title: Artificial Intelligence-powered Drug Discovery against CTLA-4 in Cancer

city: HOUSTON

first: Navid

last: Sobhani

state: TEXAS

address: 1 BAYLOR PLAZA

department: Medicine, Epidemiology and Population Sciences

institute: Baylor College of Medicine

summary: Cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) plays a pivotal role in preventing autoimmunity and fostering anticancer immunity by interacting with B7 proteins CD80 and CD86. CTLA-4 is the first immune checkpoint targeted with a monoclonal antibody inhibitor. Checkpoint inhibitors have generated durable responses in many cancer patients, representing a revolutionary milestone in cancer immunotherapy. However, therapeutic efficacy is limited to a small portion of patients, and immune-related adverse events are noteworthy, especially for monoclonal antibodies directed against CTLA-4. Previously, small molecules have been developed to impair the CTLA-4: CD80 interaction; however, they directly targeted CD80 and not CTLA-4. In this study, we performed artificial intelligence (AI)-powered virtual screening of approximately ten million compounds to target CTLA-4. We validated primary hits with biochemical, biophysical, immunological, and experimental animal assays. We then optimized lead compounds and obtained inhibitors with an inhibitory concentration of 1 micromole in disrupting the interaction between CTLA-4 and CD80. Unlike ipilimumab, these small molecules did not degrade CTLA-4. Several compounds inhibited tumor development prophylactically and therapeutically in syngeneic and CTLA-4-humanized mice. This project supports an AI-based framework in designing small molecules targeting immune checkpoints for cancer therapy.

overall_design: Tumors from CTLA-4-humanized MC38 syngeneic mice (n = 3 - 5 mice) were extracted for single cell suspension using a gentleMACSTM Octo Dissociator. The cells were stained with anti-mouse CD45 antibody (PE-Cy7, Clone 30-F11, Cat. 103114, Lot: B354212) and sorted with a BD FACSAriaII Cell Sorting Flow Cytometer. Library preparation of CD45+ sorted cells for single-cell- RNA sequencing (scRNA-seq) was performed using the 10X Genomics Chromium Single Cell 5’ Library & Gel Bead reagent kit. For TCR sequencing, the Chromium Single Cell V(D)J Enrichment kit was used. The acquired scRNA-seq reads from the 10X Genomics platform were aligned using Cell Ranger (V.7.1, 10 X Genomics) to a reference genome (mm10) using default parameters. R studio Seurat package was used for analyses.

first: Yong

last: Li


title: Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [Ribosome_Profiling]

status: Public on Feb 15 2024

city: Bethesda

first: Pedro

middle: J

last: Batista

state: MD

address: 37 Convent Street Bldg 37

department: National Cancer Institute

country: USA

institute: National Institutes of Health

type: Expression profiling by high throughput sequencing

summary: Metabolic reprogramming is a hallmark of cancer that facilitates changes in many adaptive biological processes. Mutations in the tricarboxylic acid (TCA) cycle enzyme fumarate hydratase (FH) lead to fumarate accumulation and cause hereditary leiomyomatosis and renal cell cancer (HLRCC). HLRCC is a rare, inherited disease characterized by the development of non-cancerous smooth muscle tumors of the uterus and skin, and an increased risk of a highly metastatic and aggressive form of kidney cancer. Fumarate has been shown to inhibit 2-oxyglutarate-dependent dioxygenases (2OGDDs) involved in the hydroxylation of HIF1α, as well as in DNA and histone demethylation. However, the link between fumarate accumulation and changes in RNA post-transcriptional modifications has not been defined. Here, we determine the consequences of fumarate accumulation on the activity of different members of the 2OGDD family targeting RNA modifications. By evaluating multiple RNA modifications in patient-derived HLRCC cell lines, we show that mutation of FH selectively alters the activity of demethylases acting upon N6-methyladenosine (m6A), while the demethylases acting upon N1-methyladenosine (m1A) and 5-formylcytosine (f5C) in mitochondrial RNA are unaffected. The observation that metabolites may modulate specific subsets of RNA-modifying enzymes offers new insights into their gene regulatory effects and potential strategies for therapeutic intervention.

first: Christina

middle: M

last: Fitzsimmons

first: Mariana

middle: D

last: Mandler

first: Judith

middle: C

last: Lunger

first: Dalen

last: Chan

first: Siddhardha

middle: S

last: Maligireddy

first: Alexandra

last: Schmiechen

first: Supuni

middle: T

last: Gamage

first: Courtney

last: Link

first: Lisa

last: Jenkins

first: Daniel

middle: R

last: Crooks

first: Jordan

middle: L

last: Meier

first: W

last: Linehand


title: Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [SLAM-seq]

overall_design: SLAM-seq


title: Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [m6A-IP]


title: Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [RNA-Seq]

overall_design: UOK262 RNA-seq

last: Thalalla Gamage


title: Rewiring of RNA methylation by the oncometabolite fumarate in renal cell carcinoma [miRNA-seq]

type: Non-coding RNA profiling by high throughput sequencing

overall_design: miRNA-seq


title: CASP4/Caspase-11 expression exacerbates neuroinflammation and amyloid-β deposition during Alzheimer’s disease

city: Columbus

first: Amy

last: Hite

state: OH - Ohio

address: 1800 Cannon Drive 250 Lincoln Tower

department: Biomedical Informatics

institute: The Ohio State University

type: Methylation profiling by high throughput sequencing

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus

overall_design: Refer to individual Series


title: CASP4/Caspase-11 expression exacerbates neuroinflammation and amyloid-β deposition during Alzheimer’s disease [RRBS]

summary: Alzheimer’s Disease (AD) is the 6th leading cause of death in the US. It is established that neuroinflammation contributes to the synaptic loss, neuronal death, and symptomatic decline of AD patients. Accumulating evidence suggests a critical role for microglia, innate immune phagocytes of the brain. For instance, microglia release pro-inflammatory products such as IL-1β which is highly implicated in AD pathobiology. The mechanisms underlying the transition of microglia to proinflammatory promoters of AD remain largely unknown. To address this gap, we performed Representation Bisulfite Sequencing (RRBS) to profile global DNA methylation changes in human AD brains compared to no disease controls. We identified differential DNA methylation of CASPASE-4 (CASP4), which when expressed, can be involved in generation of IL-1β and is predominantly expressed in immune cells. DNA upstream of the CASP4 transcription start site was hypomethylated in human AD brains, which was correlated with increased expression of CASP4. Furthermore, microglia from a mouse model of AD (5xFAD) express increased levels of CASP4 compared to wild-type (WT) mice. To study the role of CASP4 in AD, we developed a novel mouse model of AD lacking CASP4 (5xFAD/Casp4-/-). The expression of CASP4 was associated with increased accumulation of pathologic protein aggregate amyloid-β (Aβ) in 5xFAD mice. Utilizing RNA sequencing, we determined that CASP4 promotes unique transcriptomic phenotypes in 5xFAD mouse brains, including alterations of neuroinflammatory and chemokine signaling pathways. Notably, in vitro, CASP4 promoted generation of IL-1β from macrophages and microglia in response to cytosolic Aβ through cleavage of downstream effector GASDERMIN-D (GSDMD). We are the first to describe a role for CASP4 and GSDMD in the generation of IL-1β in response to Aβ and the progression of pathologic inflammation in AD. Overall, our results demonstrate that overexpression of CASP4 due to differential methylation in AD microglia contributes to the progression of AD pathobiology, thus identifying CASP4 as a potential target for immunotherapies for the treatment of AD.

overall_design: 5 replicates of control compared to 5 replicates of Alzheimer's

first: Kylene

middle: P

last: Daily

first: Amal

middle: O

last: Amer

last: Webb


title: CASP4/Caspase-11 expression exacerbates neuroinflammation and amyloid-β deposition during Alzheimer’s disease [RNA-seq]

overall_design: 6 replicates (3 males and 3 females) of control and CASP4/Casp11 knockout compared to 5xFAD mice with and without knockout


title: mRNA expression profile in wild-type and Lba1 (Trank1) KO bone marrow derived dendritic cell (BMDC)  infected with Sendai virus

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

country: Japan

institute: Toray Industries,Inc.

summary: mRNA expression profiles were compared between wild-type and Lba1 KO BMDC  infected with Sendai virus.

overall_design: WT and LBA1 KO BMDC were diferentiated and infected with Sendai virus for 6 hours.  Total RNA was extracted from infected BMDC.

first: Takahisa

last: Kouwaki

first: Hiroyuki

last: Oshiumi


title: Divergent learning-related transcriptional states of cortical glutamatergic neurons

city: Kingston

first: Ying

last: Zhang

state: RI

address: 120 Flagg Rd

department: Cell and Molecular Biology

institute: University of Rhode Island

summary: Experience-dependent gene expression reshapes neural circuits, permitting learning of knowledge and skills. However, the diversity of plasticity-related transcriptional responses across neurons underlying learning remains poorly understood. Here, we analyzed single-nucleus transcriptomes of L2/3 glutamatergic neurons of the primary motor cortex after motor skill training or home-cage control in water-restricted mice.

overall_design:
The caudal forelimb area of primary motor cortex for 6 mice was analyzed using snRNAseq (shallow and deep sequencing was performed for each mouse). 3 mice were control, and 3 were trained on a lever-press task.
barcode suffixes (-1 to -6) correspond to the samples titled "M1 nuclei, control, mouse1, shallow snRNAseq ", "...mouse2...", "…mouse3…", etc., respectively

first: Katie

last: Dunton

first: Nathan

middle: G

last: Hedrick

first: Saber

last: Meamardoost

first: Chi

last: Ren

first: James

last: Howe

first: Jing

last: Wang

first: Cory

last: Root

first: Rudiyanto

last: Gunawan

first: Takaki

last: Komiyama

first: Eun

last: Hwang


title: Transcriptomic signature of treatment with recombinant laminin 511-E8 and acetazolamide in human H69 cholangiocytes

city: Amsterdam

first: David

last: Trampert

address: Meibergdreef 69-71

department: Department of Gastroenterology & Hepatology

country: Netherlands

institute: Amsterdam UMC

summary: IgG4-related cholangitis (IRC) is the hepatobiliary manifestation of IgG4-related disease (IgG4-RD), a systemic, B-cell driven, fibroinflammatory disorder. To date, numerous autoantigens have been described including laminin 511-E8 and carbonic anhydrase (CA) enzymes (PMID 30089633, 15647194). Laminin 511-E8 is an extracellular matrix protein that has been shown to upregulate secretory components and aid in the cholangiocyte differentiation of induced pluripotent stem cells (PMID 27103433). Carbonic anhydrase enzymes catalyse the reversible hydration of carbon dioxide, thereby producing bicarbonate and a single proton. In humans there are 14 different CA isoforms with a confined subcellular distribution. All isoforms can be targeted by the pan-CA inhibitor acetazolamide, which is a registered drug for multiple indications. We aimed to investigate the role of IgG4-RD autoantigens laminin 511-E8 and CA enzymes in human cholangiocytes. Transcriptional profiling may provide insights into the underlying molecular mechanisms of these proteins on the cholangiocellular level. Thus, by RNA sequencing the transcriptomic signature of recombinant laminin 511-E8 and acetazolamide treatment was assessed in human H69 cholangiocytes.

overall_design: RNA quality was assessed for four biological replicates of each group by RIN scores. For each group the three samples with the highest RIN scores were selected for library preparation and mRNA sequencing. Group names are Ctrl H69, Laminin 511-E8 0.25ug/cm2 H69 and Acetazolamide 10uM H69. Dose titration experiments and available literature were taken into account to arrive at the chosen experimental concentrations.

first: Remco

middle: H

last: Kersten

first: Aldo

last: Jongejan

first: Stan

last: van de Graaf

first: Ulrich

last: Beuers


title: MAVI1, an Endoplasmic Reticulum-localized Microprotein, Suppresses Antiviral Innate Immune Response by Targeting MAVS on Mitochondrion

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

country: China

institute: Xiamen University

summary: Pattern recognition receptors (PRRs)-mediated innate immune responses are critical for host defense against microbial pathogens including RNA/DNA viruses. A growing number of coding genes and genes originally defined as non-coding RNAs (ncRNAs) are found to encode short peptides or proteins, named microproteins. However, the landscape of microproteins in responsive to virus infection and the functions of these microproteins remain uncharacterized. Here, we systematically identified microproteins, both from coding and non-coding genes, that are responsive to Vesicular Stomatitis Virus (VSV) infection. Among which, a highly conserved, endoplasmic reticulum (ER) membrane-localized microprotein, , MAVI1 (microprotein in antiviral immunity 1), was found to interact with mitochondrial localized MAVS protein, inhibiting the aggregation of MAVS and the activation of downstream type I interferon (IFN) signaling pathway. The critical role of MAVI1 was highlighted that viral infection was significantly attenuated and survival rate was significantly increased in Mavi1 knockout mice in vivo. A peptide inhibitor targeting the interaction between MAVI1 and MAVS is potent in activating the type I IFN signaling and defending viral infection both in vitro and in vivo. Our findings uncovered that microproteins could play critical roles in regulating antiviral innate immune responses via cross-organelle interaction, and targeting microproteins might represent a potential therapeutic avenue for treating viral infection in clinic.

overall_design: RNA-seq performed in this study was designed to reveal the genes that respond to VSV stimulation

first: Wen

last: Liu

last: Huang

first: Jian-cheng

first: Tao-Tao

last: Shi


title: Immunomodulatory drugs (IMiDs)- or cereblon E3 ligase modulator (CELMoD)-induced growth suppression of Adult T-Cell Lymphoma/Leukemia (ATL) cells and the intrinsic rolls of cereblon for down-regulation of target proteins and their down-stream effectors II

city: Yufu-city

first: Yoshiyuki

last: Tsukamoto

state: Oita

address: hasamacho idaigaoka 1-1

department: Molecular Pathology

institute: Oita university, Faculty of Medicine

summary: Adult T-cell lymphoma/leukemia (ATL) is an aggressive subtype of leukemia/lymphoma caused by human T-cell leukemia virus type-1 (HTLV-1) and existing chemotherapy for ATL remains with extremely poor prognosis. Therefore, more effective therapeutic options are urgent needs for this disease. Since recent two clinical studies proved promising curability of Lenalidomide (LEN, a second-generation immunomodulatory drug [IMiDs]) for ATL patients, we investigated the direct growth-inhibitory machineries of LEN on ATL cells. Among 13 ATL-related cell lines, Hut102 and TL-Om1 exhibited best response to LEN treatment and LEN-induced functional modulation of E3-ubiquitin ligase cereblon (CRBN) induced degradation of hematopoietic-specific ikaros-family transcription factors IKZF1 and IKZF3 followed by suppression of their down-stream effectors IRF4 and c-Myc (both have been implied to promote ATL cell malignancy). Additionally, Hut102 and TL-Om1 displayed impaired expression of IKZF2 (deletion in HuT102 and altered translational variants in TL-Om1). LEN-induced growth inhibition to these two cell-lines seemed to be attributed to functional deprivation of all IKZF1/2/3. While CRBN-knockdown (KD) in HuT102 imposed LEN-resistance, IKZF2-KD in LEN-resistant ED40515 induced LEN sensitivity. DNA microarray analysis on LEN-treated HuT102 and OATL4 (LEN-resistant) displayed distinct LEN-responding transcriptional profiles; restoration of immune competency and oncogenic growth promotion respectively. Oral administration of LEN to HuT102-xenographted SCID mice demonstrated significant reduction of tumor mass. Finally, a novel form of IMiDs or cereblon modulator (CELMoD), iberdomide (IBE) exerted deeper and wider range of growth suppression to ATL cells including IKZF2 down regulation. Altogether, these findings strongly indicate the therapeutic advantages of IMiDs or CELMoD against ATL.

overall_design: To identify differentially expressed genes after the treatment with Lenalidomide, ATL cell lines were treated with DMSO orLenalidomide for 24h. Then, total RNAs were collected from these cell lines and subsequently subjected to gene expression microarray analysis.

first: Yu

first: Shunsuke

last: Shimosaki

first: Emi

last: Ikebe

first: Hidekatsu

last: Iha

first: Jun-ichi

last: Yamamoto

first: Nichole

last: Fife

first: Tomonaga

last: Ichikawa

first: Mitsuo

last: Hori

first: Masao

last: Ogata

first: Naoki

last: Hijiya

first: Masatsugu

last: Moriyama

first: Shotaro

last: Hagiwara

first: Shuichi

last: Kusano

first: Masumichi

last: Saito

first: Kamruddin

last: Ahmed

first: Shuji

last: Uno

first: Kenichi

last: Minehata

first: Atsushi

last: Suzuki

first: Akira

last: Nishizono

first: Hiroshi

last: Handa

first: Kazuhiro

last: Morishita


title: Immunomodulatory drugs (IMiDs)- or cereblon E3 ligase modulator (CELMoD)-induced growth suppression of Adult T-Cell Lymphoma/Leukemia (ATL) cells and the intrinsic rolls of cereblon for down-regulation of target proteins and their down-stream effectors

first: Yoshiyuki

last: Tsukamoto

first: Yu

last: Wang

first: Shunsuke

last: Shimosaki

first: Emi

last: Ikebe

first: Hidekatsu

last: Iha

first: Jun-ichi

last: Yamamoto


title: LHFPL3-AS2 lncRNA regulates epithelial polarity and its reduced expression is linked with more severe Crohn Disease

city: Ramat Gan

first: Tzipi

last: Braun

address: Derech Sheba 2

country: Israel

institute: Sheba Medical Center at Tel Hashomer

summary: LHFPL3-AS2 knockdown  Caco-2 cells (g1 and g2) and controls (gCtl)

overall_design: A loss-of-function (LOF) system in Caco-2, We used the CRISPR interference (CRISPRi) system and two independent LHFPL3-AS2 specific guide RNAs (g1 and g2 gRNAs), which depleted LHFPL3-AS2 expression as confirmed by qPCR in comparison to control gRNA.

first: Katya

middle: E

last: Sosnovski

first: Amnon

last: Amir

first: Marina

last: BenShoshan

first: Haya

last: Abbas-Egbariya

first: Rakefet

last: Ben-Yishay

first: Liat

last: Anafi

first: Camilla

last: Avivi

first: Iris

last: Barshack

first: Lee

middle: A

last: Denson

first: Haberman

last: Yael


title: Effect of Kidney-specific deletion of ALR  on gene expression in ischemia reperfusion induced AKI

city: Yuzhong District

first: Lili

last: Huang

state: Chongqing

address: Chongqing

institute: The Second Affiliated Hospital, Chongqing Medical University

summary: To investigate the differentially expressed genes in kidney from the acute kidney injury, we establishedIschemia reperfusion model from C57 mouse.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2different grpups at  I/R 24h time points.


title: Autocrine Sfrp1 inhibits fibroblast invasion during transition to injury induced myofibroblasts - Tcf21 labeled mice

city: Biberach

first: Meshal

last: Ansari

address: Birkendorfer Straße 65

country: Germany

institute: Boehringer Ingelheim

summary: Fibroblast to myofibroblast conversion is a major driver of tissue remodeling in organ fibrosis. Here, we combined spatial transcriptomics, longitudinal single-cell RNA-seq and genetic lineage tracing to study fibroblast fates during mouse lung regeneration. We discovered a transitional fibroblast state characterized by high Sfrp1 expression, derived from both Tcf21-Cre lineage positive and negative cells. Sfrp1+ cells appeared early after injury in peribronchiolar, adventitial and alveolar locations and preceded the emergence of myofibroblasts. We identified lineage specific paracrine signals and inferred converging transcriptional trajectories towards Sfrp1+ transitional fibroblasts and Cthrc1+ myofibroblasts. Tgfβ1 downregulated Sfrp1 in non-invasive transitional cells and induced their switch to an invasive Cthrc1+ myofibroblast identity. Our study reveals the convergence of spatially and transcriptionally distinct fibroblast lineages into transcriptionally uniform myofibroblasts and identifies Sfrp1 as an autocrine inhibitor of fibroblast invasion during early stages of fibrogenesis.

overall_design: Single-cell transcriptomics experiment of Tcf21 labeled mice lungs

first: Christoph

last: Mayr

first: Arunima

last: Sengupta

first: Gerald

last: Burgstaller

first: Fabian

last: Theis

first: Herbert

middle: B

last: Schiller


title: CircRNAome of childhood B-ALL: Deciphering subtype-specific expression profiles and functional involvement

city: Montreal

first: Daniel

last: Sinnett

state: QC

address: 2900 Edouard Montpetit Blvd

country: Canada

institute: University of Montreal

summary: Childhood acute lymphoblastic leukemia (ALL) is a heterogeneous disease comprising multiple molecular subgroups with subtype-specific expression profiles. Recently, a new type of ncRNA, termed circular RNA (circRNA), has emerged as a promising biomarker in cancer, but little is known about their role in childhood B-ALL. Here, through RNA-seq analysis in 105 childhood B-ALL patients comprising 6 genetic subtypes and 7 B-cell controls from two independent cohorts, we demonstrated that circRNAs properly stratified B-ALL subtypes. By differential expression analysis, 110 overexpressed and 134 underexpressed circRNAs were identified consistently for each subtype in both cohorts. Focusing on overexpressed circRNAs, most of them had a subtype-specific expression, with 73 circRNA (66%) only expressed in one subgroup. Interestingly, TCF3/PBX1 subtype was the one with the highest number of unique circRNAs, as well as overexpressed circRNAs. Our results indicated that NUDT21, an RNA-binding protein (RBP) involved in circRNA biogenesis, contributes to this circRNA enrichment in TCF3-PBX1 ALL. Further functional characterization using CRISPR-Cas13d system demonstrated that circBARD1 (hsa_circ_0001098), overexpressed in TCF3/PBX1 subtype, was involved in cancer phenotypes. Our results suggest that circRNAs could have a role in the pathogenesis of childhood B-ALL, adding a new layer of complexity in leukemogenesis.

overall_design: Profiling the circRNAome of pediatric B cell acute lymphoblastic leukemia patients

first: Angela

last: Gutierrez-Camino


title: Role of TNFRSF13B (CD267) in prostate cancer progression identified via genetic analysis

city: Taichung

first: Wei-Chung

last: Cheng

address: No.91, Hsueh-Shih Road

country: Taiwan

institute: China Medical University

summary: We performed microarray analysis using differnt prostate cancer cell lines (PC3 and 22RV1) after TNFRSF13B (CD267) knockdown. We reported that TNFRSF13B regulates cell cycle-associated genes and P53 signaling pathway in PC3 and 22RV1 cells.

overall_design: Examination of mRNA profile of differnt prostate cancer cell lines (PC3 and 22RV1) under TNFRSF13B (CD267) knockdown.

first: Chia-Yang

last: Li

first: Bo-Ying

last: Bao


title: Microarray of brain microglia from GM-CSF-expressing B cell conditional knock-out mice at EAE peak stage

status: Public on Feb 25 2024

city: Harbin

first: Jiahui

last: Zhu

state: HEILONGJIANG SHENG

address: No.157 Baojian Road, Nangang District

department: Neurobiology

institute: Harbin Medical University

summary: We found a kind of GM-CSF producing B cells (BGM) is positively correlated with the pathogenesis of EAE. BGM cell conditional knock-out (CKO) mice showed significant resistance to EAE. To investigate the relationship between BGM cells and microglia and comprehensively evaluate the status of microglia, we obtained microglia from the brain of CKO and control mice at EAE peak stage, extracted microglial RNA, and performed microarray analysis.

overall_design: We obtained microglia from the brain of CKO and control mice at EAE peak stage, extracted microglial RNA, and performed microarray analysis.

first: Xi

last: Wang


title: Identification of the miRNA-mRNA regulatory network of Toxoplasma gondii based on RNA-seq

city: Hangzhou

first: Jia

state: Zhejiang province

address: 568 Mingshi Road, Jianggan District, Hangzhou

institute: Hangzhou Center for Disease Control and Prevention

summary: To explore the potential miRNA‑mRNA regulatory mechanism and relevant signaling pathways, we profiled host miRNA and mRNA levels during T.gondii infection with microarrays, bioinformatics, and integrated genomics analyses. Reverse transcription‑quantitative polymerase chain reaction (RT‑qPCR) was performed to validate the reliability of microarray data.The present study performed global expression analysis of 41,000 genes and 2,549 microRNAs using the Agilent Whole Human Genome 8 x 60k slide formats printed using Agilent's 60-mer SurePrint technology, respectively. Compared with the controlled cells, a total of 3,568 mRNAs were significantly differentially expressed, including 1,475 upregulated genes (fold change ≥2) and 463 downregulated genes (fold change ≤0.5).

overall_design: The SK-N-SH cells were passaged every 2‑3 days to maintain exponential growth. SK-N-SH cells were left uninfected or infected (MOI = 3) for 24 hours with RH tachyzoites.All the cells were constructed from at least three indepen¬dent experiments.


title: PTIR1 acts as a suppressor of immunoproteasome and promotes cancer immune resistance

status: Public on Feb 19 2024

city: Beijing

last: Song

state: China

address: Peking University School of Medicine, 38 Xueyuan Road, Haidian District, Beijing

institute: Peking University

summary: Cancer cells evade host immune surveillance by virtue of poor immunogenicity. We identify a novel oncogene that acts as a promotor of tumor immune resistance, designated as PTIR1. Tumor-intrinsic PTIR1 is induced by RNA splicing and highly correlated with poor outcome of patients with cancer.

overall_design: Study of  tumor infiltration lymphocytes in Mock or PTIR1 expressing CT26 tumors using 10x scRNA-seq technologies.

first: Dan

last: Lu

first: Xin

last: Zhang


title: Transcriptome profiling (RNA-seq) to identify aberrant splicing events in induced pluripotent stem cells derived from an ALS patient harboring a TDP-43(M337V) mutation

status: Public on Feb 23 2024

city: Sangareddy

first: Ashish

last: Misra

state: Telangana

address: Kandi

department: Biotechnology

country: India

institute: Indian Institute of Technology Hyderabad

summary: Mutations in the TDP-43 gene (also called TARDBP), which encodes transactive response DNA-binding protein 43 (TDP-43), have been found in 1–5% of sporadic and familial cases of the devastating adult-onset neurodegenerative disorder amyotrophic lateral sclerosis (ALS). TDP-43 is a predominantly nuclear RNA/DNA-binding protein that has diverse roles in RNA processing, but in diseased motor neurons it is depleted from the nucleus and sequestered into cytoplasmic protein aggregates that are a hallmark of the disease. How the loss of the RNA/DNA-binding activity of TDP-43 contributes to ALS pathogenesis is largely unknown. Using a large-scale RNAi screening approach, we recently identified TDP-43 as a gene required for maintaining genomic stability. We showed that induced pluripotent stem cells (iPSCs) and neurons derived from ALS patients harboring TDP-43 mutations are defective in two major pathways for repair of DNA double-strand breaks, non-homologous end joining and homologous recombination. Accordingly, TDP-43-mutant ALS iPSCs and neurons display increased DNA damage, which we also observed in brain tissues from ALS mice harboring a knock-in ALS-linked Tdp-43 mutation and from human ALS patients. To gain insight into the mechanistic basis by which ALS-associated TDP-43 mutants result in increased DNA damage, we performed transcriptome profiling (RNA-seq) in TDP-43-mutant ALS iPSCs, and found aberrant alternative pre-mRNA splicing of a number of genes involved in DNA repair. Our results suggest a role for TDP-43 in DNA repair and reveal a previously unknown mechanism that likely contributes to the pathogenesis of ALS harboring TDP-43 mutations.

overall_design: Paired-end RNA-seq to compare splicing events in TDP-43 (WT) and TDP-43(M337V) ALS iPSCs

first: Minggang

last: Fang

first: Lihua

first: Michael

last: Green


title: PPARδ inhibition blocks tumor-induced Bregs and enhances CD40 agonist immunotherapy

status: Public on Feb 20 2024

city: Changchun

first: Cong

last: Fu

state: Jilin

address: NO.17  Xinmin Street

institute: The First Hospital of Jilin University

summary: Most cancers are cold tumors characterized by a lack of effector T cells and hence unresponsive to immune checkpoint blockades, highlighting the importance of repairing the failed T cell priming in cancer immunotherapy. CD40 agonists are efficient in eliciting T cell responses and effective in converting cold tumors into hot, their clinical application, however, is limited by the very narrow window between the effective and toxic dosages. Here, we sought to reduce the effective dosage of CD40 agonists by combination therapy. We identified a CD19+CD24hiCD38lowIgDlow/- regulatory B cell (Breg) subset that is increased in tumor-bearing mice and cancer patients, and discovered that PPARδ is highly expressed in these tumor-associated Bregs and required for their proliferation and function. Inhibition of PPARδ acted synergistically with agonist anti-CD40 to enhance antitumor immunity without increasing toxicity in murine melanoma and bladder carcinoma models. Combination therapy with PPARδ inhibitor could reduce anti-CD40 dosage by over 60% to a well-tolerated level with improved or at least not compromised antitumor effects, providing a potential strategy for safely using CD40 agonists in cancer treatment. PPARδ also offers a new target for selectively blocking Breg activity while sparing immunostimulatory B cells that are known to aid antitumor immunotherapy.

overall_design: C57BL/6 mice were inoculated s.c. with 7 × 105 B16 cells and treated 8 days later by FGK45.5 or Rat IgG (peritumorally s.c.; 25 μg × 3 at day 8, 11 and 14), or GSK3787 (300 nmol; daily from day 8 to day 16), or FGK45.5 plus GSK3787. Cells of draining lymph nodes were prepared from these tumor-bearing mice at day 17 and age-matched naïve mice (n=3/group), and CD19+ B cells were sorted from pooled draining lymph nodes and analyzed for whole-transcriptome profiling by RNA-seq.

first: Chen

last: Chen

first: Jianan

last: Ma

first: Chenchen

last: Pi

first: Shulian

last: Tan

first: Tao

first: Wentao

last: Liu

first: Yong-Guang

last: Yang


title: Pancreatic Stellate Cells Promote Growth and Metastasis of Pancreatic Neuroendocrine Tumor

status: Public on Feb 22 2024

city: Taipei

first: Yu-Wen

last: Tien

address: 7 Chung-Shan S.Rd.

department: Surgery

institute: NTUH

summary: We aimed to study the interaction of PNETs and pancreatic stellate cells (PSCs) in PNET progression through exploring specific gene expression of PNETs cultured with conditional media of PSCs.

overall_design: QGP-1 cells were cultured with mock or conditional media of pancreatic stellate cells (PSCs). Total RNA was extracted and gene expression changes were analysed by microarray in comparsion to QGP-1 cultured with or without conditional media of PSCs.

first: Tsai-Chen

last: Chiang


title: RNA Sequencing of three pairs of gastric cancer tissues

city: Nanjing

first: Duochen

last: Jin

address: No. 300 of Guangzhou Road, Nanjing 210029, China.

institute: the First Affiliated Hospital of Nanjing Medical University

summary: Circular (circ) RNAs have been widely reported to be involved in gastric cancer (GC) pathogenesis and coiled coil domain containing 6 (CCDC6) is recognized as fused partner of multiple oncogenes; however, the underlying mechanisms of how circRNAs regulate CCDC6 expression in the progression and prognosis of GC remain unclear. Here, we discovered a novel circRNA derived from the DNA2 gene locus (circDNA2) through joint analysis of circRNA microarrays. By performing qRT-PCR and FISH assays with a human tissue microarray, circDNA2 was identified to be highly expressed in GC tissues and associated with lymphatic invasion of GC patients. Knockdown of circDNA2 suppressed the proliferation of GC cells by reducing CCDC6 expression in vitro. Mechanically, circDNA2 acted as a sponge for microRNA (miR)-149-5p, which was validated to target CCDC6 by dual luciferase reporter assays and rescue experiments. Both miR-149-5p low expression and CCDC6 high expression were related to unfavorable prognosis of GC patients. Moreover, GC patients with low miR-149-5p expression had shorter overall survival and higher risk of chemotherapy resistance compared with these with high miR-149-5p expression. In summary, our findings reveal that circDNA2 contributes to the growth and lymphatic metastasis of GC through upregulating CCDC6 expression via sponging miR-149-5p. The circDNA2/miR-149-5p/CCDC6 axis might be developed as a therapeutic target and prognostic indicator for GC patients.

overall_design: RNA profiles of three pairs of gastric cancer and adjacent normal gastric tissues were generated with Illumina HiSeq 4000 Sequencer.

first: Yan


title: CREBBP cooperates with cell cycle machinery to attenuate chidamide sensitivity in relapsed/refractory DLBCL

status: Public on Feb 24 2024

city: Guangzhou

first: Jianfeng

address: No.651 East Dongfeng Road

institute: Sun Yat-sen University

summary: Frequent inactivating mutations of histone acetyltransferase CREBBP is a characteristic feature of diffuse large B-cell lymphoma (DLBCL), highlighting the attractiveness of targeting the CREBBP deficiency as a therapeutic strategy. In this study, we demonstrate that chidamide, a novel histone deacetylase (HDAC) inhibitor, is effective in treating a subgroup of relapsed/refractory DLBCL patients, achieving an overall response rate (ORR) of 25.0% and a complete response (CR) rate of 15.0%. However, the clinical response to chidamide remains poor as most patients exhibit resistance, hampering the clinical utility of the drug. Functional studies in both in vitro and in vivo models showed that CREBBP loss of function is correlated with chidamide sensitivity, which is associated with modulating cell cycle machinery. A combinatorial drug screening of 130 kinase inhibitors targeting cell cycle regulators identified AURKA inhibitors, which inhibited G2/M transition during cell cycling, as top candidates that synergistically enhanced antitumor effects of chidamide in CREBBP-proficient DLBCL cells. Our study demonstrated that CREBBP inactivation can serve as a potential biomarker to predict chidamide sensitivity, while a combination of AURKA inhibitor and chidamide provides a novel therapeutic strategy for the treatment of relapsed/refractory DLBCL.

overall_design: RNA-seq for Karpas231 and SC1 treated with DMSO or Chidamide was performed (duplicate).

first: Yichen

last: Sun

last: Gao

first: Huiqiang

last: Huang

first: Choon

middle: K

last: Ong

first: Jing


title: High-throughput Sequencing Facilitates Quantitative Analysis of Transcriptome Difference Underlying Quercetin Antioxidant Action in Ox-LDL-induced HUVECs Damage [miRNA-Seq]

city: Tai’an City

first: Yang

last: Jiang

state: Shandong Province

address: 61 Daizong Street

institute: Shandong Agricultural University

summary: High-throughput Sequencing has revolutionized system-based analysis of cellular pathways. The goals of this study are to find the effect of quercetin pretreatment on the transcriptome of ox-LDL injured endothelial cells

overall_design: Complete transcriptome of normal HUVECs, ox-LDL injured HUVECs, and ox-LDL injured HUVECs pretreated with quercetin

first: Dapeng

last: Li


title: PTENα functions as an immune suppressor and promotes immune resistance in PTEN-mutant cancer

first: Yizhe

state: Beijing

address: No.38, Xueyuan Road ,Haidian District

institute: Peking University Health Science Center

summary: As a tumor suppressor, PTEN is frequently mutated in human cancers and PTEN mutants promote tumor progression and metastasis. PTEN mutations have been implicated in immune regulation, but the underlying mechanism is largely unknown. We report that PTENα, the isoform of PTEN, remains active in cancer bearing stop-gained PTEN mutations. Through counteraction of CD8+ T cell-mediated cytotoxicity, presence of PTENα leads to T cell dysfunction and accelerates immune-resistant cancer progression. Clinical analysis further uncovers that PTENα-active mutations suppress host immune responses and result in poor prognosis in cancer as relative to PTENα-inactive mutations. Furthermore, germline deletion of Ptenα in mice increases cell susceptibility to immune attack through augmenting stress granule formation and limiting synthesis of peroxidases, leading to massive oxidative cell death and severe inflammatory damage. We propose that PTENα protects tumor from T cell killing and thus PTENα is a potential target in antitumor immunotherapy.

overall_design: Study of tumor infiltration lymphocytes in Mock or PTENα expressing B16 Pten-/- tumors using 10x scRNA-seq technologies.

first: Dan

last: Lu

first: Xin

last: Zhang


title: Osteopontin isoform c promotes the survival of cisplatin-treated NSCLC cells involving NFATc2-mediated suppression on calcium-induced ROS levels

status: Public on Feb 17 2024

address: No. 10, Xitoutiao, Youanmenwai

institute: capital medical university

summary: Tumor microenvironment (TME) critically contributed to the malignant progression of transformed cells and the chemical responses to chemotherapy reagents. Osteopontin (OPN) is a secretory onco-protein with several splicing isoforms, all of which were known to regulate tumor growth and able to alter cell-cell or cell-TME communication. In this study using conditioned medium from the culture of OPNc (exon 4 excluded shorter form of OPN) overexpressing cells, we found that the survival of NSCLC cells treated with cisplatin was increased, where reduction of apoptosis by OPNc was associated with the activation of cellular calcium signals and subsequent translocation of nuclear factor of activated T cells c2 (NFATc2). The results revealed a mechanism of OPN and downstream signal for tumor cells to survive in chemo-stressed TME, which emphasized the importance of secretory proteins in alternative splicing isoforms. Our study not only demonstrated the importance of OPN neutralization for anti-tumor effects, but also implied that modulation in calcium/NFATc2/ROS axis could be a novel approach for improving the long-term outcome of NSCLC treatment.

overall_design: Total RNA  were obtained from A549 cells transfected with plasmid of NFATc2 or NFATc2M (deletion in the DNA binding domain) and induced with the conditioned medium from OPNc expressing cells. RNA-seq analysis was performed to find differentially expressed gene between NFATc2 and NFATc2M groups.

first: Huan

last: Niu

first: Shan

last: Cheng

first: Wei

last: Ding


title: High-throughput Sequencing Facilitates Quantitative Analysis of Transcriptome Difference Underlying Quercetin Antioxidant Action in Ox-LDL-induced HUVECs Damage [ncRNA-Seq]


title: Dietary restriction delays but cannot heal irradiation-induced hair graying by preserving hair follicle stem cells in quiescence

status: Public on Feb 21 2024

city: Kiel

first: Seyed Mohammd Mahdi

last: Rasa

state: Schleswig-Holstein

address: Michaelisstrasse 5

department: Institut for Immunology

institute: Universitätsklinikum Schleswig-Holstein

summary: DNA damage represents one of the cell intrinsic causes of stem cell aging, which leads to differentiation induced removal of damaged stem cells in skin and blood. Dietary restriction (DR) retards aging across various species including several strains of laboratory mice. Whether, DR has the potential to ameliorate DNA damage driven stem cell exhaustion remains incompletely understood. Here, we show that DR strongly extends the time to hair graying in response to γ–irradiation (IR) induced DNA damage of C57BL/6J mice. The study shows that DR prolongs quiescence of hair follicle stem cells (HFSCs) by silencing gene regulatory networks and metabolic switches that control proliferation and tissue regeneration. DR-mediated prolongation of HSFC quiescence blocks hair growth and prevents the depletion of HFSCs and ckit+ melanoblasts in response to IR. However, prolongation of HSFCs quiescence also leads to a suppression of DNA repair pathways and cannot prevent melanoblast loss and hair graying in the long run, when hair cycling is re- initiated even after extended periods of time. Together, these results support a model indicating that nutrient deprivation can delay but not heal DNA damage driven extinction of HFSCs and melanoblasts by stalling HSFCs in a prolonged state of quiescence coupled with inhibition of DNA repair. Disconnecting these two types of responses to DR could have the potential to delay stem cell aging.

overall_design: Transcriptional profile of mouse CD34+alpha6+ hair follicle stems cells fed with unlimited amount of food or dietary restriction diet

first: K

last: Rudolph

first: Duozhuang

last: Tang

first: Si

last: Tao

first: Yiting

last: Wang

first: Jianying

last: Wu

first: Marco

last: Groth

first: S

first: Francesco

last: Neri

first: Hui

last: Cui

first: Ting

last: Zeng

first: Lang

last: Lei

first: Hua


title: Single cell RNA-seq of forebrain cells isolated from wild-type mouse, rat, and chimeric mouse

first: Fan

last: Guo

address: 1 Beichen West Road, Chaoyang District

department: The State Key Laboratory of Stem Cell and Reproductive Biology

institute: Institute of Zoology, Chinese Academy of Sciences

summary: We performed single cell RNA-seq to quantify gene expression in forebrain tissue from the wild-type mouse, rat, and chimeric mouse. Single cell data from WT mouse or rat was used to perform integrative analysis for identifying rat cells and mouse cells in the chimaeras, respectively.

sample_organism:
Mus musculus
Rattus norvegicus

platform_organism:
Mus musculus
Rattus norvegicus

overall_design: Forebrain tissues from CCBC-Hesx1+rESCs mice (n = 3 mice) , WT rat (n =1 rat) and WT mouse (n =1 mouse) at P0 were subjected to scRNA-seq.

first: Jia

last: Huang

first: Bingbing

last: He

first: Xiali

last: Yang

first: Xin

last: Long

first: Leijie

last: Li

first: Haibo

last: Zhou

first: Jun


title: Circulating neutrophil transcriptomics in HBV-ACLF patients.

first: Shanshan

last: Sun

state: Zhejiang

address: Qingchun Road, No 79

department: State Key Laboratory for Diagnosis and Treatment of Infectious Diseases

institute: The First Affiliated Hospital, Zhejiang University School of Medicine

summary: The transcriptomic profiles of circulating neutrophils were compared between patients with ACLF (N=10), patients with CLC (N=10) and HC (N=10). Compared with CLC-neutrophils, the expression of 1022 genes were found to be upregulated in ACLF-neutrophils, and 1101 genes were downregulated. And compared to HC, the expression of 726 genes were up-regulated in ACLF-neutrophils, and 711 genes were down-regulated. The pathway analysis identified mutiple pathways enriched or down-regulated in ACLF-neutrophils when comparing with neutrophils from CLC or HC groups.

first: Wei

first: Ruihong

last: Zhao

first: Jifang

last: Sheng

first: Zhi

last: Chen

first: Yu

last: Shi


title: Inhibition of nucleotide biosynthesis to enhance responses to drugs targeting androgen biosynthesis and the androgen receptor

city: Belfast

first: Francesca

last: Amoroso

address: 97 Lisburn Road

country: United Kingdom

institute: Queen's University Belfast

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

overall_design: Refer to individual Series


title: Inhibition of nucleotide biosynthesis to enhance responses to drugs targeting androgen biosynthesis and the androgen receptor. [RNA-Seq]

summary: RNA-Seq analysis of prostate cancer cells derived from xenografts treated daily with drugs targeting androgen biosynthesis and the androgen receptor.

overall_design: Evaluation of the effects that targeting androgen biosynthesis and the androgen receptor in vivo has in prostate cancer samples.

first: Ian

last: Mills


title: Analysis of open chromatin structures in HCC827 CBX5 knockdown cells by ATAC seq analysis .

status: Public on Feb 18 2024

city: Birmingham

first: Narendra

last: Wajapeyee

state: AL

address: 720 20th Street South, Kaul 540A

department: Department of Biochemistry and Molecular Genetics

institute: University of Alabama at Birmingham

summary: Briefly, Human lung cancer HCC827 cells were stably expressing either CBX5 shRNAs or control shRNA were analysed for  open chromatin structures using ATAC seq Analysis.

overall_design: ATAC-seq analysis was done in HCC827 cells expressing either CBX5 shRNAs or control shRNA

first: Suresh

last: Bugide


title: mRNA profiles of Flammulina velutipes which of anti-disease and early fruiting by RNA sequencing

city: Shijiazhuang

first: Kun-ang

last: Liu

state: Hebei

address: No. 46, Friendship South Street, Qiaoxi District

department: Institute of Biology

institute: Hebei Academy of Sciences

summary: We isolated a bacterial identified as the genus of Mycetocola from the infected Flammulina velutipes samples collected from mushroom house in Hebei, North China. The stipe of F. velutipes appeared water-soaked, soften and browning after infected, finally, the whole plant rotten. The incidence of the disease can reach more than 80% in the serious areas, resulting in an obvious decline in the yield and quality of the F. velutipes. Furthermore, the pathogenic bacteria may occurrence in large areas by accumulated in the annual cultivation process. Therefore, the most effective measures to control this bacterial disease is screening resistant strains of F. velutipes with high yield and good agronomic traits. We obtained a white F. velutipes strain JK502 which has strong resistance to this bacterium by using the double-layer plate method combined with the sporozoite hybridization. JK501, which can early fruited, was screened using the same parent SH9 by multi spore hybridization. In order to investigate the differences of gene expression between the parent strain and the selected strains, we completed the transcriptome sequencing by Illumina HiSeq X system.

overall_design: Flammulina velutipes mRNA profiles of the selected strains JK501, JK502 and the parent strain SH9 were generated by deep sequencing, in triplicate, by Illumina HiSeq X system.


title: RNA-seq analysis CARM1 knockdown effect on MDA-MB-231 cells

city: beijing

first: yan

last: wang

address: 17 panjiayuan nanli, chaoyang district, Beijing, China

country: Zimbabwe

institute: National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences

summary: Coactivator associated arginine methyltransferase 1 has been reported to play paramount roles in estrogen receptor alpha (ERα)-positive breast cancer. It promotes breast cancer development and metastasis. However, little research about CARM1 has been focused on triple-negative breast cancer (TNBC). Here, we report that CARM1 promotes proliferation, epithelial-mesenchymal transition (EMT) and stemness in TNBC. CARM1 transactivates Hypoxia-inducible factor 1 subunit alpha (HIF1A) and is physically associated with it. They function together in a concerted complex to regulate downstream targets and promote the carcinogenesis and metastasis of TNBC.

overall_design: CARM1 siRNA or control were transfected into MDA-MB-231 cells (n=2 per group) for 48 hours. Total RNA was extracted using Trizol reagent (Invitrogen, USA). Agilent 2100 Bioanalyzer (Agilent Technologies, USA) was used to evaluate the RNA quality.

first: Dandan

last: Feng

first: Yan

last: Wang


title: Inhibition of nucleotide biosynthesis to enhance responses to drugs targeting androgen biosynthesis and the androgen receptor. [miRNA-Seq]

summary: RNA-Seq (miRNA) analysis of prostate cancer cells derived from xenografts treated daily with drugs targeting androgen biosynthesis and the androgen receptor.


title: ChIP-seq for SSRP1

city: Singapore

first: Yingying

last: Zeng

state: --- Select a state ---

address: 61 Biopolis Drive

country: Singapore

institute: Institute of Molecular and Cell Biology

type: Genome binding/occupancy profiling by high throughput sequencing

summary: SSRP1 ChIP-seq was performed in E14 cells

overall_design: Detect the genome region SSRP1 binds to.

first: Y

last: YI

middle: Y

first: H

last: Loh


title: High-throughput Sequencing Facilitates Quantitative Analysis of Transcriptome Difference Underlying Quercetin Antioxidant Action in Ox-LDL-induced HUVECs Damage

first: Yang

last: Jiang


title: RNA-SEQ analysis of P2 ALL Ret-positive (EGFP-labeled) FACSd male or female dorsal root ganglia neurons

city: Edinburgh

first: GUDMAP

last: Developers

address: Crewe Road

institute: IGMM MRC Human Genetics Unit

summary: The goal of this set is to build expression data using FACS isolated Ret-positive cells harvested from a Ret-EGFP reporter mouse P2 (post-natal day 2 male or female). These can be used as a time point in comparative analysis of ontogeny of genes expressed at various developmental time points.

overall_design: RNA was extracted from P2 FACS isolated dorsal root ganglia dissected from Ret-EGFP C57BL/6J mice (EGFP knocked-in Ret locus-heterozyotes) and sequenced using Illumina Hiseq 2500 platform. Refer to protocols on the GUDMAP website under Jain.

first: Eric

last: Tycksen

first: Masato

last: Hoshi

first: Amanda

last: Knoten


title: Rett syndrome-causing MECP2 mutations severely impact key cellular and molecular features of human astrocytes

city: stony brook

first: Jialin

last: Sun

state: New York

address: 100 Nicolls Road

institute: Stony Brook University

summary:
Purpose: The goal of this RNA sequencing (RNA-seq) study is to identify aberrations in the astrocyte transcriptional landscape caused by R270X mutation in MECP2.
Methods: mRNA-seq analysis was performed on total RNA extracted from human embryonic stem cell (ESCs)-derived wild-type (WT) and MECP2-R270X mutant astrocytes. The R270X mutation was inserted into ESCs (line H1) via CRISPR/Cas9 technology. Samples were generated in triplicates, sequenced by Illumina NovaSeq 6000 Sequencing System. Raw reads were first trimmed for 10 bases at the 5’end to remove reads with biased nucleotide (ACGT) distribution. Trimmed reads were then aligned to the Homo sapiens genome (GRCh38p12, GENCODE, primary assembly), using STAR aligner. Differential gene expression (DEG) analyses on the read counts were performed using DESeq2. Genes with sum of read counts across all samples with less 10 were filtered out from analysis.
Results: Our RNA-seq analysis showed that 1,621 genes were dysregulated in mutant astrocytes (fold-change >1.5 or <2/3; padj < 0.05, average reads count >10 in at least one genotype)

overall_design: The mutant samples  and their isogenic WT control samples were generated in triplicates.

first: Ying-Wooi

last: Wan

first: Nigel

last: Lee

first: Nurit

last: Ballas


title: PABPC1L promotes tryptophan metabolism and immune suppression by stabilizing IDO1 in renal cell carcinoma [RIP-seq]

status: Public on Feb 14 2024

first: Jiaxing

last: Zhang

address: 58 Zhongshan 2nd Road

institute: First Affiliated Hospital of Sun Yat-sen University

summary: The tumor microenvironment (TME) in renal cell carcinomas (RCC) is marked by substantial immunosuppression and immune resistance though highly infiltrated by T cells. There is an urgent need to elucidate tumor immune evasion and to develop novel therapeutic target to boost the efficacy of immune checkpoint blockade (ICB) in RCC. Our study uncovers a mechanism wherein the polyadenylate-binding protein PABPC1L modulates indoleamine2, 3dioxygenase1 (IDO1), a prospective candidate for immunotherapy. PABPC1L, markedly upregulated in RCC, correlates with unfavorable prognosis and resistance to ICB. Overexpressed PABPC1L bolsters tryptophan metabolism and induces T-cell dysfunction by stabilizing IDO1. Conversely, silencing PABPC1L diminishes IDO1 expression, mitigates cytotoxic T-cell suppression, and enhances responsiveness to anti-PD-1 therapy. Our findings underscore PABPC1L's crucial role in facilitating immune evasion in RCC, making it a potential addition to ICB therapy.

overall_design: RIP-sequencing of total RNA of 769-P cells which was immunoprecipited by anti-PABPC1L RIP-INPUT vs RIP-PABPC1L

first: Junhang

last: Luo

first: Yihui

last: Pan

first: Guocang


title: Generation of induced pluripotent stem (iPS) cells using non-viral magnet-based nanofection

status: Public on Feb 29 2024

city: Pohang, Kyungbuk

first: Sojeong

last: Yun

address: Hyoja-dong,Nam-gu

department: IBIO

country: South Korea

institute: POSTECH

summary: Using magneto-nanofection, iPS cells were efficiently generated by the transient expression of iPS genes in MEF (mouse embryonic fibroblast), suggesting that the non-viral magneto-nanofection method can be used for the efficient generation of iPS cells.

overall_design: Plasmid DNAs containing the iPS genes oct4, sox2, klf4 and C-myc were introduced into MEF cells using magneto-nanofection. ESC media were changed daily for two days after transfection, and we could observe some colonies showing ES-like morphology 6-7 days after transfection. The colonies were picked up 12 days after transfection, and then each colony was separately transferred to a new dish containing STO feeder cells.

first: Ssang

last: Cho

first: Daehee

last: Hwang

first: Kwang

last: Kim


title: Next generation sequencing facilities quantitative analysis of SHARPIN knockout or non-target LoVo cells

city: Beppu,

first: Yusuke

last: Nakano

address: 4546 Tsurumibaru

department: Department of Surgery

institute: Kyushu University Beppu Hospital

summary: Colorectal cancer (CRC) is one of the most common cancers and a major cause of cancer mortality worldwide. Further improvements are needed for the treatment of CRC. The E3 ubiquitin ligase is an enzyme that plays an important role in regulating protein expression levels via posttranslational ubiquitin-mediated proteolysis, and it is reportedly involved in the progression of various cancers, making it a target of recent interest in anticancer therapy. In this study, using comprehensive expression analysis involving spatial transcriptomic analysis with single-cell RNA sequencing in clinical CRC datasets, we identified the ubiquitin-associated protein Shank-associated RH domain interactor (SHARPIN) as a putative driver gene located on amplified chromosome 8q. SHARPIN was overexpressed in tumor cells, and high expression of SHARPIN in tumor tissues was positively correlated with lymphatic invasion and was independently predictive of a poor prognosis in CRC patients. In vitro and in vivo analyses using SHARPIN-overexpressing or -knockout CRC cells revealed that SHARPIN upregulated MDM2, resulting in subsequent downregulation of p53, which inhibits tumor cell apoptosis and promotes tumor growth in CRC. Furthermore, SHARPIN overexpression and significant effects on survival were observed in various cancers. In conclusion, SHARPIN is a novel driver gene that potentially promotes tumor growth following apoptosis inhibition in part by inhibiting p53 expression via MDM2 upregulation; therefore, SHARPIN represents a potential therapeutic target for CRC.

overall_design: To assess potential gene expression changes by SHARPIN individual knockout in LoVo cells, we performed a transcriptomic analysis using high throughput RNA sequencing (RNA-seq).Total RNA extracted from SHARPIN knockout or non-target LoVo cells .The sequencing libraries generated from the RNA were analyzed by DNBSEQ-G400. The sequencing reads were trimmed for adaptor sequence, and low-complexity or low-quality reads were removed. Subsequently, the reads were aligned to the human reference sequence and the gene annotations (UCSC hg19) using Tophat2 v2.1.1. STAR v2.7.10b was used to calculate fragments per kilobase of transcript per million fragments mapped (FPKM) values.

first: Takaaki

last: Masuda

first: Koshi

last: Mimori


title: Mitochondrial components transferred by MSC-derived exosomes promoted bone regeneration under high salt microenvironment via DRP1/Wnt signaling

city: Beijing

first: Shuai

last: Lin

address: No.22, Zhongguancun South Avenue

institute: Peking University School of StomatologyNo.22, Zhongguancun South Avenue

summary: Bone homeostasis relies on the dynamic balance of osteoblast mediated bone construction and osteoclast based bone resorption processes, which has been reported to be controlled by various mineral ions. However, there is no direct evidence of the effect and the underlying mechanism of high salt stimulation on bone metabolism. In this study, we demonstrated that high salt stimulation promoted excessive mitochondrial fission mediated by DRP1 in mesenchymal stem cells (MSCs), which resulted in impaired mitochondrial morphology and function. Consequently, this impairment hindered the bone formation of MSCs, resulting in osteopenia in mice. Mechanically, the impaired property of MSCs by high salt was controlled by DRP1 mediated mitochondrial fission, which inhibited the classical Wnt signaling pathway. Furthermore, the osteogenic property of MSC decreased by high salt could be restored by exosomes to transfer the mitochondrial DNA into the impaired MSCs. This study not only provides new strategies for promoting bone regeneration, but also provides new insights for the effect and mechanism of exosome-mediated delivery.

overall_design: Human primary bone marrow mesenchymal stem cells treated with or without 30mM NaCl for 48 hours.

first: Yiming

last: Wang

first: Ruili

last: Yang


title: RNA-seq based in vivo transcriptomes of Korean fir (Abies koreana) with enhanced drought tolerance by Aureobasidium pullulans AK10

city: Busan

first: Jungwook

last: Park

address: Pusan National University, 2, Busandaehak-ro 63beon-gil, Geumjeong-gu, Busan 609-735, Korea

department: Microbiology

institute: Pusan National University

summary: The conservation of the endangered Korean fir, Abies koreana, is of critical ecological importance. In our previous study, a yeast-like fungus identified as Aureobasidium pullulans AK10, was isolated and shown to enhance drought tolerance in A. koreana seedlings. In this study, the effectiveness of A. pullulans AK10 treatment in enhancing drought tolerance in A. koreana was confirmed. Furthermore, using transcriptome analysis, we compared A. koreana seedlings treated with A. pullulans AK10 to untreated controls under drought conditions to elucidate the molecular responses involved in increased drought tolerance.

overall_design: To induce drought stress tolerance, Korean fir seedlings were treated three times with AK10. Drought stress was simulated by withholding water. YPD broth containing 250 μg/ml Tween 20 was used as control. Three replicates were used for each group.

first: Mohamed

last: Mannaa

first: Gil

last: Han

first: Hyejung

last: Jung

first: Jin-Cheol

first: Ae

first: Young-Su

last: Seo


title: Expression data from primary human keratinocytes upon control or HERC6 knockdown using siRNA and stimulated in vitro with or without cGAMP or Poly(I:C)

city: Ann Arbor

first: Poulami

last: Dey

address: 1301 Catherine St

institute: Michigan Medicine

summary: HERC6 is an Interferon stimulated gene and expressed by epidermal keratinocytes, yet its specific role in the skin remains unclear. In this investigation, we employed bulk RNA-sequencing to explore the broader impact of HERC6 in response to sensing of cytosolic DNA mimic, cGAMP or RNA agonist, TLR3. We observed an elevated number of differentially expressed genes in keratinocytes following HERC6 knockdown, and among them, several were associated with the Interferon signaling pathway, such as OAS1, IFIT3, and STAT2, showing increased expression in HERC6 knockdown keratinocytes when stimulated with cGAMP. Additionally, our findings revealed a dysregulation in the HIPPO pathway-related genes, particularly LATS1/2, in HERC6 knockdown keratinocytes. Utilizing bulk RNA-sequencing, we identified enriched Gene Ontology terms associated with the Interferon pathway and cytosolic sensing of foreign DNA in HERC6 knockdown keratinocytes, suggesting HERC6 as a negative regulator of Interferon signaling upon DNA sensing but not RNA. This data was instrumental in elucidating the regulatory functions of HERC6 in keratinocytes during the sensing of exogenous DNA or RNA mimics.

overall_design: Three male (subjects 1, 2, and 3) and three female (subjects 4, 5, and 6) primary human keratinocytes were used to perform non-targeting control (NTC) or HERC6 knockdown using siRNA and stimulated with or without cGAMP or Poly(I:C).

first: Johann

last: Gudjonsson

first: Lam

last: Tsoi

first: Ranjitha

last: Uppala


title: GPX3 supports ovarian cancer tumor progression in vivo and promotes expression of GDF15

city: Pittsburgh

first: Nadine

last: Hempel

state: PA

address: 5051 Centre Ave

department: UPMC Hillman Cancer Center

institute: University of Pittsburgh

summary: We previously reported that high expression of the extracellular glutathione peroxidase GPX3 is associated with poor patient outcome in ovarian serous adenocarcinomas, and that GPX3 protects ovarian cancer cells from oxidative stress in culture. Here we tested if GPX3 is necessary for tumor establishment in vivo and to identify novel downstream mediators of GPX3’s pro-tumorigenic function. GPX3 was knocked-down in ID8 ovarian cancer cells by shRNA to test the role of GPX3 in tumor establishment using a syngeneic IP xenograft model. RNA sequencing analysis was carried out in OVCAR3 cells following shRNA-mediated GPX3 knock-down using two hairpins to identify GPX3-dependent gene expression signatures. GPX3 knock-down abrogated clonogenicity and intraperitoneal tumor development in vivo, and the effects were dependent on the level of GPX3 knock-down. RNA sequencing showed that loss of GPX3 leads to decreased gene expression patterns related to pro-tumorigenic signaling pathways. Validation studies identified GDF15 as strongly dependent on GPX3. GDF15, a member of the TGF-beta growth factor family, has known oncogenic and immune modulatory activities. Similarly, GPX3 expression positively correlated with pro-tumor immune cell signatures, including regulatory T-cell and macrophage infiltration, and displayed significant correlation with PD-L1 expression. We show for the first time that tumor produced GPX3 is necessary for ovarian cancer growth in vivo and that it regulates expression of GDF15. The immune profile associated with GPX3 expression in serous ovarian tumors suggests that GPX3 may be an alternate marker of ovarian tumors susceptible to immune check-point inhibitors.

overall_design: To investigate the role of GPX3 in ovarian cancer cells, GPX3 expression was knocked down using two independent shRNA hairpins (shRNA#76, shRNA#78) and RNA sequencing carried out on cells after 72hrs in culture.

first: Ya-Yun

last: Cheng


title: Linker histone H1 drives heterochromatin condensation via phase separation in Arabidopsis

city: Norwich

first: Xiaoqi

last: Feng

state: Norfolk

address: Norwich Research Park

department: Cell and Developmental Biology

institute: John Innes Centre

summary: We studied how H1 regulates higher-order chromatin architecture by performing Hi-C. In addition, we tested the effects of H1 domains on nucleosome organisation and DNA methylation by performing MNase-seq and Bisulfite-seq.

overall_design: Hi-C was performed with h1 mutant seedlings to examine chromatin interactions in the mutant. To test the functions of the C-terminal intrinsically disordered region (IDR) of H1, we generated H1.1G18IDR which contains the IDR and 18 amino acids of the globular domain nearest the IDR in h1 background. As a control, H1.2 with IDR deleted (H1.2ΔIDR) in h1 background was also generated. These transgenic plants as well as WT and h1 mutant were subject to MNase-seq and Bisulfite-seq to analyse nucleosome repeat length and DNA methylation.

first: Shengbo

last: He

last: Yu

first: Liang

first: Jingyi

last: Zhang

first: Zhengyong

last: Bai

first: Guohong

last: Li

first: Pilong


title: A multi-omics approach reveals enrichment in metabolites involved in the regulation of the glutathione pathway in LIN28B-dependent cancer cells.

city: padova

first: silvia

last: bresolin

state: padova

address: via giustiniani 3

department: department of women's and children's health

country: Italy

institute: università di padova

summary:
The RNA-binding protein LIN28B, identified as an independent risk factor in high-risk neuroblastoma patients, is implicated in adverse treatment outcomes linked to metastasis and chemoresistance. Despite its clinical significance, the impact of LIN28B on neuroblastoma cell metabolism remains unexplored. This study employs a multi-omics approach, integrating transcriptome and metabolome data, to elucidate the global metabolic program associated with varying LIN28B expression levels over time. Our findings reveal that escalating LIN28B expression induces a significant metabolic rewiring in neuroblastoma cells. Specifically, LIN28B prompts a time-dependent increase in the release rate of metabolites related to glutathione and aminoacyl-tRNA biosynthetic pathways, concomitant with a reduction in glucose uptake. These results underscore the pivotal role of LIN28B in governing neuroblastoma cell metabolism and suggest a potential disruption in the redox balance of LIN28B-bearing cells. This study contributes valuable insights into the molecular mechanisms underlying LIN28B-associated adverse outcomes in neuroblastoma, paving the way for targeted therapeutic interventions.
The study explores how the ectopic induction of the LIN28B oncogene affects the overall gene expression pattern in the SH-SY5Y neuroblastoma tumor cell line. The Tet-on system was employed in the investigation. This study reveals that escalating LIN28B expression significantly impacts neuroblastoma cell metabolism, suggesting a disruption in redox balance.

overall_design: Gene expression was measured using Affymetrix platform in neuroblastoma cell line carrying LIN28B overexpression and control

first: Sanja

last: Aveic

first: Silvia

last: Bresolin

first: Diana

last: Corallo


title: Characterization of a novel N4 -methylcytosine restriction-modification system in Deinococcus radiodurans

city: Hangzhou

first: Chenxiang

last: Shi

address: Sandun Zhen Yuhangtang Road 866

institute: Zhejiang University

summary: Deinococcus radiodurans is an extremophilic microorganism that possesses a unique DNA damage repair system, conferring strong resistance to radiation, desiccation, oxidative stress, and chemical damage. Recently, we discovered that D. radiodurans possesses a N4-methylation (m4C) methyltransferase called M.DraR1, which recognizes the 5'-CCGCGG-3' sequence and methylates the second cytosine. Here, we revealed its cognate restriction endonuclease R.DraR1 and recognized that it is the only endonuclease specially for non-4C-methylated 5'-CCGCGG-3' sequence so far. We designated the particular m4C R.DraR1-M.DraR1 as DraI R-M system. Bioinformatics searches displayed the rarity of the DraI R-M homologues system. Meanwhile, recombination and transformation efficiency experiments demonstrated the important role of the DraI R-M system in response to oxidative stress. Besides, in vitro activity experiments showed that R.DraR1 could exceptionally cleave DNA substrates with m5C-methlated 5'-CCGCGG-3' sequence besides its routine activity, suggesting that this particular R-M component possesses a broader substrate choice. Furthermore, an imbalance of the DraI R-M system led to cell death through regulating genes involved in the maintenance of cell survival such as genome stability, transporter, energy production. Thus, our research revealed a novel m4C R-M system that plays key roles in maintaining cell viability and defending foreign DNA in D. radiodurans.

overall_design: RNA-seq for KO_R.DraR1 and WT strains. All of the strains were cultured to OD600=1.0 without any stress treatment.

first: Liangyan

last: Wang

first: Yuejin

last: Hua


title: Transcriptome analysis reveals anti-cancer effects of Isorhapontigenin (ISO) on human high invasive bladder cancer cells

city: New York

first: Hong

last: Sun

state: NY

address: 341 East 25 Street

department: Medicine

institute: NYU School of Medicine

summary: Bladder cancer, the most common malignancy of the urinary tract, has a poor overall survival rate if the tumor becomes muscle invasive. The discovery and evaluation of new alternative medications targeting high-grade muscle invasive bladder cancer (MIBC) are of tremendous importance in reducing bladder cancer mortality. Isorhapontigenin (ISO), a stilbene derivative from Chinese herb Gnetum cleistostachyum, exhibits a strong anti-cancer effect on MIBCs. Here, we report the whole transcriptome profiling of ISO-treated human bladder cancer T24 cells. A total of 1047 differentially expressed genes (DEGs) were identified, including 596 downregulated and 451 upregulated genes. Functional annotation and pathway analysis revealed that ISO treatment induced massive changes in gene expression associated with cell movement, migration, invasion, metabolism, proliferation, and angiogenesis. Additionally, ISO treatment activated genes involved in the inflammatory response but repressed genes involved in hypoxia signaling, glycolysis, the actin cytoskeleton, and the tumor microenvironment. In summary, our whole transcriptome analysis demonstrated a shifted metabolism and altered actin cytoskeleton in ISO treated T24 cells, which subsequently contribute to tumor microenvironment remodeling that suppresses tumor growth and progression.

overall_design: To investigate the effect of isorhapontigenin treatment on bladder cancer cells, T24 cells were treated with 20 uM isorhapontigenin

first: Alex


title: Single-cell transcriptional response of placenta to the ablation of Caveolin-1 in mice: insights into the regulation of brain-placental axis [bulk RNA-seq]

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

summary: Bulk RNA-seq was performed to profile placental gene expression in mice lacking Caveolin-1.

overall_design: Total RNA was extarcted from day-15  placenta from Cav1-null mice (B6.Cg-Cav1tm1Mls/J). The data was compared with RNA-seq profiles of day-15 placenta from wildtype mice (C57BL6/J) generated from our earlier study (accession # GSE214759).

first: Maliha

last: Islam

first: Susanta

last: Behura


title: A cataract-causing mutation in the TRPM3 cation channel disrupts calcium dynamics in the lens

city: St. Louis

first: Philip

last: Ruzycki

department: Ophthalmology and Visual Sciences

institute: Washington University in St. Louis

summary: TRPM3 belongs to the melastatin sub-family of transient receptor potential (TRPM) cation channels and has been shown to function as a steroid-activated, heat-sensitive, calcium ion (Ca2+) channel. A missense substitution (p.I65M) in the TRPM3 gene of humans (TRPM3) and mice (Trpm3) has been shown to underlie an inherited form of early-onset, progressive cataract. Here we model the pathogenetic effects of this cataract-causing mutation using ‘knock-in’ mutant mice and human cell-lines. Trpm3 and its intron-hosted micro-RNA gene (Mir204) were strongly co-expressed in the lens epithelium and other non-pigmented and pigmented ocular epithelia. Homozygous Trpm3-mutant lenses displayed elevated cytosolic Ca2+ levels and an imbalance of sodium (Na+) and potassium (K+) ions coupled with increased water content. Homozygous TRPM3-mutant human lens epithelial (HLE-B3) cell-lines and Trpm3-mutant lenses exhibited increased levels of phosphorylated mitogen-activated protein kinase 1/extracellular signal-regulated kinase 2 (MAPK1/ERK2/p42) and MAPK3/ERK1/p44. Mutant TRPM3-M65 channels displayed an increased sensitivity to external Ca2+ concentration and an altered dose response to pregnenolone sulfate (PS) activation. Trpm3-mutant lenses shared downregulation of genes involved in insulin/peptide secretion and upregulation of genes involved in Ca2+ dynamics. By contrast, Trpm3-deficient lenses did not replicate the pathophysiological changes observed in Trpm3-mutant lenses. Collectively, our data suggest that a cataract-causing substitution in the TRPM3 cation channel elicits a deleterious gain-of-function, rather than a loss-of-function, mechanism in the lens.

overall_design: Mouse lens RNA samples (4 male and 4 female lenses per sample) were prepared in triplicate and cDNA libraries were synthesized, indexed, pooled, and sequenced.  Samples represented WT, Trpm3-KO, Trpm3-mutant (I/M), and Trpm3-mutant (M/M).

first: Yuefang

last: Zhou

first: Thomas

last: Bennett

first: Zhaohua

last: Guo

first: Yu-Qing

last: Cao

first: Mohammad

last: Shahidullah

first: Nicholas

last: Delamere

first: Alan

last: Shiels


title: Impact of modeled microgravity stress on innate immunity in a beneficial animal-microbe symbiosis

city: Hayes

first: Alexandrea

middle: (Lexi)

last: Duscher

state: VA

address: 1730 Sawgrass Pointe Dr

institute: University of Florida

summary: The innate immune response is the first line of defense for all animals to not only detect invading microbes and toxins but also sense and interface with the environment. One such environment that can significantly affect innate immunity is spaceflight. In this study, we explored the impact of microgravity stress on key elements of the NFκB innate immune pathway. The symbiosis between the bobtail squid Euprymna scolopes and its beneficial symbiont Vibrio fischeri was used as a model system under a simulated microgravity environment. The expression of genes associated with the NFκB pathway was monitored over time as the symbiosis progressed. Results revealed that although the onset of the symbiosis was the major driver in the differential expression of NFκB signaling, the stress of simulated low-shear microgravity also caused a dysregulation of expression. Several genes were expressed at earlier time points suggesting that elements of the E. scolopes NFκB pathway are stress-inducible, whereas expression of other pathway components was delayed. The results provide new insights into the role of NFκB signaling in the squid-vibrio symbiosis, and how the stress of microgravity negatively impacts the host immune response. Together, these results provide a foundation to develop mitigation strategies to maintain host-microbe homeostasis during spaceflight.

overall_design: To begin to explore how simulated microgravity alters the expression of the NFκB pathway in the E. scolopes light organ, hatchling animals were incubated in the HARVs in both the LSMMG and gravity control positions in the presence and absence of the symbiotic V. fischeri for 2, 6, 8, 10, 12, 16, 18, 24 h. Total RNA extracted from host light organs was then screened for differential expression of 33 genes associated with the NFκB pathway using NanoString nCounter direct transcript counts (Table 1; Dataset S2) (Goytain & Ng, 2020). Genes were considered significantly differentially expressed (DEGs) at an adjusted p-value cutoff of 0.10, and highly significant at a cutoff of 0.05 (Dataset S3).

first: Madeline

last: Vroom

first: Jamie

last: Foster


title: Single-cell transcriptional response of placenta to the ablation of Caveolin-1 in mice: insights into the regulation of brain-placental axis

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

overall_design: Refer to individual Series


title: Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques

city: Bethesda

first: Jason

last: Brenchley

state: MD

address: 4 Center Drive

institute: NIAID


title: Sarcoma Cell-specific Radiation Sensitization by Titanate Scrolled Nanosheets: Insights from Physicochemical Analysis and Transcriptomic Profiling

city: Gradignan

first: Hervé

last: Seznec

address: 19 Chemin du Solarium

country: France

summary: The objective of this in vitro study was to explore the potential of Titanate Scrolled Nanosheets (TNs) in improving the radiation sensitivity of sarcoma cell lines. Enhancing the response of cancer cells to radiation therapy is crucial, and one promising approach involves utilizing metal oxide nanoparticles. We focused on investigating the impact of exposing two human sarcoma cell lines to TNs and ionizing radiation (IR). Our research was prompted by previous in vitro toxicity assessments, revealing a correlation between TNs' toxicity and alterations in intracellular calcium homeostasis. TNs were synthesized via a hydrothermal process using titanium dioxide powder in alkaline solution. Our study quantified the intracellular content of TNs and analyzed their impact on radiation-induced responses. This assessment encompassed PIXE analysis, cell proliferation and transcriptomic analysis. We observed that sarcoma cells internalized TNs, causing alterations in intracellular calcium homeostasis. Irradiation was also found to influence intracellular calcium levels. Transcriptomic analysis revealed marked disparities in the gene expression patterns between the two sarcoma cell lines, suggesting a potential cell-line-dependent nano-sensitization to IR. These results significantly advance our comprehension of the interplay between TNs, IR, and cancer cells, promising potential enhancement of the radiation therapy efficacy.

overall_design: To investigate the capacity of metal oxide nanoparticles (TNs) to improve the radiation sensitivity of sarcoma cells. Two sarcoma cell lines (IB106 and IB115) were exposed to the following experimental conditions: TNs, 1Gy, 1Gy-TNs, 2Gy and 2Gy-TNs

first: Pierre

last: Beaudier

first: Florent

last: Vilotte

first: Marina

last: Simon

first: Giovanna

last: Muggiolu

first: Quentin

last: Le Trequesser

first: Guillaume

last: Devès

first: Laurent

last: Plawinski

first: Antoine

last: Mikael

first: Jérôme

last: Caron

first: Guy

last: Kantor

first: Denis

last: Dupuy

first: Marie-Hélène

last: Delville

first: Philippe

last: Barberet


title: Ongoing Production of Tissue-Resident Macrophages from Hematopoietic Stem Cells in Healthy Adult Macaques [ATAC-seq]

summary: To understand the ontogeny and longevity of tissue-resident macrophages in nonhuman primates (NHPs), we employ a model of autologous hematopoietic stem progenitor cell (HSPC) transplantation with HSPCs genetically modified to be marked with clonal barcodes, allowing for subsequent analysis of clonal ontogeny.

overall_design: Macrophages from animals that had been transplanted with barcode and GFP labeled stem cells were compared with non-GFP macrophages and macrophages from control, unmanipulated animals.

first: Andrew

last: Rahmberg

first: Chuanfeng

last: Wu

first: Taehoon

last: Shin

first: So

last: Hong

first: Luxin

last: Pei

first: Tovah

last: Markowitz

first: Heather

last: Hickman

first: Cynthia

last: Dunbar

middle: M


title: A single cell atlas of circulating immune cells involved in diabetic retinopathy

city: Chongqing

first: Wei

last: Fan

address: Youyi Road, No1

department: Urology

institute: The First affiliated hospital of Chongqing Medical University

summary: Circulating immune cells play a role in the pathophysiology of diabetic retinopathy (DR). Our study focused on examining the exact role of circulating immune cells in the development of DR.   Single-cell RNA sequencing (scRNA-seq) techniques revealed unique differentially-expressed genes and pathways in circulating immune cells among non-diabetic retinopathy (NDR) patients and DR patients. These findings highlight the notable alterations in the immunophenotypes of circulating immune cells in patients with type 1 DR.

overall_design: Peripheral blood mononuclear cells (PBMCs) were isolated from six Type 1 diabetes patients. Three of them are diagnosed with diabetic retinopathy (DR)  and the other three with non-diabetic retinopathy (NDR) . Then single-cell RNA-sequencing using 10X Genomics was conducted to examine the transcriptomic profiles of each cell subpopulation in these PBMCs.

first: Dan

last: Liao

last: Li

first: Ruonan

first: Xiaotang

last: Wang

first: Jiangyi

last: Liu

first: Hong

first: Shengping

last: Hou


title: Single-cell transcriptional response of placenta to the ablation of Caveolin-1 in mice: insights into the regulation of brain-placental axis [scRNA-Seq]

first: SUSANTA

last: BEHURA

summary: This study investigated gene expression of placental cells in a mouse model lacking Caveolin 1 (Cav1). Single-nuclei RNA-seq was performed with day-15 placenta of WT and Cav1-null mice.

overall_design: Day-15 placenta of WT (C56BL6/J) and Cav1-null (B6.Cg-Cav1tm1Mls/J) mice was used for snRNA-seq analysis by 10x Genomics.

first: Maliha

last: Islam

first: Susanta

last: Behura


title: Overexpression of aquaporin1 plays a vital role in proliferation, apoptosis and pyroptosis in Wilms’ tumor

city: Qingdao

address: 16 Jiangsu Road

institute: Qingdao University

summary: Background: Nephroblastoma, also known as Wilms’ tumor (WT), is an embryonic malignant tumor and one of the most common malignant tumors in the abdominal region of children. Previous studies have demonstrated that aquaporin 1 (AQP1), a highly expressed channel protein in the kidneys, is closely associated with various diseases and also plays a significant role in tumorigenesis and progression. However, the exact role and underlying mechanisms of AQP1 in the occurrence and development of nephroblastoma remain unclear. Methods: After overexpression of AQP1, cell proliferation was assessed using the CCK-8 proliferation assay and EdU staining. Flow cytometry was employed to detect cell apoptosis, and Western blotting (WB) analysis was conducted to validate the expression of relevant protein markers. mRNA Sequencing (mRNA-Seq) was performed on WT cells with AQP1 overexpression to predict and characterize the associated mechanisms. Transmission electron microscopy was utilized to observe changes in the ultrastructure of WT cells undergoing apoptosis and pyroptosis following AQP1 overexpression. Functional in vivo validation was conducted through animal experiments. Results: We validated at both in vitro and in vivo levels that overexpression of AQP1 inhibited cell proliferation and promoted cell apoptosis and pyroptosis. mRNA-Seq analysis of WT cells with AQP1 overexpression suggested that these effects might be mediated through the inhibition of the JAK-STAT signaling pathway, which was further experimentally validated. Additionally, we discovered that overexpression of AQP1 activated the classical pyroptosis signaling pathway dependent on Caspase-1, thereby promoting pyroptosis in WT. Conclusion: These findings highlight the significant functional role of AQP1 in the pathobiology of nephroblastoma, providing novel insights into the development of this disease. Moreover, these results offer new perspectives on the potential therapeutic targeting of AQP1 as a treatment strategy for nephroblastoma.

overall_design: The experimental objective is to investigate the precise role and underlying mechanisms of AQP1 in the occurrence and development of nephroblastoma, providing novel insights into the pathobiology of this disease and offering new perspectives on the potential therapeutic targeting of AQP1 as a treatment strategy for nephroblastoma.

first: Qian

last: Dong

first: Chen

last: Jin

last: Xia


title: Smurf1 modulates Smad signaling pathway in fibrotic cataract formation [mouse_ASC]

city: Guangzhou

first: Fanying

last: Jiang

address: No. 7, Jinsui Road

institute: Zhongshan Ophthalmic Center, Sun Yat-Sen University

summary: Purpose: TGF-β/BMP signaling pathway has a significant role in fibrotic cataract. Smurf1, a ubiquitin protein ligase, regulates the TGF-β/BMP signaling pathway through the ubiquitin-proteasome system (UPS). This study aims to investigate the role of Smurf1 in the progression of fibrotic cataract and its underlying mechanism.Method: We employed a mouse injury-induced anterior subcapsular cataract (ASC) model and administered Smurf1 inhibitor A01 through anterior chamber injection for in vivo investigation. RNA sequencing was performed to examine global gene expression changes. The volume of the subcapsular opacity was determined using whole-mount immunofluorescence of lens anterior capsules. Lentivirus was utilized to create cell lines with Smurf1 knockdown or overexpression in SRA01/04. Protein levels were assessed by Simple Western. Lens epithelial cell (LEC) proliferation was evaluated by CCK8 and EdU assays. LEC migration was measured by Transwell and wound healing assays.Results: The mRNA levels of genes associated with cell proliferation, migration, epithelial-mesenchymal transition (EMT), TGF-β/BMP pathway and UPS, including Smurf1, were upregulated in ASC model. The mRNA expression of Smurf1 was also upregulated in anterior lens capsules of age-related cataract patients. Anterior chamber injection of A01 inhibited ASC formation and EMT. In vitro knockdown of Smurf1 resulted in reduced proliferation, TGF-β2-induced migration and EMT of LECs. Smurf1 inhibition upregulated Smad1, Smad5 and pSmad1/5. Conversely, Smurf1 overexpression displayed the opposite phenotypes.Conclusion: Smurf1 regulated the progression of fibrotic cataract by influencing the proliferation, migration and EMT of LECs through regulation of Smad signaling pathway, offering a novel target for the treatment of fibrotic cataract.

overall_design: To evaluate the overall change of gene expression in fibrotic cataract, we conducted RNA-sequencing on lens capsules collected from an injury-induced ASC mouse model seven days after surgery. Lens capsules from mice that underwent a sham operation, involving only corneal incision without lens capsule incision, served as the control group. Each group has four biological replicates.


title: Pharmacological profiling of a berbamine derivative for lymphoma treatment

city: Duarte

first: Wendong

last: Huang

state: CA

address: 1500 E. Duarte Road

institute: Beckman Research Institute of the City of Hope

summary: Ca2+/calmodulin-dependent protein kinase II gamma (CAMKIIγ) has been identified as a potential target for treating cancer. Based on our previous study of Berbamine (BBM) as a CAMKIIγ inhibitor, we have synthesized a new BBM derivative termed PA4. Compared to BBM, PA4 showed improved potency and specificity, and was more cytotoxic against lymphoma and leukemia compared to other types of cancer. In addition to indirectly targeting c-Myc protein stability, we demonstrated that its cytotoxic effects were also mediated via increased ROS production in lymphoma cells. PA4 significantly impeded tumor growth in vivo in a xenograft T-cell lymphoma (TCL) mouse model. Pharmacokinetics studies depicted quick absorption into plasma after oral administration with a max concentration of 1680 ± 479 ng/mL at 5.33 ± 2.31 hr. The calculated oral absolute bioavailability was 34.1%. Toxicity assessment of PA4 showed that the therapeutic window used in our experiments was safe for future development. Given its efficacy, safety, and favorable pharmacokinetic profile, PA4 is a potential lead candidate for treating lymphoma.

overall_design: To determine the underlying mechanisms of PA4-induced cell death, we compared the global gene profiles between vehicle control (DMSO) and 1 µM PA4 treatment in H9 cells

first: Senlin

last: Xu


title: Patterning ganglionic eminences in developing human brain organoids using morphogen gradient inducing device

city: Amherst

first: Narciso

last: Pavon

state: MA

address: Life Science Laboratories, 240 Thatcher Rd

department: Biochemistry and Molecular Biology

institute: University of Massachusetts

summary: In early neurodevelopment, the central nervous system is established through the coordination of various neural organizers directing tissue patterning and cell differentiation. Better recapitulation of morphogen gradient production and signaling will be crucial for establishing improved developmental models of the brainin vitro. Here, we developed a method by assembling polydimethylsiloxane (PDMS) devices capable of generating a sustained chemical gradient to produce patterned brain organoids, which we termedMorphogen-gradientInducedBrainOrganoids (MIBOs). At 3.5 weeks, MIBOs replicated Dorsal-Ventral patterning observed in the Ganglionic Eminence (GE). Analysis of matured MIBOs through single-cell RNA sequencing revealed distinct Dorsal GE derived CALB2+ interneurons (INs), Medium Spiny Neurons (MSNs), and MGE derived cell types. Finally, we demonstrate long term culturing capabilities with MIBOs maintaining stable neural activity in cultures grown up to 5.5 months. MIBOs demonstrate a versatile approach for generating spatially patterned brain organoids for embryonic development and disease modeling.

overall_design: Gradient patterned forebrain organoid was dissociated into single cells using papain digestion methods. We used singlecell RNA sequencing (scRNA-Seq) to analyze

first: Karmen

last: Diep

first: Feiyu

last: Yang

first: Rebecca

last: Sebastian

first: Beatriz

last: Martinez-Martin

first: Ravi

last: Ranjan

first: Yubing

last: Sun

first: ChangHui

last: Pak


title: T cell-specific P2RX7 favors lung parenchymal CD4+ T cell accumulation in response to severe lung infections

city: Scottsdale

first: Henrique

last: Borges da Silva

state: Arizona

address: 13400 E Shea Blvd, 3-364 (Office)

department: Immunology

institute: Mayo Clinic Arizona

summary: CD4+ T cells are key components of the immune response during lung infections and can mediate protection against tuberculosis (TB) or influenza. However, CD4+ T cells can also promote lung pathology during these infections, making it unclear how these cells control such discrepant effects. Using mouse models of hypervirulent TB and influenza, we observed that exaggerated accumulation of parenchymal CD4+ T cells promotes lung damage. Low numbers of lung CD4+ T cells, in contrast, are sufficient to protect against hypervirulent TB. In both situations, lung CD4+ T cell accumulation is mediated by CD4+ T cell-specific expression of the extracellular ATP (eATP) receptor P2RX7. P2RX7 upregulation in lung CD4+ T cells promotes expression of the chemokine receptor CXCR3 and favors in situ proliferation. Our findings suggest that direct sensing of lung eATP by CD4+ T cells is critical to induce tissue CD4+ T cell accumulation and pathology during lung infections.

overall_design: WT CD4 T cells versus P2RX7-KO (KO) CD4 T cells, antigen-specific (2W-tetramer+), sorted from mice infected with Influenza-2W at d7 post-infection; lung parenchymal (IVNEG), lung vascular-associated (IVPOS) and spleen (SPL) were separated; two replicates each sample.


title: Long-term intermittent hypoxia in mice induces inflammatory pathways implicated in sleep apnea and steatohepatitis in humans

city: Grenoble

first: Florent

last: Chuffart

state: La Tronche

address: Site Santé - Allée des Alpes

institute: IAB - INSERM (U1209) - CNRS (UMR5309)

summary: Obstructive Sleep Apnea (OSA) engenders repetitive desaturation-reoxygenation sequences called intermittent hypoxia (IH), now widely accepted as an independent risk factor for the occurrence and progression of non-alcoholic fatty liver disease (NAFLD). The specific molecular mechanisms linking IH and the development and progression of NAFLD remain elusive. NAFLD pathogenesis is multifactorial including immune cell-driven inflammation as a key mechanism in the transition from  fatty liver to steatohepatitis (NASH). The overall goal of this study was to identify the specific impact of IH on liver inflammation in the absence of major confounders frequently encountered in OSA clinical research (i.e., obesity, diabetes, reduced physical activity). We employed a model of lean mice exposed to long-term IH (16 weeks) and a cohort of lean OSA patients free of comorbidities (n=71) coupled with high-throughput hepatic transcriptomics, lipidomics and targeted serum proteomics. For the first time, we have demonstrated that long-term IH is an independent “hit” sufficient by itself to induce the NASH molecular signatures found in human steatohepatitis transcriptomic datasets.We identified a unique set of biomarkers in mice and humans (PPARs, NRFs,  arachidonic acid, IL16, IL20, IFNB and TNFa) associated with early hepatic and systemic inflammation. This molecular connection between IH, sleep apnea and steatohepatitis warrants further investigation in clinical trials and support the systematic implementation of sleep apnea diagnosis in liver disease phenotyping. Our original signatures could allow the identification of potential diagnostic and treatment response markers, as well as therapeutic targets in the comorbid association between NAFLD and OSA.

overall_design: Sixteen-week-old male C57BL/6JRj mice (Janvier Labs, France) were housed with ad libitum food and water access on a 12 h light/12 h dark cycle (light ON at 8 am and light OFF at 8 pm). Mice were maintained with regular chow diet (LASQC diet, Rod 16, Altromin international) during all the experiment. Mice were randomly assigned to either intermittent hypoxia (IH) or normoxic control (NC) and directly exposed in their housing cages to 16 weeks of NC or IH, 8h per day during their sleeping period (IH from ZT0=8 am to ZT8=4 pm and NC the rest of the day). The IH stimulus consisted of 60 sec cycles alternating 30 sec of hypoxia (hypoxic plateau at 5% FiO2) and 30 sec of NC (normoxic plateau at 21% FiO2). NC mice were exposed to similar air-air cycles in order to avoid bias from noise and turbulence related to gas flow. After 16 weeks of exposure, mice were sacrificed by decapitation, livers were harvested and immediately frozen in liquid nitrogen until further analysis. For RNA extraction, 50mg of frozen liver tissues were homogenized in TRIzol Reagent and RNA was extracted after precipitation with isopropanol and ethanol washes according to the manufacturer’s protocol. RNA quality was monitored for quality control using Agilent Bioanalyzer Nano RNA chip and Nanodrop absorbance ratios of 260/280 nm and 260/230 nm. Library construction was performed according to the Illumina kit protocol (TruSeq stranded mRNA sample preparation).The multiplexed libraries were sequenced on one lane using single-end 100 cycles chemistry for the NovaSeq 6000 (Illumina)

first: Jonathan

last: Gaucher

first: Emilie

last: Montellier

first: Guillaume

last: Vial

first: Maëlle

last: Guellerin

first: Sophie

last: Bouyon

first: Emeline

last: Lemarie

first: Yoshiki

last: Botté

first: Aya

last: Dirani

first: Raoua

last: Messaoud

first: Marie

last: Joyeux-Faure

first: Diane

last: Godin-Ribuot

first: Charlotte

last: Costentin

first: Renaud

last: Tamisier

first: Cyril

first: Saadi

last: Khochbin

last: Rousseaux

first: Jean-Louis

last: Pépin


title: Smurf1 modulates Smad signaling pathway in fibrotic cataract formation [cell line]

first: Fanying

last: Jiang

overall_design: To investigate the function of Smurf1 in the regulation of the biological behavior of lens epithelial cells, we established SRA01/04 cell lines in which Smurf1 has been knocked down  by shRNA. We then performed gene expression profiling analysis using data obtained from RNA-seq of Smurf1 knockdown and negative control cell lines treated with TGF-β2  for 48 hours.Each group has four biological replicates.


title: Functional genomics of TFEB overexpression

city: Los Angeles

first: Constanza

middle: J

last: Cortes

state: California

address: 3715 McClintock Ave

institute: University of Southern California


title: Skeletal muscle TFEB overexpression transcriptionally remodels the mouse hippocampal landscape throughout lifespan in a sex-dependent manner [RNA-seq]

summary: Skeletal muscle has recently arisen as a novel regulator of Central Nervous System (CNS) function and aging, secreting bioactive molecules known as myokines with proteostasis- and metabolism-modifying functions in targeted tissues, including the CNS. We generated a novel transgenic mouse that has overexpression of Transcription Factor E-B (TFEB), a master regulator of proteostasis and lysosomal function, in skeletal muscle. We discovered that the resulting changes in muscle function promotes transcriptional remodeling of the aging CNS, as well as preserves cognition and memory in aging mice. Our results implicate the maintenance of autophagic skeletal muscle signaling throughout aging to the direct regulation of the CNS metabolism and function, and suggest that skeletal muscle originating factors may act as novel therapeutic targets against age-associated neurodegenerative diseases.

overall_design:
mice with overexpression of Transcription Factor EB in skeletal muscle tissue were examined for age-associtated gene expression profile changes in the hippocampus compared to age and sex-matched littermate controls (no skeletal muscle TFEB overexpression) to further comprehend the muscle-to-brain axis implicated in age-related cognitive decline.
Gene expression profiling by high-throughput sequencing for hippocampi of 6-month and 24-month, mice with skeletal muscle Transcription Factor EB overexpression and wild-type controls. Profiles for both male and female mice were generated

first: Allison

last: Birnbaum

first: Kailin

last: Liu