title: Single-cell RNA sequencing revealed the role of the Th17 pathway in the development of anti HLA antibodies in a highly sensitized mouse model

city: Seoul

first: Hanbi

last: Lee

address: 222 Banpo-daero, Seocho-gu

department: Division of Nephrology, Department of Internal Medicine

institute: Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea

summary: The aim of this study is to investigate the specific pathway involved in HLA sensitization using single-cell RNA sequencing analysis and an allo-sensitized mouse model developed with an HLA.A2 transgenic mouse. For sensitization, wild-type C57BL/6 mouse received two skin grafts from C57BL/6-Tg (HLA-A2.1)1Enge/J mouse (allogeneic mouse (ALLO)). For syngeneic control (SYN), skin grafts were transferred from C57BL/6 to C57BL/6. We performed single-cell RNA sequencing analysis on splenocytes isolated from ALLO and SYN mice and compared the gene expression between them. We generated 9,190 and 8,890 single-cell transcriptomes from ALLO and SYN control mice, respectively. Five major cell types (B-cells, T-cells, NK cells, macrophages, and neutrophils) and their transcriptome data were annotated according to the representative differentially expressed genes of each cell cluster. The percentage of B-cells was higher in allogeneic mouse than it was in syngeneic control mouse. KEGG enrichment analyses indicated that the highly expressed genes in the B-cells from ALLO mouse were mainly associated with antigen processing and presentation pathways, allograft rejection, and the Th17 cell differentiation pathway. Upregulated genes in the T-cells of ALLO mouse were involved in the IL-17 signaling pathway. The ratio of Th17 cluster and Treg cluster was increased in the ALLO mouse. On flow cytometry, the percentage of Th17 (IL-17+/CD4+ T) cells was higher and regulatory T cells (FOXP3+/CD4+ T) was lower in the ALLO mouse compared to those in the SYN mouse. Our results indicate that not only the B cell lineage, but also the Th17 cells and their cytokine (IL-17) are involved in the sensitization to HLA.

overall_design: For sensitization (Allogeneic (ALLO) mouse), wild-type C57BL/6 mouse was sensitized twice with skin allografts from C57BL/6-Tg(HLAA2.1)1Enge/J mouse (0 and 5 weeks). Syngeneic (SYN) mouse received skin transplants from wild-type C57BL/6 mouse using the same procedure. Both the donor and recipient mice were anesthetized with intraperitoneal (i.p.) injections of Zoletil®50 (Tiletamine and Zolazepam) 30 mg/kg and Rompun® (Xylazine) 10 mg/kg. Tail skin, segmented into 8 × 8 −10 mm2 sizes, was obtained from the donor mice and grafted onto the dorsal area of the recipient mice. The mice were sacrificed using a CO2 chamber at four weeks after the second skin transplant, and mice spleens were harvested for scRNA-seq analysis.

first: Yoo-Jin

last: Shin

first: Xianying

last: Fang

first: Sheng

last: Cui

first: Sun

last: Lim

first: Sang

middle: H

last: Eum

first: Ji-Won

last: Min

first: Chang-Won

last: Hong

first: Hae-Ock

first: Eun-Jee

last: Oh

first: Chul

last: Yang

first: Byung

last: Chung


title: Rapid retinoic acid-induced trophectoderm model from human induced pluripotent stem cells

status: Public on Aug 15 2024

city: Minneapolis

first: Samira

last: Azarin

state: MN

address: 421 Washington Ave SE, RM151R Amundson Hall

department: Chemical Engineering and Materials Science

country: USA

institute: University of Minnesota

type: Expression profiling by high throughput sequencing

summary: A limited number of accessible and representative models of human trophoblast cells currently exist for disease modeling and improving our understanding of placentation. Current stem cell models involve either a transition through a naïve stem cell fate or precise dynamic control of multiple interacting growth factor and small molecule cues. Here, we show that simple exposure of hiPSCs to two small molecules, retinoic acid (RA) and the Wnt signaling agonist CHIR 99021 (CHIR), results in rapid, synergistic upregulation of CDX2, an important transcription factor for trophectoderm cell induction and maintenance of the trophoblast cell population. RA+CHIR-treated cells have a transcriptional profile with high similarity to that of primary trophectoderm cells, and they can also be further differentiated into cells with features of syncytiotrophoblasts and extravillous trophoblasts. We assessed RA+CHIR-treated cells for the established set of criteria defining a trophectoderm cell model, and the cells possess all of the features necessary to be considered a valid model. Taken together, our data demonstrate the development of a simple method for the generation of functional trophoblast-like cells that can be used to better understand mechanisms and interactions involving the placenta.

overall_design: Gene expression profiling analysis of RNA-seq data from IMR90-4 iPS cells during differentiation toward trophoectoderm. Samples were collected from days 0, 1, 3, and  5 of the differentiation in duplicate.

first: Kristen

middle: A

last: Lemke

first: Casim

last: Sarkar

middle: M


title: CPSF6 regulates alternative polydenylation and proliferation of cancer cell through phase separation Ⅱ

city: Guangzhou

first: Wu

last: Runze

address: SUN YAT-SEN UNIVERSITY

country: China

institute: SUN YAT-SEN UNIVERSITY

summary: To verify the effect of phosphorylation of CPSF6 by CLK2 on APA, we co overexpressed CLK2 and wild-type CPSF6 or phosphorylated mutant CPSF6 in HEK293T cells

overall_design: Compare the changes in APA length between IVT-SAPAS groups

first: Susu

last: Liu

first: Runze

last: Wu

first: Liutao

last: Chen


title: Fumarylacetoacetate hydrolase targeted by a Fusarium graminearum effector positively regulates wheat FHB resistance and yield and promotes heading

city: shanxi

first: Yiwei

last: wang

address: Taiyuan, Shanxi Province

institute: TYUT

summary: Fusarium head blight (FHB), caused by Fusarium graminearum is a devastating disease that affects global wheat production. F. graminearum encodes many effector proteins; however, its virulence mechanisms are poorly understood. In this study, we identified a secretory effector candidate protein (FgEC10) that is essential for the virulence of F. graminearum and suppresses the basal immune response. FgEC10 interacted strongly with wheat fumarylacetoacetate hydrolase (TaFAH) and accelerated its degradation via the 26S proteasome pathway. In addition, we showed that TaFAH interacted with TaPSMD, an important component of the 26S proteasome and that FgEC10 enhanced the interaction between TaFAH and TaPSMD. RNA silencing or overexpression of TaFAH in wheat plants showed that TaFAH positively regulated wheat FHB resistance, heading period, and grain yield. Transcriptomic analysis revealed that TaFAH promoted the expression of genes associated with disease resistance and the heading period. Metabolomic analysis revealed that overexpression of TaFAH increased the levels of several amino acids that inhibited F. graminearum growth and enhanced wheat resistance to FHB. Collectively, our study reveals a novel pathogenic mechanism and provides a valuable genetic resource for improving FHB resistance and grain yield in wheat.

overall_design: To investigate the function wheat TaFAH in the regulation of wheat growth and resistance to Fusarium graminearum, we generated transgenic wheat plants overexpressing or RNAi silencing TaFAH gene. We then performed gene expression profiling analysis using data obtained from RNA-seq of these transgenic plants.

first: Shengping

last: Shang

first: Yuhan

last: He

first: Qianyong

last: Hu

first: Ruihua

last: Zhao

first: Yujin

last: Fan

last: Wang

first: Penghao

first: CuiJun

last: Zhang


title: Berberine mitigates 5-fluorouracil-induced intestinal mucosal damage without impairing anti-tumor effect of 5-Fu by regulating the intestinal flora

city: hangzhou

first: wu

middle: chang

last: hong

state: zhejiang

address: binwen street num 548

institute: The Second Clinical Medical College, Zhejiang Chinese Medical  University

summary: To investigate the mechanism of BBR improved intestinal mucosa induced by 5-fluorouracil-induced  in mice

overall_design: The colonic tissue from the 5-Fu and 5-Fu + BBR group were collected for RNA-sequencing analysis to identify BBR-associated genes.

first: Changhong

first: Chenxiao

last: Ye

first: Haitao


title: AS-exos exacerbates microglial ferroptosis-driven neuroinflammation

city: Wuhan, Hubei

first: Minghao

last: Dong

address: No. 1095, Jiefang Avenue

institute: Tongji Hospital

summary: Experimental atherosclerosis was established by feeding Apoe KO mice a Western, high-fat diet for 12 weeks and experimental cerebral ischemia was established by middle cerebral artery occlusion. RNA-seq was perfomed to investigate the potential gene regulation of AS (LAA)-exo-dependent changes of microglia.

overall_design: Transcriptional profiles of microglia sorted from Sham mice, MCAO mice, MCAO mice treated with  Ctrl-exos, and MCAO mice treated with  AS-exos.

first: Ming-Hao

first: Luo-Qi

last: Zhou

first: Yue

last: Tang

first: Yun-Hui

last: Chu

first: Chuan

last: Qin

first: Dai-Shi

last: Tian

first: Wei


title: Idasanutlin differential expression in MOLM13 and OCIAML3

city: Portland

first: Peter

last: Ryabinin

state: OR

address: 3181 SW Sam Jackson Park Rd

institute: Oregon Health and Science University

summary: Targeting MDM2 is an attractive therapeutic approach for TP53 wild-type (WT) tumors, including the majority of de novo acute myeloid leukemia (AML) cases. However, patients with WT TP53 have shown variable responses to MDM2 inhibitors in clinical trials, highlighting the need to identify additional biomarkers to maximize the chances of clinical success. We performed CRISPR-Cas9 knockout screens to identify genes that confer resistance to an MDM2 inhibitor idasanutlin. We did not find recurrent sgRNA hits or mutations in p53 downstream targets, such as CDKN1A, BAX, PMIAP1, and BBC3, apart from TP53. This was consistent with the results of individual knockout validation experiments and exome sequencing data from idasanutlin resistant cell lines generated form long-term exposure to low doses of idasanutlin. RNA-seq differential expression analysis revealed that major p53 downstream targets were upregulated in both idasanutlin-sensitive MOLM13 and resistant OCIAML3 cell lines after idasanutlin treatment. These findings highlight the pleiotropic functions of TP53 and suggest that the loss of individual downstream targets of TP53 does not significantly contribute to MDM2 inhibitor resistance.

overall_design: MOLM13 and OCIAML3 cells were treated with 300nM idasanutlin overnight. Total RNA was extracted using Qiagen RNeasy Mini Kit according to the manufacturer’s instructions. RNA-seq libraries were constructed using the TruSeq protocol (Illumina ) and sequenced on the Novaseq 6000.

first: Daniel

last: Bottomly

first: Shannon

last: McWeeney

first: Haijiao

first: Basil

last: Allen

first: Lindsey

last: Savoy

first: Anthony


title: Effect of murine RIPK1 T169A mutation to the LPS and LPS/5z7 response in bone marrow derived macrophages

city: Medford

first: rebecca

last: batorsky

state: MA

address: 177 College Ave

department: Tufts Institute of Artificial Intelligence

institute: Tufts University

summary: RIPK1 plays an important role initiating inflammatory signaling downstream of TLR4 and TNFR1, acting as a polyubiquitinated scaffold for the recruitment and activation of NFkB and MAPK signaling. We geneerated a murine model inhibitng the autophosphorylation of threonine 169 (T169) on murine Ripk1 to determine the effect on cell death complex formation and caspase activation. Due to the dual role of RIPK1 in inflammatiton and cell death we first sought to confirm that tthis mutation did not disturb the scaffolding functions of RIPK1 and did not alter tthe inflammatory response after stimulation of TLR4.

overall_design: We engineered a mouse with T169 substitution to alanine. BMDMs from B6 and RIPK1 T169A mutant knock in mice were collected and stimulated with LPS or LPS/5z7 for 2 hours.

first: David

last: Jetton

first: Alexander

last: Poltorak

first: Rebecca

last: Batorsky


title: NOVA1 HITS-CLIP in wild-type mouse diencephalon/ mesencephalon (P21)

city: New York

first: Yoko

last: Tajima

state: NY

address: 1230 York avenue

institute: The Rockefeller University

summary: Mouse diencephalon/ mesencephalon samples from P21 wild-type were subjected to HITS-CLIP to detect NOVA1 binding positions on RNA

overall_design: Mouse diencephalon/ mesencephalon samples were UV-irradiated and subjected to NOVA1 HITS-CLIP (detailed desription in accompanying paper)

first: Robert

middle: B

last: Darnell


title: Identification of IKKβ Inhibitor by utilizing a novel KLF15 High-Throughput Screen for Proteinuric Kidney Disease

city: Stony Brook

first: Sandeep

last: Mallipattu

address: HSC-T16 Room 80E

department: Division of Nephrology and Hypertension

institute: Stony Brook University School of Medicine

summary: To investigate the expression profile in human podocytes treated with or without BT503 with or without LPS stress. to compare the expression profile of human podocytes at 33c vs 37c treated with or without BT503

overall_design:
To investigate the potential pathways by which BT503-KLF15 restores podocyte injury, we conducted RNA-sequencing in cultured human podocytes treated with and without BT503 in the setting of LPS treatment.
To investigate the potential binding target of BT503 and the involved pathway, we conducted RNA-sequecing in culture human podocytes treated with and without BT503 under nonpermissive (37C) conditions as compared to permissive (33C) conditions.

first: Yiqing

last: Guo

first: Andrew

middle: K

last: Chow

first: Nehaben

last: Gujarati


title: Roles of NOVA1 in inhibitory neurons

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

overall_design: Refer to individual Series


title: The IL-33/ST2 axis and tissue Treg maintains epithelial homeostasis in the skin and restrains cancer development

city: London, United Kingdom

first: Norzawani

middle: Binti

last: Buang

state: London

address: 9N15 Commonwealth Buidling, Ducane Road

country: United Kingdom

institute: Imperial College London

summary: IL-33 is constitutively expressed in many epithelial tissues at steady state and signals through the receptor, ST2. IL-33 is released upon tissue injury and functions as an endogenous danger signal to alert the immune system to tissue damage. Here we investigate the physiological role of the IL-33/ST2 axis in skin homeostasis and cancer development. We show that expression of IL-33 differentiates malignant from normal/benign human tissues and that in mouse models of cutaneous squamous cell carcinoma the IL-33/ST2 axis protects against carcinogenesis. Tissue Treg are the predominant cells expressing ST2 in the skin and localise around the hair follicle and IL-33+ epithelial cells (EC). Adoptive transfer experiments demonstrate that skin Treg regulate EC differentiation, minimizes mutational load and retrains cancer development following exposure to an environmental carcinogen. Our findings indicate an important role for direct EC-Treg cross-talk as an early checkpoint to contain tissue damage and carcinogenesis.

overall_design: Tcrb-/- or wild type FVB background were topically treated with 200ng of DMBA weekly for 6 weeks. Additonally, CD3+CD4+CD25+ Tregs were purified from the spleen of WT donors and were transferred i.v. into Tcrb-/- recipients before treatment with DMBA. Total RNA was extracted from whole skin biopsies using RNEasy kits and RNA-seq was performed on Illumina Hiseq 4000.

first: Jessica

last: Strid


title: Genome-wide CRISPR  screen of MOLM13 cells after Idasanutlin treatment

first: Peter

last: Ryabinin

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: MOLM13 cells constitutively expressing Cas9 and were transduced with a CRISPR library virus and puromycin-selected and then treated with Idasanutlin or DMSO control for 14 days.

first: Daniel

first: Shannon

last: Zhang

last: Wang


title: CLIP-seq of VSV-infected HEK293T cells overexpressed PTENα

city: Beijing

first: Zeliang

last: Yang

address: No.38 Xueyuan Road,Haidian

institute: Peking University Health Science Center

summary: To determine whether PTENα directly binds to viral RNA, we performed  Cross-Linking and Immunoprecipitation (CLIP) sequencing of HEK293T cells transfected with vector encoding PTENα under VSV (vesicular stomatitis virus) infection

sample_organism:
Homo sapiens
Vesicular stomatitis Indiana virus

overall_design: Ten 10cm2 dishes of HEK293T cells at 70% confluency were transfected with 10μg of FLAG-PTENα plasmid per dish. At 24 h after transfection, the cells were stimulated with VSV (MOI = 0.01) in the presence of 100μM 4-thiouridine. 14 h later, cells were irradiated with 365nm UV wavelength of 150mJ/cm2 energy. Then, cells were collected and resuspended with co-IP lysis buffer. After rotation at 4℃ for 15 min, the lysates were centrifuged at 13000 × g and the pellets were discarded. After saving 1/20 of the sample as input, the supernatant was predigested with RNase T1 (1U/μl) at 22℃ for 15 min, and the RNA-protein complex were enriched using ANTI-FLAG M2 beads with slow rotation at 4℃ for 2 h. Next, the beads were washed with IP washing buffer three times, and treated with DNase I (2U/μl) and RNase T1 (100U/μl) at 22℃ for 15 min. Finally, the protein-RNA complexes were digested with Proteinase K (0.5mg/mL) and 0.1% SDS at 56℃ for 15 min and the bound RNA was separated using TRIzol reagent.

first: Yue

last: Yin

first: Dan

last: Lv


title: A Trisomy 21 Lung Cell Atlas

city: Rochester

first: Soumyaroop

last: Bhattacharya

address: 601 Elmwood Ave Box 703

department: Pediatrics

institute: University of Rochester

summary: Trisomy 21 (T21), resulting in Down Syndrome (DS), is the most prevalent chromosomal abnormality worldwide. While pulmonary disease is a major cause of morbidity and mortality in DS, the ontogeny of pulmonary complications remains poorly understood. We recently demonstrated that T21 lung anomalies, including airway branching and vascular lymphatic abnormalities, are initiated in utero. Here, we aimed to describe molecular changes at the single cell level in prenatal T21 lungs. Our results demonstrate differences in the proportion of cell populations and detail changes in gene expression at the time of initiation of histopathological abnormalities. Notably, we identify shifts in the distribution of alveolar epithelial progenitors, widespread induction of key extracellular matrix molecules in mesenchymal cells and hyper-activation of IFN signaling in endothelial cells. This single cell atlas of T21 lungs greatly expands our understanding of antecedents to pulmonary complications and should facilitate efforts to mitigate respiratory disease in DS.

overall_design: human fetal lung tissue samples from Trsomy 21 subjects (n=5) and age matched controls (n=4)

first: Bhattacharya

last: Soumyaroop

first: Danopoulos

last: Soula


title: Tumor-intrinsic CD74 expression mediates immune evasion in lung cancer with COPD

city: Chengdu

first: Chunyan

last: Yu

state: Sichuan

address: 37 Guoxue street

institute: Sichuan University

summary: To better elucidate the complex interaction between COPD and NSCLC, we comprehensively characterized immune cell dynamics and transcriptome profiles of malignant cells in tumor tissues from NSCLC patients with COPD using single-cell RNA sequencing (scRNA-seq). We observed increased fractions of exhausted CD8+ T cells, CCL18+ tumor-associated macrophages (TAMs), and LAMP3+ dendritic cells (DCs) in the immune component of NSCLC with COPD compared with the findings in NSCLC without COPD. Remarkably, a critical cluster of malignant cells from NSCLC with COPD samples, characterized by high expression of CD74, significantly exhibited an epithelial-immune dual signature and was associated with poor prognosis. Interestingly, we found that CD74 facilitated phosphorylation of MAPK/STAT3 to mediate PD-L1 expression and further suppressed CD8+ T cell function, triggering LC progression. Our study provides a comprehensive profiling of the multi-cellular ecosystem of NSCLC with coexisting COPD and reveals that CD74+ cancer cells are potential targets for immunotherapy.

overall_design: To systematically elucidate the cellular diversity of NSCLC with or without COPD, we performed scRNA-seq (10X Genomics) of primary tumors from eight patients, including tumors samples (four NSCLC samples without COPD (Tumor) and four NSCLC samples with COPD (CTumor)) and matched adjacent samples (four normal tissues (Normal) and four COPD tissues (COPD))

first: Weimin

last: Li

first: Denian

first: Sixiang


title: Modulation of Integrin α9β1 in Macrophages Reduces Periodontal Inflammation and Supports Alveolar Bone Preservation in Periodontitis [RNA-seq]

status: Public on Aug 14 2024

city: Guangdong

first: Shihan

last: Xu

address: North Campus, Sun Yat-Sen University, No. 74, 2nd Yat-Sen Road/Street, Yuexiu District, Guangzhou City

institute: Sun Yat-sen University

summary: Bone marrow-derived macrophages (BMMs) from Itga9-Lyz2-cKO and Itga9-Lyz2-cHet mice  were stimulated with Porphyromonas gingivalis (Pg) for 2 hours, then subjected to mRNA sequencing.

overall_design: Induce bone marrow mononuclear cells from 8-week-old male Itga9-Lyz2-cKO and Itga9-Lyz2-cHet mice to BMMs by 50 ng/mL macrophage colony-stimulating factor (M-CSF).After stimulation with Pg (MOI = 1:20) for 2 hours, total RNA was extracted using Trizol and subjected to sequencing.

first: Junji

first: Jianyu

last: Gu

first: Wen

last: Pan

first: Xiaohui

first: Tingwei

first: Songlin

first: Jinlin

last: Song


title: NPM1-fusion proteins promote myeloid leukemogenesis  through XPO1-dependent HOX activation

city: Minato-ku

first: Yuko

last: Shimosato

state: Tokyo

address: 4-6-1 Shirokanedai

department: Molecular Oncology

country: Japan

institute: Tokyo university

summary: Nucleophosmin (NPM1) is a nucleolar protein and one of the most frequently mutated genes in acute myeloid leukemia (AML). In addition to the commonly detected frameshift mutations in exon12 (NPM1c), previous studies have identified NPM1 gene rearrangements leading to the expression of NPM1-fusion proteins in pediatric AML. However, whether the NPM1-fusions are indeed oncogenic and how the NPM1-fusions cause AML have been largely unknown. In this study, we investigated the subcellular localization and leukemogenic potential of two rare NPM1-fusion proteins, NPM1-MLF1 and NPM1-CCDC28A. NPM1-MLF1 is present in both the nucleus and cytoplasm and occasionally induces AML in the mouse transplantation assay (2/12). NPM1-CCDC28A localizes predominantly to the cytoplasm, immortalizes mouse bone marrow cells in vitro and efficiently (5/6) induces AML in vivo. Mechanistically, both NPM1-fusions bind to the HOX gene cluster and, like NPM1c, cause aberrant upregulation of HOX genes in cooperation with XPO1. The XPO1 inhibitor selinexor suppressed HOX activation and colony formation driven by the NPM1-fusions. Thus, our study provides experimental evidence that both NPM1-MLF1 and NPM1-CCDC28A are oncogenes with functions similar to NPM1c. Inhibition of XPO1 may be a promising strategy for the NPM1-rearranged AML.

overall_design: To examine the molecular changes induced by NPM1 fusions, we first examined the gene expression profiles of cells expressing vector, NPM1-MLF1 or NPM1-CCDC28A. We transplanted bone marrow cells transduced with retrovirus vector harboring, NPM1-MLF1 or NPM1-CCDC28A into recipient mice, and harvested GFP+ bone marrow cells two months after transplantation.

first: Keita

last: Yamamoto

first: Susumu

last: Goyama


title: Molecular mechanisms of BCAT1 in ASK120067-resistant NSCLC cells

city: Shanghai

first: Zilu

address: No. 555 Zuchongzhi Road

institute: Shanghai Institute of Materia Medica

summary: To investigate the mechanism of BCAT1 in mediating resistance to third-generation EGFR-TKI, we employed RNA-seq analysis to compare the transcriptome signature of ASK120067-resistant NSCLC cells with or without BCAT1 knockdown. Here, gene set enrichment (GSEA) revealed a significant decrease in the expression of genes in glycolysis pathway following small interfering RNA (siRNA)-mediated BCAT1 knockdown, which indicated the role for BCAT1 in supporting TKI resistance through upregulation of glycolysis.

overall_design: Total mRNA profiles of 67R (ASK120067-resistant NCI-H1975) cells with and without BCAT1 knockdown.

first: Tao

last: Zhang

first: Zillu

first: Hua

last: Xie


title: Transcriptional analysis of CD8+ T lymphocytes isolated from syngeneic MC38 tumors implanted in young adult or aged mice

city: Boston

first: Amy

last: Huang

address: 25 Shattuck St

department: Immunology

institute: Harvard Medical School

summary: Evaluation of transcriptional changes associated with advanced age in tumor-infiltrating CD8+ T lymphocytes from within MC38 colorectal tumors.

overall_design: Single-cell transcriptional analysis of CD8+ T lymphocytes isolated 12 days post-implantation from subcutaneous MC38 tumors in young adult (~3 months) or aged (~21-22 months) C57BL6 mice. Each sample contains tumor-infiltrating CD8+ cells combined from 3-4 mice, individually barcoded using hashing antibodies.

first: Alison

middle: E

last: Ringel

first: SeongJun

last: Han

first: Peter

last: Georgiev

first: Jefte

last: Drijvers

first: Brian

middle: C

last: Miller

first: Arlene

last: Sharpe

first: Marcia

last: Haigis


title: Gene expression profile of olive oil- and ozonated olive oil-treated B16F10 murine melanoma cell lines

city: Sapporo-shi

first: Seong-jin

last: An

state: Hokkaido

address: Kita 12 nishi 6, kita-ku

department: Graduate School of Pharmaceutical Sciences

institute: Hokkaido university

summary: We analyzed the effect of ozonated olive oil on gene expression of B16F10 murine melanoma cells.

overall_design: B16F10 cells were treated with olive oil and ozonated olive oil for 6 h and gene expression profile was analyzed by NGS.

first: Jun-ichi

last: Kashiwakura

first: Sumihito

last: Togi

first: Tadashi

last: Matsuda


title: Modulation of Integrin α9β1 in Macrophages Reduces Periodontal Inflammation and Supports Alveolar Bone Preservation in Periodontitis [scRNA-seq]

first: Shihan

last: Xu

summary: Establish an experimental periodontitis model using Itga9-Lyz2-cKO mice and Itga9-Lyz2-cHet mice, and collect gingival tissues for single-cell analysis.

overall_design: An experimental periodontitis model was established in transgenic mice by performing silk suture ligation and applying Porphyromonas gingivalis to the maxillary second molar. After 14 days, gingival tissues were harvested for single-cell sequencing.

first: Junji

first: Jianyu

last: Gu

first: Wen

last: Pan

first: Xiaohui

first: Tingwei

first: Songlin

last: Wang

first: Jinlin

last: Song


title: Differential Induction of Interferon-Stimulated Genes by Cell-Based Versus Egg-Based Quadrivalent Influenza Vaccines in Children During the 2018-2019 Season

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

state: PA

address: 4401 Penn Avenue

institute: University of Pittsburgh

summary: Background: Cell-based quadrivalent-inactivated influenza vaccine has been shown to have higher vaccine effectiveness than traditional egg-based quadrivalent-inactivated influenza vaccine. This is observed despite similar levels of serum hemagglutinin antibodies induced by each vaccine. Results: Cell-based influenza vaccine induced greater interferon-stimulated and innate immune gene activation compared with egg-based influenza vaccine. Participants who seroconverted had increased interferon-signaling activation versus those who did not seroconvert. Conclusions: These data suggest that cell-based influenza vaccine stimulates immune activation differently from egg-based influenza vaccine, shedding light on reported differences in vaccine effectiveness.

overall_design: Methods: In this study, we examine peripheral immune activation after egg-based or cell-based influenza vaccination in a clinical trial in children. Peripheral blood mononuclear cells were isolated, and ribonucleic acid was sequenced from 81 study participants (41 Fluzone, egg based and 40 Flucelvax, cell based) pre- and 7 days postvaccination. Seroconversion was assessed by hemagglutinin inhibition assay. Differential gene expression was determined and pathway analysis was conducted.

first: Judith

last: Martin

first: Krissy

last: Geffel

first: Marianna

last: Ortiz

first: Mary

middle: P

last: Nowalk

first: Richard

last: Zimmerman

first: John

middle: F

last: Alcorn


title: Gene expression profiling of C57BL/6J wildtype and IFNAR1 knockout mice following LPS and IFNβ stimulation

city: Ottawa

first: Alexandre

last: Blais

state: ON

address: 451 Smyth Road

country: Canada

institute: University of Ottawa

summary: Type-I interferon signalling plays a critical role in immunity especially during viral infections. IFNAR1-deficent macrophages are highly resistant to Salmonella typhimurium (ST) infection and to the stimulation with LPS, poly I:C and TNFα. We have used microarray expression profiling on bone marrow derived macrophage cells as a discovery platform to identify genes that play a role in their resistance. Several genes were identified downregulated in IFNAR1-deficient macrophages compared to WT control sample. The Expression of identified genes will be quantified by qRT-PCR followed by knockdown of identified genes using si-RNA approach. The identified genes will help us to understand how IFNβ mediates susceptibility to bacterial infection in macrophages.

overall_design: Gene expression was measured in wildtype and IFNAR1-deficient macrophages in various conditions including: no treatment, LPS and IFNβ.

first: Norah

last: Alturki

first: Subash

last: Sad

first: Ellias

last: Horner


title: Effects of Nova1 Deletion on Gene Expression in Tissues and Cells

first: Yoko

last: Tajima

summary: To elucidate the function of Nova1 in neurons, especially in inhibitory neurons, gene expression profiling analysis (RNAseq, TRAP-seq) was performed using Nova1 conditional knockout mice and their primary neurons.

overall_design: To analyze changes in gene expression in inhibitory neuron specific Nova1 knockout (cKO) mice, we performed RNA sequencing analysis of each brain region (hypothalamus, substantia nigra, periaqueductal gray, caudate putamen) and pituitary gland. In addition, TRAP-seq was performed on whole brains of neonatal mice to capture changes occurring in inhibitory neurons. Finally, primary neurons were used to assess the effects of Nova1 loss and the impact of overexpression of Impact, a Nova1 target gene.

first: Robert

last: Darnell


title: LncRNA and mRNA expression profiling from purified CD19+CD24hiCD27+ B cells and CD19+CD24loCD27- B cells of Hashimoto Disease patients and healthy donors

first: Luman

address: 130 Dong'an Road

institute: Fudan University

summary:
Recent studies have indicated that B cells act as a crucial regulator in autoimmune diseases. However, little is known about their role in Graves’ Disease (GD) which is an important autoimmune thyroid disease. There is now accumulating evidence that mRNA and lncRNA are important regulators of B cell function, we explored the functional lncRNA and mRNA expression profiles from purified CD19+ B cells of GD patients and healthy individuals.
We compared lncRNA and mRNA expression profiles from isolated B cells of GD patients and normal control using microarray to examine the mechanisms involved in the pathogenesis of GD.

overall_design: RNA samples from purified CD19+ B cells of GD patients and healthy individuals were collected for hybridization on Affymetrix microarrays. Each sample was the pool of RNA from 3 donors.

first: Bingbing

last: Zha

first: Yiwei

last: Chu


title: Axonopathy precedes cell death in ocular damage mediated by blast exposure

city: Iowa City

first: Todd

last: Scheetz

state: IA

address: 3181B MERF

institute: UNIVERSITY OF IOWA

summary: Traumatic brain injuries (TBI) of varied types are common across all populations and can cause visual problems. For military personnel in combat settings, injuries from blast exposures (bTBI) are prevalent and arise from a myriad of different situations. To model these diverse conditions, we are one of several groups modeling bTBI using mice in varying ways. Here, we report a refined analysis of retinal ganglion cell (RGC) damage in male C57BL/6J mice exposed to a blast-wave in an enclosed chamber. Ganglion cell layer thickness, RGC density (BRN3A and RBPMS immunoreactivity), cellular density of ganglion cell layer (hematoxylin and eosin staining), and axon numbers (paraphenylenediamine staining) were quantified at timepoints ranging from 1 to 17-weeks. RNA sequencing was performed at 1-week and 5-weeks post-injury. Earliest indices of damage, evident by 1-week post-injury, are a loss of RGC marker expression, damage to RGC axons, and increase in glial markers expression. Blast exposure caused a loss of RGC somas and axons-with greatest loss occurring by 5-weeks post-injury. While indices of glial involvement are prominent early, they quickly subside as RGCs are lost. The finding that axonopathy precedes soma loss resembles pathology observed in mouse models of glaucoma, suggesting similar mechanisms.

overall_design: We performed gene expression profile analysis on retinas from male C5BL/6J mice exposed to a blast-wave in an enclosed chamber at 1-week and 5-weeks post-injury. The retina was from the eye exposed directly to the blast wave. There were 12 mice at each time-point 6 sham and 6 injured.

first: Nickolas

last: Boehme

first: Adam

last: Hedberg-Buenz

first: Nicole

last: Tatro

first: Michael

last: Bielecki

first: William

last: Castonguay

middle: G

last: Anderson

first: Laura

last: Dutca


title: Gene expression profile of olive oil- and ozonated olive oil-treated A375 human melanoma cell lines

first: Seong-jin

last: An

summary: We analyzed the effect of ozonated olive oil on gene expression of A375 human melanoma cells

overall_design: A375 cells were treated with olive oil and ozonated olive oil for 6 h and gene expression profile was analyzed by NGS.

first: Jun-ichi

last: Kashiwakura

first: Sumihito

last: Togi

first: Tadashi

last: Matsuda


title: Feedback regulation between ALKBH3-mediated glycolysis and histone lactylation promotes age-related macular degeneration

city: Nanjing

first: Ying

last: Wang

address: Guangzhou Road

institute: NanJing Medical University

summary: Age-related macular degeneration (AMD) is a leading cause of blindness among the elderly. Using clinical samples and knockout mice, we reported that the m1A eraser ALKBH3 reshaped retinal metabolism to promote AMD. In retinal pigment epithelium (RPE), the dm1ACRISPR system demonstrated that ALKBH3 demethylated the glycolytic enzyme HK2 to activate anaerobic glycolysis, producing excessive lactate. The lactate promoted histone lactylation at H3K18, which in turn bound to ALKBH3 to amplify its transcription, establishing a positive feedback loop. The ALKBH3 inhibitor HUHS015 disrupted this loop, effectively mitigating RPE degeneration. Furthermore, ALKBH3 directly targeted the pro-angiogenic factor VEGFA to modulate the metabolic cross-talk between RPE and choroidal capillaries, thus promoting choroidal neovascularization (CNV). HUHS015 inhibited CNV synergistically with the anti-VEGF drug Aflibercept. Our study provides critical insights into the molecular mechanisms and metabolic events facilitating the progression from RPE degeneration to CNV in AMD, laying the groundwork for new treatments of AMD.

overall_design: Extracted and purified total RNA was evaluated for quantity and integrity. Ideal RNA samples were sent for library construction using the Directional RNA Library Prep Kit (GenSeq, Shanghai, China), according to the manufacturer’s instructions. The mRNA is typically fragmented into pieces of ~300 nucleotides in length. cDNA synthesis form the mRNA fragments was then carried out using reverse transcriptase and random hexamer primers. The resulting cDNA fragments were subjected to end-repair and dA-tailing, followed by adapter ligation. These adapter-ligated cDNA samples were subsequently amplified via PCR and purified to yield sequencing libraries. Finally, the libraries were sequenced on an Illumina Novaseq 6000 platform (Illumina) using a paired-end 150 bp mode. Raw sequencing data were processed and filtered to produce clean reads, which were aligned to the human genome using the STAR software. To generate expression levels, we used the HTSeq v0.6.0 to calculate the fragments per kilobase per million mapped reads (FPKM) of each gene or transcript. The DESeq2 algorithm was applied to identify differentially expressed genes.

first: Xue

last: Chen

first: Qinghuai

last: Liu


title: Cell type-specific dysregulation of gene expression due to Chd8 loss of function during mouse cortical development [snRNA-seq]

city: New Haven

first: James

last: Noonan

state: CT

address: 333 Cedar St

department: Genetics

institute: Yale School of Medicine

summary: Disruptive variants in the chromodomain helicase CHD8, which acts as a transcriptional regulator during neurodevelopment, are strongly associated with risk for autism spectrum disorder (ASD). Loss of CHD8 function is hypothesized to perturb gene regulatory networks in the developing brain, thereby contributing to ASD etiology. However, insight into the cell type-specific transcriptional effects of CHD8 loss of function remains limited. We used single-cell and single-nucleus RNA-sequencing to globally profile gene expression and identify dysregulated genes in the embryonic and juvenile wild type and Chd8+/− mouse cortex, respectively. Chd8 and other ASD risk-associated genes showed a convergent expression trajectory that was largely conserved between the mouse and human developing cortex, increasing from the progenitor zones to the cortical plate. Genes associated with risk for neurodevelopmental disorders and genes involved in neuron projection development, chromatin remodeling, signaling, and migration were dysregulated in Chd8+/− embryonic day (E) 12.5 radial glia. Genes implicated in synaptic organization and activity were dysregulated in Chd8+/− postnatal day (P) 25 deep- and upper-layer excitatory neurons, suggesting a delay in synaptic maturation or impaired synaptogenesis due to CHD8 loss of function. Our findings reveal a complex pattern of transcriptional dysregulation in Chd8+/− developing cortex, potentially with distinct biological impacts on progenitors and maturing neurons in the excitatory neuronal lineage.

overall_design: Single-nucleus RNA-seq (snRNA-seq) was performed on cortical tissue from postnatal day (P) 25 litter- and sex-matched pairs of wild type and Chd8+/- mice. Tissue from four pairs of mice was collected and processed individually

first: Kristina

last: Yim

first: Marybeth

last: Baumgartner

first: Martina

last: Krenzer

first: María

last: Rosales-Larios

first: Timothy

last: Nottoli

first: Rebecca

last: Muhle

first: Guillermina

last: Hill-Terán


title: NPM1-fusion proteins promote myeloid leukemogenesis through XPO1-dependent HOX activation [Cut & Run]

first: Yuko

last: Shimosato

overall_design: To identify genes that are directly regulated by NPM1-fusions, we then performed CUT & RUN analysis using NPM1-CCDC28A cells, which revealed NPM1-CCDC28A specific peaks around 4725 genes (FDR < 0.1).

first: Keita

last: Yamamoto

first: Wenyu

last: Zhang

first: Yuhan

last: Jia


title: Characterization of CD8+ virtual memory T cells in IL-4 knockout mice using single-cell RNA sequencing

city: Seoul

first: Jaeil

last: Lee

address: 103 Daehak-ro, Jongno-gu

country: South Korea

institute: Seoul National University

summary: We profiled the heterogeneity of virtual memory T cells and observed changes in virtual memory T cell subsets under conditions of IL-4 deficiency in mouse spleens using single-cell RNA sequencing.

overall_design: Using DEG analysis, we distinguished virtual memory T cells from splenocytes of wild-type B6 mice and IL-4 knock-out mice and compared virtual memory T cells of each condition.

first: Sung

last: Choi

first: Hi

middle: J

last: Park

first: Hyun

last: Boo

first: Kyeong

last: Jung

first: Jae

middle: I


title: Cell type-specific dysregulation of gene expression due to Chd8 loss of function during mouse cortical development [scRNA-seq]

first: James

last: Noonan

overall_design: Single-cell RNA-seq (scRNA-seq) was performed on developing cortical (i.e., dorsal telencephalon) tissue from embryonic day (E) 12.5, E14.5, E16.0, and E17.5 litter- and sex-matched pairs of wild type and Chd8+/- embryos.Tissue from four pairs of mice was collected for each time point and processed individually.

first: Kristina


title: Copy number variation analysis of 18,000 fetuses in southern China

city: Fuzhou

first: Yanting

last: Que

address: No. 88, Jiaotong Road, Taijiang District, Fuzhou City, Fujian Province

institute: Fujian Medical University

summary:
Chromosomal microarray analysis (CMA) in prenatal diagnosis detects copy number variations (CNVs) in many fetuses; however, the low penetrance and phenotypic diversity of CNVs complicate genetic counseling, resulting in limited understanding of intrauterine ultrasound phenotypes linked to CNVs.
In a retrospective analysis of 25,000 cases at Fujian Maternal and Child Health Hospital, 18,000 pregnant women underwent SNP array testing (December 2015 to June 2023).

first: Meiying

last: Cai

first: Hailong

last: Huang


title: Amelioration of nonalcoholic fatty liver disease by inhibiting the deubiquitylating enzyme RPN11 [MeRIP-m6A]

first: Yunchen

last: Luo

address: shanghai hongkou

institute: Shanghai Jiao Tong University School of Medicine

type: Methylation profiling by high throughput sequencing

summary: Nonalcoholic fatty liver disease (NAFLD) including its more severe manifestation, nonalcoholic steatohepatitis (NASH), is a global public health challenge with no approved pharmacological therapies. Here, we reveal an indispensable role for the deubiquitinating enzyme RPN11 in the development of NAFLD and NASH. Ablation of hepatic RPN11 markedly protected mice from several diets-induced liver steatosis, insulin resistance and steatohepatitis, whereas RPN11 overexpression had the opposite effects. Mechanistically, RPN11 interacts with and stabilizes METTL3 via deubiquitination initiated at lysine 241, to increase the m6A modification and expression of acyl-CoA synthetase short chain family member 3 (Acss3). RPN11-Acss3 axis generates propionyl-CoA and functions in histone propionylation to transcriptionally upregulate lipid metabolism-related genes. Of pathophysiological significance, RPN11-METTL3-Acss3-histone propionylation modification pathway is activated in the livers of patients with NAFLD and positively correlated with hepatic triglyceride contents. More importantly, pharmacological inhibition of RPN11 by Capzimin showed dramatic beneficial effects in ameliorating NAFLD, NASH and related metabolic disorders in mice. Capzimin also reduces intracellular lipid contents in human primary hepatocytes cultured in 2D and 3D spheroids. Together, these results demonstrate that RPN11 is essential for the development of NAFLD/NASH and that suppressing RPN11 has therapeutic potential for the treatment.

overall_design: Genome-wide methylated RNA immunoprecipitation sequencing (MeRIP-Seq)  for db/db mice and lean control mice.

first: Bing

last: Zhou

last: Zhao

first: Yao

last: Li

first: Cheng

last: Hu

first: Yan

last: Lu


title: Cell type-specific dysregulation of gene expression due to Chd8 loss of function during mouse cortical development [bulk RNA-seq]

overall_design: Bulk RNA-seq validation experiments were performed on developing cortical tissue from embryonic day (E) 12.5 and E17.5 and on cortical tissue from postnatal day (P) 25 litter- and sex-matched pairs of wild type and Chd8+/- mice. Tissue from six pairs of mice was collected for each time point and processed individually.

last: Yim

first: Marybeth

last: Baumgartner

first: Martina

last: Krenzer

first: María

last: Rosales-Larios

first: Timothy

last: Nottoli

first: Rebecca

last: Muhle

first: Guillermina

last: Hill-Terán


title: Amelioration of nonalcoholic fatty liver disease by inhibiting the deubiquitylating enzyme RPN11 (MeRIP-m6A-mRNA-seq)

overall_design: Genome-wide methylated RNA immunoprecipitation sequencing (MeRIP-Seq)  for RPN11 HKO and METTL3 HKO mice with their respective flox/flox mice.


title: Amelioration of nonalcoholic fatty liver disease by inhibiting the deubiquitylating enzyme RPN11 [mRNA-seq]

overall_design: Comparative gene expression profiling analysis of RNA-seq data for RPN11 HKO and METTL3 HKO mice with their respective flox/flox mice.


title: Amelioration of nonalcoholic fatty liver disease by inhibiting the deubiquitylating enzyme RPN11 (mRNA-seq db vs. lean)

overall_design: Comparative gene expression profiling analysis of RNA-seq data for db/db mice and lean control mice.


title: Effect of heparan sulfate cleavage on homeostatic gene expression in microvascular endothelial cells

city: Birmingham

first: Jillian

last: Richter

state: AL

address: 1900 University Blvd

department: Surgery

institute: University of Alabama at Birmingham

summary: Heparan sulfate (HS) in the vascular endothelial glycocalyx (eGC) is a critical regulator of blood vessel homeostasis. Trauma results in HS shedding from the eGC, but the impact of HS shedding on mechanisms of vascular injury and repair has not been evaluated. The objective of this work was to characterize the effect of eGC HS shedding on the transcriptional landscape of vascular endothelial cells. In vitro work was performed using flow conditioned primary human lung microvascular ECs treated with vehicle or heparin lyase III to simulate human heparanase activity. Bulk RNA sequencing was performed to determine differentially expressed gene-enriched pathways following heparin lyase III treatment. Pathway analysis demonstrated downregulation of genes that support cell junction integrity, EC polarity, and EC senescence while upregulating genes that promote cell differentiation and proliferation following HS shedding.

overall_design: Primary human lung microvascular ECs (HLMVEC) were conditioned under shear stress (15 dynes/cm2) for 48 hours prior to a 6-hour treatment with vehicle (PBS) or heparin lyase III (n = 4 per group). After treatment, flow was discontinued, and cell monolayers were washed thrice with PBS prior to RNA harvest. Total RNA was isolated from HLMVEC, and cell lysate from 2 slides was combined into a single sample to ensure robust RNA quantity, which generated 2 RNA samples per treatment group for bulk sequencing.

first: Robert

last: Odum

first: Camilla

last: Margaroli

first: Lei

last: Zheng


title: Distance-depending transcriptome changes of pancreatic stellate cells in paracrine pancreatic ductal adenocarcinoma co-culture models

city: Halle (Saale)

first: Anais

last: Zourelidis

state: Sachsen-Anhalt

address: Ernst-Grube-street 40

department: General Surgery

country: Germany

institute: University hospital Halle

summary: Pancreatic stellate cells (PSC) are one source of cancer-associated fibroblasts (CAF) and play, therefore, an essential role in pancreatic ductal adenocarcinoma (PDA). Paracrine signalling between PDA cancer cells and CAF has been widely studied, yet external influences on paracrine crosstalk are poorly understood. This study aimed to gain a deeper insight into the communication of PSC and cancer cells under different co-culture conditions via analysis of PSC gene expression profiles. Two contactless co-culture models with tumor cells from the p48-Cre; lox-stop-lox-KrasG12D/+; lox-stop-lox-Trp53R172H/+ mouse model (KPC) and murine PSC separated through a microporous membrane and grown in different compartments (standard co-culture) or on different sides of the same membrane (inverse co-culture), were established. RNA-Sequencing analysis of PSC mRNA was performed 24 h and 72 h after co-culture with KPC cells. For selected genes, results were confirmed by quantitative RT-PCR and immunocytochemistry. Standard co-culture displayed 19 differentially expressed genes (DEG) at 24 h and 52 DEG at 72 h. In inverse co-culture, 800 DEG at 24 h and 2213 DEG at 72 h were enriched. PSC showed great heterogeneity in their gene expression profiles; however, mutually regulated genes of both co-cultures, such as VCAN and CHST11, could be identified. VCAN-protein-protein interaction-network analysis revealed several shared genes between co-culture models, such as SDC4 and FN1. In conclusion, PSC show a varying susceptibility to cancer cell signals depending on the co-culture method, with intensified transcriptome changes with closer proximity.

overall_design: To investigate PSC gene expression under different conditions, we developed two contactless, paracrine co-culture models: in standard-co culture, PSC grew on top of a microporous membrane with 1 μm pores, with KPC cells growing in the lower compartment, in inverse co-culture PSC and KPC cells were grown on different sides of the same microporous membrane. RNA-Seq was performed from PSC at two different time points, 24 h and 72 h.

first: Bogusz

last: Trojanowicz

first: Yoshiaki

last: Sunami

first: Gerd

last: Hause

first: David

last: Vieweg

first: Joerg

last: Kleeff


title: Amelioration of nonalcoholic fatty liver disease by inhibiting the deubiquitylating enzyme RPN11

first: Yunchen

last: Luo

type: Genome binding/occupancy profiling by high throughput sequencing

overall_design: Chromatin Immunoprecipitation DNA-sequencing (ChIP-seq) for H3K23 propionylation in RPN11 WT and RPN11 HKO mice.

first: Bing

last: Zhou

last: Zhao

first: Yao

last: Li

first: Cheng

last: Hu

first: Yan

last: Lu


title: Exposure of Ldlr-/- mice to a PFAS mixture increased circulating cholesterol and decreased bile acid excretion with concurrent increases in male ileal ASBT

city: Detroit

first: Katherine

last: Gurdziel

state: MI

address: 275 E. Hancock

institute: Wayne State University

summary: Background: Previous epidemiological studies have repeatedly found per- and polyfluoroalkyl substances (PFAS) exposure associated with higher circulating cholesterol, one of the greatest risk factors for development of coronary artery disease. The main route of cholesterol catabolism is through its conversion to bile acids, which circulate between the liver and ileum via enterohepatic circulation. Patients with coronary artery disease have decreased bile acid excretion, indicating that PFAS-induced changes of enterohepatic circulation may play a critical role in cardiovascular risk.  Objectives: Using a mouse model with high LDL-VLDL cholesterol and aortic lesion development similar to humans, the current study investigates mechanisms linking exposure to a PFAS mixture with increased cholesterol.  Methods: Male and female Ldlr-/- mice were fed an atherogenic diet (Clinton/Cybulsky low fat, 0.15% cholesterol) and exposed to a mixture of 5 PFAS representing legacy, replacement, and emerging subtypes (i.e., PFOA, PFOS, PFNA, PFHxS, GenX), each at a concentration of 2 mg/L, for 7 weeks. Blood was collected longitudinally for cholesterol measurements and mass spectrometry was used to measure circulating and fecal bile acids. Transcriptomic analysis of ileal samples was performed via RNA-sequencing. Results: After 7 weeks of PFAS exposure, average circulating PFAS levels were measured at 21.6, 20.1, 31.2, 23.5, and 1.5 µg/mL in PFAS-exposed females and 12.9, 9.7, 23, 14.3, and 1.7 µg/mL in PFAS-exposed males for PFOA, PFOS, PFHxS, PFNA, and GenX, respectively. PFAS exposure led to elevated circulating cholesterol levels after 7 weeks compared to vehicle mice, with females increasing 18% and males increasing 24%. Total circulating bile acid levels were elevated in PFAS-exposed mice by 230% in males and 290% in females compared to vehicle. PFAS decreased fecal bile acid levels by 62% in females and 59% in males. In the ileum, expression levels of the bile acid reuptake transporter ASBT were increased due to PFAS exposure. Discussion: Mice exposed to a PFAS mixture display increased circulating cholesterol and bile acids perhaps due to changes in enterohepatic circulation. This study implicates PFAS-mediated effects at the site of the ileum as a possible critical mediator of increased cardiovascular risk due to PFAS.

overall_design: Ldlr KO mice were fed an atherogenic diet (Clinton/Cybulsky low fat, 0.15% cholesterol) an exposured to water containing a PFAS mixture for 7 weeks. Ileums from the male mice were collected. RNA was harvested from the ileums to compare transcriptional differences between control water and PFAS water exposure.

last: Roth

first: Zhao

last: Yang

first: Manisha

last: Agarwal

first: Johnna

last: Birbeck

first: Judy

last: Westrick

first: Todd

last: Lydic

first: Michael

last: Petriello


title: Adipose microenvironment promotes hypersialylation of ovarian cancer cells

first: Grace

middle: Michelle

last: Swanson

address: 275 E. Hancock, C.S. Mott Center room 271

summary: Sialylation, the addition of negatively charged sialic acid sugars to terminal ends of glycans, is upregulated in most cancers. Hypersialylation supports multiple pro-tumor mechanisms such as enhanced migration and invasion, resistance to apoptosis and immune evasion. A current gap in knowledge is the lack of understanding on how the tumor microenvironment regulates cancer cell sialylation. The adipose niche is a main component of most peritoneal cancers’ microenvironment. This includes ovarian cancer (OC), which causes most deaths from all gynecologic cancers. In this report, we demonstrate that the adipose microenvironment is a critical regulator of OC cell sialylation.In vitroadipose conditioning led to an increase in both⍺2,3 and⍺2,6-linked cell surface sialic acids in both human and mouse models of OC.Adipose-induced sialylation reprogramming was also observedin vivofrom intra-peritoneal OC tumors seeded in the adipose-rich omentum. Mechanistically, we observed upregulation of at least three sialylatransferases, St3gal1, St6gal1 and St3galnac3.Hypersialylated OC cells consistently formed intra-peritoneal tumors in both immune-competent mice and immune-compromised athymic nude mice. In contrast, hyposiaylated OC cells persistently formed tumors only in athymic nude mice demonstrating that sialylation impacts OC tumor formation in an immune dependent manner. To our knowledge, this is the first demonstration of the effect of adipose microenvironment on OC tumor sialylation. Our results set the stage for translational applications targeting sialic acid pathways in OC and other peritoneal cancers.

overall_design: mRNA-seq primed from the polyA was used to determine expression profiles. Lexogen’s QuantSeq 3’mRNA-seq Library Prep Kit (FWD for Illumina) was utilized for building RNA-seq librariesfrom 0.1-200ng of total RNA in 5 µl of nuclease-free ultrapure water.Libraries were quantified on the Qubit and Agilent 2200 Tapestation using the DNA High Sensitivity Screen tape. The electrophoretogram, RNA Integrity Number (RIN), and the ratio of the 28S:18S RNA bands are collectively examined to determine overall quality of the RNA. The barcoded libraries were multiplexed at equimolar concentrations and sequenced with 75 bp reads on an Illumina NovaSeq SP flow cell. Data was demultiplexed using Illumina's CASAVA 1.8.2 software. After read quality was assessed[44], reads were aligned to the human genome (Build hg38)[45]and tabulated for each gene region[46]. Differential gene expression analysis was used to compare transcriptome changes between conditions using a paired design[47]. Significantly altered genes (p-value ≤ 0.05) were input in iPathwayGuide (Advaita Bioinformatics, Ann Arbor, MI) to identify differentially regulated Pathways.

first: Alexandra

last: Fox

first: Garry

middle: D

last: Leonard

first: Nicholas

last: Adzibolosu

first: Terrance

last: Wong

first: Roslyn

last: Tedja

first: Sapna

last: Sharma

first: Radhika

last: Gogoi

first: Robert

last: Morris

first: Gil

last: Mor

first: Charlie

last: Fehl

first: Ayesha

last: Alvero


title: Respiratory infection with influenza A virus delays remyelination and alters oligodendrocyte metabolism.

city: Urbana

first: Andrew

last: Steelman

state: IL

address: 1201 West Gregory

institute: University of Illinois

summary: Peripheral viral infection disrupts oligodendrocyte homeostasis such that endogenous remyelination may be affected. Here, we demonstrate that influenza A virus infection perpetuated a demyelination- and disease-associated oligodendrocyte (OL) phenotype following cuprizone-induced demyelination that resulted in delayed OL maturation and remyelination in the prefrontal cortex. Furthermore, we assessed cellular metabolism ex-vivo, and found that infection altered brain OL and microglia metabolism in a manner that opposed the metabolic profile induced by remyelination. Specifically, infection increased glycolytic capacity of OLs and microglia, an effect that was recapitulated by LPS stimulation of mixed glia cultures. In contrast, mitochondrial respiration was increased in OLs during remyelination, which was similarly observed in OLs of myelinating P14 mice compared to adult and aged mice. Collectively, our data indicate that respiratory viral infection is capable of suppressing remyelination, and suggest that metabolic dysfunction of OLs is implicated in remyelination impairment.

overall_design: Spatial transcriptomic analysis was performed on brains from non-cuprizone control mice ("Normal"), cuprizone-fed mice at peak demyelination (“Demyelinated”), and saline-inoculated (“Saline”) or influenza virus-inoculated (“Flu”) mice during active remyelination

first: Allison

middle: Y

last: Louie

first: Jenny

last: Drnevich

first: Jennifer

middle: L

last: Johnson

first: Meagan

last: Woodard

first: Anna

middle: V

last: Kukekova

first: Rodney

middle: W


title: The effect of myeloid STING knockout after tumor formation on gene expression in AOM/DSS-induced CAC mice

city: Beijing

first: Runping

last: Liu

state: Beijing

address: 11 Beisanhuandonglu

institute: Beijing University of Chinese Medicine

summary: Myeloid-derived STING has been recognized to play a vital role in mediating the development of colitis-associated carcinoma (CAC). We here report that myeloid-specific knockout of STING after tumor formation enhanced tumor growth by modifying the tumor microenvironment to a more immunologically inactive state. Pathways related to antigen presentation, macrophage and DC activation, T cell chemotaxis and activation, T cell-mediated cytotoxicity and other immune responses to tumor cells were all inhibited by lateral myeloid STING kncckout after tumor formation.

overall_design: Tmem173fl/fl mice and Tmem173fl/flLzym-Creert2 mice were performed tamoxifen administration after three circles of AOM/DSS induction. Total tumor RNA was extracted and RNA-sequecing was performed.


title: Expression Data from ST2 cells transfected with a Wnt1 expressing plasmid

city: Hamburg

first: Thorsten

last: Schinke

address: Martinistr. 52

department: Department of Osteology and Biomechanics

institute: University Medical Center Hamburg-Eppendorf

summary:
Wnt1 has major anabolic functions in bone metabolism. We investigated the effect of of Wnt1 on the mesenchymal cell line ST2 by transfecting it with a pLNCX-Wnt1 expression plasmid.
We used microarray analysis to detail the global gene expression of ST2 cells 5 days after transfection with 1 µg pLNCX-Wnt1.

overall_design: 2 samples generated from pools of 3 independent experiments each were analyzed. Effects of transfection with pLNCX-Wnt1 were compared to transfection with the empty pLNCX vector.

first: Wenbo

last: Zhao

first: Timur

last: Yorgan


title: The effect of STING knockout on gene expression in DMXAA-induced BMDMs and BMDCs

summary: Myeloid-derived STING has been recognized to play a vital role in mediating the development of colitis. We here report that in BMDMs and BMDCs, knockout of STING inhibited pathways related to IL-12/23 production and IL-12 signaling, inflammation, and the maturation and activation of macrophages and DCs.

overall_design: BMDMs and BMDCs were isolated from tamoxifen-induced Tmem173fl/fl mice and Tmem173fl/flLzym-Creert2 mice. Isolated BMDMs and BMDCs were stimulated by 40 μM DMXAA. Total cellular RNA was extracted and RNA-sequecing was performed.


title: EV-miRNAs as biomarkers of breast cancer recurrence

city: Barretos

first: Rhafaela

middle: Lima

last: Causin

state: SP

address: Antenor Duarte Villela, 1331

department: Molecular Oncology Research Center

country: Brazil

institute: Barretos Cancer Hospital

summary: To evaluate the miRNAs expression related to breast cancer recurrence

overall_design: This retrospective observational study utilized convenience sampling and was conducted at the Molecular Oncology Research Center of the Barretos Cancer Hospital. Initially, a total of 177 medical records of women with BC were available at the Biobank of Barretos Cancer Hospital (20). However, only 24 patients were by all the inclusion criteria previously described. Samples were divided into two groups: group 1 represents the samples with BC recurrence (n=10), and group 2 was without recurrence disease (n=13).

first: Márcia

middle: M

last: Marques;


title: The Impact of PAD4-dependent Neutrophil Extracellular Trap formation on the Early Development of Intestinal Fibrosis in Crohn’s Disease

city: Florence

first: Gabriele

last: Dragoni

address: Viale Pieraccini, 6

country: Italy

institute: University of Florence

summary: To explore the potential profibrotic effect of neutrophil extacellular traps (NETs), we investigated the transcriptional modification that NET stimulation determines in the intestine of patients with Crohn's disease(CD). To this end, primary intestinal fibroblasts derived from the ileum of patients with CD were either coltured with NETs for 24 hours or left untreated. Bulk RNA sequencing (RNA-seq) was performed to evaluate the differentially expressed genes and determine the possible profibrogenic signature of this interaction.

overall_design: Transcriptomic analysis of primary intestinal fibroblasts stimulated in vitro with NETs (1 ug/mL) compared to transcriptome of untreated fibroblasts from the same CD patients (n = 3).

first: Bo-Jun

last: Ke

first: Lucia

last: Picariello

first: Saeed

last: Abdurahiman

first: Elisabetta

last: Ceni

first: Francesca

last: Biscu

first: Tommaso

last: Mello

first: Simone

last: Polvani

last: Innocenti

first: Valérie

last: Spalart

first: Stefano

last: Milani

first: André

last: D'Hoore

last: Bislenghi

last: Scaringi

first: Bram

last: Verstockt

first: Gert

last: De Hertogh

first: Kimberly

last: Martinod

first: Andrea

last: Galli

first: Gianluca

last: Matteoli

first: Séverine

last: Vermeire


title: RNA Sequencing Analysis of Brain Transcriptomes of Ischemic Stroke Treated With or Without Lactate

city: Chengdu

first: Xiao-Yi

last: Xiong

address: 37 Shierqiao Road, 610075, Chengdu, China

institute: Chengdu University of Traditional Chinese Medicine

summary: We report the application of RNA sequencing technology for high-throughput profiling of brain transcriptomes in ischemic stroke mice. We find that changes in gene expression were detected in vehicle-treated ischemic brains when compared with the sham groups, with 1159 upregulated genes and 529 downregulated genes. While, the lactate preconditioning further enlarged the changes in gene expression of ischemic brains, with 2071 upregulated genes and 1003 downregulated genes. Finally, we show that the ischemic brains are much more immunologically activated by the lactate treatment. This study shows that the contributing roles of lactate in the brain injury after cerebral ischemia are complex and immunological mechanisms may be the major effects that exacerbate the brain injury of mice with cerebral ischemia.

overall_design: Methods: Brain mRNA profiles of ischemic mice treated with or without lactate were generated by deep sequencing, in quadruplicate, using PromthION.

first: Jing

last: Yuan

first: Su-Hao

last: Yang

first: Qing-Wu


title: Transcription Factor Activity Regulating Macrophage Heterogeneity  during Skin Wound Healing

city: Chicago

first: Timothy

middle: Jon

last: Koh

address: 1919 W Taylor Room 650

institute: University of Illinois at Chicago

summary: We aimed to study chromatin accessibility for TF binding sites for inferring TF activity in monocytes and macrophages during skin wound healing. Monocytes and macrophages isolated from skin wounds on male C57BL6/J mice on day 3 and 6 post-injury, subjected to enzymatic digestion to obtain single cells and pooled from two mice per time point. Nuclei were processed using the 10x Chromium platform. Libraries sequenced on NovaSeq 6000 with paired-end reads. Fastq files were generated and demultiplexed into single cells using Cell Ranger software.

overall_design: Monocytes and macrophages isolated from skin wounds on male C57BL6/J mice on day 3 and 6 post-injury by magnetic sorting and nuclei was isolated and processed for scATACseq according to manufacturer’s instructions.

first: Jingbo

last: Pang

first: Mark

last: Maienschein-Cline


title: The Pgb1 locus controls glycogen aggregation in astrocytes of the aged hippocampus without impacting cognitive function.

status: Public on Aug 13 2024

city: Berlin

first: Rupert

last: Overall

state: Berlin

address: Philippstraße 13

institute: Humboldt University of Berlin

summary: In aged humans and mice, aggregates of hypobranched glycogen molecules called polyglucosan bodies (PGBs) accumulate in hippocampal astrocytes. PGBs are known to drive cognitive decline in neurological diseases but remain largely unstudied in the context of typical brain aging. Here, we show that PGBs arise in autophagy-dysregulated astrocytes of the aged C57BL/6J mouse hippocampus. To map the genetic cause of age-related PGB accumulation, we quantified PGB burden in 32 fully sequenced BXD-recombinant inbred mouse strains, which display a 400-fold variation in hippocampal PGB burden at 16-18 months of age. A major modifier locus was mapped to chromosome 1 at 72–75 Mb, which we defined as the Pgb1 locus. To evaluate candidate genes and downstream mechanisms by which Pgb1 controls the aggregation of glycogen, extensive hippocampal transcriptomic and proteomic datasets were produced for aged mice of the BXD family. We utilized these datasets to identify Smarcal1 and Usp37 as potential regulators of PGB accumulation. To assess the effect of PGB burden on age-related cognitive decline, we performed phenome-wide association scans, transcriptomic analyses as well as conditioned fear memory and Y-maze testing. Importantly, we did not find any evidence suggesting a negative impact of PGBs on cognition. Taken together, our study demonstrates that the Pgb1 locus controls glycogen aggregation in astrocytes of the aged hippocampus without affecting age-related cognitive decline.

overall_design: 234 samples from 74 mouse strains of the BXD population.

first: A

last: Gómez-Pascual

first: D

last: Glikman

first: H

middle: X

last: Ng

first: J

last: Tomkins

first: L

last: Lu

first: Y

last: Xu

last: Ashbrook

first: C

last: Kaczorowski

first: G

last: Kempermann

last: Killmar

first: K

last: Mozhui

first: O

last: Ohlenschläger

first: R

last: Aebersold

middle: K

last: Ingram

first: E

last: Williams

first: M

last: Jucker

last: de Bakker


title: mTORC1 hyperactivation blocks pluripotent stem cells fate transitions through TFE3-NuRD association [CUT&Tag]

city: Guangzhou

first: shuhui

last: xu

address: 190 Kaiyuan Avenue, Huangpu District

institute: Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences

summary: As an evolutionarily conserved master regulator of metabolism, mechanistic target of rapamycin complex 1 (mTORC1) regulates cell states and fates in development, cancer and aging. mTORC1 activity regulation was critical for pluripotent stem cells maintenance and cell fate transitions. Inhibition of mTORC1 induces embryonic stem cells (ESCs) entry into a paused state which reversibly arrests self-renewal leaving pluripotency intact. Hyperactivation of mTORC1 impedes both pluripotency re-establishment and exit of PSCs. As shown that mTORC1 mediates TFE3 nuclear translocation block pluripotency exit, whether similar mechanisms through transcription factor TFE3 are involved in these processes, and the detailed mechanism by which mTORC1-TFE3 regulates critical transcriptional processes for these transitions, remain unclear. In this study, we demonstrate that the nuclear translocation of TFE3, induced by hyperactivation of mTORC1, results in its binding to the nucleosome remodeling and deacetylation (NuRD) complex in both re-establishment and exit of pluripotency. This interaction inhibits the expression of various crucial genes during different fate transitions of PSCs. Our findings uncover a common and key role of TFE3-NuRD association as mediator of mTORC1 to block pluripotent cell fate transitions, with implications for various fields including physiological and pathological diseases.

overall_design: We performed experiments to identify the binding sites of TFE3 and HDAC2 at a later stage (Day 10) from MEFs reprogramming to iPSCs. Using TFE3 and HDAC2 antibodies, we performed CUT&Tag in these stages of Tsc1 WT and Tsc1 KO cell lines to determine where these factors bind.

first: Peizhi

last: Li

first: Xueting

first: BaoMing

last: Qin

first: Shuhui


title: The effect of myeloid STING knockout on gene expression in colitic mice

first: Runping

last: Liu

summary: Myeloid-derived STING has been recognized to play a vital role in mediating the development of colitis. We here report that myeloid-specific knockout of STING in adult mice ameliorates DSS-induced acute colitis through inhibiting macrophage maturation, reducing DC cell activation, and suppressing pro-inflammatory Th1 and Th17 cells.

overall_design: Tmem173fl/fl mice and Tmem173fl/flLzym-Creert2 mice were injected intraperitoneally with tamoxifen for five continuous times before 7d-DSS administration. Total colonic RNA was extracted and RNA-sequecing was performed.


title: Epigenetic insights into GABAergic development in Dravet Syndrome iPSC and therapeutic implications

city: Uppsala

first: Xingqi

last: Chen

address: Husargata

department: Immunology, Genetics and Pathology

country: Sweden

institute: uppsala university

summary: Dravet syndrome (DS) is a devastating early onset refractory epilepsy syndrome caused by variants in the SCN1A gene. A disturbed GABAergic interneuron function is implicated in the progression to DS but the underlying developmental and pathophysiological mechanisms remain elusive, in particularly at the chromatin level. In this study, we utilized induced pluripotent stem cells (iPSCs) derived from DS cases and healthy donors to model disease-associated epigenetic abnormalities of GABAergic development. Employing the ATAC-Seq technique, we assessed chromatin accessibility at multiple time points (Day 0, Day 19, Day 35, and Day 65) of GABAergic differentiation. Additionally, we elucidated the effects of the commonly used anti-seizure drug valproic acid (VPA) on chromatin accessibility in GABAergic cells. The distinct dynamics in chromatin profile of DS iPSC predicted accelerated early GABAergic development, evident at D19, and diverged further from the pattern in control iPSC with continued differentiation, indicating a disrupted GABAergic maturation. Exposure to VPA at D65 reshaped the chromatin landscape at a variable extent in different iPSC-lines and rescued the observed dysfunctional development in some DS iPSC-GABA. This study provides the first comprehensive investigation on the chromatin landscape of GABAergic differentiation in DS-patient iPSC, offering valuable insights into the epigenetic dysregulations associated with interneuronal dysfunction in DS. Moreover, our detailed analysis of the chromatin changes induced by VPA in iPSC-GABA holds the potential to improve development of personalized and targeted anti-epileptic therapies.

overall_design: Dynamic change of chromatin accessbility in  GABAergic development from Dravet Syndrome iPSC

first: chen

last: xingqi


title: SLU7 downregulation results in an aberrant expression of mRNA transcripts

city: Pamplona

first: Carmen

last: Berasain

state: Navarra

address: Avda. Pio XII 55

country: Spain

institute: CIMA

summary: SLU7 (Splicing factor synergistic lethal with U5 snRNA 7) was first identified as a splicing factor necessary for the correct selection of 3' splice sites, strongly impacting on the diversity of gene transcripts in a cell. More recent studies have uncovered new and non-redundant roles of SLU7 as an integrative hub of different levels of gene expression regulation, including epigenetic DNA remodeling, modulation of transcription and protein stability. Aim: to generate the transcript landscape in control and SLU7 knock-down PLC/PRF/5 human hepatocellular carcinoma cells.

overall_design: The expression of the splicing factor SLU7 in the human hepatocellular carcinoma cell line PLC/PRF/5 was knocked down with specific siRNAs (siSlu7). An irrelevant siRNA (siGL2) was used as negative control. The RNA to perform the array analysis was extracted 48h after transfection.


title: Cerebral hypoperfusion exacerbates traumatic brain injury in male mice

city: Morgantown

first: Zachary

last: Weil

state: WV

address: 108 Biomedical Road, 313 BMRC

institute: WVU

summary: Traumatic brain injury (TBI) has been postulated to initiate a disease process that interacts with vascular dysfunction. However, the combined effects of preexisting cerebral hypoperfusion and TBI remain poorly explored. This study aimed to investigate the combined effects of bilateral carotid artery stenosis (BCAS) and mild-moderate TBI on cerebral blood flow (CBF), cognitive function, histology, and transcriptomics in Swiss-Webster mice. Male and female mice underwent BCAS using steel microcoils around the carotid arteries, followed by TBI 30 days post coil implantation. CBF, spatial learning and memory, axonal damage, and gene expression profiles were assessed. BCAS led to a ~10% reduction in CBF, while TBI caused a similar decrease. However, mice exposed to both BCAS and TBI exhibited more pronounced reductions in CBF, associated with marked spatial learning and memory deficits, particularly in males. Axonal damage in male mice was also exacerbated by the combination of BCAS and TBI. Notably, females demonstrated differential vascular and cognitive responses to BCAS and TBI, suggesting sex-specific protective mechanisms. Single nuclei RNA sequencing revealed unique, cell type-specific gene expression alterations due to BCAS, TBI, or the combination. Moreover, BCAS and TBI induced significant gene expression changes in various cell types, hinting at complex cellular interactions following vascular challenges and trauma. The cellular and molecular interplay between hypoperfusion and TBI points to intricate vascular-neuronal interactions and potential avenues for targeted interventions.

overall_design: A 2mm cube of perilesional forebrain tissue was dissected from male Swiss Webster mice that underwent control, BCAS, TBI, or a combination of BCAS+TBI surgeries and frozen in liquid nitrogen. Frozen tissue was submitted to Genewiz for 10X snRNA sequencing on the 10X Genomics Chromium System.

first: Bailey

last: Whitehead

first: Corbin

last: Deborah

first: Alexander

last: Megan

first: Bumgarner

last: Jacob

first: Zhang

last: Ning

first: Kate

last: Karelina


title: Multiomics analysis of canine myocardium after circumferential pulmonary vein ablation: Effect of NPY on long-term reinduction of atrial fibrillation

city: Jinan

first: Yinglong

last: Hou

state: ShanDong

address: No. 16766, Jingshi Road, Lixia District, Jinan City, Shandong Province, China

institute: Qianfoshan Hospital of Shandong Province

summary: In this study,We established a long-term model of beagle canines after circumferential pulmonary vein ablation (CPVA). The transcriptome and proteome were obtained using high-throughput sequencing and TMT-tagged LC‒MS/LC analysis. Differentially expressed genes and proteins were screened and enriched, and the effect of fibrosis was found and verified in tissues

overall_design: Beagles underwent thoracotomy in the right fourth intercostal space, followed by circumferential pulmonary vein catheter ablation(CPVA). After 6 months of feeding, bullseye atrial muscle tissues were collected (CPVA:Control=5:5).

first: Juanjuan

last: Du

first: Qiyuan

last: Song


title: The mRNA and microRNA expression profiles of ovarian cancer in chicken

first: guoqiang

last: zhu

address: No. 24, Section 1, South Section 1, First Ring Road

institute: sichuan university

type: Non-coding RNA profiling by high throughput sequencing

summary: The laying hen is the only spontaneous model of ovarian tumor. But no studies have systematically compared the molecular mechanisms of ovarian cancer in hens and women. We performed RNA sequencing of nine chicken ovarian tumor samples and four normal ovarian samples.

overall_design: We perform transcriptome sequencing of mRNAs and microRNAs from five late-stage ovarian tumor samples, four early-stage ovarian tumor samples and four normal ovarian samples


title: Early Decline of Conventional NK Cells During Acute Pseudomonas aeruginosa Lung Infection

first: Duo

last: Su

address: Street Dongdajie

institute: Beijing Institute of Microbiology and Epidemiology

summary: To assess gene expression changes, RNA-sequencing technology was employed to map the temporal shifts in the transcriptional profile of the host lung post-infection. Our findings provide novel insights into the pathogenesis of PA pulmonary infections and offer valuable suggestions for inhalational infection protection and immunotherapy.

overall_design: Lung mRNA profiles of 8 week-old female wild type (WT) mice infected with PAO1 by aerosolized intratracheal inoculation and control mice were genreated by deep sequencing on the Illumina sequencing platform NovaSeq 6000. RT–PCR validation was performed using  SYBR Green assays.

first: Fuliang

last: Zong

last: Xiao

first: Yifeng

last: Wang

first: Huiying

last: Yang


title: Transcriptomic profiling of the intermediate cell carcinoma of the primary liver cancer

city: Suwon

first: Hyun Goo

last: Woo

address: 164 Worldcup-ro Yeongtong-gu

institute: Ajou University School of Medicine

summary:
Introduction: Combined hepatocellular-cholangiocarcinoma (cHCC-CCA) is a mixed-type tumor of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), which is classified into classical type (i.e., c-CHC) and intermediate cell type (i.e., i-CHC). c-CHC harbors both HCC and iCCA cells, whereas i-CHC is comprised of intermediate cell types lacking classical regions of HCC or iCCA cells. Notwithstanding the unique pathological feature of i-CHC, its molecular characteristics is not fully elucidated yet.
Methods: To obtain molecular insights on the i-CHC, RNA-sequencing (RNA-Seq) and whole genome sequencing (WGS) profiling were performed on the tissues of i-CHC, HCC, and iCCA, respectively.
Results: i-CHC showed unique transcriptomic features differing from HCC and iCCA, showing higher expression of Notch signaling and frequent splicing events of intron-retention (IR). Noticeably, we found that i-CHC had DNA-copy number loss and concomitant transcriptional suppression of METTL16, which may contribute to the aggressive progression of i-CHC via Notch activation.
Conclusions: We suggest that i-CHC had unique transcriptomic features, providing new insights into the pathobiology of i-CHC.

overall_design: Trnascriptomic profiling from 7 cases of NT, 5 cases of HCC, 8 cases of i-CHC, and 5 cases of iCCA tissue were performed. Four tissue types: NT, HCC, i-CHC, iCCA

first: Hyun


title: Epithelial and mesenchymal pancreatic cancer cells exhibit different stem cell phenotypes being associated with different metastatic propensity

city: Lübeck

first: Hauke

last: Busch

state: Schleswig-Holstein

address: Ratzeburger Allee 160

department: Lübeck Institute of Experimental Dermatology

institute: University of Lübeck

summary: Pancreatic ductal adenocarcinoma (PDAC) is the most common malignant pancreatic tumor in western countries, characterized by a low 5-year survival rate of only 11 %. Owing to a lack of early and specific symptoms, most patients are diagnosed at advanced or even me-tastasized stages essentially impairing treatment efficacy. Metastatic outgrowth requires a high plasticity of tumor cells implying phenotypic switching in response to changing envi-ronments. One important process leading to phenotypic switching is the Epithelial-Mesenchymal-Transition (EMT) and its reversion, the Mesenchymal-Epithelial-Transition (MET). This process has been associated with the gain of cancer stem cell (CSC) properties being regarded as drivers of tumor initiation at primary and secondary sites. Still, it is poorly understood whether different CSC phenotypes exist along the EMT/MET axis and how these impact malignancy associated properties. Thus, this study aimed to characterize CSC popula-tions of epithelial and mesenchymal PDAC cells and how these relate to functional pheno-types.  Methods: For this purpose, single-cell-cloning of the two PDAC cell lines Panc1 and Panc89 was performed to isolate and expand CSC- (Holoclone cells) and non-CSC (Paraclone cells) clones. Cell variants were characterized regarding cell growth, migration, invasion, cell ad-hesion and tumorigenicity. Results: Panc1 Holoclone cells showed a mesenchymal phenotype dominated by high ex-pression of the stemness marker Nestin, while Panc89 Holoclone cells exhibited an epitheli-al phenotype with elevated expression of the stemness marker SOX2. Moreover, Panc89 Holoclone cells showed enhanced cell growth and colony formation ability compared to Panc1 Holoclone cells. In contrast, slowly proliferating Panc1 Holoclone cells were highly invasive, while Panc89 Holoclone cells showed a slow cluster-like invasion. In line with these findings, a higher number of metastases was formed by Panc1 Holoclone cells in vivo. How-ever, Panc89 Holoclone cells led to formation of larger tumors limiting survival of inoculated mice. Moreover, epithelial and mesenchymal CSC-clones showed clear differences with re-spect to organ manifestation. Conclusion: Overall, these data support the view of different CSC phenotypes in PDAC cells that are linked to distinct EMT/MET phenotypes and that manifest in a different metastatic propensity.

overall_design: Single-cell-cloning of the two PDAC cell lines Panc1 and Panc89 was performed to isolate and expand CSC- (Holoclone cells) and non-CSC (Paraclone cells) clones. Gene expression of the parental, holocone and paraclone cell lines were quantified by RNA-seq in triplicates.

first: Susanne

last: Sebens

first: Lisa-Marie

last: Philipp


title: Widespread regulation of the maternal transcriptome by Nanos in Drosophila

city: Columbus

first: Mohammad

last: Marhabaie

state: OH

address: 700 Children's Dr

institute: Nationwide Children's Hospital

summary: The translational repressor Nanos (Nos) regulates a single target, maternal hunchback (hb) mRNA, to govern abdominal segmentation in the early Drosophila embryo. Nos is recruited specifically to sites in the 3'-UTR of hb mRNA in collaboration with the sequence-specific RNA-binding protein Pumilio (Pum); on its own, Nos has no binding specificity. Nos is expressed at other stages of development, but very few mRNA targets that might mediate its action at these stages have been described. Nor has it been clear whether Nos is targeted to other mRNAs in concert with Pum or via other mechanisms. In this report, we identify mRNAs targeted by Nos via two approaches. In the first method, we identify mRNAs depleted upon expression of a chimera bearing Nos fused to the nonsense mediated decay (NMD) factor Upf1. We find that, in addition to hb, Upf1-Nos depletes ~2600 mRNAs from the maternal transcriptome in early embryos. Virtually all of these appear to be targeted in a canonical, hb-like manner in concert with Pum. In a second, more conventional approach, we identify mRNAs that are stabilized during the maternal zygotic transition (MZT) in embryos from nos- females. Most (86%) of the 1185 mRNAs regulated by Nos are also targeted by Upf1-Nos, validating use of the chimera. Previous work has shown that 60% of the maternal transcriptome is degraded in early embryos. We find that maternal mRNAs targeted by Upf1-Nos are hypo-adenylated and inefficiently translated at the ovary-embryo transition; they are subsequently degraded in the early embryo, accounting for 59% of all destabilized maternal mRNAs.We suggest that the late ovarian burst of Nosrepresses a large fraction of the maternal transcriptome, priming it for later degradation by other factors during the MZT in the embryo.

overall_design:
To identify mRNAs targeted by Nos we took two approaches. In the first method, we identify mRNAs depleted upon expression of a chimera bearing Nos fused to the nonsense mediated decay factor Upf1. In addition to Upf1-Nos and wild type embryos, we also prepared triplicate samples from 3 more experimental embryos: Upf1, Nos, and Upf1-NosL7.
In a second one, we took a more conventional approach and identify mRNAs that are stabilized during the maternal zygotic transition in embryos from nos- females compared to wild type w strain.

first: Tammy

middle: H

last: Wharton

first: Sung

last: Yun-Kim

first: Robin


title: Sfrp4 is Required to Maintain Ctsk-Lineage Periosteal Stem Cell Niche Function

city: Boston

first: Francesca

last: Gori

state: MA

address: 188 Longwood Avenue

institute: Harvard School of Dental Medicine

summary: The periosteum contains cells which function as a reservoir of stem cells and progenitors and contribute to cortical expansion during growth, cortical bone homeostasis and repair. However, the local or paracrine factors that govern stem cell renewal and differentiation within the periosteal niche remains elusive. Cathepsin K (Ctsk) together with additional cell surface markers marks a subset of stem cells in the periosteum (PSC) which possess self-renewal ability and inducible multipotency. These PSCs produce osteoblasts mediating periosteal bone formation and fracture repair. Sfrp4 is expressed in periosteal Ctsk-lineage cells and using CtskCre mice that are either wild type or Sfrp4-/-, we report here that Sfrp4 deletion decreases the pool of PSCs, impairs their self-renewal, their ability to give rise to their derivatives and their clonal multipotency for differentiation into osteoblasts and chondrocytes in vitro and formation of bone organoids in vivo. Bulk RNA sequencing analysis in Ctsk-lineage PSCs demonstrated that Sfrp4 deletion leads to downregulation of signaling pathways associated with skeletal development, positive regulation of bone mineralization and wound healing. Sfrp4 deletion hampers the Ctsk-lineage PSC response and recruitment after bone injury and leads to an impaired periosteal response. Periosteal Ctsk-lineage cells respond to PTH(1-34) treatment with an increase in the % of PSCs, a response not seen in the absence of Sfrp4. Importantly, bone histomorphometry analysis showed that in the absence of Sfrp4, PTH(1-34)-dependent increase in cortical thickness, periosteal bone formation is markedly impaired.

overall_design: To gain insight into the function of Sfrp4 in the regulation of the Ctsk-lineage periosteal stem cell (PSC) stemness, differentiation and function, we generated CtskCre;mTmG;wt (GFP+) and CtskCre;mTmG;Sfrp4-/- (GFP+;Sfrp4-/-) mice and investigated Ctsk+ (GFP+) labeled and GFP+;Sfrp4-/- PSC. To better understand the changes occurring in the Ctsk-lineage PSC population in the absence of Sfrp4 we performed bulk RNA-seq analysis. Two biological samples were collected per GFP+ PSC and GFP+Sfrp4-/- PSCs, each composed of the pooled cells yield from n=3 mice.

first: Ruiying

last: Chen

first: Han

last: Dong

first: Roland

last: Baron

first: Matthew

middle: B

last: Greenblatt


title: Single-cell RNA-seq profiling of cardiopharyngeal progenitor maturation in Ciona Robusta

status: Public on Aug 12 2024

city: Qingdao

first: WEI

last: WANG

state: Shandong

address: 23 Hongkong east road haier building G zone

institute: Ocean University of China

summary: During development, stem and progenitor cells divide and transition through germ layer- and lineage-specific multipotent states to generate the diverse cell types that compose an animal. Defined changes in biomolecular composition underlie the progressive loss of potency and acquisition of lineage-specific characteristics. For example, multipotent cardiopharyngeal progenitors display multilineage transcriptional priming, whereby both the cardiac and pharyngeal muscle programs are partially active and coexist in the same progenitor cells, while their daughter cells engage in a cardiac or pharyngeal muscle differentiation path only after cell division. Here, using the tunicate Ciona, we studied the acquisition of multilineage competence and the coupling between fate decisions and cell cycle progression. We showed that multipotent cardiopharyngeal progenitors acquire the competence to produce distinct Tbx1/10 (+) and (-) daughter cells shortly before mitosis, which is necessary for Tbx1/10 activation. By combining transgene-based sample barcoding with single cell RNA-seq (scRNA-seq), we uncovered transcriptome-wide dynamics in migrating cardiopharyngeal progenitors as cells progress through G1, S and G2 phases. We termed this process “transcriptome maturation”, and identified candidate “mature genes”, including the Rho GAP-coding gene Depdc1, which peak in late G2. Functional assays indicated that transcriptome maturation fosters cardiopharyngeal competence, in part through multilineage priming and proper oriented and asymmetric division that influences subsequent fate decisions, illustrating the concept of “behavioral competence”. Both classic feedforward circuits and coupling with cell cycle progression drive transcriptome maturation, uncovering distinct levels of coupling between cell cycle progression and fateful molecular transitions. We propose that coupling competence and fate decision with the G2 and G1 phases, respectively, ensures the timely deployment of lineage-specific programs.

overall_design: Samples from 5-14hpf Ciona embryos were tagged with a pair of sample barcoding (SBC) constructs as unique labels for the multiplexing strategy. Singel-cell suspensions were prepared as described in the manuscripts. FACS-purified B7.5 lineage cells were used to generate single-cell libraries following a modified 10X protocol to capture the sequencing reads from both the transcriptome and SBC transcripts.

first: Wei

first: Lionel

last: Christiaen


title: Smad7-based biologic targeting epidermis and stroma promotes healing of diabetic wounds in mice and pigs

city: Aurora

first: Ben-Zheng

last: Li

state: CO

department: Department of Physiology and Biophysics

institute: University of Colorado Anschutz Medical Campus

summary: Impaired healing of diabetic wounds causes significant morbidity and mortality. This study aimed to identify novel mechanisms of diabetic wound healing defects and test a therapeutic intervention using diabetic mouse and pig models. We found Smad7 transgene expression in mouse epidermis promoting wound healing in diabetic db/db mice, with reductions in obesity and blood glucose. To isolate effects of Smad7 on wounds, we created a Smad7-based biologic (Tat-PYC-Smad7) that penetrates wound cells. Topical application of Tat-PYC-Smad7 to diabetic pig and mouse wounds accelerated healing compared to controls. RNAseq analysis of mouse wound samples showed reduced TGFβ/NFκB signaling, leading to faster re-epithelialization and better extracellular matrix remodeling. Tat-PYC-Smad7 also attenuated neutrophil degranulation and NETosis by blocking histone 3 citrullination and inhibiting myeloperoxidase activities. Our study reveals that Tat-PYC-Smad7 promotes diabetic wound healing by targeting keratinocytes and neutrophils, providing insight into cellular mechanisms of diabetic wound healing defects targetable by Smad7-based therapy.

overall_design: To understand the molecular basis of Tat-PYC-Smad7 effects, we performed RNA-seq on db/db mouse wound samples excised at identical locations treated with vehicle or Tat-PYC-Smad7 on days 9 and 11.

first: Yao

last: Ke

first: Fulun

first: Donna

first: Suyan

first: Sam

middle: T

last: Hwang

first: Scott

last: Simon

first: Sean

middle: R

last: Collins

first: Christian

last: Young

first: Xiao-Jing


title: JNK signalling regulates self-renewal of proliferative urine-derived renal progenitor cells via inhibition of ferroptosis.

city: Düsseldorf

first: Wasco

last: Wruck

address: Moorenstr. 5

institute: Universitätsklinikum Düsseldorf

summary: With a global increase in chronic kidney disease patients, alternatives to dialysis and organ transplantation are needed. Stem cell-based therapies could be one possibility to treat chronic kidney disease. Here, we used multipotent urine-derived renal progenitor cells (UdRPCs) to study nephrogenesis. UdRPCs treated with the JNK inhibitor- AEG3482, displayed decreased proliferation and downregulated transcription of cell cycle-associated genes as well as the kidney progenitor markers -SIX2, CITED1, and SALL1. In addition, levels of activated SMAD2/3, which is associated with the maintenance of self-renewal in UdRPCs, were decreased. JNK inhibition resulted in less efficient oxidative phosphorylation and more lipid peroxidation via ferroptosis- an iron-dependent non-apoptotic cell death pathway linked to various forms of kidney disease. Our study reveals the importance of JNK signalling in maintaining self-renewal as well as protection against ferroptosis in SIX2-positive UdRPCs.  We propose that UdRPCs can be used for modelling ferroptosis-induced kidney diseases.

overall_design: The transcriptomes of UdRPCs  with and without JNK inhibition were compared by microarray analysis (Clariom-S Human Gene Expression Array, Affymetrix, Thermo Fisher Scientific).

first: Wruck

last: Wasco

first: Nguyen

last: Lisa

first: Adjaye

last: James


title: mTORC1 hyperactivation blocks pluripotent stem cells fate transitions through TFE3-NuRD association [RNA-Seq]

first: shuhui

last: xu

overall_design: RNA-seq data included Tsc1 loxp/loxp MEFs cells with or without AAV-cre cleavage (Tsc1 WT and Tsc1 KO), and reprogrammed cells with ectopically expressed OSKM (Oct4, Sox2, Klf4, c-Myc),along with either control transfection(shLuc) or two shRNAs for Tfe3 Knockdown. Two time points in the reprogramming time course were profiled: Day 5(early) and Day 10 (late)

first: Peizhi

first: Xueting

last: Xu

first: BaoMing

last: Qin

first: Shuhui


title: MALAT1 is required for phenotypic consequences of TET2 mutations in myeloid neoplasms.

city: Tampa

first: Ben-Crentsil

last: Nana Adjoa

address: 12902 USF Magnolia Drive

institute: Moffitt Cancer Center

summary: Loss of function mutations inTET2(LOF) occur in up to 58% and 30% of myeloid malignancies and clonal hematopoiesis (CH) respectively. Genetically engineered murine models of Tet2 LOF display splenomegaly, granulomonocytic expansion, and increased bone marrow hematopoietic stem and progenitors. However, the direct downstream effectors of TET2 LOF leading to this phenotype are unknown. Using multiome single cell sequencing from a cohort of severe COVID patients with or without TET2 mutations we show that MALAT1, a therapeutically tractable long non-coding RNA, is overexpressed and is both necessary and sufficient to induce TET2 LOF phenotypes. We additionally demonstrate that TET2 LOF leads to decrease activity of the transcriptional repressor EGR1 leading to upregulation of MALAT1. This upregulation then leads to sustained NFkB activity by inhibiting the phosphatase activity of PP2A on P65 resulting in increased pro-inflammatory cytokines such as IL-6 required for TET2 LOF phenotypes in MALAT1 overexpressing mice

overall_design: Bone marrow mononuclear cells were obtained from 8 week old male wild type (WT), Tet2-/- and Tet2-/-;Malat1-/- (TKM) mice and lineage negative, ckit+, sca1+ (LSK) cells were sorted by FACS. Total mRNA was extracted from these LSK cells and bulk RNA extracted for sequencing. Cells from WT mice were used as controls and the transcriptome differences between the various groups were determined.

first: Nana

middle: A

last: Ben-Crentsil

first: Surendra

last: Neupane

first: Hannah

last: Newman

first: Eric

last: Padron