% of all lung cancer cases are small cell lung cancer (SCLC), which originates from neuroendocrine cells lining the airways (bronchi) of the lung. SCLC is known for its aggressive nature and swift growth, resulting in a five-year survival rate of around 6%. Understanding the genetic pathways that drive tumor development remains an ongoing challenge. In our study, we employed an in vivo multiplexed approach, known as Tuba-seq, to investigate the impact of the functional loss of 18 putative tumor suppressors. Our screening unveiled Pten and Keap1 as top candidates; knocking out either one promoted both tumor initiation and progression. We identified the Keap1/Cul3/Nrf2 pathway as a pivotal regulator for SCLC development, particularly in regulating the susceptibility of SCLC to ferroptosis. Our work not only established an in vivo multiplexed approach for assessing the role of tumor suppressors in SCLC but also uncovers a previously unappreciated role of Keap1 in SCLC.

overall_design: In this study a multiplex approach was used to examine the consequences of loss of putative 18 tumor suppressors (TS) in vivo. The 18 TSs were selected based on their mutation prevalence in human SCLC patients, in addition to the genes of personal interest. To stimulate SCLC development  Rb1;p53;p130;p107 quadruple knockout mice (hereafter referred to as QKO) was used. To study the roles of putative tumor suppressors, the QKO mice was bred with H11loxP-STOP-loxP-Cas9 mice (QKO;Cas9). The sgRNA for each putative tumor suppressor gene was cloned into the Lenti-U6-sgRNA/PGK-Cre vector. To facilitate the multiplexed study, the Tuba-seq approach was utilized. A unique barcode was assigned to each Lenti-sgRNA/Cre vector: an sgRNA ID (a specific eight-nucleotide sequence) and a tumor ID (a string of hemi-random nucleotides). All the barcoded vectors (including 18 putative tumor suppressors and one non-targeting control) were pooled at an equal ratio, encapsulated them into a lentivirus pool using a PEG8000-mediated precipitation method. The lentivirus titer was determined by FACS with 3T3 cells expressing Cre-reporter. Next, small cell lung cancer formation was induced. The barcoded lentivirus pool was injected into the QKO;Cas9 mice, with each mice receiving 9.7×10^5 ifu (infectious units) of virus. The entire lung was harvested from each mouse at the survival end point (median survival time ~13 weeks).


title: In vivo multiplexed screen reveals a critical role of Keap1/Nrf2 pathway in small cell lung cancer


title: A multidimensional atlas of human glioblastoma-like organoids reveals highly coordinated molecular networks and effective drugs [RNA-seq]

first: Haikun

last: Liu

address: INF 581

summary: We use bulk-RNA sequencing to gain deeper insights into the impact of genetic modifications on phenotypic changes in two-month-old organoids derived from two iPSC lines

overall_design: Bulk-RNA sequencing data for 2-month-old WT (wildtype), PT (PTEN-/-; TP53-/-), PTCC (PTEN-/-; TP53-/-; CDKN2A-/-; CDKN2B-/-), and PTN (PTEN-/-; TP53-/-; NF1-/-) organoids samples

first: Changwen

last: Wang


title: Laser Capture Microdissection-based RNAseq for Profiling Mouse and Human Sebaceous Gland Transcriptomes

city: Philadelphia

first: Jordan

last: Harris

state: PA

address: 3620 Hamilton Walk

institute: University of Pennsylvania

summary:
We describe the use of laser capture microdissection (LCM) to isolate human and murine sebaceous glands (SGs) for transcriptomic analysis and publish this SG transcriptomic data for reference.
We show that compared to whole skin RNA sequencing, LCM RNA sequencing allows for high resolution in identifying and describing SG genes at homeostasis.
Lastly, we compare this LCM of sebaceous glands to published SG clusters from single cell RNA sequencing of skin, and show that we achieve greater resolution and depth with the LCM approach.

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Gene expression profiling analysis of laser capture microdissection derived bulk RNA-seq data from mouse and human sebaceous glands.

middle: C

first: Stephen

middle: M

last: Prouty

first: Molly

middle: A

last: Nelson

first: Derek

last: Sung

first: Amanda

first: John

middle: T

last: Seykora

first: Taku

last: Kambayshi

first: Elizabeth

last: Grice


title: Genetically defined human GBM organoids reveal principles of GBM development and actionable targets

summary: We used single cell RNA sequencing (scRNA-seq) to analysis the cellular state of organoids harboring different genetic mutations

overall_design: scRNA-sequencing data for 1- and 4-month-old WT (wildtype), PT (PTEN-/-; TP53-/-), PTCC (PTEN-/-; TP53-/-; CDKN2A-/-;  CDKN2B-/-), and PTN (PTEN-/-; TP53-/-; NF1-/-) organoids samples

first: Chunxuan

last: Shao


title: In vivo multiplexed screen reveals a critical role of Keap1/Nrf2 pathway in small cell lung cancer [RNAseq]

overall_design: Tuba-seq approach was utilized to profile effects of inactivating 18 putative tumor suppressors in SCLC. Keap1 was identified as a robust tumor suppressor in this study, with its inactivation promoting tumor iniation and progression in SCLC. To investigate how Keap1 regulates SCLC development transcriptomes were profiled in control and Keap1 depleted QKO tumors (about 4 months after virus injection) by mRNA-seq (paired-end, 3 control samples and 3 Keap1 knockout samples).


title: A multidimensional atlas of human glioblastoma-like organoids reveals highly coordinated molecular networks and effective drugs

summary: Genome-wide DNA Methylation array on iPSCs and organoids with different genetic mutations.

overall_design: DNA methylation array on organoids with Illumina Infinium MethylationEPIC array. Samples include 1-, 2- and 3-month-old organoids from WT (wildtype), PT (PTEN-/-; TP53-/-), PTCC (PTEN-/-; TP53-/-; CDKN2A-/-;  CDKN2B-/-), and PTN (PTEN-/-; TP53-/-; NF1-/-) samples. Four replicates for 3-month-old PT, PTCC and PTN organoids, and three replicates for the rest of the groups. DNA methylation array on organoids with Illumina Infinium HumanMethylation450 array. Samples include human iPSC cell line and 2-month-old organoids from WT (wildtype), PT (PTEN-/-; TP53-/-), PTCC (PTEN-/-; TP53-/-; CDKN2A-/-;  CDKN2B-/-), and PTN (PTEN-/-; TP53-/-; NF1-/-) samples (Three replicates in each group).


title: Epigenetic Small Molecule Library Screen for Inhibition and Reversal of Acinar to Ductal Metaplasia in a Mouse Pancreas 3-Dimensional Organoid Model

city: Gainesville

first: Alberto

last: Riva

state: FL

address: 2033 Mowry Rd

department: ICBR

institute: University of Florida

summary: We used in vitro mouse pancreatic 3-D organoid model to screen for possible compounds that inhibit or reverse Acinar-to-Ductal Metaplasia, which is a known intial stage of pancreatic ductal adenocarcinoma (PDAC). This model has higher translational value due to the harbored KRASG12D mutation which is common in  PDAC patients and is considered a driving mutatrion for cancer development. Observed transcriptomic differences with select hit compounds compared to vehicle control could be very useful for future targeted therapy approach, as well as for further understanding of the driving mechanisms involved in pancreatic metaplasia and PDAC. Some of the hit compounds are already FDA approved drugs that could be easily re-purposed for PDAC treatment or prevention.

overall_design: Mouse 3D organoids harboring an KRASG12D mutation were grown in vitro and left to undergo acinar-to-ductal metaplasia for two days. Then organoids were treated with Largazole (10 µM and 1 µM), its stable homodimer (10 µM and 1 µM), FK228 (1 µM) or Chaetocin (1 µM) at two concentrations.

first: Kalina

last: Atanasova

first: Ranjala

last: Ratnayake

first: Thomas

last: Schmittgen

first: Hendrik

last: Luesch


title: high-throughput sequencing of circRNAs in T-BEAS-2B cells and C-BEAS-2B cells

city: Wuhan

first: Xue

last: Zhou

state: Hubei

address: 13 Hangkong Road

department: Department of Occupational and Environmental Health, School of Public Health, Tongji Medical College

institute: Huazhong University of Science and Technology

summary: We report the differential expression of circRNAs between T-BEAS-2B cells (cadmium-transformed BEAS-2B cells) and C-BEAS-2B cells (passage-matched control BEAS-2B cells) by high-throughput sequencing. T-BEAS-2B cells are BEAS-2B cells transformed by cadmium at 2.0 μM for twenty weeks, and C-BEAS-2B cells are their passage-matched control. RNAs were sequenced on Illumina HiSeq Xten platform in triplicates, and expressions of circRNAs were calculated by TPM (transcripts per kilobase of exon model per million mapped reads). Clean data per sample exceeds 10 GB. We find 235 significantly up-regulated circRNAs and 271 significantly down-regulated circRNAs in T-BEAS-2B cells relative to C-BEAS-2B cells. Our work provides clues and evidence for exploring the mechanism of circRNAs in cadmium carcinogenesis.

overall_design: circRNA profiles in T-BEAS-2B cells and C-BEAS-2B cells

first: Qin


title: A first truly systems level mechanistic model  unravelling the gene regulation of Th2 differentiation [IRF4]

city: Linköping

first: Danuta

last: Gawel

address: Garnisonsvägen

country: Sweden

institute: Linköping University

summary: Recent and ongoing revolutions in measurement technologies imply completely new possibilities for genome research: today, time-resolved, quantitative, and systems-level data are available. Nevertheless, without a corresponding revolution in methods for data analysis, these new data tend to drown researchers and doctors, rather than provide clear and useful insights. Such new methods are developed within the field of systems biology. Systems biology has two main approaches: mechanistically detailed and well-determined simulation models for small subsystems, and more approximative statistical models for the entire genome. However, there are few, if any, methods that combine the strengths of these two approaches. Herein, we present LASSIM, a new simulation-based approach, which can be applied to systems of the size of the entire genome. The superior performance of LASSIM is demonstrated in three examples: i) an example with simulated data shows that unlike traditional large-scale methods, LASSIM correctly identifies the true behavior between measured data-points, ii) LASSIM outperforms the winner of a previous DREAM challenge, the most competitive benchmarking approach available, iii) based on new data from TH2 differentiation, LASSIM identifies a first mechanistic model for the entire genome. The key predictions of this model are typically enriched for DNA bindings, which suggests that most predicted interactions are direct. Moreover, in silico knockdowns were experimentally validated. In summary, LASSIM opens the door to a new type of model-based data analysis: to models that combine the strengths of reliable mechanistic models with truly systems-level data.

overall_design: Human naive CD4+ T cells were isolated from fresh buffy coats with Miltenyis Naïve CD4+ T Cell Isolation Kit II according to the manufacturers instructions. 1x106 cells were either transfected in a cuvette with 600nM human on target plus SMART pool against IRF4 (Dharmacon, USA), non-targeting siRNA (Dharmacon) or with transfection buffer using the Amaxa transfection program U-014. Six hours after the nucleofection cells were washed, activated and polarized towards Th2 for 12 hours. The cells were activated with platebound anti-CD3 (500 ng/ml), 500 ng/ml soluble anti-CD28, 5 ug/ml anti-IL-12, 10 ng/ml IL-4 and 17 ng/ml IL-2 (R&D Systems). For microarray experiments the cells were harvested at 12 hours of polarization and lysed in 600 ll Qiazol. For the gene expression microarray analysis 200 ng total RNA was Cy3-labeled using the Agilent Quick Amp Labeling Kit, one color. The labeled cRNA was purified with the RNeasy Mini Kit from Qiagen. After checking the labeling efficiency using the NanoDrop ND-1000 UVVIS Spectrophotometer, 1.65 ug Cy3 labeled RNA from each sample was hybridized to Agilent Sure-Print G3 Human GE 4 x 44 K slides (Agilent Gene Expression Hybridization Kit). The microarray slides were incubated for 17 h at 65 C in a rotating hybridization oven. After washing according to the manufacturers protocol the slides were analyzed using the Agilent Microarray scanner (2505C) with default settings for all parameters. Microarray expression data were obtained by use of Agilent feature extraction software (version 10.7.3.1).

first: Mattias

last: Köpsén

first: William

last: Lövfors

first: Sören

last: Bruhn

first: Gunnar

last: Cedersund

first: Mikael

last: Benson

first: Mika

last: Gustafsson


title: mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors [KR158 RNA-TCR]

status: Public on Jan 25 2024

first: Duane

last: Mitchell

state: Florida

address: 1333 Center Drive, BSB B1-150

summary: mRNA-based immunotherapeutics have garnered widespread interest for their potential to revolutionize cancer treatment. In this study, we have established a personalized and customizable mRNA-therapeutic approach that effectively targets a plurality of tumor antigens and demonstrated potent anti-tumor response in preclinical brain tumor models. Our platform uniquely addresses the challenge of tumor heterogeneity and low antigen burden, two key deficiencies in targeting classically immunotherapy-resistant CNS malignancies.

overall_design: We created GBM tumor antigen-specific RNA and loaded it into dendritic cells for anti-tumor vaccine. We performed in vivo anti-tumor efficacy study with antigen loaded dendritic cells in combination with adoptive T cell therapy with relevant controls in the KR158 murine GBM model. Post therapy, we isolated the CD45+ve immune cells from the brain tumor microenvironment and performed TCR seq analysis from the RNA.

first: Vrunda

last: Trivedi

first: Changlin

last: Yang

last: Micthell


title: mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors

overall_design: We created GBM tumor antigen-specific RNA and loaded it into dendritic cells for anti-tumor vaccine. We performed in vivo anti-tumor efficacy study with antigen loaded dendritic cells in combination with adoptive T cell therapy with relevant controls in the KR158 murine GBM model. Post therapy, we isolated the CD45+ve immune cells and CD45 -ve tumor cells from the brain tumor microenvironment and performed scRNA-seq analysis. The samples from each treatment arm were multiplexed together to minimize batch effect. Each treatment arm had 4 replicates for CD45 +ve immune cell subset divided across 3 multiplexed pools and 1 combined replicate for CD45 -ve tumor cells multiplexed into 1 pool.


title: mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors [KR158 RNA-Seq]

overall_design: We created GBM tumor antigen-specific RNA and loaded it into dendritic cells for anti-tumor vaccine. We performed in vivo anti-tumor efficacy study with antigen loaded dendritic cells in combination with anti-PD1 immune checkpoint blockade therapy with relevant controls in the KR158 murine GBM model. Post therapy, we isolated the CD45+ve immune cells from the brain tumor microenvironment and performed bulk RNA-seq analysis.


title: mRNA-based precision targeting of neoantigens and tumor-associated antigens in malignant brain tumors [GL261 RNA-Seq]

overall_design: We created GBM tumor antigen-specific RNA and loaded it into dendritic cells for anti-tumor vaccine. We performed in vivo anti-tumor efficacy study with antigen loaded dendritic cells in combination with anti-PD1 immune checkpoint blockade therapy with relevant controls in the GL261 murine GBM model. Post therapy, we isolated the CD45+ve immune cells from the brain tumor microenvironment and performed bulk RNA-seq analysis.


title: RNA-seq gene expression profiling comparing WT and DccrM Ptac-ccrM Agrobacterium tumefaciens C58 cells cultivated in ATGN+/-IPTG.

city: Lausanne

first: Karolina

last: Bojkowska

address: Unil, Genopode

country: Switzerland

institute: University of Lausanne

summary: The cell cycle-regulated DNA methyltransferase CcrM is conserved in most Alphaproteobacteria, but its role in bacteria with complex or multicentric genomes remains unexplored. Here, we compare the methylome, the transcriptome and the phenotypes of wild-type and CcrM-depleted Agrobacterium tumefaciens cells with a dicentric genome with two essential replication origins. We find that DNA methylation has a pleiotropic impact on motility, biofilm formation and viability. Remarkably, CcrM promotes the expression of the repABCCh2 operon, encoding proteins required for replication initiation/partitioning at ori2, and inhibits gcrA, encoding a conserved global cell cycle regulator. Imaging ori1 and ori2 in live cells, we show that replication from ori2 is often delayed in cells with a hypo-methylated genome, while ori2 over-initiates in cells with a hyper-methylated genome. We thus propose that methylation by CcrM stimulates RepABC-dependent chromosomal origins, uncovering a novel and original connection between CcrM-dependent DNA methylation and genome maintenance in an Alphaproteobacterial pathogen.

overall_design:
To investigate the impact of DNA methylation by CcrM on the transcriptome of an A. tumefaciens C58 derivative strain with a dicentric chromosome, we engineered a conditional ccrM mutant. A second copy of ccrM (Atu0794) under the control of the IPTG-inducible Ptac promoter was introduced into the dicentric chromosome of A. tumefaciens and then the native ccrM gene was deleted following a standard double recombination procedure, generating strain JC2307 (DccrM Ptac-ccrM) on ATGN minimal medium containing IPTG.
We then performed gene expression profiling analyses using RNA-seq data comparing viable A. tumefaciens JC2307 cells incubated for 7 hours in ATGN without IPTG with that of control mutant cells cultivated in ATGN with IPTG and WT cells cultivated in ATGN without IPTG.
Comparative gene expession profiling analysis of RNA-seq data for three types of cell cultures in exponential phase: DccrM Ptac-ccrM + IPTG, WT and DccrM Ptac-ccrM -IPTG.

first: Sandra

last: MARTIN

first: Florian

last: FOURNES

first: Giovanna

last: AMBROSINI

first: Christian

last: ISELI

last: BOJKOWSKA

first: Julien

last: MARQUIS

first: Nicolas

last: GUEX

first: Justine

last: COLLIER


title: Differentially expressed messenger RNAs and long noncoding RNAs after spinal cord injury

city: Tianjin

first: Shiqing

last: Feng

address: 154 Anshan Road, Heping District, Tianjin, China, 300052

institute: Tianjin Medical University General Hospital

summary: Spinal cord injury (SCI) is a severely disastrous event that occurs in the central nervous system (CNS) that is associated with high disability and mortality rates.To further explore the  expression of mRNAs and lncRNAs and the potential roles of differentially expressed  mRNAs and lncRNAs after SCI, we examined the expression of mRNAs and lncRNAs in a rat model at 2 hours, 2 days and 7 days after SCI and identified the differentially expressed lncRNAs (DE lncRNAs) and differentially expressed mRNAs (DE mRNAs) using microarray analysis. A total of 992 mRNAs were differentially expressed at 2 hours after SCI, among which 730 mRNAs were up-regulated and 262 mRNAs were down-regulated. A total of 4308 mRNAs were differentially expressed at 2 days after SCI, including 2229 mRNA with up-regulated expression and 2079 mRNAs with down-regulated expression. A total of 4113 mRNAs were differentially expressed at 7 days after SCI, including 2339 up-regulated  and 1774  down-regulated mRNAs. After SCI, 772 lncRNAs were differentially expressed in the 2-hour group (528 were up-regulated, 244 were downregulated) , 3193 lncRNAs were differentially expressed in the 2-day group (1332 were up-regulated, 1861 were downregulated) ,3093 lncRNAs were differentially expressed in the 7-day group (1290 were up-regulated, 1803 were downregulated) .The current study on provides novel insights into how lncRNAs and mRNAs regulate the pathogenesis of the immediate phase after SCI.

overall_design: The spinal cord contusion model of rats was first built, and the mRNA and lncRNA expressions at 2 hours, 2 days and 7 days after SCI were detected by microarray. 36 rats were randomly divided into four groups (2-hour, 2-day, 7-day and control), each group contains 9 animals.  A total of 12 samples were detected and each sample contained 3 rats spinal cord.

first: Hengxing

last: Zhou


title: Pervasive environmental chemicals impair oligodendrocyte development

city: Cleveland

first: Erin

last: Cohn

state: OH

address: 2109 Adelbert Rd

institute: Case Western Reserve University School of Medicine

summary: Exposure to environmental chemicals can impair neurodevelopment, and oligodendrocytes may be particularly vulnerable as their development extends from gestation into adulthood. However, few environmental chemicals have been assessed for potential risks to oligodendrocytes. Here, using a high-throughput developmental screen in cultured cells, we identified environmental chemicals in two classes that disrupt oligodendrocyte development through distinct mechanisms. Quaternary compounds, ubiquitous in disinfecting agents and personal care products, were potently and selectively cytotoxic to developing oligodendrocytes, whereas organophosphate flame retardants, commonly found in household items such as furniture and electronics, prematurely arrested oligodendrocyte maturation. Chemicals from each class impaired oligodendrocyte development postnatally in mice and in a human 3D organoid model of prenatal cortical development. Analysis of epidemiological data showed that adverse neurodevelopmental outcomes were associated with childhood exposure to the top organophosphate flame retardant identified by our screen. This work identifies toxicological vulnerabilities for oligodendrocyte development and highlights the need for deeper scrutiny of these compounds’ impacts on human health.

overall_design: OPCs were plated in 6-well plates coated with poly-L-ornithine (Sigma, P3655) and laminin (Sigma, L2020) in differentiation permissive media and allowed to attach for one hour. OPCs were incubated with vehicle (DMSO), cetylpyridinium chloride (Tox1), C12-C14-Alkyl(ethylbenzyl)dimethylammonium chloride (Tox2), or methyltrioctylammonium chloride (Tox3), at their respective IC75 for 4 hours. OPCs were then lysed in TRIzol (Invitrogen, 15596018) and RNA was extracted by phenol-chloroform extraction and purified using the Rneasy Mini Kit (Qiagen, 74104). Samples were sent to Novogene for library preparation and mRNA sequencing. Libraries were generated according to protocols from the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB, E7490L) and NEBNext Ultra RNA Library Prep Kit for Illumina (NEB, E7530L) and then evenly pooled and sequenced on the Illumina NovaSeq with 150bp paired-end reads and a read depth of at least 20 million reads per sample.

first: Paul

last: Tesar


title: Circulating microRNA analysis in a prospective co-clinical trial identifies biomarker of response and mechanisms of resistance to regorafenib in colorectal cancer

city: Bellinzona

first: Luciano

last: Cascione

state: Ticino

address: Via Chiesa 5

department: Lymphoma & Genomics Research Program

institute: IOR

summary: MicroRNA profiling was performed on baseline bloods using the NanoString nCounter platform in a serial liquid biopsies obtained at baseline in chemo-refractory mCRC patients treated with regorafenib in a phase II clinical trial (PROSPECT-R n=40; NCT03010722).

overall_design: Examination of global miRNA expression profile in liquid biopsy of 40 chemo-refractory mCRC patients treated with regorafenib in a phase II clinical trial (PROSPECT-R n=40; NCT03010722)

first: Nicola

last: Valeri


title: ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [RNA-Seq]

city: Yokohama

first: Tomohiko

last: Akiyama

state: Kanagawa

address: 3-9 Fuku-ura

department: School of medicine

institute: Yokohama city university

summary: The Zinc finger and SCAN domain containing 4 (Zscan4) protein, expressed transiently in pluripotent stem cells as well as in gamete and embryonic development, regulates genome stability in addition to telomere elongation and karyotype correction in mouse ES cells. However, the mechanism underlying Zscan4’s ability to counter the toxic effects of DNA/chromatin remodeling is not fully understood. In this study, we used ChIP-seq technology with Zscan4 antibodies to identify genome-wide binding sites in mouse and human ES cells. We discovered that both mouse and human Zscan4 bind to specific simple sequence repeats, (TG/CA)n, that have a propensity to induce genomic instability through a left-handed helix and stem-loop structure. Furthermore, we found that Zscan4 removes active histone marks from (TG/CA)n regions to maintain the closed/inactive chromatin state. These results demonstrate that Zscan4 protects unstable genomic regions by directing chromatin condensation.

overall_design: RNA-sequencing analysis for DUX4 treated ZSCAN4 (+/-) and ZSCAN4 (-/-) human ES cells. We used hES cells, in which Emerald GFP replaces one allele of hZSCAN4, and the other allele is either intact (+/-) or disrupted by CRISPR-Cas9 (-/-). Those cells were transfected with synthetic mRNA of DUX4.

first: Minoru

last: Ko


title: ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes

type: Genome binding/occupancy profiling by high throughput sequencing

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

overall_design: Refer to individual Series


title: Effects of gene-by-environment interaction on the H3K4me3 profile in the light of differential susceptibility

first: Konrad

last: Förstner

address: Gleueler Str. 60

summary:
Purpose: Investigation of effects of early adversity in mice deficient for serotonin transporter on H3K4me3 enrichment in the context of differential susceptibility
Methods: Following prenatal stress and behavioural screening in adulthood, 3 month old females, either wildtype or carrying a heterozygous knockout of the serotonin transporter gene, were sacrificed, brains extracted, the hippocampi of both hemispheres dissected, blended and separated in two protions. For one of these portions  the material was split again in two portions, of which one was fixed using 1% PFA, and was subsequently processed using a standard Chromatin immuno precipitation protocol. Following ChIP, the samples were processed by Nxt-Dx Belgium. Library preparation was performed using the NEBNext Ultra II DNA Library prep kit for Illumina (NEB, Ipswitch, Massatchusettes, USA). Subsequently, the whole IP material was subjected to ends prep and ligation of Illumina adaptors. A clean up of the adaptor-ligated DNA with AMPure XP beads (Beckman Coulter) was performed without size selection. The eluted material was subjected to enrichment PCR (14 cycles) with the NEBNext Index primers, and a last clean up with AMPure XP beads followed. The quality of the final libraries was checked on a Bioanalyzer 2100 DNA 1000 chip (Agilent, Santa Clara, CA, USA). The concentration was determined by performing qPCR on the samples using a dilution of PhiX index3 as standard. The concentration of all indexed samples was adjusted to 10 nM and samples were pooled for sequencing. Sequencing was performed on an Illumina HiSeq4000 (read-length of 50 bp with 25-30 million reads/sample, paired-end).
Results: dependent on the serotonin transporter genotype and behaviourally determined susceptibility to early life adversity, animals displayed distinct H3K4me3 enrichment. As expected, the effect sizes and significances were rather subtle.
Conclusion: the epigenetic regulation by prenatal stress seems to be modulated by the serotonin transporter genotype

overall_design:
H3K4me3 enrichment affected in serotonin transporter deficient or wildtype offspring of prenatal stress that do or do  not succumb to the adverse effects of prenatal stress, i.e. vulnerable or resilient offspring
[contributor] Nxt-Dx (Ghent, Belgium)

first: K

middle: P

last: Lesch

first: D

last: van den Hove

first: M

last: Weidner

middle: U

first: L

last: Eijjsen

first: R

last: Lardenoije


title: RNA-seq analysis of myeloid cells in dLNs post-administration of mRNA vaccine

city: Tsukuba

first: Kenji

last: Kubara

state: Ibaraki

address: Tokodai 5-1-3

department: Tsukuba Research Laboratories

institute: Eisai Co., Ltd.

summary: To investigate transcriptional signatures of myeloid cells in dLNs post-administration of mRNA vaccine, we collected dLNs from mice 24 h post-vaccination, sorted six types of myeloid subsets using FACS, and performed RNA-seq analysis. RNA-seq data showed increased expression of markers related to proinflammation and antigen presentation throughout myeloid subsets in dLNs post-administration of the mRNA vaccine.

first: Yuta

last: Suzuki

first: Takayuki

last: Miyazaki

first: Daisuke

last: Kurotaki

last: Tamura


title: Diacylglycerols and lysophosphatidic acid, enriched on Lipoprotein(a), contribute to monocyte inflammation

city: Amsterdam

first: Jeffrey

last: Kroon

address: Meibergdreef 9

department: Experimental Vascular Medicine

country: Netherlands

institute: Amsterdam UMC

summary: Background: OxPLs play a key role in the atherogenic potential of Lp(a), however Lp(a) is a complex particle that warrants research into additional pro-inflammatory mediators. We hypothesized that additional Lp(a)-associated lipids contribute to the atherogenicity of Lp(a). Methods: Untargeted lipidomics was performed on plasma and isolated lipoprotein fractions. The atherogenicity of the observed Lp(a)-associated lipids was tested ex vivo in primary human monocytes by RNAseq, ELISA, Western Blot and transendothelial migratory assays. Using immunofluorescence staining and single-cell RNA sequencing, the phenotype of macrophages was investigated in human atherosclerotic lesions. Results: Compared to healthy individuals with low/normal Lp(a) levels [median 7 mg/dL (18 nmol/L); N=13], individuals with elevated Lp(a) levels [median 87 mg/dL (218 nmol/L); N=12]  demonstrated an increase in lipid species, particularly diacylglycerols (DGs) and lysophosphatidic acid (LPA). DG and the LPA precursor lysophosphatidylcholine were enriched in the Lp(a) fraction. Ex vivo stimulation with DG(40:6) demonstrated a significant upregulation in pro-inflammatory pathways related to leukocyte migration, chemotaxis, NF-κB signalling and cytokine production. Functional assessment showed a dose-dependent increase in the secretion of IL-6, IL-8 and IL-1β after DG(40:6) and DG(38:4) stimulation, which was in part mediated via the NLRP3-inflammasome. Conversely, LPA-stimulated monocytes did not exhibit an inflammatory phenotype. Furthermore, activation of monocytes by DGs and LPA increased their transendothelial migratory capacity. Human atherosclerotic plaques from patients with high Lp(a) levels demonstrated co-localisation of Lp(a) with M1 macrophages, and an enrichment of CD68+IL18+TLR4+TREM2+ resident macrophages and CD68+CASP1+IL1B+SELL+ inflammatory macrophages compared to patients with low Lp(a). Finally, potent Lp(a) lowering treatment (pelacarsen), resulted in a reduction in specific circulating DG lipid subspecies in cardiovascular disease patients with elevated Lp(a) levels [median 82 mg/dL (205 nmol/L)]. Conclusions: Lp(a)-associated DGs and LPA have a potential role in Lp(a)-induced monocyte inflammation by increasing cytokine secretion and monocyte transendothelial migration. This DG-induced inflammation is in part NLRP3-inflammasome dependent.

overall_design: In order to investigate the potential impact of DG and LPA plasma levels on promoting an increased pro-inflammatory monocyte phenotype in individuals with elevated Lp(a) levels, we conducted a functional proof-of concept study using commercially available DGs and LPA. The lipid species DG(38:4) (18:0-20:4; 1-stearoyl-2-arachidonoyl-sn-glycerol), DG(40:6) (18:0-22:6; 1-stearoyl-2-docosahexaenoyl-sn-glycerol) and LPA were selected, as these lipid species are significantly increased in individuals with high levels of Lp(a) (p=0.0007; p=0.0067; p=0.0044, respectively) and were commercially available (Figure 4A and Supplemental Figure 5). Transcriptomic analysis was performed on DG-and LPA-stimulated primary human monocytes.

first: Kim

middle: E

last: Dzobo

first: Arjen

last: Cupido

first: Barend

last: Mol

first: Lotte

last: Stiekema

first: Miranda

last: Versloot

first: Maaike

last: Winkelmeijer

first: Jorge

last: Peter

first: Anne-Marije

last: Pennekamp

first: Stefan

last: Havik

first: Frédéric

last: Vaz

first: Michel

last: van Weeghel

first: Koen

middle: H

last: Prange

first: Johannes

last: Levels

first: Menno

last: de Winther

first: Sotirios

last: Tsimikas

first: Albert

last: Groen

first: Erik

middle: S

last: Stroes

first: Dominique

last: de Kleijn


title: ZSCAN4-binding motif - TGCACAC is conserved and enriched in CA/TG microsatellites in both mouse and human genomes [ChIP-Seq]

first: Tomohiko

last: Akiyama

overall_design: Chromatin immunoprecipitation DNA sequencing (ChIP-seq) for 1) Zscan4 in mouse embryonic fibroblasts (MEF), mouse ES cells (ES), and retinoic acid treated mouse ES cells (RA), and 2) ZSCAN4 in human ES cells treated with or without DUX4

first: Minoru

last: Ko


title: 5-Hydroxymethylcytosine signals in serum are a predictor of chemoresistance in high-grade serous ovarian cancer

city: Chicago

first: Xiaolong

last: Cui

state: IL

address: 680 N Lake Shore Drive

department: Department of Preventive Medicine

institute: Northwestern University

type: Methylation profiling by high throughput sequencing

summary: The genome-wide profiling of 5-hydroxymethylcytosine (5hmC) on circulating cell-free DNA (cfDNA) has revealed promising biomarkers for a variety of diseases. The purpose of our study is to investigate if 5hmC profiles from serum cfDNA are novel predictive biomarkers for the development of chemoresistance in high-grade serous ovarian cancer (HGSOC). We hypothesized that 5-hmC profiles associate with the development of chemoresistance and elucidate pathways that may drive chemoresistance in HGSOC. We developed a novel multivariate model based on clinico-pathologic data and a cfDNA-derived 5hmC-annotated gene that can predict response to platinum-based chemotherapy in intermediate-sensitive HGSOC. These results merit further investigation of our model as a predictive model.

overall_design: Patients diagnosed with HGSOC and with known platinum sensitivity status (Across all cohorts: sensitive n= 40, intermediate n= 34, resistant n= 37, and recurrent n= 20) were selected for this study. Nano-hmC-Seal was performed on cfDNA isolated from archived serum samples and differential 5hmC annotations were identified using DESeq2 to establish a model predictive of chemoresistance.

first: Melanie

last: Weigert

first: Xiao-Long

first: Diana

last: West-Szymanski

first: Wei

last: Zhang

first: Chuan

last: He

first: Ernst

middle: R

last: Lengyel


title: miRNA-Seq analysis differentially expressed miRNAs in intestinal tissues of ASMVT rat

city: Yunnnan province

first: kunmei

last: Gong

address: Jinbi Road 157

institute: The first People's Hospital of Yunnan Province

summary: Acute superior mesenteric vein thrombosis (ASMVT) decreases the expression of junction-associated proteins and the number of intestinal epithelial cells, which leads to intestinal epithelial barrier disruption. Thermoprotein deposition has also recently been identified as an important cause of mucosal barrier defects. However, the role and mechanism of thermoprotein deposition in asmvt is not fully understood. Differentially expressed microRNAs (miRNAs) in the intestinal tissues of ASMVT mice were detected by transcriptome sequencing (RNA-Seq). To identify miRNAs involved in intestinal barrier disruption, we performed RNA-Seq analysis of intestinal tissues from ASMVT mice . Sixty miRNAs were abnormally expressed in normal intestinal tissues compared with ASMVT-induced intestinal tissues.

overall_design: 6-8 weeks male Sprague Dawley rats (weight, 300–350 g) were supplied by the Hunan SJA Laboratory Animal Co., Ltd and housed individually in a temperature-controlled barrier facility with light-dark (12:12) cycles at 22 ℃ with 50% humidity, and received ad libitum food and water. The animal experiments have been approved by the Animal Ethics Committee of Kunming University of Science and Technology.The ASMVT rat model was established according to the method described in a previous study [25]. The rats were fasted for 12 hours before the operation and were given free access to water. In the lower abdomen of the rat, the rat was anesthetized with 5% ketamine 2 ml + 0.05% atropine 1 ml + 2.5% promethazine 2 ml at 5% ketamine 2 ml + 0.05% atropine 1 ml + 2.5% promethazine 2 ml at 2 ml/kg, and a midline incision of approximately 2 cm in length was made in the upper abdomen. The position of the cecum was determined after entering the abdominal cavity. The small intestine was pulled 5 cm away from the ileocecal region and the mesentery was exposed. The main branches of the mesenteric vein and the ends of the arch vein are ligated with 7-0 nylon thread. During mesenteric vein clamping, approximately 15-20 ml/kg of saline is injected intraperitoneally intermittently to prevent transient hypovolemia after loosening of the arterial clamp. Mesenteric vein dilatation and intestinal congestion were dark red, indicating successful modeling. After closing the abdomen, 25-30 m/kg of saline (containing gentamicin 320,000 U/L) was added into the abdominal cavity to prevent abdominal surgical infection. After surgery, the rats were placed back into the feeding cage for observation, one rat per cage, and were allowed to eat and drink freely. Rats were randomly divided into the following groups: (1) Sham group: after surgical exposure of the superior mesenteric vein; (2) ASMVT group;Rats were executed by spinal dislocation method under deep anesthesia. The affected intestine was cut down the middle and the intestinal contents were washed with normal saline. Small intestinal tissues were stored at -80°C until use.


title: Verteporfin targets CCR5 to inhibit TNBC growth and metastasis via YAP1

city: Shanghai

first: Ling

last: Chen

state: Shanghai

address: 800 Dingchuan Road

institute: Shanghai Jiao Tong univesity

summary: CCL5/CCR5 axis is an immunotherapeutic target for triple-negative breast cancer (TNBC). However, the signaling mechanism is poorly understood and its antagonists have not been reported. Here, we developed a high-throughput screening (HTS) assay for discovering its antagonists. Verteporfin was identified as a specific and more potent inhibitor than maraviroc. It significantly reduced TNBC tumor growth in an immunologically dependent manner, and lung metastasis in a cell-intrinsic way. Mechanistically, CCR5 was co-expressed with Yes-associated protein 1 (YAP1) in TNBC patients. RNA-sequencing and expression silencing further revealed that CCR5 promoted the expression of YAP1 through HIF-1α in TNBC cells, and through YAP1 to regulate β-catenin, ZEB1/ZEB2 for metastasis, as well as CXCL16 and CXCL8 for immune cell migration and tumor growth. In essence, verteporfin may have potential immunotherapeutic applications for diseases co-expressing CCR5 and YAP1 such as TNBC. The HTS assay can be adapted for unveiling antagonists of broader signaling pathways.

overall_design: RNA-seq of knockdown of CCR5 in human triple-nagative breast cancer MDA-MB-231 cells.

first: Xiaojing

last: Ma

first: Jing

last: Yu


title: Single-cell atlas of human infrapatellar fat pad and synovium unravels mechanisms of osteoarthritis-induced joint pathology

city: Shenyang

first: Lutian

last: Yao

address: 155 Nanjing st

department: Department of Orthopedic

institute: the First Affiliated Hospital of China Medical University

summary: Infrapatellar fat pad (IPFP) and synovium, two joint tissues next to each other, play essential roles in regulating joint homeostasis and the progression of knee osteoarthritis (OA). However, the mechanisms regulating their function under healthy and diseased conditions are largely unknown. This study aims to analyze the cellular heterogeneity of these two tissues from normal and OA patients. Single cell and single nuclei transcriptomic profiling were performed on IPFP/synovium cells from four healthy donors and five OA patients. Subsequent bioinformatic analyses identified cell clusters, delineated differentiation routes of mesenchymal cells and macrophages, and identified novel cell-to-cell communication pathways in joint tissue.

overall_design: IPFP/synovium cells from four healthy donors and five OA patients were harvest and analyzed by scRNA-seq

first: Changhai

last: Ding

last: Qin

first: Su'an

last: Tang


title: RNA-seq transcriptional profiling in primary human hepatocytes, short- and long-term cultured Proliferating human hepatocytes (in vitro/in vivo)

first: Lijian

last: Hui

address: yueyang road 320

department: SIBCB

institute: CEMCS, CAS

summary: One of the major challenges of cell therapy is manufacturing of the effective seed cells, which inevitably requires the expansion of cells in vitro. Although considerable progresses have been achieved in expansion of primary human hepatocytes (PHH) in vitro, the transplantation efficiency of proliferating human hepatocytes was decreased with the extended culture. The mechanism of declined transplantation is not clear.Here, we found that long-term cultured proliferating human hepatocytes (lc-ProliHH) significantly upregulated chemokines and proinflammatory cytokines associated with innate immune response. Moreover, lc-ProliHH elicited robust recruitment of macrophages and neutrophils at early stage of transplantation, and being cleared by macrophages caused the engraftment efficiency reduction.Based on these findings, we designed to treat recipient with Dexamethasone (Dex), which decreased the response of innate immune cells and significantly increased the transplantation efficiency to a level approximate to PHH in the liver-injured mice. Furthermore, ProliHH organoid reduced the expression of cytokine genes and behaved close to mature hepatocyte, and as a result, ameliorated their transplantation efficiency as well.

overall_design: During the culture process, transcriptional profiling in PHH, sc-ProliHH and lc-ProliHH were generated by RNA-seq analysis. Transcriptional profiling in lc-ProliHH-repopulated Fah-/-Rag2-/-IL2rg-/- mouse liver were generated by RNA-seq analysis.

first: Chenhua

last: Wang

first: Baihua

last: Wu


title: Expression analysis of SPDEF KO and hRosa26 clones of hF27, CFPAC1 and HPAF-II orthotopically grafted into the pancreata of NSG mice.

city: Cold Spring Harbor

first: David

last: Tuveson

state: New York

address: 1 Bungtown Road

department: Cancer Center

institute: Cold Spring Harbor Laboratory

summary: This study used Illumina RNA-sequencing to examine gene expression differences following Spdef deletion in hF27, CFPAC1 and HPAF-II orthotopically grafted tumor models.

overall_design: RNA-sequencing of tumor RNA isolated from hF27, CFPAC1 and HPAF-II orthotopically grafted models of SPDEF KO and hRosa26 clones in NSG mice.

first: Claudia

last: Tonelli

first: Astrid

last: Deschenes


title: Tongue RNA expression after oropharyngeal candidiasis in mice deficient in CCL28

city: Milwaukee

first: Anna

last: Huppler

state: WI

address: 8701 Watertown Plank Road

department: Pediatrics

institute: Medical College of Wisconsin

summary: We report the RNA expression using RNAseq in tongue tissue of mice with and without infection with oropharyngeal candidiasis.  CCL28 KO mice are compared to C57BL/6 WT mice.

overall_design: RNAseq on tongue tissue 1 day after oropharyngeal innoculation with Candidia albicans or sham innoculation in WT or CCL28-/- mice. Four replicates were performed for each experimental condition.

first: Jie


title: Hypoxa-actived XBP1s recruits HDAC2-EZH2 to engage epigenetic suppression of DNp63 expression and promotes breast cacner metastasis independent HIF1a

status: Public on Jan 24 2024

city: Chengdu

first: Hu

last: CHEN

state: Sichuan

address: No, 278, Baoguang Road, Xindu District, Chengdu

department: School of Clinical Medicine

institute: Chengdu Medical College

summary: Hypoxia is a hallmark of cancer development. However, the molecular mechanisms by which hypoxia promotes tumor metastasis are not fully understood. In this study, we demonstrate that hypoxia promotes breast cancer metastasis through suppression of ΔNp63α-dependent in a HIF1α-independent manner. We show that hypoxia activates unfolded protein response (UPR) to elevate XBP1s, which in turn forms stable repressor protein complexes with HDAC2 and EZH2 in suppression of ΔNp63α. Notably, while H3K27ac is predominantly presented in the ΔNp63 promoter under normoxia, it is switched to H3K27me3 under hypoxia. We show that XBP1s binds to the ΔNp63 promoter to recruit HDAC2 and EZH2 in facilitating the H3K27ac-H3K27me3 switch. Knockdown or pharmacological inhibition of either HDAC2 or EZH2 leads to increased H3K27ac concomitant with reduced H3K27me3, which effectively restores ΔNp63α expression suppressed by hypoxia, resulting in inhibition of cell migration. Clinical analyses reveal that reduced p63 expression is correlated with the elevated expression of XBP1, HDAC2, or EZH2, and is associated with poor overall survival in human breast cancer patients. Together, these results indicate that hypoxia-activated XBP1s modulates the epigenetic program in suppression of ΔNp63α to promote breast cancer metastasis independent of HIF1α and provides a molecule basis for targeting the XBP1s/HDAC2/EZH2-ΔNp63α axis as a putative strategy in the treatment of breast cancer metastasis.

overall_design: HCC1806 cells, which were cultured under normoxic or hypoxic conditions, with ChIP-IT Kit (53009, Active Motif, USA) using antibodies specific for H3K27me3 (9733, CST, 1:50), H3K27ac (ab4729, abcam, 1: 50) or normal rabbit IgG (2927, CST, 1:50), as described previously18. Immunoprecipitated DNA was used to construct sequencing libraries according to the protocol provided by the TruePrep DNA library Prep kit (Vazyme #TD501) and sequenced on Illumina Nova Seq6000 (Gene Denovo CO., Ltd., Guangzhou, China)

first: Shuhan

first: Ruidong

first: Liyuan

last: Deng

first: Jingsong

last: Li

first: Yong

last: Yi

first: Lanxin

last: Ye

last: Xu

first: Mengmeng

last: Niu

first: Zhi-Xiong

last: Xiao


title: NAC61 regulates late- and post-ripening osmotic, oxidative, and biotic stress responses in grapevine

city: VR

first: Alessandra

last: Amato

address: strada le grazie 15

country: Italy

institute: University of Verona

summary: During late- and post-ripening stages, grape berry undergoes profound biochemical and physiological changes whose molecular control is poorly understood. Here, we report the role of NAC61, a grapevine NAC transcription factor, in regulating different processes featuring the berry ripening progression. NAC61 is highly expressed during post-harvest berry dehydration and its expression pattern is closely related to sugar concentration. The ectopic expression of NAC61 in Nicotiana benthamiana leaves determines low stomatal conductance, high leaf temperature, tissue collapse and a higher relative water content. Transcriptome analysis of grapevine leaves transiently overexpressing NAC61, and DNA affinity purification and sequencing analyses allowed us to narrow down a list of NAC61-regulated genes. Direct regulation of the stilbene synthase regulator MYB14, the osmotic stress-related gene DHN1b, the Botrytis cinerea susceptibility gene WRKY52 and the NAC61 itself, is validated. We also demonstrate that NAC61 interacts with NAC60, a proposed master regulator of grapevine organ maturation, in the activation of MYB14 and NAC61 expression. Overall, our findings establish NAC61 as a key player in a regulative network that governs stilbenoid metabolism and osmotic, oxidative and biotic stress responses that hallmark late- and post-ripening grape stages.

overall_design: For transient transformation of Vitis vinifera cv. Thompson Seedless, the 35S:NAC61 construct was transferred to Agrobacterium tumefaciens strain C58C1 by electroporation. As control, Agrobacterium was also transformed with an empty pK7WG2 containing a non-coding sequence. Seven in vitro six-week-old plants of grapevine cv. Thompson Seedless for overexpression and five for the control were immersed in each bacterial suspension and vacuum infiltrated (2 X 2 min at 90kPa). After agroinfiltration, plantlets were allowed to recover in vitro for seven days before collecting material for RNA extraction and transcriptomic analysis.

first: Chiara

last: Foresti

first: Luis

last: Orduña

first: José

last: Matus

first: Elodie

last: Vandelle

first: Davide

last: Danzi

first: Oscar

last: Bellon

first: Giovanni

middle: B

last: Tornielli

first: Sara

last: Zenoni


title: Prospective Approach to Deciphering the Impact of Intercellular Mitochondrial Transfer from Human Neural Stem Cells and Brain Tumor-Initiating Cells to Neighboring Astrocytes

first: Jason

last: Wood

address: 900 S Ashland Ave rm 1057

department: Research Informatics Core

institute: University of Illinois at Chicago

summary: The communication between neural stem cells (NSCs) and surrounding astrocytes is essential for the homeostasis of the NSC niche. Intercellular mitochondrial transfer, a unique communication system that utilizes the formation of tunneling nanotubes for targeted mitochondrial transfer be-tween donor and recipient cells, has recently been identified in a wide range of cell types. Intercel-lular mitochondrial transfer has also been observed between different types of cancer stem cells (CSCs) and their neighboring cells, including brain CSCs and astrocytes. CSC mitochondrial transfer significantly enhances overall tumor progression by reprogramming neighboring cells. Despite the urgent need to investigate this newly identified phenomenon, mitochondrial transfer in the central nervous system remains largely uncharacterized. In this study, we found evidence of intercellular mitochondrial transfer from human NSCs and from brain CSCs, also known as brain tumor-initiating cells (BTICs), to astrocytes in co-culture experiments. Both NSC and BTIC mito-chondria triggered similar transcriptome changes upon transplantation into the recipient astro-cytes. In contrast to NSCs, the transplanted mitochondria from BTICs had a significant prolifera-tive effect on the recipient astrocytes. This study forms the basis for mechanistically deciphering the impact of intercellular mitochondrial transfer on recipient astrocytes, which will potentially provide us with new insights into the mechanisms of mitochondrial retrograde signaling.

overall_design: Astrocytes were transplanted with mitochondria that was extracted from Radia Glia (RG) cells or Brain tumor initiating cells (BTIC), that were compared with the non-transplanted astrocytes as a control. The RNA was extracted from the cells after 7 days of cell culture with the transplanted mitochondria.

first: Jerusha

last: Boyineni

first: Aditya

last: Ravindra

first: Ethan

last: Boley

first: Sarah

last: Donohue

first: Marcelo

last: Soares

first: Sergey

last: Malchenko


title: AML Relapse After BET Inhibition and Chemotherapy Is Characterized by Myc-Ras Transcriptional Remodeling

city: San Francisco

first: Benjamin

last: Huang

state: CA

address: 1450 3rd Street

institute: University of California San Francisco

summary: Genome-wide analysis of adult and pediatric acute myeloid leukemias (AMLs) revealed distinct mutational profiles characterized by a higher incidence of RAS mutations in young patients. Here we show that the BET inhibitor PLX51107 potently suppresses the growth and promotes apoptosis of NRAS-mutant monocytic AML cell lines, and that these activities are enhanced by co-treatment with the MEK inhibitor PD0325901. Controlled preclinical trials in primary mouse Nras-mutant monocytic AMLs revealed single agent efficacy of PLX51107 that was enhanced by PD0325901. Leukemias that relapsed during treatment developed intrinsic drug resistance characterized by transition to a more primitive state, up-regulation of Myc target genes, and down-regulation of Ras-associated transcriptional programs. AMLs that relapsed after frontline chemotherapy showed similar transcriptional remodeling. These studies demonstrate transcriptional plasticity in primary AMLs that relapse following in vivo treatment with either targeted agents or chemotherapy, and support evaluating BET inhibition in leukemias with monocytic differentiation and RAS mutations.

overall_design: To investigate mechanisms of response and resistance to BET and MEK inhibition in acute myeloid leukemia (AML), primary mouse AMLs were transplanted and then exposed in vivo to the BET inhibitor PLX51107 with and without the MEK inhibitor PD0325901 (PD901). Mice were treated and observed daily. Moribund mice were euthanzied and bone marrow was collected. Cells underwent RNA extraction (with or without preceding 24 hour ex vivo exposure drug exposure) for bulk RNA sequencing.

first: Kevin

last: Shannon


title: Postnatal Subventricular Zone Injury Predicts Motor Impairment in Preterm Infants Following Intestinal Disease

city: Durham

first: Adrian

last: Epstein

state: NC

address: 300 N Duke

department: Pediatrics, Neonatology

institute: Duke University

summary: Following intestinal perforation in neonatal mice there is an injury to the subventrcular zone stem cell niche. These files are the raw data from mouse brain sections, transecting SVZ in controls and mice with modeled instestinal perforation.

overall_design: On postnatal day 5, mice were divided into controls and modeled intestinal perforation. After 48 hours, the brain was removed, formalin fixed, paraffin embeded and sectioned coronally and processed for spatial transcriptomics.

first: Eric

last: Benner

first: Vaibhav

last: Jain

first: Simon

middle: G

last: Gregory


title: Mechanical confinement governs phenotypic plasticity in melanoma [HMGB2OE_ATACseq]

city: New York

first: Miranda

last: Hunter

state: NY

address: 418 E 68th St

institute: Memorial Sloan Kettering Cancer Center

summary: Phenotype switching is a form of cellular plasticity in which cancer cells reversibly move between two opposite extremes - proliferative versus invasive states. While it has long been hypothesised that such switching is triggered by external cues, the identity of these cues has remained elusive. Here, we demonstrate that mechanical confinement mediates phenotype switching through chromatin remodelling. Using a zebrafish model of melanoma coupled with human samples, we profiled tumour cells at the interface between the tumour and surrounding microenvironment. Morphological analysis of these rare cells showed flattened, elliptical nuclei suggestive of mechanical confinement by nearby adjacent tissue. Spatial and single-cell transcriptomics demonstrated that the interface cells adopted a gene program of neuronal invasion, including acquisition of an acetylated tubulin cage that protects the nucleus during migration. We identified the DNA-bending protein HMGB2 as a confinement-induced mediator of the neuronal state. HMGB2 is upregulated in confined cells, and quantitative modelling revealed that confinement prolongs contact time between HMGB2 and chromatin, leading to changes in chromatin configuration that favour the neuronal phenotype. Genetic disruption of HMGB2 showed that it regulates the trade-off between proliferative and invasive states, in which confined HMGB2high tumour cells are less proliferative but more drug resistant. Our results implicate the mechanical microenvironment as a mechanism for phenotype switching in melanoma.

overall_design: ATAC-sequencing of A375 human melanoma cells overexpressing HMGB2 relative to empty vector control.

middle: V


title: Mechanical confinement governs phenotypic plasticity in melanoma [HMGB2OE_RNAseq]

overall_design: Bulk RNA-sequencing of A375 human melanoma cells overexpressing HMGB2, relative to empty vector control.


title: Mechanical confinement governs phenotypic plasticity in melanoma [confined_RNAseq]

overall_design: Bulk RNA-sequencing of A375 human melanoma cells confined at 3 µm height for 18 hours, relative to unconfined control.


title: Precision Cut Lung Slices as an ex vivo model to study Pneumocystis murina survival and antimicrobial susceptibility

city: New Orleans

first: Jay

last: Kolls

state: LA

address: 1430 Tulane Ave

department: Medicine

institute: Tulane University

summary: This study was done to show the utility of precision-cut lung slices (PCLS) in supporting the survival of Pneumocystis murina in vitro.

overall_design:
We cultured PCLS derived from wild type C57BL/6 and immunocompromised Rag2-/-Il2rγ-/-  mice with a P. murina inoculum in submerged or air-liquid interface models for up to 14 days.
We isolated total RNA from the cultured lung tissues at days 0, 3, 7, 10 and 14 and analyzed for the expression of host lung genes and P. murina genes (Gsc1 for asci and Sp for trophs) by real-time qPCR.
We then performed gene expression profiling analysis using data obtained from RNA-seq of  naïve and  P. murina - inoculated PCLS on day 3 and day 14 of culture in comparison to  in vivo  P. murina infected mice on day 14.

first: Ferris

last: Munyonho

first: D

last: Robert

first: Lin

last: Dong

first: Shamima

last: Khatun

first: Dora

last: Pungan

first: Dai

last: Guixiang

middle: K


title: Multilineage pituitary neuroendocrine tumors with PIT1/SF1 co-expression

city: Hamburg

first: Matthias

last: Dottermusch

address: Martinistr. 52

department: Institute of Neuropathology

institute: University Medical Center Hamburg-Eppendorf

type: Methylation profiling by genome tiling array

summary: Pituitary neuroendocrine tumors (PitNET)/adenomas are classified according to cell lineage, which requires immunohistochemistry for the transcription factors (TFs) PIT1, SF1, and TPIT. Co-expression of PIT1/SF1 was previously reported in PitNETs, which otherwise correspond to the somatotroph lineage. However, little is known about the clinicopathological features of these tumors.  We compiled an in-house case series of 100 tumors, previously diagnosed as densely or sparsely granulated somatotroph PitNETs. Following TF staining, histopathological features associated with PIT1/SF1-coexpression were assessed. Global DNA methylation profiling was conducted on 31 of 100 in-house samples and integrated with publicly available sample data.   The majority (74%, 52/70) of our densely granulated somatotroph PitNETs (DGST) unequivocally co-expressed PIT1 and SF1 (DGST-PIT1/SF1). None of our SGST (0%, 0/30) stained positive for SF1 (SGST-PIT1). Integrated molecular analyses including publicly available sample data confirmed that DGST-PIT1/SF1, DGST-PIT1 and SGST-PIT1 represent distinct tumour subtypes.   In summary, we spotlight that a substantial proportion of previously diagnosed densely granulated somatotroph PitNET co-express PIT1 and SF1 and exhibit clinical, histopathological, and molecular distinctness from other pure PIT1-lineage somatotroph PitNET.

overall_design: The Infinium MethylationEPIC BeadChip Array (Illumina) was used for global DNA methylation profiling of 31 somatotroph PitNETs.

first: Alice

last: Ryba

first: Franz

middle: L

last: Ricklefs

first: Jörg

last: Flitsch

first: Simone

last: Schmid

first: Markus

last: Glatzel

first: Wolfgang

last: Saeger

first: Julia

last: Neumann

first: Ulrich

last: Schüller


title: Fate-mapping via Spp1-expression history revealed innate immune memory of microglia imprinted by neonatal injury [Spp1GFP]

city: Hangzhou

first: DANYANG

last: HE

state: Zhejiang

address: 600 Dunyu Road Sandun Town

department: School of Life Sciences

institute: Westlake Univeristy

summary: Microglial reactivity to injury and disease is emerging as a heterogeneous, dynamic, and crucial determinant in neurological disorders. However, the plasticity and ultimate fate of disease-associated microglia (DAM) remains largely unknown. We established a lineage tracing system, leveraging the expression dynamics of Spp1, which allows for genetic labeling of DAM-like microglia and tracking their behavior during brain injury and recovery. Fate-mapping of Spp1+ microglia in juvenile stroke revealed an irreversible state of reactive microglia that are ultimately eliminated from the injured brain. In contrast, DAM-like microglia in the neonatal context exhibit high plasticity, capable of regaining a homeostatic signature and integrating into the global microglial network after recovery. Furthermore, neonatal injury has a lasting impact on microglia, rendering them intrinsically sensitized to subsequent immune challenges. Therefore, by unraveling the fate of DAM-like microglia in various neuropathological conditions, our work highlights the exceptional plasticity and innate immune memory of neonatal microglia.

overall_design: To further explore the heterogeneity and the underlying molecular signature of microglial reactivity across neurological disorders, we performed bulk RNA Seq  and sc RNA-seq of Spp1-GFP+ microglia from four disease models.

first: Yangning

last: Lan

first: Shaorui

last: Liu

first: Hui

last: Li


title: Effect of Regnase-2/MCPIP2/ZC3H12B overexpression in human glioblastoma U-251 MG cell line.

city: Kraków

first: Mateusz

last: Wawro

address: Gronostajowa 7

department: Cell Biochemistry

country: Poland

institute: Jagiellonian University

summary: Regnase-2/MCPIP2/ZC3H12B is a protein belonging to the ZC3H12 protein family. There are three other proteins of this family present in humans of which Regnase-1/MCPIP1/ZC3H12A is the founder member as well as the best-described protein.  All proteins of this family contain a NYN domain with endoribonuclease activity and a CCCH-type zinc finger responsible for interaction with substrate RNA. Although the NYN domain has a high degree of similarity across all four members the in vitro RNase activity was shown only for two of them, namely Regnase-1 and Regnase-3. Interestingly the ZC3H12 family proteins have unique expression patterns with Regnase-2 being expressed almost solely in the central nervous system. What is more, Regnase-2 is downregulated in human glioblastoma, and its expression is inversely correlated with tumor grade. To decipher the role of Regnase-2 in human glioblastoma we performed RNA sequencing of U-251 MG cells overexpressing Regnase-2 and control, mock-transfected cells.

overall_design:
To investigate the role of Regnase-2 in U-251 MG cells we established two U-251 MG cell lines with doxycycline-inducible overexpression of Regnase-2 or luciferase (control/mock) and we induced the expression of transgenes for 24 hours.
Differential expression profiling was performed using data obtained from RNA-seq of the two cell lines (outsourced to QIAGEN Genomic Services, Germany).

first: Weronika

last: Sowinska

first: Jakub

last: Kochan

first: Aneta

last: Kasza


title: Fate-mapping via Spp1-expression history revealed innate immune memory of microglia imprinted by neonatal injury

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

overall_design: Refer to individual Series


title: Expression Analysis of Mouse Tumor Pancreatic Ductal Adenocarcinoma (PDA) Organoids upon Spdef deletion and re-instatement

status: Public on Jan 29 2024

first: David

middle: A.

last: Tuveson

address: 1 Bungtown Rd.

summary: This study used Illumina strand-specific, paired-end RNA-sequencing to examine gene expression differences following Spdef deletion and re-instatement in epithelial organoid cultures of primary tumor cells from KrasLSLG12D/+; Trp53LSLR172H/+; Pdx1-Cre (KPC) mice.

overall_design: Strand-specific RNA-sequencing of epithelial organoid cultures of primary cells from KrasLSLG12D/+; Trp53LSLR172H/+; Pdx1-Cre (KPC) mice following Spdef deletion and re-instatement.

first: Claudia

last: Tonelli

first: Astrid

last: Deschenes


title: Transcriptional profiling of CD4 T cells from control mice and from mice lacking BCL6 expression in CD4+ T cells 4+4

city: Columbia

first: Jerod

last: Skyberg

state: MO

address: Veterinary Pathobiology, 1500 Bouchelle

institute: University of Missouri

summary: We isolated CD4+ T cells from mice vaccinated against, and challenged with, Brucella to investigate the function of CD4+ T cell intrinsic BCL6 signaling

overall_design: Comparative gene expression profiling analysis of CD4+ T cells with and without BCL6 signaling after four weeks of vaccination and four weeks of  challenge with Brucella melitensis.

first: Mostafa

last: Abushahba

first: Skyberg

last: Jerod


title: Universal STING Mimic Boosts Antitumour Immunity via Preferential Activation of Tumour Control Signalling Pathways

city: Chapel Hill

first: Ying

last: Wang

address: 125 Mason Farm Road, 3118G Marsico Hall, Marsico Hall/3118G/3nd

institute: University of North Carolina at Chapel Hill

summary: The efficacy of stimulator of interferon genes (STING) agonists is compromised by various factors, primarily inefficient intracellular delivery, low/lack of endogenous STING expression in many tumours and a complex balance between tumour control and progression. Here, we report a universal STING mimic (uniSTING) based on a polymeric architecture. The uniSTING activates STING signalling in a range of mouse and human cell types, independent of endogenous STING expression, and selectively stimulates tumour control IRF3/IFN-I pathways, but not tumour progression NF-κB pathways. Intratumoural or systemic injection of uniSTING-mRNA via lipid nanoparticles (LNP) results in potent anti-tumour efficacy across established and advanced metastatic tumour models, including triple negative breast cancer, lung cancer, melanoma and orthotopic/metastatic liver malignancies. Furthermore, uniSTING displays an effective antitumour response superior to 2’3’-cGAMP and ADU-S100. By favouring IRF3/IFN-I activity over the pro-inflammatory NF-κB signalling pathway, uniSTING promotes dendritic cell maturation and antigen specific CD8+ T cell responses. Extracellular vesicles released from uniSTING-treated tumour cells further sensitise dendritic cells via exosome containing miRNAs that reduced the immunosuppressive Wnt2b and a combination of LNP-uniSTING-mRNA with α-Wnt2b antibodies synergistically inhibit tumour growth and prolong animal survival. Collectively, these results demonstrate the LNP-mediated delivery of uniSTING-mRNA as a strategy to overcome the current STING therapeutic barriers, particularly for the treatment of multiple cancer types in which STING is downregulated or absent.

overall_design: To investigate the function of uniSTING in the regulation of Type I IFN signaling pathways, we performed RNA-seq on 4T1 tumor cells post treatments with either uniSTING mRNA or Mock (EGFP) mRNA. Moreover, the uniSTING’s effect on downstream pathways in an unbiased fashion was also examined on 4T1 tumor cells. The gene expression profiling analysis was performed using the RNA-seq data of 4T1 tumor cells after indicated treatments above.

first: Sirui

first: Mengying

last: Hu

first: Yuchen

last: Yang

first: Jenny

last: Ting

first: Rihe


title: Fate-mapping via Spp1-expression history revealed innate immune memory of microglia imprinted by neonatal injury [Spp1Tdt]

first: DANYANG

last: HE

overall_design: To explore the transcriptional dynamics in DAM-like microglia following stroke induction and upon seconday immune challenge, we performed bulk RNA Seq, single cell RNA-Seq and ATAC-Seq of Tdt+ microglia at multiple time points after SIMPLE.

first: Yangning

last: Lan

first: Shaorui

first: Hui


title: Transcriptional profiling of CD4 T cells from control mice and from mice lacking BCL6 expression in CD4+ T cells 4+2

overall_design: Comparative gene expression profiling analysis of CD4+ T cells with and without BCL6 signaling after four weeks of vaccination and two weeks of  challenge with Brucella melitensis.


title: Transcriptional profiling of CD4 T cells from control mice and from mice lacking BCL6 expression in CD4+ T cells


title: Snai2-mediated upregulation of NADSYN1 promotes bladder cancer progression by interacting with PHB

city: Guangzhou

first: Xiao-Peng

last: Tian

address: 651 Dong Feng RD East

department: Department of Medical Oncology

institute: Sun Yat-sen University Cancer Center

summary: Prohibitin (PHB) plays a significant role in cancer processes whereas its mechanism in bladder cancer (BC) aggressiveness is not fully understood. This study aimed to investigate the role of PHB in BC aggressiveness. The study employed a range of in vivo and in vitro assays to elucidate the interaction between PHB-NADSYN1 and its underlying function in BC progression. We found that PHB was upregulated in muscle-invasive bladder cancer tissues, and bound to NADSYN1 mRNA in BC tissues more than in adjacent normal tissues. NADSYN1 and PHB were upregulated and positively correlated both in BC tissues and cell lines. We further revealed that deleting NADSYN1 prevented PHB-mediated cell invasiveness of BC in vivo and in vitro. PHB could directly bind to NADSYN1 mRNA, and it was found that the PHB domain was responsible for the PHB-NADSYN1 interaction. Depletion of NADSYN1 expression significantly decreased the protein level of PHB. In addition, Snai2 positively correlated with NADSYN1 and depletion or mutation of Snai2 binding sites inhibited NADSYN1-PHB-mediated BC progression. The study highlights a novel Snai2-NADSYN1-PHB mechanism in BC progression and indicates that PHB and NADSYN1 could serve as a therapeutic target for BC

overall_design:
We initially utilized high-throughput RNAseq method to identify differential gene expressions between MIBC and NMIBC tisseus.By intersecting three different groups, we pinpointed 10 specific genes that exhibited differential expression. MIBC, muscle-invasive bladder cancer; NMIBC, non-muscle-invasive bladder cancer.
We repeated the high-throughput RNAseq 3 times (2 pairs of specimens at a time) to compare the differential genes between MIBC and NMIBC, and by taking the intersection of the differential genes 3 times, we obtained 10 differential genes

first: Li-Juan

last: Jiang

first: Xiao

last: P-Tian


title: Effect of lysosomal alkalinization on nutrient-rich and nutrient-depleted Caco-2 cells

city: Cankaya

first: Sreeparna

last: Banerjee

state: Ankara

address: Universiteler Mah., Dumlupinar Bulvari No:1

department: Biological Sciences

country: Turkey

institute: Middle East Technical University

summary: Nutrient restriction in cancer cells can activate a number of stress response pathways for cell survival. We aimed to determine mechanistically how nutrient depletion (ND) in colorectal cancer (CRC) cells leads to cellular adaptation. Caco-2 cells under ND showed high viability, tumor-forming ability, and increased expression of one or more epithelial and mesenchymal markers, suggesting the activation of partial (p)-EMT. Lysosomes are activated with ND; therefore, we incubated the ND cells with the V-ATPase inhibitor Bafilomycin A1 (ND+Baf). We observed a further increase in p-EMT markers, numerous membrane protrusions, decreased cell-cell adhesion in 3D, and increased motility in ND+Baf Caco-2 cells. The protrusions in the ND+Baf cells were primarily mediated by microtubules and enabled the relocalization of lysosomes from the perinuclear region to the periphery. Overall, our data show that ND activated p-EMT in CRC cells, which was exacerbated with lysosomal alkalinization.

overall_design: To investigate the effect of nutrient depletion and lysosomal alkalinization in Caco-2 cells, Caco-2 cells were grown in a complete medium and treated with either vehicle or 100nM BafA1. Additionally, Caco-2 cells were also grown in a nutrient-depletion medium and treated with 100nM BafA1. Three replicates were collected for each condition.

first: Hazal

last: Husnugil

first: Aliye

last: Gulec Taskiran

first: Ismail

last: Guderer

first: Leman

middle: N

last: Nehri

first: Goksu

last: Oral

first: Nazli

last: Menemenli

first: Ozun

last: Ozcan

first: Ariana

last: Noghreh

first: Aytekin

last: Akyol


title: Impact of plastic-related compounds on the gene expression signature of HepG2 cells transfected with CYP3A4

city: Mainz

first: Federico

last: Marini

address: Obere Zahlbacher Strasse 69

department: Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)

institute: University Medical Center - Mainz

summary: The presence of plastic and microplastic within the oceans as well as in marine flora and fauna have caused a multitude of problems which have been topic of numerous investigations for many years. However, their impact on human health remains largely unknown. Such plastic and microplastic particles have been detected in blood and placenta, underlining their ability to enter the human body. Plastics also contain other compounds, such as plasticizers, antioxidants, or dyes, whose impact on human health is currently being studied. Critical enzymes within the metabolism of endogenous molecules, especially of xenobiotics, are the cytochrome P450 monooxygenases (CYPs). Although their importance in maintaining cellular balance has been confirmed, their interactions with plastics and related products are poorly understood. In this study, the possible relationship between different plastic-related compounds and CYP3A4 as one of the most important CYPs was analyzed using hepatic cells overexpressing this enzyme. Beginning with virtual compound screening and molecular docking of more than 1,000 plastic-related compounds, several candidates were identified to interact with CYP3A4. In a second step, RNA-sequencing was used to study in detail the transcriptome-wide gene expression levels affected by the selected compounds. The results showed that three candidate molecules (2,2'-methylene bis(6-tert-butyl-4-methylphenol, 1,1-bis(3,5-di-tert-butyl-2-hydroxyphenyl)ethane, and 2,2'-methylene bis(6-cyclohexyl-4-methylphenol) had an excellent binding affinity to CYP3A4 in silico as well as cytotoxic effects and interactions with several metabolic pathways in vitro. We identified common pathways influenced by all three selected plastic-related compounds. In particular, the suppression of pathways related to mitosis and ‘DNA-templated DNA replication’. Furthermore, several mis-regulated metabolic and inflammation-related pathways were identified, suggesting the induction of hepatotoxicity at different levels. These findings imply that these compounds may cause problems in the liver, which could subsequently affect the entire organism.

overall_design: To investigate whether plastic-related compounds may have a toxic effect on liver cells overexpressing cytochrome CYP3A4

first: Matteo

last: Rosellini

first: Alicia

last: Schulze

first: Ejlal

last: Omer

first: Jan-Heiner

last: Küpper

first: Thomas

last: Efferth


title: Mus Musculus Brain FMR1KO, FMR1WT small RNA seq

city: Baltimore

first: Mollie

last: Meffert

address: 725 N. Wolfe St.

institute: Johns Hopkins University School of Medicine

overall_design: siblings

first: William

last: Mills IV


title: Fosfomycin uptake in Escherichia coli is mediated by the outer membrane porins OmpF, OmpC and LamB

city: Tübingen

first: Kay

last: Nieselt

state: DE

address: Sand 14

department: Department for Computer Science

institute: Institute for Bioinformatics and Medical Informatics

summary: The antibiotic fosfomycin is widely recognized for treatment of lower urinary tract infections caused by Escherichia coli and lately gained importance as a therapeutic option to combat multidrug resistant bacteria. Still, resistance to fosfomycin frequently develops through mutations reducing its uptake. Whereas the inner membrane transport of fosfomycin has been extensively studied in E. coli, its outer membrane (OM) transport remains insufficiently understood. While evaluating minimal inhibitory concentrations in OM porin-deficient mutants, we observed that the E. coli ΔompCΔompF strain is five times more resistant to fosfomycin than the wild type and the respective single mutants. Continuous monitoring of cell lysis of porin-deficient strains in response to fosfomycin additionally indicated the relevance of LamB. Furthermore, the physiological relevance of OmpF, OmpC and LamB for fosfomycin uptake was confirmed by electrophysiological and transcriptional analysis. This study expands the knowledge of how fosfomycin crosses the OM of E. coli.

overall_design: To investigate the expression of genes encoding for porins RNA sequencing was conducted for three biological replicates of E.coli BW25113

first: Martina

last: Bianchi

first: Theresa

last: Harbig

first: Christoph

last: Mayer


title: Adipocyte hypertrophy associates with differential in vivo postprandial fatty acid metabolism, adipose single-cell landscape and transcriptional dynamics

city: Sherbrooke

first: Run Zhou

last: Ye

state: QC

address: 3001 12e Avenue Nord

country: Canada

institute: Université de Sherbrooke

summary: We employed a combination of oral and i.v. tracers with positron emission tomography imaging to measure systemic and organ-specific fatty acid metabolism in 40 men and women with normal or impaired glucose tolerance (NCT02808182), and single nuclei RNA-sequencing to perform an unbiased comparison of cellular heterogeneity and transcriptional dynamics of all subcutaneous AT cell types between individuals with AT hypertrophy vs. hyperplasia matched for the same sex, ethnicity, glucose-tolerance status, BMI, total and percent body fat, and waist circumference.

overall_design: We have also used single-nuclei RNA sequencing of frozen human subcutaneous AT with adipocyte hypertrophy and hyperplasia in order to perform an unbiased assessment of the single-cell landscape of all AT cell types, including mature adipocytes.

first: Run

middle: Z

first: Emilie

last: Montastier

first: Frédérique

last: Frisch

first: Christophe

last: Noll

first: Hugues

last: Allard-Chamard

first: Nicolas

last: Gévry

first: André

last: Tchernof

middle: C

last: Carpentier


title: Single-Cell Transcriptomics Identifies Pituitary Gland Population Changes in Diet-Induced Obesity

city: Riverside

first: Djurdjica

last: Coss

address: 109 Picnic Hill Rd

department: Biomedical Sciences

institute: University of California Riverside

summary: The obesity incidence is increasing worldwide with the urgent need to identify new therapeutics. Obesity is associated with endocrine alterations, arising from changes in the hypothalamic-pituitary hormone axes, leading to reproductive disorders, altered basal metabolism and stress hormone production. The focus of this study was to determine if diet induced obesity alters pituitary gland plasticity, gene expression and hormone production and secretion. Here we performed single cell RNA-sequencing (scRNA-seq) on pituitary glands from control (CTRL) and high fat diet (HFD) fed males and looked at cell type population dynamics and gene expression changes between HFD and CTRL for all hormone-producing cell types. Our study revealed diet-induced changes in pituitary gland plasticity and hormone production that may play a role in altered hormone production in obese patients and consequently, dysregulation of pituitary gland homeostasis.

overall_design: WT male mice were placed on CTRL or HFD for 12 weeks. After 12 weeks on their respective diets, pituitary glands were collected and enzymatically digested separately into single cell suspensions. Cell suspensions were counted and scRNA-seq was performed using the 10x Genomics Chromium Next GEM Single Cell 3’ v.3.1 Dual Index kit and protocol.

first: Rebecca

last: Ruggiero-Ruff

first: Brandon

last: Le


title: Id3 is required for the maintenance of tissue-infiltrating alloreactive T cells in GVHD but not anti-leukemia responses

city: Nutley

first: Ying

last: Wang

state: NJ

address: 111 Ideation Way

institute: Hackensack Meridian Health Center for Discovery and Innovation


title: Comparative transcriptome analysis of testes and ovaries reveals sex-biased genes and pathways in zebrafish

city: Hefei

first: Qiang

last: Hong

address: Hefei

institute: Anhui Medical University

summary: The goals of this study are to compare the differentially expressed genes between testes and ovaries of zebrafish  based on RNA-seq data and some of these genes were validated by qRT–PCR.Further, the differentially expressed genes were devided into up-regulated and down-regulated genes for GO and KEGG analysis.

overall_design: Testes and ovaries  mRNA profiles of adult  zebrafish were generated by deep sequencing. Every sample was compose of three  adult individuals.

first: Cong

last: Li

first: Rui

last: Cai

first: Wenhui

last: Shi


title: Id3 is required for the maintenance of tissue-infiltrating alloreactive T cells in GVHD but not anti-leukemia responses [scRNA-Seq]

summary: To identify how Id3 transcriptionaly regulate alloreactive CD4 T cells and whether this leads to the generation of distinct alloreactive donor T cell populations.

overall_design: WT or Id3-KO CD4 T cells were transplanted to lethally irradiated Balb/c mice. Donor CD4 T cells were seperated from the spleens and  livers of recipient mice 3 weeks after hematopoietic stem cell transplantation for scRNAseq library preparation.

first: Shan

last: He

first: Gennaro

last: Calendo

first: Tien

last: Bui

first: Yuanyuan

last: Tian

first: Che

last: Lee

first: Xin

last: Zhao

first: Ciril

last: Abraham

first: Wenbin

last: Mo

first: Mimi

last: Chen

first: Ruqayyah

last: Sanders Braggs

first: Jozef

last: Madzo

first: Jean-Pierre

last: Issa

first: Elizabeth

last: Hexner

first: David

last: Wiest

first: Ran

last: Reshef

first: Haihui

last: Xue

first: Yi

last: Zhang


title: RNA -seq analysis of cells co-culture with ROS producing cells

city: Dallas

first: Matt

last: Sieber

state: Texas

address: 5323 Harry Hines blvd, MC 9040 ND12.214

institute: UT Southwestern Medical Center

summary: The the experiment examines the non-cell autnomous effetc og ROS productionn on adjacent cells.

overall_design: We co-cultured HEK293(+GFP) with ROS producing HEK293 (+DAAO) cells for 10 hr and FACS sorted out the GFP positive cells. We then compared the gene expression profiles of HEK293(+GFP) to HEk293 (+GFP) cells co-culture with ROS producing HEK293(DAAO) cells. Both GFP + WT controls and  and ROS-co-culture cells  were FASC sorted in this experiment.

first: Mathew