title: The pivotal role of the Hes1–Piezo1  pathway in the pathophysiology of glucocorticoid-induced osteoporosis [human_GIOP]

city: Saitama

first: Nagahiro

last: Ochiai

address: Yoshino-cho 1-403, Kita-ku

institute: Taisho Pharmaceutical, Co., Ltd

summary: Glucocorticoid-induced osteoporosis (GIOP) lacks fully effective treatments. This study investigated the role of Piezo1, a mechanosensitive ion channel component 1, in GIOP. We found reduced Piezo1 expression in cortical bone osteocytes from patients with GIOP and a GIOP mouse model. Yoda1, a Piezo1 agonist, enhanced the mechanical stress response and bone mass and strength, which were diminished by dexamethasone (DEX) administration in GIOP mice. RNA sequencing revealed that Yoda1 elevated Piezo1 expression by activating the key transcription factor Hes1, followed by enhanced CaM kinase II and Akt phosphorylation in osteocytes. This improved lacuno-canalicular network and reduced sclerostin production and receptor activator of nuclear factor kappa beta/osteoprotegerin ratio, which were mitigated by DEX. Comparative analysis of mouse models and human GIOP cortical bone revealed downregulation of mechano-stimulated osteogenic factors, such as osteocrin, and cartilage differentiation markers in osteoprogenitor cells. In human periosteal-derived cells, DEX suppressed differentiation into osteoblasts, but Yoda1 rescued this effect. Our findings suggest that reduced Piezo1 expression and activity in osteocytes and periosteal cells contribute to GIOP, and Yoda1 may offer a novel therapeutic approach by restoring mechanosensitivity.

overall_design: To investigate the differences in gene expression between non-GIOP and GIOP patients, RNA sequencing analysis was performed on RNA extracted from the cortical bone of age- and sex-matched patients with non-GIOP and GIOP conditions.

first: Shohei

last: Ito


title: Dual roles of histone H3 lysine-4 in antagonizing Polycomb group function and promoting target gene expression

status: Public on Dec 18 2024

city: Chapel Hill

first: Daniel

middle: J.

last: McKay

state: NC

address: 250 Bell Tower Drive

country: USA

institute: University of North Carolina at Chapel Hill

type: Expression profiling by high throughput sequencing

summary: Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the ON/OFF state of targets like the Hox genes. Trithorax encodes a methyltransferase specific to histone H3 lysine-4 (H3K4). However, there is no direct evidence that H3K4 regulates Polycomb group target genes in vivo. Here, we demonstrate two key roles for replication-dependent histone H3.2K4 in target control. We find that H3.2K4 antagonizes Polycomb group catalytic activity and that it is required for proper target gene activation. We conclude that H3.2K4 directly regulates expression of Polycomb targets.

overall_design: Comparative gene-expression analysis of RNA-seq data collected from mutant H3.2-K4R and wild-type H3.2-K4 16-18hr Drosophila melanogaster embryos.

first: Cyril

middle: S

last: Anyetei-Anum

first: Mary

middle: P

last: Leatham-Jensen

first: Geoffrey

middle: C

last: Fox

first: B

middle: R

last: Smith

first: Krzysztof

last: Krajewski

first: Brian

middle: D

last: Strahl

first: Jill

middle: M

last: Dowen

first: A

middle: G

last: Matera

first: Robert

middle: J

last: Duronio


title: The pivotal role of the Hes1–Piezo1  pathway in the pathophysiology of glucocorticoid-induced osteoporosis

country: Japan

overall_design: To investigate the mechanisms of glucocorticoid-mediated mechanical stress response, an RNA-seq analysis was conducted comparing the mouse tibial axial loading responses between the vehicle- and DEX-treated groups over five days.


title: Single cell RNA sequence data from intrahepatic immune cells of CHB(chronic hepatitis B) mice

city: Suita

first: Takahiro

last: Kodama

state: Osaka

address: 2-2 Yamadaoka

department: Department of Gastroenterology and Hepatology

institute: Osaka university, Graduate School of Medicine

summary: We successfully established a novel immunocompetent mouse model of CHB(chronic hepatitis B)  at the immune-active phase by a simple combination of a Fumarylacetoacetate hydrolase (FAH) knockout mouse, hydrodynamic tail vein injection, and sleeping-beauty transposon system. The employment of single-cell RNA sequence in this model revealed the comprehensive intrahepatic immune landscape in the immune-active phase, which contributes to the persistence of HBV infection. Our model also made it possible to profile the intrahepatic immune response to the immunomodulators.

overall_design: Hepatic immune cells were analysed by scRNA-seq at the chronic inflammation phase .


title: Characterization of Dipyridamole as a Novel Ferroptosis Inhibitor and its Therapeutic Potential in Acute Respiratory Distress Syndrome Management

city: Hefei

first: yun

middle: xiao

last: Fan

address: 218 Jixi Road, Shushan District

country: China

institute: Department of Geriatric Respiratory and Critical Care, the First Affiliated Hospital of Anhui Medical University

summary: Ferroptosis in lung epithelium and endothelium contributes to the pathogenesis of acute respiratory distress syndrome (ARDS), a critical and frequently fatal condition marked by acute inflammation and elevated pulmonary vascular permeability. Despite this, there are currently no FDA-approved therapeutics specifically targeting ferroptosis for ARDS management. In this investigation, we identified Dipyridamole (DIPY) as a potent ferroptosis inhibitor in pulmonary epithelial and endothelial cells via screening 259 FDA-approved drugs. The anti-ferroptotic and therapeutic efficacy of DIPY was validated in two ARDS mouse models (LPS-induced acute lung injury and CLP-induced sepsis) and human airway organoids (hAOs).

overall_design: To explore the molecular mechanism of DIPY against ferroptosis, we performed RNA-Seq analysis by utilizing RSL3- or RSL3 plus DIPY-treated A549 cells.


title: Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner [scRNA-seq]

city: Jerusalem

first: Yasmin

last: Jaber

address: Hadassah Ein-Kerem

country: Israel

institute: Hebrew University

summary: Understanding the impact of the microbiota on oral mucosal epithelial barriers, particularly within the gingiva, is essential for elucidating the mechanisms underlying oral health and disease. The gingiva exhibits intricate tissue architecture and undergoes dynamic microenvironmental shifts influenced by various factors. Notably, microbial colonization emerges as an early-life factor that plays a significant role in shaping the functional and immunological maturation of the gingival epithelium. This study utilizes spatial transcriptomic analysis to unveil distinct immunological characteristics between the buccal and palatal regions of the murine gingiva, impacting natural alveolar bone loss. Moreover, the analysis identifies a significant influence of the microbiota on the development and function of the junctional epithelium, which faces the oral microbial plaque, offering new insights into neutrophil recruitment to this strategic location. Additionally, the microbiota is found to impact fundamental functions of the gingival epithelium, including proliferation kinetics and barrier sealing. In conclusion, this study emphasizes the crucial role played by the microbiota in regulating gingival barriers and brings attention to its unique influence on specific epithelial regions within the gingiva.

overall_design: One SPF sample pooled from four SPF mice was compared with one GF sample pooled from four GF mice

first: Avital

last: Sarusi-Portuguez

first: Yasmine

last: Netanely

first: Reem

last: Naamneh

first: Shahd

last: Yacoub

first: Or

last: Saar

first: Nadeem

last: Drawshave

first: Luba

last: Eli-Berchoer

first: Hagit

last: Shapiro

first: Eran

last: Elinav

first: Asaf

last: Wilensky

first: Avi-Hai

last: Hovav

first: Abed

last: Nasereddin

first: Idit

last: Shiff


title: Transcriptional profiling of EZM8266 treatment in a syngeneic model of PARPi-resistant ovarian cancer.

city: Aurora

first: Lily

last: Nguyen

state: CO

address: 1635 Aurora Ct

institute: UNIVERSITY OF COLORADO DENVER

summary: Euchromatin methyltransferase1/2 (EHMT1/2) have been correlated with tumorigenesis and therapy resistance through unknown mechanisms of action. Using a combination of experimental and bioinformatic analyses in several PARP inhibitor resistant ovarian cancer models, we demonstrate that combinatory EHMT and PARP inhibition is effective in treating PARP inhibitor resistant ovarian cancers. Our in vitro studies show that combinatory therapy reactivates transposable elements and increased immunostimulatory dsRNA formation and several immune signaling pathways. Our in vivo studies show that single EHMT and combinatory EHMT and PARP inhibition reduces tumor burden and that this reduction is dependent on CD8 T cells. Together, our results show a direct mechanism by which transposable elements are regulated and how an epigenetic therapy can be used as a fine tune agent to treat cancers with specific genetics.

overall_design: Transcriptional profiling (RNA-seq) of a syngeneic model of PARPi-resistant ovarian cancer - ID8-OR  cells - were treated with DMSO, a PARP inhibitor (olaparib), an EHMT1/2 inhibitor (EZM8266) or combinatory PARP/EHMT inhibitors.

middle: L

first: Benjamin

last: Bitler

first: Edward

middle: B

last: Chuong


title: Treatment with obinutuzumab and venetoclax reshapes the TRB repertoire of CLL patients

city: Rotterdam

first: Paul

last: Hengeveld

address: Dr Molewaterplein 40

department: Immunology

country: Netherlands

institute: Erasmus MC

summary: Anti-leukemic treatment in chronic lymphocytic leukemia (CLL) impacts  autologous T cells through various direct and indirect mechanisms. However,  how first-line treatment with venetoclax and obinutuzumab impacts the TRB  repertoire has not been studied. Here, we have used next-generation sequencing to  longitudinally characterize the TRB repertoire of previously untreated CLL patients  who received treatment with obinutuzumab and venetoclax in the HOVON-139/ GIVE trial. Following treatment, due to the emergence of a polyclonal population of  small-sized, diverse clonotypes, TRB repertoire diversity increased (Shannon’s H;  trial entry 5.5 [95%CI 5.2-6.2] vs end of induction treatment [EOiT] 6.2 [95%CI 5.7- 6.7], P=0.001). In contrast, treatment with obinutuzumab and venetoclax did not  ameliorate TRB oligoclonality (EOiT, cumulative frequency of top 10 clonotypes  32.5% [95%CI 25.3-39.9], P=0.10; R+12 CF10 31.2% [95%CI 24.3-38.1], P=0.17), due  to the persistence of large pre-treatment clonotypes. Patients with IGLV3-21R110 CLL had weaker recovery of TRB repertoire diversity (mean Shannon’s H 5.2  [95%CI 4.0-6.3] vs 6.8 [95%CI 6.3-7.3], P=0.01). TRB clonotypes that were shared  among patients could be identified, a minority of which had known pathogenic  or auto-antigenic affinity. The concurrent presence or future resurgence of MRD  did not impact the TRB repertoire, but low TRB diversity (Poisson regression  coefficient -0.32±0.15, P=0.046) and high oligoclonality (Poisson regression  coefficient 0.02±0.009, P=0.02) were associated with an increased risk of infection.  These data provide the groundwork for the future investigation of the fitness of  autologous T cells for T cell-mediated immunotherapy, following treatment with  obinutuzumab and venetoclax.

overall_design: TRBV sequences were amplified from PBMC DNA using the EuroClonality TRBV two-step assay on an Illumina Miseq platform. FASTQ files were processed downstream in the Arrest/Interrogate immunoprofiler.

first: Joyce

last: Schilperoord-Vermeulen

first: P

last: Kolijn

first: Julie

last: Dubois

first: Sabina

last: Kersting

first: Arnon

last: Kater

first: Peter

middle: E

last: Westerweel

first: Mark-David

last: Levin

first: Anton

middle: W

last: Langerak


title: Gene expression data of Lin28a-positive MuSCs using RNA-seq and RIP-seq

city: Beijing

first: Dan

last: Song

state: Beijing

address: 3 Datun Road, Chaoyang District, Beijing 100101, P.R.china

institute: CHINESE ACADEMY OF SCIENCES STEM CELL AND REGENERATIVE MEDICINE INNOVATION INSTITUTE

summary: During the early stages of embryonic development, Lin28a is expressed at high levels and gradually decreases as the embryo develops. As an RNA-binding protein, Lin28a maintains a subset of adult muscle stem cells (MuSCs) in an embryonic-like state. However, the specific mechanism for regulating RNA metabolism is not yet clear. Through the analysis of Lin28a-associated genes, we have revealed that Lin28a promotes the expression of Igf2bp3 and interacts with the Igf2bp3 protein, controlling the proliferation of MuSCs. In response to stress stimuli, Lin28a rapidly upregulates the expression of Igf2bp3, recruits mRNAs by interacting with the N6-methyladenosine (m6A) reader Igf2bp3, and forms protein complexes with G3bp1 in stress granules. Sequencing of the transcriptome and RNAs immunoprecipitated by Lin28a, Igf2bp3, and m6A antibodies in Lin28a+ MuSCs further revealed that Lin28a and Igf2bp3 collaboratively regulate the expression of DNA repair-related genes such as Fancm and Usp1 to promote DNA repair after oxidative stress. Therefore, Lin28a regulates the expression of DNA damage repair-related genes and upregulates the DNA stress response of MuSCs through stress granule regulation of m6A-modified mRNAs. This positive regulation contributes to the self-renewal of MuSCs.

overall_design: To investigate the crucial role of lin28a in MuSCs, we assessed the gene expression data of Lin28a-positive MuSCs using RNA-seq and RIP-seq methods.

first: Yu

last: Chen

first: Peng

last: Wang

first: Ng

last: Shyh-Chang


title: Reduction of SIRPα connects podocyte metabolism dysfunction to inflammatory activation via promoting PKM2 nuclear translocation in diabetes nephropathy II

city: Nanjing

first: Yang

address: 639 Longmian Avenue

institute: Chinese Pharmaceutical University

summary: A central cause of diabetic nephropathy (DN) is podocyte injury. There are many factors causing podocyte injury in DN, such as hyperglycemia, oxidative stress and inflammation. In this study, a signal regulator protein α (SIRPα) was found to play a critical role in regulating podocyte metabolism, oxidative stress and inflammatory.

overall_design: To explore the relationship between molecular pathways regulated by down-regulation of SIRPα expression and podocyte injury in Primitive cells of mice renal podocytes

first: Limin

last: Li


title: Siglec-G suppresses CD8+ T cells responses through metabolic rewiring and can be targeted to enhance tumor immunotherapy

city: shang hai

first: yin

middle: shen

last: hui

address: xiangyin road 800

institute: Second military medical university

summary: CD8+ T cells play a critical role in cancer immune-surveillance and pathogens elimination. However, their effector function can be severely impaired due to inhibitory receptors such as PD-1 and Tim-3. Here we identify Siglec-G as a novel coinhibitory receptor that limits CD8+ T cell function. Siglec-G is highly expressed on tumor-inﬁltrating T cells and is enriched in the exhausted T cell subset. Ablation of Siglec-G enhances the efficacy of adoptively transferred T cells and CAR T cells to repress the growth of solid tumors. Mechanistically, sialic acids on tumor cells trigger Siglec-G-SHP2 axis in CD8+ T cells, and impairs metabolic reprogramming from OXPHOS to glycolysis, which dampens CTL activation, expansion and cytotoxicity. These findings deﬁne a critical role for Siglec-G in inhibiting CD8+ T cell responses, which strongly suggests its therapeutic effect in adoptive T cell therapy and tumor immunotherapy.

overall_design: To compare the difference between TILs and Teff, we isolated TILs from MC38-OVA-bearing mice and Teff from LM-OVA infected mice


title: Differentially expressed long non-coding RNAs and mRNAs in DRG of bone cancer pain and sham group rats based on microarray and bioinformatic analysis

city: Jiaxing

first: Huadong

last: Ni

address: zhonghuan nan road 1882

institute: Department of Anesthesiology and Pain Research Center, The Affiliated Hospital of Jiaxing University

summary: Objective: The diagnostic roles of long non-coding RNAs (lncRNAs) and mRNAs in bone cancer pain are still not well defined. We aimed to identify differentially expressed DRG mRNAs in bone cancer pain and sham group rats systematically. Methods: Expression profile of mRNAs in DRG from bone cancer pain and sham group rats was analyzed by microarray assay. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway based approaches were used to investigate biological functions and signaling pathways affected by the differentially expressed mRNAs. GPR160 was selected for validation using Real-Time PCR. Results: Compared with sham group, a total of 807 differentially expressed mRNAs were revealed by heatmap and volcano-plot, including up-regulation in 720 and down-regulation in 87 (fold change ≥ 2 and P < 0.05), respectively. Pathways analysis based on upregulated mRNAs were mainly involved in antigen processing and presentation and phagosome pathway (P < 0.05). We first reported differentially expressed mRNAs in bone cancer pain and sham group rats systemically. Combined with the published dataset, we identified several differentially expressed mRNAs which might to be diagnostic or prognostic markers. The biological functions of those mRNAs should be further validated. Taken together, this study provided the basis for future treatment of bone cancer pain.

overall_design: 3 cases of bone cancer pain rats and 4 sham group were enrolled in this study. Ipsilateral DRG was collected from each rats followed by centrifugation at 1,000 g for 10 min at 4°C.   then transferred to sterile polypropylene tubes on ice and centrifuged again at 10,000g for 10 min at 4°C to remove cell debris.

first: Chengfei

last: Xu

first: Yahui

first: Miao

first: Ming

last: Yao


title: Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner

first: Inbar

last: Plaschkes

address: The Hebrew University of Jerusalem - Ein Kerem

department: The Faculty of Medicine - Ein Kerem

institute: HUJI

first: Yasmin

last: Jaber

first: Avital

last: Sarusi-Portuguez

first: Yasmine

last: Netanely

first: Reem

last: Naamneh

first: Shahd

last: Yacoub

first: Or

last: Saar

first: Nadeem

last: Drawshave

first: Luba

last: Eli-Berchoer

first: Hagit

last: Shapiro

first: Eran

last: Elinav

first: Asaf

last: Wilensky

first: Avi-Hai

last: Hovav

first: Abed

last: Nasereddin

first: Idit

last: Shiff


title: Cell-permeated peptide P-T3H2 inhibits malignancy on hepatocarcinoma through stabilizing HNF4α protein

city: shanghai

first: sihan

last: wu

address: 上海市杨浦区翔殷路800号

institute: Naval medical university

summary:
Objectives: Hepatocyte nuclear factor 4α (HNF4α) is a key regulator of hepatocyte function and has a strong therapeutic effect on hepatocellular carcinoma (HCC) by inducing  the differentiation of hepatoma cell into hepatocytes. Our previous study showed that Tribbles homolog 3 (TRIB3) directly interacts with and promotes the degradation of HNF4α in non-alcoholic fatty liver disease (NAFLD). Disrupting the TRIB3-HNF4α interaction by using a cell-permeating peptide called P-T3H2 stabilizes HNF4α protein. This study aimed to assess the anti-tumor impact of P-T3H2 in HCC.
Methods: The expression of TRIB3 and HNF4α was assessed using western blot and immunohistochemistry staining (IHC). Hepatic functions in HCC cells were evaluated through periodic acid-Schiff (PAS) staining and acetylated low-density lipoprotein (ac-LDL) uptake. Senescence-associated β-galactosidase (SA-β-gal) activity staining was used to detected the cellular senescence in HCC cells. RNA-Seq analysis was carried out to identify differentially expressed genes in Huh-7 cells treated with the peptide P-T3H2 compared to the control peptide P-T3H2-2A. The impact of P-T3H2 on hepatocarcinoma malignancy was evaluated in HCC cells, a Huh-7 xenograft mouse model, an orthotopic model, and a C-MET/ΔN90-β-catenin-driven HCC model.
Results: TRIB3 exhibited a negative correlation with HNF4α in both human and mouse HCC tissues. The administration of P-T3H2 significantly inhibited the malignancy of HCC cells. Additionally, P-T3H2 stabilized the HNF4α protein and facilitated the restoration of hepatic functions and the cellular senescence in HCC cells. RNA-Seq analysis demonstrated that P-T3H2 enhanced the transcriptional activity of HNF4α in HCC. Furthermore, P-T3H2 effectively suppressed the growth of HCC tumors in both of the Huh7 xenograft and orthotopic mouse models in vivo. Notably, P-T3H2 also inhibits hepatocarcinogenesis in the C-MET/ΔN90-β-catenin-driven HCC model.

overall_design: To investigate the inhibitory effect of P-T3H2 on HCC by enhancing the transcriptional activity of HNF4α, Huh7 cells were treated with  P-T3H2-2A and P-T3H2. We then performed gene expression profiling analysis using data obtained from RNA-seq of three groups of Huh7 cells were treated with  P-T3H2-2A and P-T3H2.

first: S

last: Wu

first: M

last: Xiao

first: H

last: Hong

first: C

last: Ding


title: Severe Fever with Thrombocytopenia Syndrome Virus Induces Lactylation of m6A Reader Protein YTHDF1 to Facilitate Viral Replication

first: Bingxin

last: Liu

state: Jiangsu province

address: 22 Hankou Road

department: Medical school

institute: Nanjing University

summary: To investigate the role of m6A modification during SFTSV infection, we established a SFTSV-infected cell model, in which each m6A modification change was identified.

overall_design: We then performed gene expression profiling analysis using data obtained from MeRIP-seq of HeLa cells and SFTSV-ifected HeLa cells.

first: Zhiwei


title: Multiprotein bridging factor 1 is required for robust activation of the integrated stress response on collided ribosomes

city: St Louis

first: Hani

last: Zaher

state: MO

address: 1 Brookings Drive

department: Biology

institute: Washington University in St. Louis

summary: The multiprotein bridging factor 1 (Mbf1) proteins are a family of conserved eukaryotic proteins thought to mediate the activity of stress-induced transcription factors. In yeast, Mbf1 has been proposed to function in the integrated stress response (ISR) by mediating an interaction between the basal transcription machinery and the process’s key effector Gcn4. Curiously, mounting recent evidence has strongly suggested that the factor and its human homologue to be recruited to collided ribosomes, the very signal newly recognized to activate the ISR. Here we provide data that connect these otherwise supposedly disparate functions of the factor. Our findings revealed that Mbf1 functions as a core factor in the ISR process, responding early to stress and mediating the activation of Gcn2. We further show that the factor serves no role as a transcriptional coactivator of Gcn4; instead, it is required for optimal stress-induced eIF2a phosphorylation and downstream de-repression of GCN4 translation. Detailed mutational and biochemical analysis, together with a cryo-EM structure of the factor bound to collided ribosomes, showed that Mbf1’s activity in the ISR is enabled through its interaction with ribosomes. Collectively, our data resolve an important question about how Mbf1 factors function in signaling by acting as sensors of stress-induced ribosomes collisions, and not as coactivators of the effector proteins as widely accepted in the field.

overall_design: RNA-seq analysis of wild type, gcn2Δ, gcn4Δ, and mbf1Δ strains treated with 0.1% methyl methanesulfonate (MMS) for one hour, as well as their matched no treatment controls. Each condition had three biological replicates and differential gene expression analysis was done using a Salmon-DESeq2 pipeline to investigate the interaction effect of treatment with genotype.

first: K

middle: Q

last: Kim


title: Gingival spatial analysis reveals geographic immunological variation in a microbiota-dependent and -independent manner [Spatial Transcriptomics]

first: Yasmin

last: Jaber

overall_design: A total of four samples from two different SPF mice was analyzed and compared to three samples analyzed from one GF mouse

first: Avital

last: Sarusi-Portuguez

first: Yasmine

last: Netanely

first: Reem

last: Naamneh

first: Shahd

last: Yacoub

first: Or

last: Saar

first: Nadeem


title: CX43-mediated Mitochondria Transfer from Bone Marrow Stromal Cells Promotes the Stemness of Leukemia Stem Cells

city: Chongqing

first: Hui

middle: hui

last: Fu

address: 181 Hanyu Road, Shapingba District, Chongqing

institute: Affiliated Cancer Hospital of Chongqing University

summary: Acute myeloid leukemia (AML) is characterized by abundant immature myeloid cells, relapse and refractory AML are associated with leukemic stem cells (LSCs). Bone marrow mesenchymal stem/ stromal cells (BMSCs) support LSCs survival. Connexin 43 as the most intercellular gap junction, was improved expressed in patients who received chemotherapy. The functionality of CX43 is yet to be determined between BMSCs and LSCs. CX43 improved BMSCs transport mitochondria to LSCs, LSCs utilized more mitochondria to increase oxidative phosphorylation (OXPHOS) and support the cells' proliferation. Therefore, CX43 played an important role in AML relapse patients and could be a novel therapeutic target.

overall_design:
To investigate the effects of CX43-regulated mitochondrial transfer in BMSCs and LSCs on the dryness of LSCs, we established a BMSCs cell line overexpressing CX43 (CX43-BMscs) and a control BMSCs cell line overexpressing CX43-BMscs (EV-BMSCs).
Then, after co-culture of LSCs with CX43-BMSCs/EV-BMSCs for 48 hours, gene expression profiling of rna-1 sequence data of LSCs was performed.
Comparative gene expression profiling of RNA-seq data from LSCs monoculturated or co-cultured with BMSCs.

first: Huihui

first: Xiaoqing

last: Xie

first: Yao

first: Xiaomei

last: Zhang

first: Zailin

last: Yang


title: Chromatin dynamics of Phytophthora during host infection [ChIP-seq]

first: Haidong

last: Shu

state: Jiangsu

address: Weigang NO.1

department: Department of Plant Pathology

institute: Nanjing Agricultural University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: Dynamic regulation of silencing histone marks, specifically H3K9me3 and H3K27me3, provide effector gene expression plasticity, which enables adaptative responses to environmental fluctuations in plant fungal pathogens. It remains an unanswered question whether the epigenetic regulatory mechanisms governing gene expression during infection stages in Phytophthora are the same as in fungal pathogens. We performed chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) of three histone modifications, H3K4me3, H3K36me3, and H3K27me3 in P. sojae and P. infestans, encompassing both the mycelium stage, and infection stages (12h post-inoculation (hpi), and 24hpi in soybean, as well as 3dpi in potato respectively).Integrative analysis of ChIP-seq and RNA-seq data of mycelium and infection stages was performed.Overall, our work provides a comprehensive and detailed view of distinctive chromatin dynamic patterns during the infection stages of Phytophthora.

sample_organism:
Phytophthora infestans
Phytophthora sojae

overall_design: ChIP-seq of H3K4me3, H3K36me3, and H3K27me3 in P. sojae and P. infestans, encompassing both the mycelium stage, and infection stages (12h post-inoculation (hpi), and 24hpi in soybean, as well as 3dpi in potato respectively) were performed. Each ChIP-seq experiment was performed with two biological replicates.

first: Han

last: Chen

first: Suomeng

last: Dong


title: Eif2s2 deficiency causes oocyte arrest at the early diplotene stage and apoptosis in mice

city: Guangzhou

first: Wenjun

last: Zhou

state: Guangdong

address: Waihuan East Road, Mega center city

department: School of Medicine

institute: South China University of Technology

summary: Mutations in translation initiation factors are associated with premature ovarian insufficiency. Here, we used signle-cell RNA sequencing method to investigate the effect of Eif2s2 deletion in premeiotic germ-cells on primordial formation.

overall_design: Two pooled samples of ovaries from Eif2s2 floxed and cKO mice. Each sample includes 6 ovaries from 3  Eif2s2 floxed and cKO mice.

first: Meijia


title: Identification of microRNAs contained in extracellular vesicles derived from Pg-infected macrophages  Description

city: Kamakura

first: Satoshi

last: Kondo

state: Kanagawa

address: 10-1 tebiro 6-chome

institute: Toray Industries,Inc.

summary: Although miRNA analysis within Extracellular vesicles (EVs) has been explored in the context of various inflammatory diseases, limited research has been reported on EV-contained miRNAs associated with periodontal disease. Therefore, we comprehensively identified the specific miRNAs contained within EVs produced by macrophage-like cells infected with Pg.

overall_design: THP-1 macrophage-like cells were infected with Pg for 4 hours. Subsequently, both Pg and EVs were removed from the medium. miRNAs contained within EVs, released from infected cells into the medium within 48 hours, were identified using miRNA microarray analysis.

first: Kayo

last: Yoshida

first: Kaya

first: Yasuhiro

last: Mouri

first: Ayu

last: Takai

first: Mariko

last: Seyama

first: Mana

last: Mekata

first: Noriko

last: Mizusawa

first: Keiko

last: Miyoshi

first: Yasusei

last: Kudo

first: Kazumi

last: Ozaki


title: Single cell sequencing of hypoimmunogenic neonatal islet beta cells

city: Yangling

first: Pengxiu

last: Dai

address: No.3 Taicheng Road,

institute: Northwest A&F University (Northwest Agriculture and Forestry University)

summary: In this study, 7530 newborn pancreatic β-cells were analyzed by single-cell sequencing. Cell Ranger was used to compare the original sequencing data, count the genome, filter background cells and cell transcript UMI, and use cell barcode to generate gene-barcode matrix. Then the samples were grouped, gene expression analysis, etc., and the statistical results of each sample sequencing data were output

overall_design: scRNA-Seq; Islet beta cells derived from MSCs


title: Identification of the YAP1-MAML2 fusion-regulated genes in ovarian cancer ES-2 cells

city: Gainesville

first: Lizi

last: Wu

state: FL

address: 2033 Mowry Road

institute: University of Florida

summary: Gene expression profiling was conducted to identify genes affected by shRNA targeting MAML2 in ovarian cancer ES-2 cells compared to scrambled shRNA control cells.

overall_design: The study included two groups of ES-2 cells: one transduced with pLKO.1 lentiviruses expressing shRNA targetingMAML2 (to knock down YAP1-MAML2 fusion and MAML2 proteins), and the other with nontargeting control shRNA. Each group had two biological replicates. Cells from each group were cultured independently, and RNAs were subsequently harvested for RNA-seq analysis.


title: German cockroach subcutaneous immunotherapy: Impact on nasal responses and allergen-specific immunity among urban children with asthma

city: Seattle,

first: Stephanie

last: Osmond

state: WA

address: 1201 9th Ave

institute: Benaroya Research Institute

summary: Background: Cockroach allergy contributes to morbidity among urban children with asthma. Few trials address the effect of subcutaneous immunotherapy (SCIT) with cockroach allergen among these at-risk children.Objective: To determine if nasal allergen challenge (NAC) responses to cockroach allergen would improve following one year of SCIT.Methods: Urban children with asthma, cockroach-sensitized (skin prick test [SPT] and serum specific IgE) and reactive on NAC, participated in a yearlong randomized double-blind placebo-controlled SCIT trial using German cockroach extract. The primary endpoint was the change in mean total nasal symptoms scores (TNSS) during NAC after 12 months of SCIT. Changes in nasal transcriptomic responses during NAC, SPT wheal size, serum allergen-specific antibody production and T-cell responses to cockroach allergen were assessed.Results: Changes in mean NAC TNSS did not differ between SCIT-assigned (n=28) versus placebo-assigned (n=29) participants (p=0.63). Nasal transcriptomic responses correlated with TNSS, but a treatment effect was not observed. Cockroach sIgE decreased to a similar extent in both groups, while decreased cockroach SPT wheal size was greater among SCIT participants (p=0.04). A 200-fold increase in cockroach sIgG4 was observed among subjects receiving SCIT (p<0.001) but was unchanged in the placebo group. T-cell interleukin-4 responses following cockroach allergen stimulation decreased to a greater extent among SCIT versus placebo (p=0.002), while no effect was observed for interleukin-10 or interferon-gamma.Conclusion: A year of SCIT failed to alter NAC TNSS and nasal transcriptome responses to cockroach allergen challenge despite systemic effects on allergen-specific skin tests, induction of serum sIgG4 production and down-modulation of allergen stimulated T-cell responses.

overall_design: CRITICAL (ClinicalTrials.gov NCT03541187) was a randomized, double-blind, placebo-controlled, multicenter trial of non-standardized aqueous glycerinated German cockroach (Blattella germanica) allergenic extract (Stallergenes Greer USA, Lenoir, NC) or placebo administered by subcutaneous injection completed between July 2018 and June 2022. Children ages 8-17 years, with persistent asthma for at least one year and living in low income areas of 10 large US cities were eligible if sensitized to German cockroach extract by both prick skin test and cockroach-specific IgE ≥ 0.35 kUA/L. A positive graded cockroach NAC, defined as either a Total Nasal Symptom Score (TNSS) ≥ 6 on a 12-point scale or a TNSS sneeze score of 3, was also required.Key exclusion criteria included National Asthma Education and Prevention Program classification of severe persistent asthma at randomization; AIT in the last year or anti-IgE, anti-IL-4R-alpha, anti-IL-5/IL5R therapy within six months of the NAC procedure; nasal polyposis or structural nasal abnormalities; a history of anaphylaxis grade 3 or higher; more than 2 courses of systemic corticosteroids within the 12 months or one course within the last 3 months prior to enrollment; or medication use or medical conditions potentially posing additional risk.


title: Convergent transcriptomic signatures across brain structures in eating disorders and obsessive compulsive disorder

city: New York City

first: Michael

last: Breen

state: NY

address: 1468 Madison Ave

department: Depts. of Psychiatry, Genetics and Genomic Sciences

institute: Icahn School of Medicine at Mount Sinai

summary: The objective of this study was to delineate the transcriptomic landscapes of the caudate and dorsolateral prefrontal cortex (DLFPC) in individuals with ED and OCD to identify common and distinct molecular pathways that may underlie these disorders.

overall_design: A cross-sectional study was conducted, leveraging postmortem brain samples to perform a transcriptomic analysis of the DLPFC and caudate nucleus from 86 control participants, 57 individuals diagnosed with ED, and 27 with OCD.

first: Andy

last: Yang

first: Xuran

last: Wang

first: Pardis

last: Amini

first: Miguel

last: Rodriguez de los Santos

first: Dorothy

last: Grice

first: Joseph

last: Buxbaum


title: Transcriptional and UV-response regulatory role of PPARb in Normal Human Keratinocytes

city: Lausanne

first: Paris

last: Jafari

address: Genopode Building

department: Center for Integrative Genomics

country: Switzerland

institute: University of Lausanne

summary: Solar radiation is the major source of human exposure to UV radiation, the major carcinogen in skin cancers, by triggering a number of cellular responses that can indirectly or directly induce DNA damage. Skin cells attempt to repair these damages by activating cascades of DNA Damage Response mechanisms to safeguard genome integrity, thereby preventing skin cancers. The role of PPARb - a druggable transcription factor, in the development of UV-dependent skin cancers is not mechanistically elucidated. We have shown previously that PPARb knockout mice are less prone to UV-induced skin cancers. Here, we report on our global transcriptomic analysis revealing that PPARb directly regulates gene expression programs associated with cell cycle and DNA repair pathways in normal human epidermal keratinocytes. We show that in these cells, as well as in malignant human keratinocytes and in human melanoma cells, PPARb controls cellular proliferation and cell cycle progression and its depletion leads to cell cycle arrest. We also show that PPARb controls the response of normal human epidermal keratinocytes to UV-induced DNA damage. PPARb depletion decreases the expression and/or activation of multiple effectors of DNA Damage Response (DDR) pathway and favours the apoptotic response of human keratinocytes to UV irradiation. Our preclinical data of a PDX melanoma model demonstrated that the depletion or inhibition of PPARb delays of blocks tumor formation. Our data suggest that PPARb inhibition can be considered as a therapeutic target for the prevention of UV-induced skin cancers in vulnerable population, by attenuating the DDR and eliminating skin cells with high UV-induced mutational burden.

overall_design: To study the regulatory role of PPARb on gene expression in NHEK cells, we downregulated PPARb gene (PPARD) in NHEK cells using two different siRNAs (siPPARD D, and siPPARD 2)

first: Nguyen

last: ThanhNhan

first: Jafari

last: Paris

first: Michalik

last: Liliane


title: TR-107, An Agonist of Caseinolytic Peptidase Proteolytic Subunit, Disrupts Mitochondrial Metabolism and Inhibits the Growth of Human Colorectal Cancer Cells

city: Stony Brook

first: Agnieszka

last: Bialkowska

address: 100 Nicolls Road

department: Medicine

institute: Stony Brook University

summary: Oxidative phosphorylation (OXPHOS) is an essential metabolic process for cancer proliferation and therapy resistance. The ClpXP complex maintains mitochondrial proteostasis by degrading misfolded proteins. Madera Therapeutics has developed a class of highly potent and selective small-molecule activators (TR compounds) of the ClpXP component caseinolytic peptidase proteolytic subunit (ClpP). This approach to cancer therapy eliminates substrate recognition and activates non-specific protease function within mitochondria, which has shown encouraging preclinical efficacy in multiple cancer types. The class-leading compound, TR-107, has demonstrated significantly improved potency in ClpP affinity and activation and enhanced pharmacokinetic properties over the multi-targeting clinical agent ONC201. In this study, we investigate the in vitro efficacy of TR-107 against human colorectal cancer (CRC) cells. TR-107 inhibited CRC cell proliferation in a dose- and time-dependent manner and induced cell cycle arrest at low nanomolar concentrations. Mechanistically, TR-107 downregulated the expression of proteins involved in the mitochondrial unfolded protein response (UPRmt) and mtDNA transcription and translation. TR-107 attenuated oxygen consumption rate and glycolytic compensation, confirming inactivation of OXPHOS and a reduction in total cellular respiration. Multi-omics analysis of treated cells indicated a downregulation of respiratory chain complex subunits and an upregulation of mitophagy and ferroptosis pathways. Further evaluation of ferroptosis revealed a depletion of antioxidant and iron toxicity defenses that could potentiate sensitivity to combinatory chemotherapeutics. Together, this study provides evidence and insight into the subcellular mechanisms employed by CRC cells in response to potent ClpP agonism. Our findings demonstrate a productive approach to disrupting mitochondrial metabolism, supporting the translational potential of TR-107.

overall_design: To investigate the mechanism of action and efficacy of TR-107 in vitro, we treated the human CRC cell line, HCT116, with vehicle control (DMSO, 0.1%) and 50nM TR-107 for 24 hours. Total RNA was isolated and RNA-seq was conducted. We then performed differential gene expression analysis using RNA-seq data from three biological replicates of each treatment condition to characterize significant transcriptomic changes in response to TR-107 treatment. Additionally, we conducted KEGG pathway analysis to identify upregulated and downregulated gene pathways following TR-107 treatment.

last: Giarrizzo

middle: F

last: LaComb

first: Hetvi

last: Patel

first: Rohan

last: Reddy

first: John

last: Haley

first: Lee

last: Graves

first: Edwin

last: Iwanowicz


title: Chromatin dynamics of Phytophthora during host infection [RNA-seq]

first: Haidong

last: Shu

overall_design: RNA-seq of P. sojae infection stages (12h post-inoculation (hpi), and 24hpi in soybean) were performed. Each RNA-seq experiment was performed with two biological replicates.

first: Han

last: Chen

first: Suomeng

last: Dong


title: CDC7 Inhibition Potentiates Antitumor Efficacy of PARP Inhibitor in Advanced Ovarian Cancer

first: Peng

last: Deng

address: Panyu

institute: SYSUCC

summary: PARP inhibitors have demonstrated remarkable clinical efficacy in treating ovarian cancer (OV) patients with BRCA1/2 mutations. However, drug resistance inevitably limits their clinical applications and there is an urgent need for improved therapeutic strategies to enhance the clinical utility of PARP inhibitors, such as Olaparib. Here, we present compelling evidence that PARP inhibitor sensitivity is associated with cell cycle dysfunction, independent of homologous recombination deficiency (HRD) /BRCA status. Through high-throughput drug screening with a cell cycle kinase inhibitor library, we identified XL413, a potent CDC7 inhibitor, which can synergistically enhance the anti-cancer efficacy of Olaparib. Mechanistically, we demonstrate that the combined administration of XL413 and Olaparib induced considerable DNA damage and DNA replication stress, leading to increased sensitivity to Olaparib. Additionally,  a robust type-I interferon response was triggered through the induction of the cGAS/STING signaling pathway. Using a murine syngeneic tumor model, we further demonstrate that the combination treatment enhanced antitumor immunity, resulting in tumor regression. Collectively, this study presents a novel treatment strategy for patients with advanced OV by combining CDC7 and PARP inhibitiors, offering a promising therapeutic approach forpatients whith limited response to PARP inhibitors.

overall_design: RNA-sequencing (RNA-seq) was conducted in OVCAR5 cells treated with Olaparib in the presence or absence of XL413.

first: Shini

last: Liu

first: Jing

last: Tan


title: Ancestral beta-globin gene haplotypes modify beta-thalassemia severity in a mouse model [Ery]

city: Memphis

first: Mitchell

last: Weiss

state: Tennessee

address: 262 Danny Thomas Place

department: Hematology

institute: St. Jude Children's Research Hospital

summary: beta-Thalassemia is a prevalent anemia caused by mutations in the HBB (beta-globin) gene. We show that the severity of beta-thalassemia in the frequently studied Hbb(th3/+) mouse model is influenced by ancestral beta-globin gene (Hbb) haplotypes that differ in common strains.

overall_design: Gene expression profiling of RNA-Seq data from 4 single Hbb and 4 diffuse Hbb mice.  Profiling was done on freshly sorted murine peripheral blood reticulocytes and bone marrow CD71hiFSChi (Ery. A) and CD71hiFSClo (Ery. B) cells.

first: Christophe

last: Lechauve

first: Julia

last: Keith

first: Alfonso

last: Fernandez

first: Eugene

last: Khandros

first: Kalin

last: Mayberry

first: Thiyagaraj

last: Mayuranathan

first: Lance

last: Palmer

first: Xiaohui

last: Qiu

first: Heather

last: Sheppard

first: Rahul

last: Telange

first: Hans-Martin

last: Herz


title: Ancestral β-globin gene haplotypes modify β-thalassemia severity in a mouse model [bone marrow, spleen]

summary: β-Thalassemia is a prevalent anemia caused by mutations in the HBB (β-globin) gene. We show that the severity of β-thalassemia in the frequently studied Hbbth3/+ mouse model is influenced by ancestral β-globin gene (Hbb) haplotypes that differ in common strains.

overall_design: To investigate to what degree the single and diffuse Hbb haplotypes modify the severity of β-thalassemia in mice.


title: The lectin Siglec-G functions as an inhibitory receptor in CD8+ T cell and can be targeted to enhance therapeutic antitumor immunity.

first: yin

last: hui

address: xiangyin road 800

institute: Second military medical university

summary: CD8+ T cells play a critical role in cancer immune-surveillance and pathogens elimination. However, the effector function of CD8+ T cells may be severely influenced due to inhibitory receptors. Here we identify Siglec-G as a coinhibitory receptor that plays a critical role in limiting the function of CD8+ T cells. Siglec-G is highly expressed on both human and murine tumor-inﬁltrating T cells, and SiglecG+ T cells enriched in the exhausted T cell subset. CD24-Siglec-G-SHP2 axis negatively regulates PI3K-AKT signaling and impairs metabolic reprogramming in CD8+ T cells and thereby dampens their activation, expansion and cytotoxicity. Genetic ablation of Siglec-G can enhance the efficacy of adoptively transferred T cells and CAR T cells to repress the growth of solid tumors. These results deﬁne a key role for Siglec-G in inhibiting CD8+ T cell-dependent responses, which strongly suggested its therapeutic effect in adoptive T cell therapy and tumor immunotherapy.

overall_design: To elucidate the mechanism that mediates the damped function of Siglec-G+ CD8+ T cells, we isolated Siglec-G+ and Siglec-G- OT-I effector cell subsets from LM-OVA infected mice and conducted RNA-seq.

first: Sheng

last: Xu

first: Chunzhen

last: Li

first: Xin

last: Shen


title: CAR-NK cells derived from cord blood predominantly originated from CD56-CD7+CD34-HLA-DR- lineage markers- NK progenitor cells

city: Suita

first: Daisuke

last: Motooka

address: 3-1, Yamadaoka

institute: NGS core facility, Research Institute for Microbial Diseases, Osaka University

summary: Cord blood (CB)-derived chimeric antigen receptor (CAR)-natural killer (NK) cells targeting CD19 has been shown to be effective against B cell malignancies. While human CD56+ NK cells can be expanded in vitro, it is also known that NK cells can be differentiated from hematopoietic progenitor cells. It is still unclear whether CAR-NK cells are originated from mature NK cells or NK progenitor cells in CB. Here we found that CAR-NK cells are predominantly derived from the CD56- NK progenitor cells. We first found that substantial numbers of CD19 CAR-NK cells were produced from the CD56- CB mononuclear cells after in vitro culture for two weeks. Single cell RNAseq analysis of CD56-CD3-CD14-CD19- CB mononuclear cells revealed that those cells were subdivided into three subpopulations based on the expression of CD34 and HLA-DR. NK cells were predominantly produced from the CD34-HLA-DR- cells. In addition, in the CD34-HLA-DR- cells, only CD7+ cells could differentiate into NK cells. These results indicate that CD56-CD7+CD34- HLA-DR-lineage marker (Lin)- cells are the major origin of human CB-derived CAR-NK cells, indicating that we need to develop methods to enhance the quality and quantity of NK cells produced from these NK cell progenitor cells.

overall_design: CD56-CD3-CD14-CD19- cord blood mononuclear cells from three independent donors were FACS-sorted and subjected to the analysis

first: Tansri

last: Wibowo

first: Yosuke

last: Kogue

first: Naoki

last: Hosen


title: Endothelial POFUT1 controls injury-induced liver fibrosis by repressing fibrinogen synthesis

city: Xi'an

first: Luo

last: Yuru

state: Shannxi

address: 28 Xianning West Road

department: Health Science Center

institute: Xi'an Jiaotong University

summary: Background & Aims: NOTCH signaling in liver sinusoidal endothelial cells (LSECs) regulates liver fibrosis, a pathological feature of chronic liver diseases. POFUT1 is an essential regulator of NOTCH signaling. Here, we investigated the role of LSECs-expressed POFUT1 in liver fibrosis. Methods: Endothelial-specific Pofut1 knockout mice were generated and subjected to experimental liver fibrosis by chronic carbon tetrachloride exposure or by common bile duct ligation. Liver samples were assessed by ELISA, histology, electron microscopy, immunostaining and RNA in situ hybridization. LSECs and hepatic stellate cells (HSCs) were isolated for gene expression analysis by RNA-seq, qPCR, and Western blotting. Signaling crosstalk between LSECs and HSCs was investigated by treating HSCs with supernatant from LSECs cultures. Liver single-cell RNA-seq data sets from cirrhotic patients and healthy individuals were analyzed to evaluate the clinical relevance of gene expression changes observed in mouse studies.  Results: POFUT1 loss promoted injury-induced LSECs capillarization and HSC activation, leading to aggravated liver fibrosis. RNA-seq analysis revealed that POFUT1 deficiency upregulated fibrinogen expression in LSECs. Consistently, fibrinogen was elevated in LSECs of cirrhotic patients. HSCs treated with supernatant from LSECs of Pofut1 null mice showed exacerbated activation compared to treatment with supernatant from control LSECs, and this effect was attenuated by knockdown of fibrinogen or by pharmacological inhibition of fibrinogen receptor signaling, altogether suggesting that LSEC-derived fibrinogen induced the activation of HSCs. Mechanistically, POFUT1 loss augmented fibrinogen expression by enhancing NOTCH/HES1/STAT3 signaling.  Conclusions: Endothelial POFUT1 prevents injury-induced liver fibrosis by repressing the expression of fibrinogen which function as a profibrotic paracrine signal to activate HSCs. Therapies targeting the POFUT1/NOTCH/HES1/STAT3/fibrinogen axis offer a promising strategy for the prevention and treatment of fibrotic liver diseases.

overall_design: To further elucidate the molecular mechanism through which POFUT1 regulates the phenotype of LSECs and HSCs, LSECs were isolated from the CTL and P1KO mice treated with CCl4 and subjected to RNA-seq analysis.

first: Shan

last: He

first: Yuru

last: Luo


title: Increased PTCHD4 expression via m6A modification of PTCHD4 mRNA promotes senescent-cell survival [CLIP-seq]

city: Baltimore

first: Supriyo

last: De

state: Maryland

address: 251 Bayview Blvd

department: Laboratory of Genetics and Genomics

institute: NIA-IRP, NIH

summary: RNA modifications, including m6A, critically modulate protein expression program in a range of cellular processes.  Although cellular senescence has been linked to age-related diseases and functional declines, the landscape and impact of m6A modification are poorly understood. Here, we report a robust m6A modification of Patched-Domain Containing Protein 4 (PTCHD4) mRNA at m6A in senescent cells.  The METTL3/METTL14 complex was found to mediate the m6A modification of PTCHD4 mRNA, which increased PTCHD4 mRNA stability and PTCHD4 production.  MeRIP RT-qPCR and eCLIP analyses were used to map this m6A modification to the last exon of PTCHD4 mRNA.  Further investigation identified IGF2BP1, but not other m6A readers, as being responsible for stabilization and increased abundance of PTCHD4 mRNA by m6A modification.  Silencing PTCHD4, a transmembrane protein, enhanced growth arrest and DNA damage in pre-senescent cells, and sensitized them to senolytic treatments and apoptosis.  Our results support the notion that m6A modifications critically control senescence programs, and that factors such as METTL3/METTL14 and IGF2BP1, implicated in PTCHD4 mRNA m6A metabolism, could be exploited to eliminate senescent cells for therapeutic benefit.

overall_design: To investigate the role of m6A in PTCHD4, eCLIP analysis was performed on proliferating and senescent samples.


title: Antiandrogen Flutamide-Induced Restoration of miR-449 Expression Mitigates Molecular  Markers Associated with Ovarian Cancer Risk

city: Tucson

first: Michelle

last: Wei

state: AZ

address: 1200 E University Blvd

institute: University of Arizona

type: Non-coding RNA profiling by high throughput sequencing

summary: The involvement of the androgen receptor (AR) pathway in the development of epithelial ovarian cancer is increasingly recognized. We examined the effects of the anti-androgen agent flutamide on miRNA expression in women at high risk (HR) for ovarian cancer. Flutamide treatment restored the reduced expression of miR-449a and miR-449b-5p in HR tissues, thereby decreasing CSF1R and AR expression associated with an increased risk of ovarian cancer. In addition to the known direct binding of flutamide to the AR, we found that flutamide also suppresses AR expression via miR-449a and miR-449b-5p upregulation, revealing a novel dual-inhibitory mechanism on the AR pathway. Taken together, our study highlights the chemopreventive potential of flutamide in ovarian cancer and suggests avenues for future research and clinical applications.

overall_design: We conducted miRNA-sequencing profiling in the two ovarian cancer-related tissues, the ovary and fallopian tube, from HR and LR patients (with high- and low-risk for ovarian cancer, respectively). HR group was further divided into two cohorts: those treated with flutamide (the “flutamide” cohort) and those not treated with flutamide (the “HR” cohort). The samples across the three cohorts (flutamide, HR, and LR) were matched for body mass index (BMI) and menopausal status. The HR and flutamide cohorts were defined for the high-risk status and balanced for germline BRCA1/2 conditions

first: Xia

last: Wang

first: Ho-Hyung

last: Woo

first: Steven

last: Gibson

first: Mitzi

last: Miranda

first: Demaretta

last: Rush

first: Janiel

last: Cragun

first: Wenxin

last: Zheng

first: Guang

last: Yao

first: Setsuko

middle: K

last: Chambers


title: The role of CMTM3 in a sepsis mouse model

city: Beijing

first: Haiyan

last: Xue

address: 11th Xizhimen South Street

institute: Peking University People's Hospital

summary: Sepsis is a life-threatening condition characterized by an imbalanced immune response to infection, leading to multiple organ dysfunction. It has a high incidence and mortality rate. CMTM3 is a member of the CKLF-like MARVEL transmembrane domain (CMTM) gene superfamily, and it is widely expressed in the immune system, playing a critical role in immune response. However, the precise role of CMTM3 in sepsis remains yet to be determined.

overall_design: To investigate the role of CMTM3 in sepsis, we generated Cmtm3 knock-out mice. Subsequently, we induced sepsis in both Cmtm3 wild-type and knock-out mice by performing cecal ligation and puncture (CLP) surgery. After 24 hours of modeling, we isolated bone marrow cells for transcriptome sequencing.

first: Fengxue

last: Zhu


title: Differentiating erythroblasts adapt to turbulent flow by accelerating maturation and activating cholesterol biosynthesis.

city: Amsterdam

first: Giulia

last: Iacono

address: Plesmanlaan 125

institute: Sanquin

summary: In vitro culture of erythroblasts and production of mature erythrocytes for transfusion purposes requires upscaling in bioreactors with turbulent fluidic environments, resulting in membrane shear stress. For the implementation of erythroid cultures in bioreactors, further understanding of the effects of mechanical stress on terminal erythroblast differentiation are required. To this end, we investigated the effect of orbital shaking-induced shear stress on differentiation of CD49d+CD235low primary human erythroblast (EBL) towards enucleated reticulocytes at the molecular, cellular, and functional level. Orbital shaking at the onset of erythroblast differentiation enhanced cell maturation and increased enucleation percentage compared to static cultures, without loss of cell viability. Transcriptome analysis uncovered 505 genes to be differentially expressed between static and non-static cultures, where genes involved in lipids and cholesterol biosynthesis pathways where upregulated in non-static conditions. In line with this finding, cells differentiated in orbital shakers showed an increased cholesterol concentration and higher osmotic resistance compared to cells differentiated in static condition. HMGCR (3-Hydroxy-3-Methylglutaryl-CoA-Reductase), a rate limiting enzyme of the cholesterol biosynthesis pathway, is significantly increased and showed earlier induction during differentiation in shear stress environments. Inhibition of HMGCR using lovastatin led to severe loss of EBL differentiation in shear environments but not in static conditions. In conclusion, differentiating EBL display a dynamic capability to adapt to shear stress environments, by modulating their transcriptional program and consequently upregulating cholesterol biosynthesis, which is critical for their survival. This work sheds light into specific mechanisms which will assist on the successful upscaling of erythroid differentiation in turbulent bioreactors.

overall_design:
To understand the effect of mechanical forces on erythroblasts differentiation we performed RNAseq analysis of erythroblast differentiated in static and dynamic conditions.
We then compared the RNA-seq data obtained from 4 different donors during 3 culture time points: day of differentiation 1, 2 and 4, determining 3 different expression profiles.

first: Asena

last: Abay

first: Arthur

last: Flohr Svendsen

first: Emile

last: van den Akker


title: RNAseq analysis of IL-18 WT- and IL-18 D69A-overexpressing B16-F10 tumors

city: Shanghai

first: junchen

last: Shen

address: 320 yueyang road.

institute: Shanghai institute of immunity and infection

summary: To gain insights into the function and mechanism of Interleukin (IL)-18 in cancer cells, we conducted RNA-seq analysis to compare the gene expression profiles between IL-18 WT- and IL-18 D69A (IL-18 mutagenesis replacing aspartate (D) with alanine (A) at position 69)-overexpressing B16-F10 tumors. As expected, many genes were upregulated in IL-18 WT samples. Notably, transcripts related to many signaling pathways such as interferon signaling pathway were significantly enriched in samples expressing IL-18 WT.

overall_design:
We established B16-F10 cancer cell lines overexpressing IL-18 WT or IL-18 D69A (IL-18 mutagenesis replacing aspartate (D) with alanine (A) at position 69).
C57BL/6 mice were s.c. engrafted with 4 × 105 B16-F10 cells harboring IL-18 WT or IL-18 D69A. Mice were sacrificed on day 11. Five IL-18 WT-overexpressing tumor samples and five IL-18 D69A-overexpressing tumor samples were collected for RNAseq analysis.
Comparative gene expression profiling analysis of RNA-seq data for B16-F10 tumors expressing IL-18 WT or IL-18 D69A. We conducted RNA-seq analysis to compare the gene expression profiles.

first: Guangxun

last: Meng

first: Junchen

first: Yu

last: Zhang


title: TAF15 overexpression impairs memory in mice by inhibiting the transcription of Npas4

city: Hefei

first: Ding

middle: Mei

last: Jie

state: Anhui

address: Huangshanlu

department: life science

institute: the University of science and technology of China

summary: TAF15, a DNA and RNA-binding protein primarily localized in the nucleus, has been reported to be associated with the aging process and neurodegenerative diseases accompanied by cognitive decline. However, its role in regulating learning and memory remains unclear. Here, we discovered that TAF15 accumulates in the hippocampus of aged mice, and TAF15 overexpressing in hippocampal neurons led to spatial learning and memory impairments in young mice. These finding are further supported by the significant reduction of dendritic spines density and synaptic proteins level. Further studies revealed that overexpression of TAF15 is likely to reduce the number of dendritic spines by inhibiting the expression of Npas4 (among the most rapidly induced immediate-early genes) and its target gene Nptx2. Notably, the expression of Npas4 and Nptx2 in the hippocampus of aged mice is also downregulated. Additionally, we demonstrated that TAF15 binds to the core promoter of Npas4 gene and inhibits its transcription, and neuronal depolarization induces the dissociation of TAF15 from Npas4 promoter. Together, these findings uncover a direct role of TAF15 in regulating spatial learning and memory formation, which may provide new insights into aging-related cognitive deficits.

overall_design: The transcriptome profiles in the hippocampus of control and TAF15 overexpressing (TAF15 OE) mice were sequenced on an Illumina NovaSeq 6000 platform. Briefly, total RNA was extracted with Trizol Reagent, and the cDNA libraries were prepared according to the manufacturer’s protocol. Three replicates were sequenced (each replicate represents one mouse) for each group.

first: Meijie

last: Ding

first: Dingfeng

last: Li

first: Juan

first: Qiang

last: Liu


title: Hepatic Vagal Afferents Convey Clock-Dependent Signals to Regulate Circadian Food Intake Patterns

city: Philadelphia

first: Mohit

middle: K.

last: Midha

state: PA

address: 3400 Civic Center Blvd

institute: University of Pennsylvania

summary: Circadian desynchrony induced by shiftwork or jetlag is detrimental to metabolic health, but how synchronous or desynchronous signals are transmitted among tissues is unknown. We report that liver molecular clock dysfunction is signaled to the brain through the hepatic vagal afferent nerve (HVAN), leading to altered food intake patterns that are corrected by ablation of the HVAN. Hepatic branch vagotomy also prevents food intake disruptions induced by high-fat diet feeding and reduces body weight gain. Our findings reveal a homeostatic feedback signal that relies on communication between the liver and the brain to control circadian food intake patterns. This identifies the hepatic vagus nerve as a potential therapeutic target for obesity in the setting of chrono-disruption.

overall_design: Arcuate nucleus microdissections and left nodose ganglia from control and HepDKO animals were collected every 6hrs for 24hrs and sequenced. 3-4 arcuate nuclei per group per time point were pooled for each biological replicate. 4 left nodose per group per time point were pooled for each biological replicate.

first: Lauren

middle: N

last: Woodie

first: Mitchell

middle: A

last: Lazar


title: Asynchronous female reproductive organ ageing as revealed by single-cell transcriptomic atlas

city: Wuhan

first: Shixuan

last: Wang

state: Hubei

address: Jiefang Avenue

institute: Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology

summary: Successful pregnancies require fine coordination among the reproductive organs. Reproductive research has focused on ovarian ageing, the uterus and oviduct have received much less attention; whether these organs age synchronously with the ovaries remains unclear. Here, we established a single-cell transcriptomic atlas of the ovary, oviduct, and uterus across the murine reproductive lifespan. Organ–organ communication patterns were identified using cell-specific hormone receptor analysis. The ageing hallmarks (including DNA damage, cellular senescence, and apoptosis, etc.) were evaluated for each cell type. Analysis of these ageing-related gene set scores combined with changes in morphology and molecular signatures revealed that the ovary aged earlier and faster than the oviduct and uterus; this was also confirmed in human reproductive tissues. Our single-cell transcriptomic atlas provides molecular insights into reproductive ageing and its asynchronization for the reproductive organs across the murine reproductive lifespan, which may reveal the causes of declining fertility at advanced ages.

overall_design: We performed scRNA-seq analyses of the ovary, oviduct, and uterus across the female reproductive lifespan of Mus musculus [C57BL/6 mice, 5 days (5D), 5 weeks (5W), 3 months (3M), 6 months (6M), 9 months (9M), 12 months (12M), and 15 months (15M)].

first: Jinjin

first: Qianyu

first: Yun

last: Han

first: Xiaofan

last: Gao

first: Suzhen

last: Yuan

first: Bo

first: Tong

last: Wu

first: Yueyue

first: Qian

last: Chen

first: Jingyi

last: Wen

first: Yan

first: Milu

first: Dianxing

last: Hu

first: Xianan

last: Tang

first: Yingying

first: Huan

last: Lu

first: YanZhi

last: Feng

first: Yaling

first: Xingyu

first: Jun

last: Dai

first: Meng

first: Pengfei

last: Cui

first: Xiaoyan

first: Guoping

first: Aiyue

last: Luo

first: Mo


title: Increased PTCHD4 expression via m6A modification of PTCHD4 mRNA promotes senescent-cell survival [RNA-seq]

first: Supriyo

last: De

overall_design: To investigate the functions of PTCHD4, the gene was silenced using 2 different methods. Each condition was sequenced in replicates of 3.  PTCHD4 silencing was compared to  control.


title: Increased PTCHD4 expression via m6A modification of PTCHD4 mRNA promotes senescent-cell survival [array]

summary: RNA modifications, including m6A, critically modulate protein expression program in a range of cellular processes.  Although cellular senescence has been linked to age-related diseases and functional declines, the landscape and impact of m6A modification are poorly understood.  Here, we report a robust m6A modification of Patched-Domain Containing Protein 4 (PTCHD4) mRNA at m6A in senescent cells.  The METTL3/METTL14 complex was found to mediate the m6A modification of PTCHD4 mRNA, which increased PTCHD4 mRNA stability and PTCHD4 production.  MeRIP RT-qPCR and eCLIP analyses were used to map this m6A modification to the last exon of PTCHD4 mRNA.  Further investigation identified IGF2BP1, but not other m6A readers, as being responsible for stabilization and increased abundance of PTCHD4 mRNA by m6A modification.  Silencing PTCHD4, a transmembrane protein, enhanced growth arrest and DNA damage in pre-senescent cells, and sensitized them to senolytic treatments and apoptosis.  Our results support the notion that m6A modifications critically control senescence programs, and that factors such as METTL3/METTL14 and IGF2BP1, implicated in PTCHD4 mRNA m6A metabolism, could be exploited to eliminate senescent cells for therapeutic benefit.

overall_design: Detection of m6A modification in proliferating (PDL22) and senescent (RS PDL50, IR-IS: 10 Gy (PDL22) human WI-38 diploid fibroblasts was performed using the ArrayStar mRNA&LncRNA Epitranscriptomic Array Service on anti-N6-methyadenosine (m6A) antibody immunoprecipitated total RNA (N= 3 biological replicates per condition)> The modified RNA (IP RNA) and the unmodified RNAs supernatants (Sup RNA) for each sample were recovered, the IP and Sup RNAs labeled with Cy5 and Cy3, respectively, and arrayed on the Arraystar Human mRNA&lncRNA Epitranscriptomic microarray (8x60K, Arraystar).

first: Martina

last: Rossi

first: Nirad

last: Banskota

first: ChangHoon

last: Shin

first: Carlos

last: Anerillas

first: Dimitrios

last: Tsitsipatis

first: Jen-Hao

last: Yang

first: Rachel

last: Munk

first: Jennifer

last: Martindale

first: Xiaoling

first: Yulan

last: Piao

first: Krystyna

last: Mazan-Mamczarz

first: Jinshui

last: Fan

first: Elin

last: Lehrmann

first: Kwan-Wood

last: Lam

first: Kotb

last: Abdelmohsen

first: Myriam

last: Gorospe


title: Regulation of GLIS3 in neonatal kidney development

city: Research Triangle Park

first: Anton

middle: M

last: Jetten

state: NC

address: 111 TW Alexander Drive

department: DIR

institute: NIEHS, NIH

summary: Loss of transcription factor GLIS3 function in humans and mice leads to the development of neonatal polycystic kidney disease (PKD). To investigate how loss of GLIS3 function in kidney affects postnatal kidney development and PKD, we analyzed the gene expression profiles of kidneys from WT and Glis3-null mice at P7, P14, and P28 by RNA-Seq analysis using Glis3 global KO model Glis3-mCherry.

overall_design: Total kidney RNAs were isolated from WT and Glis3-null mice and gene expression profiles were analyzed by RNA-Seq.

first: Yun-Gil

last: Roh

first: Chitrangda

last: Srivastava

first: Hong

middle: S

last: Kang

first: Justin

last: Collier

first: Sara

last: Grimm


title: Targeted degradation of oncogenic KRAS G12V triggers antitumor immunity in lung cancer [scRNA-seq]

city: New York

first: Yuan

last: Hao

address: Laura and Isaac Perlmutter Cancer Center

institute: NYU Langone Health

summary: We performed single cell RNA sequencing analysis from KRAS G12V mouse tumor nodules from different treatment.

overall_design: KRAS G12V mutant mice with lung tumors were treated with either vehicle or dTAGV-1. Tumor nodules were collected for sequencing.

first: Hua

last: Zhang


title: Comprehensive analysis of mesenchymal cells reveals a deregulated TGF-B/Wnt/HOXB7 axis in patients with myelofibrosis [RNA-seq]

city: paris

first: SARAVANAN

last: GANESAN

state: Paris

address: 1 Avenue Claude Vellefaux, 75010 Pa

country: France

institute: IRSL, Hopital Saint Louis

summary: In this study, through a patient-sample driven transcriptomic and epigenetic description of the MF microenvironment landscape and cell-based analyses, we identify HOXB7 overexpression and more precisely a novel TGF-B-Wnt-HOXB7 pathway as associated to a pro-fibrotic and pro-osteoblastic biased differentiation of mesenchymal stromal cells (MSCs).

overall_design:
Characterizing MSCs from myelofibrosis patients by RNA-seq.

**Submitter declares that the raw data have not been deposited due to patient privacy concerns**

first: Saravanan

last: Ganesan

first: Bruno

last: Cassinat

first: Christine

last: Chomienne


title: Comprehensive analysis of mesenchymal cells reveals a deregulated TGF-B/Wnt/HOXB7 axis in patients with myelofibrosis [ATAC-seq]

overall_design:
Characterizing MSCs from myelofibrosis patients by ATAC-seq.

**Submitter declares that the raw data have not been deposited due to patient privacy concerns**


title: Comprehensive analysis of mesenchymal cells reveals a deregulated TGF-B/Wnt/HOXB7 axis in patients with myelofibrosis

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

overall_design: Refer to individual Series


title: DAB2IP Loss in Luminal A Breast Cancer Leads to NF-kB- Associated Aggressive Oncogenic Phenotypes

city: Chapel Hill

first: Albert

middle: S.

last: Baldwin

state: North Carolina

address: 450 West Drive, Room 21-211

department: Lineberger Comprehensive Cancer Center

institute: UNC at Chapel Hill

summary:
Despite proven therapy options for estrogen receptor (ER)-positive tumors, a significant number of patients with these cancers exhibit relapse with associated metastasis. Studies have shown that the loss of expression of RasGAPs leads to aggressive phenotypes and poor outcomes in several cancers including breast cancer. In our study, mining TCGA gene expression profiles of ER-positive breast tumors, we found that low expression of the RasGAP, DAB2IP is associated with a significant decrease in relapse-free survival in patients with Luminal A breast tumors. Immunostaining found that DAB2IP loss occurs in grade 2 tumors and higher. Consistent with this, genes upregulated in low DAB2IP Luminal A tumors are shared with more aggressive tumor subtypes, and are associated with proliferation, metastasis, and enhanced ER-signaling. In addition, cell-based studies reveal that low DAB2IP expression in ER-positive breast cancer cells is associated with increased proliferation, enhanced stemness phenotypes, and activation of IKK, the upstream regulator of the NF-B signaling pathway. Further, integrating cell-based ChIP-seq with motif analysis and TCGA RNA-seq data, we identify a candidate set of NF-B target genes that are upregulated with loss of DAB2IP and are proposed to regulate several oncogenic phenotypes, including altered RNA processing. This study provides new insight into mechanisms associated with aggressiveness and recurrence within a subset of Luminal A breast cancers that are otherwise typically less aggressive.
Gene expression profiling by RNA-sequencing of DAB2IP knockdown and control MCF10A cells.

overall_design: Total RNA was isolated from MCF10A DAB2IP knockdown and control cells using Quick-RNA kits, Zymo Research following manufacturer’s instructions. The RNA samples were then submitted to Novogene Corporation Inc., California for library preparation, RNA sequencing, and analysis.

first: Angana

last: Mukherjee


title: Molecular Response to Biomechanical Loading in Human Growth Plate Cartilage

city: Solna

first: Nageswara Rao

last: Boggavarapu

state: stockholm

address: Visionsgatan 4

department: Women and Children health

country: Sweden

institute: Karolinska Institutet

summary: Understanding the effects of biomechanical loading on human growth plate cartilage, which are unknown so far, could uncover diagnostic and therapeutic avenues. To address this, we used rare human growth plate biopsies obtained from children undergoing epiphysiodesis. These biopsies were exposed to a precisely controlled mechanical loading application using a microloading device. Subsequently, the biopsies were cultured for 24 hours post-mechanical loading, followed by RNA-sequencing analyses to decipher the molecular responses.

overall_design: Biopsies from three patients were divided into two groups: mechanical loading (9 biopsies) and control (9 biopsies). Mechanical loading was applied using a custom device at 0.4N and 0.77Hz for 30 seconds, while the control group underwent the same procedure without loading. After 24 hours, RNA was extracted and DNA libraries were prepared for next-generation sequencing using the Smart-seq2 protocol.

first: Nageswara

middle: R


title: Targeted degradation of oncogenic KRAS G12V triggers antitumor immunity in lung cancer


title: Effect of GFI1B ectopic expression in the hematopoietic or endothelial commitment of human iPSC derived CD34+CD43-CD73- hemogenic endothelium (HE)

first: Emile

last: van den Akker

institute: Sanquin Research Amsterdam

summary: In this study we focused on unrevealing the role of major transcriptional factor GFI1B and its cofactor, LSD1 in human endothelial to hematopoietic transition (EHT). We applied irreversible LSD1 inhibitor (GSK-LSD1) to healthy iPSC lines. Interestingly, LSD1 inhibited healthy lines which showed complete absence of hematopoietic cell output, did not showed detection of GFI1B expression, suggesting a timed transcriptional program. In order to test this hypothesis, we ectopically expressed GFI1B in the uncommitted HE cells, leading to downregulation of endothelial genes and an upregulation of hematopoietic genes, including GATA2, KIT, RUNX1 and SPI1.

overall_design: To investigate this, we enriched CD34+ HE cells from iPSC differentiation. We lentivirally transduced these cells with empty vector (EV) or GFI1B, and harvested them 3 days after transduction for RNA seq analysis. We had three replicates for each condition

first: Huan

first: Marten

last: Hansen

first: Franca

last: di Summa

first: Marieke

last: von Lindern

first: Nynke

last: Gillemans

first: Wilfred

last: van IJcken

first: Arthur

last: Svendsen

first: Sjaak

last: Philipsen

first: Bert

last: van der Reijden

first: Eszter

last: Varga


title: High resolution analysis of heterogeneous alveolar type II cells in emphysema and health reveals an airway origin of impaired alveolar regeneration

city: Pittsburgh

first: Melanie

last: Königshoff

state: Pennsylvania

address: 200 Lothrop St

institute: University of Pittsburgh

summary: Emphysema is a major pathological phenotype of chronic obstructive pulmonary disease (COPD) that is characterized by progressive and irreversible alveolar tissue destruction caused by several stressors, such as tobacco smoke and air pollution. It remains incurable in part due to an incomplete understanding of cellular and molecular mechanisms underlying the failure of tissue repair. Here, we have generated a single cell RNA sequencing dataset of enriched epithelial cells from emphysematous parenchymal lung tissue of COPD patients and from healthy controls.Using this dataset, we performed high resolution analysis of 78,699 ATII cells and reveal novel ATII cell subsets in severe emphysema and health. These include two ATII sub-clusters expressing various secretoglobin mRNAs (SCGBpos) in COPD that present distinct transcriptomic profiles compared to healthy sub-clusters. These ATII sub-clusters that are present in human COPD are also found in a mouse emphysema model. Importantly, the COPD specific ATII cells from both species demonstrate airway origins and fail to undergo alveolar differentiation in organoid cultures, thereby suggesting that a common mechanism in emphysema pathogenesis.

overall_design:
Emphysematous parenchymal lung tissues were surgically dissected from explanted lung lobes of deidentified patients with end-stage COPD (N=6), who received lung transplantation. Protocol was approved by UC Health University of Colorado Hospital (COMIRB 11–1664). Healthy lung tissues of deidentified donors without lung diseases (N=4) were obtained from the Human Lung Tissue Consortium at National Jewish Health. (NJHIRB HS-1797)

**RAW data not provided due to patient privacy concerns**

first: Yan

last: Hu

first: Qianjiang

last: Koenigshoff


title: Chronic Interferon Stimulated Gene Transcription Promotes Oncogene Induced Breast Cancer [RNA-Seq]

first: Hexiao

last: Wang

address: 1275 York Ave

institute: Memorial Sloan Kettering Cancer Center

summary: The Mre11 complex (comprising Mre11, Rad50, Nbs1) is integral to the maintenance of genome stability. We previously showed that a hypomorphic Mre11 mutant mouse strain (Mre11ATLD1/ATLD1) was highly susceptible to oncogene induced breast cancer. Here we used a mammary organoid system to examine which Mre11 dependent responses are tumor suppressive. We found that Mre11ATLD1/ATLD1 organoids exhibited an elevated interferon stimulated gene (ISG) signature and sustained changes in chromatin accessibility. This Mre11ATLD1/ATLD1 phenotype depended on DNA binding of a nuclear innate immune sensor, IFI205. Ablation of Ifi205 in Mre11ATLD1/ATLD1 organoids restored baseline and oncogene-induced chromatin accessibility patterns to those observed in WT. Implantation of Mre11ATLD1/ATLD1 organoids and activation of oncogene led to aggressive metastatic breast cancer. This outcome was reversed in implanted Ifi205-/- Mre11ATLD1/ATLD1 organoids. These data reveal a connection between innate immune signaling and tumor suppression in mammary epithelium. Given the abundance of aberrant DNA structures that arise in the context of genome instability syndromes, the data further suggest that cancer predisposition in those contexts may be partially attributable to tonic innate immune transcriptional programs.

overall_design: To investigate DNA damage response after oncogene activation in mammary epithelia. We performed RNA-Seq in WT and Mre11ATLD1/ATLD1 mammary organoids at day 0, day 14, day 28 after oncogene neuT activation.

first: Claudia

last: Canasto-Chibuque

first: Jun

middle: H

last: Kim

first: Marcel

last: Hohl

first: Christina

last: Leslie

first: Jorge

last: Reis-Filho

first: John

last: Petrini


title: Diverse Epithelial Lymphocytes in Zebrafish Revealed Using a Novel Scale Biopsy Method

city: Oklahoma City

middle: Kimble

last: Frazer

state: Oklahoma

address: 941 Stanton L Young Blvd

department: Pediatrics

institute: University of Oklahoma Health Sciences Center

summary: Zebrafish (Danio rerio) are a compelling model to study lymphocytes because zebrafish and humans have similar adaptive immune systems, including their lymphocytes. Antibodies that recognize zebrafish proteins are sparse, so many investigators utilize transgenic, lymphocyte-specific fluorophore-labeled lines. Human and zebrafish lymphocyte types are conserved, but many aspects of zebrafish lymphocyte biology remain uninvestigated, including lymphocytes in peripheral tissues, like epidermis. Here, we report the first study focused on zebrafish epidermal lymphocytes, using scales. Obtaining zebrafish blood via non-lethal methods is difficult; scales represent a source to longitudinally sample live fish. We developed a novel biopsy technique, collecting scales to analyze epithelial lymphocytes from several fluorescently-labeled lines. We imaged scales via confocal microscopy and demonstrated multiple lymphocyte types in scales/epidermis, quantifying them flow cytometrically. We profiled gene expression of scale, thymic, and marrow lymphocytes from the same animals, revealing B- and T-lineage signatures. Single-cell qRT-PCR and RNA sequencing (scRNA-seq) show not only canonical B and T cells, but also novel lymphocyte populations not described previously. To validate longitudinal scale biopsies, we serially sampled scales from fish treated with dexamethasone (DXM), demonstrating epidermal lymphocyte responses. To analyze cells functionally, we employed a bead-ingestion assay, showing thymic, marrow, and epidermal lymphocytes have phagocytic activity. In summary, we establish a novel, non-lethal technique to obtain zebrafish lymphocytes, providing the first quantification, expression profiling, and functional data (DXM responses and phagocytosis) from epidermal lymphocytes in the zebrafish model.

overall_design: This experimental study aimed to investigate the gene expression profiles of individual lymphocytes from the zebrafish lck:GFP transgenic line by using single-cell RNA sequencing (scRNA-seq) analysis. We performed scRNA-seq on GFPhi thymocytes and GFPlo scale/marrow cells from lck:GFP fish which mark different lymphocyte populations. scRNA-seq data reveal diverse thymic, scale, and marrow lymphocyte populations for subsequent transcriptomic analysis and isolation of specific cell types.

first: Gilseung

last: Park

first: Clay

last: Foster

first: Megan

last: Malone-Perez

first: Ameera

last: Hasan

first: Jose

last: Macias

first: J


title: Tumorigenic effect of knockout HKDC1 on A549 in vivo

city: Guangzhou

first: YAO

last: LUO

address: Dong Feng East Road

institute: SYSUCC

summary: To investigate the tumorigenic function of HKDC1 in vivo, we established A549 cell lines in which HKDC1 has been knockout by CRISPER/Cas9 genome editing. We then performed gene expression profiling analysis using data obtained from RNA-seq of 6 different tumors from sgCtrl or sgHKDC1-1 groups.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for 6 different tumors from sgCtrl or sgHKDC1-1 groups.

first: Peng

last: Huang

first: Panpan

last: Liu

first: Yao

last: Luo

first: Jianan

last: Li


title: Vascular rarefaction mediates whitening of brown fat in obesity

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Brown adipose tissue (BAT) is a highly vascularized organ with abundant mitochondria that produce heat through uncoupled respiration. Obesity is associated with a reduction of BAT function; however, it is unknown how obesity promotes dysfunctional BAT. Here, using a murine model of diet-induced obesity, we determined that obesity causes capillary rarefaction and functional hypoxia in BAT, leading to a BAT “whitening” phenotype that is characterized by mitochondrial dysfunction, lipid droplet accumulation, and decreased expression of Vegfa. Targeted deletion of Vegfa in adipose tissue of nonobese mice resulted in BAT whitening, supporting a role for decreased vascularity in obesity-associated BAT. Conversely, introduction of VEGF-A specifically into BAT of obese mice restored vascularity, ameliorated brown adipocyte dysfunction, and improved insulin sensitivity. The capillary rarefaction in BAT that was brought about by obesity or Vegfa ablation diminished β-adrenergic signaling, increased mitochondrial ROS production, and promoted mitophagy. These data indicate that overnutrition leads to the development of a hypoxic state in BAT, causing it to whiten through mitochondrial dysfunction and loss. Furthermore, these results link obesity-associated BAT whitening to impaired systemic glucose metabolism.

overall_design: Brown adipose tissue was collected from adipose-specific Vegfa knockout animals and littermate controls, and gene expression was profiled using Mouse Gene 1.0 ST microarrays.

first: Ippei

last: Shimizu

first: Kenneth

last: Walsh


title: Compensatory mechanisms in non-muscle organs in myotubular myopathy

city: Illkirch-Graffenstaden

first: Jocelyn

last: Laporte

address: 1 rue Laurent Fries

institute: IGBMC

summary: X-Linked myotubular myopathy (XLMTM), is associated with very severe muscle weakness and reduced life expectancy. Liver dysfunction was also reported. The pathomechanism and the impact of non-muscular defects affecting survival are barely known. Here, we investigated organ-specific effects of XLMTM in the faithful Mtm1-/y mouse model. We performed RNA-sequencing to identify a shared mechanism in several skeletal muscles, and to investigate potential phenotypes and/or compensation in heart and liver. The cardiac and hepatic function and structural integrity were also studied in vivo and in vitro. There was no defect in liver function and morphology. A disease signature shared across several skeletal muscles including diaphragm highlighted dysregulations of muscle development, inflammation, cell adhesion and oxidative phosphorylation as main pathomechanisms. Heart displayed only slight functional alterations without obvious structural defects. An opposite dysregulation of specific pathways in cardiac compared to skeletal muscles was revealed at the transcriptome level. More specifically, biochemical and cellular experiments demonstrated that OXPHOS mitochondrial function, cell adhesion and beta integrin trafficking were strongly affected in skeletal muscle and normal in cardiac muscle. Moreover, biomarkers reflecting the molecular activity of MTM1, such as PtdIns3P and dynamin 2 levels, were increased in the skeletal muscles but not in cardiac muscle. Overall, these data identified a compensatory mechanism preserving cardiac function, indicating therapeutic targets to cure the severe skeletal muscle defects in XLMTM.

overall_design: To assess the impact of XLCNM on gene expression in different muscle and non-muscle tissues, we performed RNA-seq in Mtm1-/y mice and their wild-type (WT) littermates at 5 weeks in the heart, the liver, the gastrocnemius and the diaphragm.

first: Alix

last: Simon


title: StCDF1 transcription factor: "The jack of all trades" and its nitrogen signalling regulation in potato [DAP-seq]

city: Madrid

first: Jose M.

last: Franco-Zorrilla

state: Madrid

address: Darwin, 3

department: Plant Molecular Genetics

country: Spain

institute: Centro Nacinal de Biotecnologia-CSIC

summary: Due to the sessile nature of plants, they are under increased risk of environmental threats,aggravated by climate-change induces abiotic stress. However, plants have adapted toachieve growth development and reproduction by modulating their molecular stressresponse. Transcription factors (TFs) encoded belonging to DNA-BINDING WITH ONEFINGER (DOF) as CYCLING DOF FACTOR (CDFs) have been implicated in diverseprocesses, including nitrogen response. In potato,StCDF1TF plays a central role as a clockoutputthat regulatestuberizationand we previously demonstrated that it is also involved indrought response together with its antisense lncRNAthroughstomata regulation.Using arecently developed high-throughput DNA-affinity purification sequencing technology(DAP-Seq) we were able to identify the molecular targets of StCDF1. We further combinedDAP-Seq & RNA-Seq data from overexpressed and knockdownStCDF1transgenic plants,to specify its downstream candidate targets. We found that in addition to its canonical roleas a repressor, StCDF1 can also act as an activator of target genes involved in a range ofbiological processes, including the regulation of nitrogen metabolism. Finally, wedemonstrated that plants overexpressingStCDF1are more sensitive to lownitrogenconditions compared to the knockoutStCDF1

overall_design: DAP-seq experiments

first: Lorena

last: Gonzales

first: José

first: Maroof

last: Shaikh

first: Christian

last: Bachem

first: Salomé

last: Prat


title: Single-nucleus RNA sequencing-based construction of a hippocampal neuron atlas in mice with epileptic memory impairment

city: Xi'an City

first: Bei

state: Shaanxi province

address: No.569 Xinsi Road

institute: Tangdu Hospital

summary: In this study, we utilized snRNA-seq to explore the transcriptional changes in hippocampal neurons of drug-resistant mice with memory disorder in epilepsy, and analyzed the inter-group heterogeneity of 20 subclasses of neurons, focusing on aspects such as cell communication, gene expressions, GO and KEGG enrichment analysis, and module gene set analysis. Our data provides a comprehensive transcriptomic description of the neuronal population affected by drug-resistant epileptic memory disorders. Further studies have shown that specific neuronal subpopulations impact synaptic plasticity through the regulation of relevant target genes by specific transcription factors.

overall_design: Comparative gene expression analysis of SnRNA seq data between drug-resistant epileptic memory impairment and normal mouse hippocampal tissue.

first: JiaQi

last: Ma

first: Lu

last: Wang

first: Yue

last: Zhang

first: YongQian

last: Bian

first: XiaoPeng

last: Qu

first: LiJia

last: Song

first: Chao

first: Li

last: Gao

first: DeChang

last: Zhao

first: QiXing

last: Fang

first: LiangLiang

last: Shen


title: StCDF1 transcription factor: "The jack of all trades" and its nitrogen signalling regulation in potato

first: Jose M.


first: Albert

last: Baldwin

summary: Despite proven therapy options for estrogen receptor (ER)-positive tumors, a significant number of patients with these cancers exhibit relapse with associated metastasis. Studies have shown that the loss of expression of RasGAPs leads to aggressive phenotypes and poor outcomes in several cancers including breast cancer. In our study, mining TCGA gene expression profiles of ER-positive breast tumors, we found that low expression of the RasGAP, DAB2IP is associated with a significant decrease in relapse-free survival in patients with Luminal A breast tumors. Immunostaining found that DAB2IP loss occurs in grade 2 tumors and higher. Consistent with this, genes upregulated in low DAB2IP Luminal A tumors are shared with more aggressive tumor subtypes, and are associated with proliferation, metastasis, and enhanced ER-signaling. In addition, cell-based studies reveal that low DAB2IP expression in ER-positive breast cancer cells is associated with increased proliferation, enhanced stemness phenotypes, and activation of IKK, the upstream regulator of the NF-B signaling pathway. Further, integrating cell-based ChIP-seq with motif analysis and TCGA RNA-seq data, we identify a candidate set of NF-B target genes that are upregulated with loss of DAB2IP and are proposed to regulate several oncogenic phenotypes, including altered RNA processing. This study provides new insight into mechanisms associated with aggressiveness and recurrence within a subset of Luminal A breast cancers that are otherwise typically less aggressive.

overall_design: Genome binding profiling by chromatin immunoprecipitation -sequencing (ChIP-seq) for RelA, RelB and NFKB2 in stable DAB2IP knockdown and empty vector containing control T47D cells.

first: Angana

last: Mukherjee


title: Ivermectin inhibits the growth of esophageal squamous cell carcinoma by activating ATF4-mediated endoplasmic reticulum stress-autophagy pathway

city: Kaifeng

first: Mengmeng

last: Lu

state: Henan

address: Henan Kaifeng

department: School of life Sciences

institute: Henan Univesity

summary: Esophageal squamous cell carcinoma (ESCC) is one of the most common form of malignancies in the world. However, there is currently a lack of effective chemotherapeutic drugs for ESCC, and it is urgent to develop new and safe drugs for this disease. Ivermectin is a broad-spectrum antiparasitic drug with demonstrable antitumor activity. However, the precise cellular and molecular mechanisms of ivermectin in cancers growth inhibition remain unclear. In this study, we report a role of ivermectin in ESCC suppression by activating the endoplasmic reticulum (ER) stress and autophagy. In transcriptome analysis, we found that ATF4 and DDIT3 are involved in ER stress activation by ivermectin. Moreover, ivermectin treatment suppressed the growth of ESCC xenograft tumors in nude mice. Taken together, our results identify the antitumor molecular basis of ivermectin targeting the ER stress-autophagy pathway and suggest that ivermectin is a potential drug for the treatment of ESCC.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of 2 different cells.

last: Mengmeng

first: Wang

last: Yanming


title: The gene expression profiling of 3'2'-cCAMP signaling and 2'3'-cGAMP signaling in the BMDMs of WT and STING deficienc mice

city: Shanghai

first: Haiyang

last: Hu

address: 320 Yueyang Road

institute: PICB

summary: 3'2'-cCAMP represents a new class of  endogenous Cyclic GMP-AMP second messenger. Here, we examined gene expression profiling of 3'2'-cCAMP signaling in the BMDMs of WT and STING deficienc mice

overall_design: Total RNA of BMDMs from WT or STING knockout mouse after stimulating with 3'2'-cCAMP or 2'3'-cGAMP was isolated and sequenced by deep sequencing using Illumina HiSeq 2500

first: Ze

last: Hong

first: Munire

last: Maimaiti


title: StCDF1 transcription factor: "The jack of all trades" and its nitrogen signalling regulation in potato [RNA-seq]

last: Franco-Zorrilla

overall_design: 2 replicates for wild-type, StCDF1 overexpressor and RNAi

first: Lorena

last: Gonzales

first: José

first: Maroof

last: Shaikh

first: Christian

last: Bachem

first: Salomé

last: Prat


title: Replication Fork-Associated RNA-DNA Hybrids Safeguard Genomic Stability in Transcriptionally Active Regions [HeLa REFORC]

city: Beijing

first: Jiadong

last: Wang

address: 38 College Road, Haidian District

department: Department of Radiation Medicine

institute: Peking University Health Science Center

summary: Safeguarding replication fork stability in transcriptionally active regions, which require high DNA replication accuracy, is crucial for precise DNA replication and prevention of mutations. However, how cells ensure the stability of replication forks in these regions remains a critical challenge. Here, we discovered the pervasive existence of replication forks-associated RNA-DNA hybrids (RF-RDs) within transcriptionally active regions, where they act as a protective barrier against DNA2-mediated nascent DNA degradation and prevent replication fork collapse upon replication stress. Subsequently, the RNA helicase DDX39A dismantles RF-RDs, facilitating proper DNA2-mediated DNA resection and replication fork restart. Excessive dissolution of RF-RDs causes replication fork collapse and genomic instability, while insufficient dissolution of RF-RDs under replication stress increases fork stability, resulting in chemoresistance that can be reversed by eliminating RF-RDs. In summary, we elucidated the prevalence of RF-RDs at replication forks within transcriptionally active regions, revealed their pivotal role in safeguarding replication fork stability, and proposed that targeting RF-RDs holds promise for augmenting chemotherapeutic efficacy.

overall_design: We developed a method called Replication Fork RNA Capture (REFORC) to exact the RNA associated with nascent replication fork DNA, and prepared for cDNA library building and related high-throughput sequencing.

first: Zhanzhan

last: Xu

first: Chen

last: Nie

first: Weibin


title: Comparision of Differential methylation between Control and mutant Dnmt3a

status: Public on Dec 17 2024

city: St. Louis

first: Andrew

middle: Lee

last: Young

state: MO

address: 660 South Euclid Ave

institute: Washington University in St. Louis

type: Methylation profiling by high throughput sequencing

summary: Dnmt3a is the most recurrently mutated gene in clonal hematopoiesis (CH), and it is a critical regulator of hematopoietic stem cells (HSCs). Conditional deletion of Dnmt3a in mouse HSC results in enhanced self-renewal but impaired differentiation. Dnmt3a encodes for a de novo DNA methyltransferase enzyme but both mouse and human cells with loss of Dnmt3a show minimal change in DNA methylation levels which do not correlate with gene expression differences. To understand if there are methylation differences between control and mutant (R878H) Dnmt3a, we are performing WGBS.

overall_design: To investigate the differential DNA methylation in hematopoietic cells expressing Dnmt3a mutant with reduced DNA methyltransferase activity, we established Cre-mediated knock in mouse model. Competitive HSC transplantation was performed.  Cells were isolated 18-weeks post-transplant for analysis of DNA methylation patterns by whole genome bisulfite sequencing.

first: Infencia

middle: X

last: Raj

first: Won

last: Koh

first: Jessica

last: Harrison

first: Christine

last: Zhang

first: Barbara

last: Soares

first: Aishwarya

last: Krishnan

first: Hassan

last: Bjeije

first: Tyler

last: Parsons

first: Wentao

last: Han

middle: L

first: Ting

first: Luis

last: Batista

first: Grant

last: Challen