title: Spindle cell lesions with oncogenic EGFR kinase domain aberrations: expanding the spectrum of protein kinase-related mesenchymal tumors

city: Rome

first: Evelina

last: Miele

address: Piazza di Sant'Onofrio 4

department: Oncoematologia

institute: Ospedale Pediatrico Bambino Gesù

summary: EGFR aberrations are reported in a subset of myofibroblastic lesions with kinase domain duplication (EGFR-KDD) and exon 20 mutations being assigned to infantile fibrosarcomas (IFS), mesoblastic nephroma and fibrous hamartoma of infancy (FHI), respectively. In this retrospective study, we correlated molecular findings with histomorphology of 14 myofibroblastic lesions harboring such genetic changes identified by NGS. We additionally performed DNA methylation profiling (DNAmp) and immunohistochemistry. Lesions were from 10 males and 4 females with a mean age of 3 years (range, 0.3 -14) and occurred subcutaneously in the upper limbs (n = 5), lower limbs (n = 3), back/thorax (n = 5), and the nasal cavity (n = 1). Eleven were cured by surgery, including one relapsed case. Two patients were lost to follow-up. One case was very recent, and the patient was biopsied. Histologically, the lesions showed a wide spectrum varying from classic FHI (n=9) to IFS (n=1) or lipofibromatosis-like tumors (LFT) (n=2) or dermatofibrosarcoma protuberans-like (DFSP) (n=1) to a predominantly-myxoid spindle cell lesion (n=1). Immunohistochemically, all neoplasms stained with CD34, while S100 was positive in 2/14. EGFR expression was observed in 9/10 cases. Molecularly, the IFS and one LFT harbored EGFR-KDD, while an exon 20 mutation was identified in all FHI, one LFT and in the DFSP and predominantly myxoid spindle cell lesion. By DNAmp, all but two cases formed a well-defined cluster, demonstrating that these lesions are also epigenetically related. In conclusion, EGFR kinase domain aberrations found in FHI, IFS, LFN, DFSP and a spindle cell lesion with a predominant myxoid stroma of children and adolescents show that these neoplasms with a broad morphological spectrum belong to the group of protein kinase-related lesions with a distinct epigenetic signature. Molecular analyses, including DNAmp, help to identify and characterize this emerging category and become mandatory when targeted treatment is considered.

overall_design: Generated methylation data were compared to sarcoma classifier v12.2-v12.3 (Koelsche et al, 2021), that also allowed for determining copy number alterations. We also carried out t-distributed stochastic neighbor embedding (t-SNE) analysis, with R package Rtsne version 0.16, using the first 94 principal components computed on the top 32000 DNA methylation values with highest standard deviation as described by Capper et al.


title: Chronic pharmacologic manipulation of dopamine transmission ameliorates metabolic disturbance in a syndrome caused by mutated trappc9

status: Public on Jun 17 2024

city: Shanghai

first: Yan

last: Li

state: Shanghai

address: 800 Dong Chuan Road

country: China

institute: Shanghai Jiao Tong University

type: Expression profiling by high throughput sequencing

summary: Loss-of-function mutations of the gene encoding the trafficking protein particle complex subunit 9 (trappc9) cause autosomal recessive intellectual disability and obesity by unknown mechanisms. Genome-wide analysis links trappc9 to non-alcoholic fatty liver disease (NAFLD). Trappc9-deficient mice have been shown to appear overweight shortly after weaning. Here, we analyzed serum biochemistry and histology of adipose and liver tissues to determine the incidence of obesity and NAFLD in trappc9-deficient mice and combined transcriptomic and proteomic analyses, pharmacological studies, and biochemical and histological examinations of postmortem mouse brains to unveil mechanisms involved. We found that trappc9-deficient mice presented with systemic glucose homeostatic disturbance, obesity and NAFLD, which were relieved upon chronic treatment combining dopamine receptor D2 (DRD2) agonist quinpirole and DRD1 antagonist SCH23390. Blood glucose homeostasis in trappc9-deficient mice was restored upon administrating quinpirole alone. RNA-sequencing analysis of DRD2- containing neurons and proteomic study of brain synaptosomes revealed signs of impaired neurotransmitter secretion in trappc9-deficient mice. Biochemical and histological studies of mouse brains showed that trappc9-deficient mice synthesized dopamine normally, but their dopamine-secreting neurons had a lower abundance of structures for releasing dopamine in the striatum. Our study suggests that trappc9 loss- of-function causes obesity and NAFLD by constraining dopamine synapse formation.

overall_design: Abdominal fat pads were collected aseptically from three WT and three trappc9 KO mice aged 3-4 weeks. Tissues were washed three times in Hank’s balanced salt solutions, minced into small pieces, and then treated with 1 mg mL-1 type-I collagenase at 37 oC with gentle mixing at 120 rpm. Enzymatic digestions were terminated by adding 10 mL of α-MEM media containing 10% FBS, 1x L-glutamine, and 1x penicillin/ streptomycin. The digestion mixtures were filtered through a 70-μm cell strainer (ThermoFisher), and the filtrates were centrifuged at 1200 rpm for 5 min. The cell pellets were washed once in phosphate saline and resuspended in 1 mL TRIzol reagents (Invitrogen) for RNA sequencing (RNAseq) analysis.

first: Muhammad

last: Usman

first: Ellen

last: Sapp

first: Yuting

last: Ke

first: Zejian

last: Wang

first: Adel

last: Boudi

first: Marian

last: DiFiglia

first: Xueyi


title: RNA binding protein PCBP2 regulates pancreatic β cell function and adaptation to glucose

city: Philadelphia

first: Doris

middle: A

last: Stoffers

state: PA

address: 3400 Civic Center Blvd

department: IDOM

country: USA

institute: University of Pennsylvania

summary: Glucose plays a key role in shaping pancreatic β cell function. Thus, deciphering the mechanisms by which this nutrient stimulates β cells holds therapeutic promise for combating β cell failure in type 2 diabetes (T2D). β cells respond to hyperglycemia in part by rewiring their mRNA metabolism, yet the factors governing these changes remain poorly understood. Here, we interrogate the transcriptomes of control β cells and mutant β cells lacking the RNA binding protein PCBP incubated with low or high glucose for 72 hours.

overall_design: RNASeq was performed in control and Pcbp2 null  β cells exposed to low or high glucose for 72 hours.

first: Matthew

middle: W

last: Haemmerle

first: Kristen

middle: L

last: Wells


title: Cytosolic dopamine determines hypersensitivity to blunt force trauma

city: Dallas

first: Peter

middle: M

last: Douglas

state: Tx

address: 6000 Harry Hines Blvd

department: Molecular Biology

institute: University of Texas Southwestern Medical Center

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

overall_design: Refer to individual Series


title: Complement Membrane Attack Complexes Disrupt Proteostasis to Function as Intracellular Alarmins

city: New Haven

first: Daniel

last: Jane-Wit

state: CT

address: 10 Amistad St

institute: Yale University

summary: We report bulk RNA-seq data of A197-270 tandem plasmids of human C9 protein in HEK cell lines.

overall_design: HEK cell lines were transduced with vector or A197-270 tandem plasmids with or without IFN-gamma, then harvested. Total RNA was isolated using a RNeasy Mini Kit (74104, Qiagen), and sent for bulk RNA-seq with polyA selection.

first: Guiyu

last: Song

last: Jane-wit


title: Cytosolic dopamine determines hypersensitivity to blunt force trauma [N2 injury timeline]

summary: The selective vulnerability of dopaminergic neurons to trauma-induced neurodegeneration is a conserved phenomenon across species, extending from nematodes to humans. However, the molecular mechanisms contributing to this hypersensitivity to blunt force injury remain poorly understood. We find that dopamine oxidation, a key driver of Parkinson’s Disease, extends its toxic role to the acute challenges of blunt force trauma. Ectopic synthesis of dopamine in serotonergic neurons alone proves sufficient in determining neuronal subtype sensitivity to trauma-induced death. While dopaminergic neurons maintain this neurotransmitter in a functional and benign state, trauma-induced subcellular redox imbalances elicit dopamine-dependent cytotoxicity. Perturbing dopamine synthesis and its packaging into synaptic vesicles further demonstrate how cytosolic dopamine is both necessary and sufficient to drive cell loss upon mechanical stress and during aging. Additionally, trauma activates the B-Zip transcription factor, fos-1, which exacerbates this toxic cascade by transcriptionally upregulating the rate-limiting enzyme in dopamine synthesis, cat-2. In summary, our study unravels the molecular intricacies that render dopaminergic neurons uniquely prone to physical perturbation, highlighting a shared vulnerability across different evolutionary lines.

overall_design: Day 1 adult N2 worms were subjected to mechanical trauma (8600 RPM, 16s) and placed on recovery plates. Worms were collected in Trizol 8, 48, and 96 hours after injury. To prevent progeny contamination worms were kept sterile by maintaining all conditions on cdc-25.1 RNAi.

first: Kielen

last: Zuurbier


title: Lactylation of NAT10 promotes N4‐acetylcytidine modification on tRNASer-CGA-1-1 to boost oncogenic DNA virus KSHV reactivation

city: Nanjing

first: jing

last: zhou

address: longmian Street No.101

institute: Nanjing Medical University

summary: N4-acetylcytidine (ac4C), a conserved but recently rediscovered RNA modification on tRNAs, rRNAs and mRNAs, is catalyzed by N-acetyltransferase 10 (NAT10). Lysine acylation is a ubiquitous protein modification that controls protein functions. Our latest study demonstrates a NAT10-dependent ac4C modification, which occurs on the polyadenylated nuclear RNA (PAN) encoded by oncogenic DNA virus Kaposi's sarcoma-associated herpesvirus (KSHV), can induce KSHV reactivation from latency and activate inflammasome. However, it remains unclear whether a novel lysine acylation occurs in NAT10 during KSHV reactivation and how this acylation of NAT10 regulates tRNAs ac4C modification. Here, we showed that NAT10 was lactylated by α-tubulin acetyltransferase 1 (ATAT1), as a writer at the critical domain, to exert RNA acetyltransferase function and thus increase the ac4C level of tRNASer-CGA-1-1. Mutagenesis at the ac4C site in tRNASer-CGA-1-1 inhibited its ac4C modifications, translation efficiency of viral lytic genes, and virion production. Mechanistically, KSHV PAN orchestrated NAT10 and ATAT1 to enhance NAT10 lactylation, resulting in tRNASer-CGA-1-1 ac4C modification, eventually boosting KSHV reactivation. Our findings reveal a novel post-translational modification in NAT10, as well as expand the understanding about tRNA-related ac4C modification during KSHV replication, which may be exploited to design therapeutic strategies for KSHV-related diseases.

overall_design: To investigate the effects of knocking down NAT10 and overexpressing ATAT1 on tRNA ac4C modification, tRNA ac4C-seq was performed on iSLK-RGB WT,iSLK-RGB KO NAT10+/-,iSLK-RGB pCDH and iSLK-RGB ATAT1.

first: Qin

last: Yan

first: Jing

last: Zhou

first: Guochun

last: Chen

first: Haoran

last: Zhang


title: Cytosolic dopamine determines hypersensitivity to blunt force trauma [PMD216 EV, cat-1, cat-2]

overall_design: C. elegans expressing sid-1 and rde-1 in dopaminergic neurons in a rde-1 mutant background raised on EV, cat-1 or cat-2 RNAi. Worms were collected at day 1 of adulthood.


title: A novel MYC-ZNF706-SLC7A11 regulatory circuitry contributes to cancer progression and redox balance in human hepatocarcinoma (ChIP-Seq)

city: Xi’an

first: jie

last: Chu

address: 169 Changle West Road

institute: Air Force Medical University

type: Genome binding/occupancy profiling by high throughput sequencing

summary: ZNF706 belongs to a member of C2H2-type zinc finger proteins which exerts pivotal roles in cancer progression. However, the biological function and mechanism of ZNF706 are rarely investigated.   Using qRT-PCR and Western blot assays, we identified ZNF706 was frequently amplified in human hepatocarcinoma and high ZNF706 expression was associated with unfavorable HCC patient survival based on TCGA database. In vitro and in vivo experiments revealed that ZNF706 promoted HCC cell growth. Mechanistically, RNA-seq and ChIP-seq identified SLC7A11 was a critical target of ZNF706, and depletion of ZNF706 increased lipid peroxidation, cell death and decreased cystine uptake medicated by SLC7A11 contributing to redox homeostasis disruption. Furthermore, using luciferase report assays and ChIP-qPCR, we found MYC could regulate ZNF706 transcription by binding to ZNF706 promoter region, and further assay indicated MYC also involved in redox balance by modulating SLC7A11. Collectively, our study uncovers that the oncogenic role of ZNF706 in liver cancer, indicating that ZNF706 inhibition could be a potential treatment strategy for liver cancer.

overall_design: Given ZNF706 is a DNA-binding protein, there are no studies that describe the binding motif of ZNF706. Therefore, we performed ChIP-seq to search for specific DNA binding site of ZNF706 in LM3 cells.


title: A novel MYC-ZNF706-SLC7A11 regulatory circuitry contributes to cancer progression and redox balance in human hepatocarcinoma


title: FGF1 supports metabolic reprogramming through the estrogen receptor in endocrine-resistant and obesity-associated breast cancer

city: Sheridan

first: Kenneth

last: Jones

state: Wyoming

address: 1309 Coffeen Avenue STE 10090

institute: Bioinformatic Solutions LLC

summary: Obesity is associated with elevated breast cancer risk and with breast cancer-specific mortality, particularly for people with estrogen receptor (ER) positive tumors. Body mass index (BMI) is commonly used to define obesity, but it may not be the best predictor of breast cancer risk or prognosis on an individual level. Adult weight gain is an independent prognostic indicator of breast cancer risk, and many patients undergoing cancer treatment experience the side effect of weight gain. Our previous work described a murine model of obesity, ER-positive breast cancer, and weight gain, and identified fibroblast growth factor receptor (FGFR) as a potential driver of tumor progression in some cases. During adipose tissue expansion, the FGF1 ligand is produced by hypertrophic adipocytes as a stimulus to stromal preadipocytes that proliferate and differentiate to provide additional lipid storage capacity. In the breast adipose tissue, FGF1 production may stimulate cancer cell proliferation and tumor progression.

overall_design: We explored the effects of FGF1 on ER-positive endocrine-sensitive and -resistant breast cancer and compared that to the effects of the canonical ER ligand, estradiol. We used untargeted proteomics, specific immunoblot assays, gene expression profiling, and functional metabolic assessments of breast cancer cells. Results were validated in tumors from obese mice and breast cancer datasets from women with obesity.

first: Marisol

last: Castillo-Castrejon

first: Elizabeth

last: Wellberg


title: A multi-cancer CRISPR/Cas9 reveals distinct gene dysregulation by noncoding MSTRG transcripts

city: Guangzhou

first: wei

last: xiong

state: Guangdong

address: No.1023,South Shatai Road

department: Bioinformatics Section

institute: Southern Medical University

summary: Long noncoding RNAs (lncRNAs) regulate gene expression with their functional domains without being translated into proteins. Whether wrong noncoding transcripts have functions is of special interest and lacks systematic investigation.  Our study identified several MSTRG transcripts that may have regulatory functions through specific DNA-binding domains (DBDs). We selected three MSTRG noncoding transcripts and validated their roles in cancer through CRISPR/Cas9-mediated knockout experiments, using A549 and HCT116 cell lines as experimental models. Then, we conducted a comparative gene expression analysis using RNA-seq data to compare the knockout of three aberrant human non-coding transcripts to their respective wild-type controls.

overall_design: We selected three MSTRG transcripts for knockout of their DNA-binding domains (DBDs), including MSTRG.4401.1, MSTRG.2513.6, and MSTRG.34636.7. Specifically, MSTRG.4401.1 and MSTRG.2513.6 were knocked out in both A549 and HCT116 cell lines, while MSTRG.34636.7 was knocked out only in HCT116 cells. Both before and after the knockout, RNA sequencing (RNA-seq) was performed on the samples.

first: Hao

last: Zhu


title: Analysis of CD70 wild type or CD70 knock out CD70-specific nanoCAR T cells

city: Ghent

first: Stijn

last: De Munter

address: Corneel Heymanslaan 10

country: Belgium

institute: Ghent University

summary: CD70 is an attractive target for chimeric antigen receptor (CAR) T cell therapy as treatment for both solid and liquid malignancies. However, functionality of CD70-specific CAR T cells is only modest. Here, we optimized a CD70-specific VHH based CAR (nanoCAR). We evaluated the nanoCARs in clinically relevant models in vitro, using co-cultures of CD70-specific nanoCAR T cells with malignant rhabdoid tumor organoids, and in vivo by using a diffuse large B cell lymphoma (DLBCL) patient-derived xenograft (PDX) model. Whereas the nanoCAR T cells were highly efficient in organoid co-cultures, they showed only modest efficacy in the PDX model. Knocking out CD70 expression in the nanoCAR T cells resulted in dramatically enhanced functionality in the PDX model, suggesting that CD70 interaction in cis with the nanoCAR induces exhaustion. Through single-cell transcriptomics, we obtained evidence that CD70 KO CD70-specific nanoCAR T cells are protected from antigen-induced exhaustion. Our data show that CARs targeted to endogenous T cell antigens, negatively affect CAR T cell functionality by inducing an exhausted state, which can be overcome by knocking out the specific target, in this case CD70.

overall_design: CD70 WT and CD70 KO CD70-specific nanoCAR T cells were isolated by Fluorescence-activated cell sorting (FACS) from bone marrow of mice injected with the Raji cell line. Sorting was performed based on CD45 and eGFP expression. Sorted cells were analyzed using scRNAseq.

first: Laurenz

last: De Cock

first: Bart

last: Vandekerckhove


title: Signaling in microglia after anti-PD-1 treatment

city: Freiburg

first: Robert

last: Zeiser

address: Hugstetter Strasse 53

department: Inner Medicine 1

country: Germany

summary: In this experiment, we studied how anti-PD-1 effects microglial kinase signaling

overall_design: Murine Microglia isolated from B16F10 melanoma bearing mice  that received ISO (n=3) or PD-1 antibody (n=4)

first: Zeiser

last: Robert

first: Janaki

last: Vinnakota


title: Transcriptome profiling of muscle stem cell subpopulations based on differential expression of Myf5

city: Lausanne

first: Jerome

last: Feige

address: EPFL Innovation Park, Building H

department: Musculo-Skeletal Health

country: Switzerland

institute: Nestle Institute Of Health Sciences

summary: To identify genes and pathways differentially expressed in Myf5 subpopulations of muscle stem cells

overall_design: Myf5 subpopulations (Myf5High and Myf5Low) of muscle stem cells were isolated from hindlimb muscles of Pax7/Myf5 reporter mice by fluorescence-activated cell sorting (FACS). Myf5High and Myf5Low cells were defined as two Pax7-positive subpopulations at opposite ends of the Myf5-E2Crimson fluorescence spectrum. In total, 4 different conditions were analyzed: male Myf5High, male Myf5Low, female Myf5High, and female Myf5Low. We performed two independent replicates per condition, each replicate consisting in a pool of 4 mice.

first: S

last: Ancel

first: E

last: Migliavacca

last: Metairon

first: P

last: Stuelsatz

first: J

middle: N


title: MHC class II proteins mediate sialic acid independent entry of human and avian H2N2 influenza A viruses

city: Zuerich

first: Lennart

last: Opitz

address: Winterthurerstr. 190

institute: FGCZ Zuerich

summary: Influenza A viruses (IAV) cause seasonal outbreaks that pose a substantial burden on human health. They are also a zoonotic threat as avian and swine IAV can be a source for pandemic influenza. Receptor specificity is a critical determinant of tropism, host range and transmissibility of IAV and thus, plays a crucial role in zoonotic IAV infections1-3. Avian, swine and human IAV bind sialic acid on host cell glycans as their common receptor but differ in sialic acid specificity4,5. In contrast, bat IAV of the H17 and H18 subtypes cannot use sialic acid and require MHC class II complexes for host cell entry6-8. It is unknown how this difference in receptor specificity evolved and if dual receptor specificity for sialic acid and MHC class II is possible. Here, we show that human H2N2 IAV and related avian H2N2 possess dual receptor specificity. In addition to their known sialic acid-dependent entry they can use MHC class II as alternative entry pathway, independent of sialic acid. Of note, MHC class II from humans, pigs, ducks, swans and chickens but not from bats can mediate H2 IAV entry and the ability to use this alternative entry pathway is conserved in current Eurasian avian H2 IAV. Our results demonstrate that IAV can possess dual receptor specificity for sialic acid and MHC class II and suggest a role for MHC class II-dependent entry in zoonotic IAV infections.

overall_design: We used primary human airway epithelial cells of bronchial origin and generated airway cultures at air-liqwid interface. These cultures were subjected to single cell RNA sequencing in order to identify the different cell types present along with their transcriptomic profile. In particular, we aimed to determine transcript levels for HLA-DR expression in the different cell types.

first: Umut

last: Karakus

first: Milagros

last: Sempere Borau

first: Patricia

last: Martínez-Barragán

first: Josephine

last: von Kempis

first: Soner

last: Yildiz

first: Laura

last: Arroyo-Fernández

first: Marie

middle: O

last: Pohl

first: Julia

last: Steiger

first: Irina

last: Glas

first: Annika

last: Hunziker

first: Adolfo

last: García-Sastre

first: Silke

last: Stertz


title: Comparative seq Between Killifish Species

city: Stanford

first: Anne

last: Brunet

state: California

address: 290 Jane Stanford Way

department: Genetics

institute: Stanford University

sample_organism:
Aphyosemion australe
Austrofundulus limnaeus
Iconisemion striatum
Nothobranchius furzeri

first: Param

middle: P

last: Singh

first: G

last: Reeves

first: Kévin

last: Contrepois

first: Katharina

last: Papsdorf

first: Jason

last: Miklas

first: Chi-Kuo

last: Hu

first: Mathew

last: Ellenberger

first: Michael

last: Snyder


title: Comparative RNAseq Between Killifish Species

summary: We evaluate the global gene expression changes that occur during a stage-matched developmental window in a closely related set of killifish species.

sample_organism:
Aphyosemion australe
Iconisemion striatum
Nothobranchius furzeri

overall_design: Single timepoint examination the global gene expression changes during pre-diapuase development in the African turquoise killifish, the red-striped, and the lyretail killifish.


title: Analysis of CD70 wild type or CD70 knock out CD70-specific nanoCAR T cells [RNA-Seq]

first: Stijn

last: De Munter

summary: CD70 is an attractive target for chimeric antigen receptor (CAR) T-cell therapy for the treatment of both solid and liquid malignancies. However, the functionality of CD70-specific CAR T-cells is modest. We optimized a CD70-specific VHH-based CAR (nanoCAR). We evaluated the nanoCARs in clinically relevant models in vitro, using co-cultures of CD70-specific nanoCAR T-cells with malignant rhabdoid tumor organoids, and in vivo using a diffuse large B-cell lymphoma (DLBCL) patient-derived xenograft (PDX) model. Whereas the nanoCAR T-cells were highly efficient in organoid co-cultures, they showed only modest efficacy in the PDX model. Fratricide was not causing this loss in efficacy but rather CD70 interaction in cis with the nanoCAR, as validated by imaging flowcytometry, induces exhaustion. Knocking out CD70 expression in nanoCAR T-cells using CRISPR/Cas9, resulted in dramatically enhanced functionality in the DLBCL PDX model. Through single-cell transcriptomics, we obtained evidence that CD70 knock out (KO) CD70-specific nanoCAR T-cells were protected from antigen-induced exhaustion. In addition, we were able to demonstrate that WT CD70-specific nanoCAR T-cells already exhibit signs of exhaustion shortly after production. Their gene signature strongly overlapped with gene signatures of exhausted CAR T-cells. On the other hand, the gene signature of KO nanoCAR T-cells overlapped with the gene signature of CAR T-cell infusion products that led to complete responses in chronic lymphatic leukemia patients. Our data show that CARs targeting endogenous T-cell antigens, negatively affect CAR T-cell functionality by inducing an exhausted state, which can be overcome by knocking out the specific target, in this case CD70.

overall_design: To investigate the effect of CD70 expression on CD70-and CD20-specific nanoCAR T cells, we knocked out CD70 at the beginning of the nanoCAR T cell prodution. At day 12 of the production process, we harvested the cells and assessed the transcriptome. This was done on three independent healthy donors.

first: Laurenz

last: De Cock

first: Bart

last: Vandekerckhove


title: Comparative ATACseq Between Killifish Species

summary: We evaluate the global chromatin changes that occur during the developmental progression and development-to-diapause transition in a closely related set of killifish species.

platform_organism:
Aphyosemion australe
Austrofundulus limnaeus
Iconisemion striatum
Nothobranchius furzeri

overall_design: Time-course examination the global chromatin landscape changes during the tranistion from development-to-diapause in the African turquoise killifish, South American killifish, and equivalent developmental stages in the red-striped and lyretail killifish.

first: Micael


title: A novel MYC-ZNF706-SLC7A11 regulatory circuitry contributes to cancer progression and redox balance in human hepatocarcinoma (RNA-Seq)

first: jie

last: Chu

overall_design: To better determine the molecular mechanisms underlying ZNF706-modulated the biological process, we performed RNA-seq to explore the gene expression profiles using LM3 cells with stable ZNF706 knockdown or vector control and identified the DEGs


title: Glucose deprivation effect on Hepatocellular carcinoma cell line: Huh-7

city: Hong Kong

first: Chi Ho

last: Lin

address: 6th Floor, The Hong Kong Jockey Club Building for Interdisciplinary Research, 5 Sassoon Road, Pokfulam

department: Centre for PanorOmic Sciences

country: Hong Kong

institute: The University of Hong Kong

summary: Analysis of Hepatocellular carcinoma (HCC) cell line - Huh7 deprived of glucose. Glucose restriction promotes a liver tumor-initating cell phenotype. Results provide insight into the molecular mechanism of glucose deprivation in HCC.

overall_design: mRNA profiles of Huh7 cells culture in high glucose (HG; 4.5g/L) and low glucose (LG; 0.45g/L) medium.

first: Ho

middle: C

last: Loong

first: Stephanie

last: Ma


title: LncRNA HIF1A-AS1 regulates the apoptosis and proliferation of vascular endothelial cells through globally regulating miRNAs expression

city: WuHan

first: Guosong

last: Jiang

state: Hubei Province

address: Jiefang Road, No. 1277

department: Department of Urology

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

type: Non-coding RNA profiling by high throughput sequencing

overall_design: Refer to individual Series


title: LncRNA HIF1A-AS1 regulates the apoptosis and proliferation of vascular endothelial cells through globally regulating miRNAs expression [miRNA-Seq]

summary: In the current study, on the basis of establishment of PA-induced damage model of HUVECs, the silencing and overexpression (OE) of HIF1A-AS1 were implemented in the HUVECs, and the effects on cell viability, apoptosis, migration and invasion were explored, respectively. Functionally, the results indicated silencing of HIF1A-AS1 promoted the proliferation migration and invasion, and reduced the apoptosis of HUVECs. In contrast, OE of HIF1A-AS1 reduced proliferation transwell and invasion, promoted the apoptosis, suggesting that HIF1A-AS1 play vital roles in regulating HUVECs. Moreover, miRNA sequencing (miRNA-seq) and RNA sequencing (RNA-seq) were carried out, and the results indicated that HIF1A-AS1 globally mediate expression of miRNA and mRNA. The multiple target genes of DEmiRNA were associated with cell proliferation and apoptosis, and overlapped with the DEGs from RNA-seq, suggestion that HIF1A-AS1 might regulate the proliferation and apoptosis of HUVECs by regulating miRNA expression.

overall_design: Examination the silencing and overexpression of HIF1A-AS1 in HUVECs

first: Lingqiang

last: Chen


title: LncRNA HIF1A-AS1 regulates the apoptosis and proliferation of vascular endothelial cells through globally regulating miRNAs expression [RNA-Seq]


title: The transcriptome data of immature dendritic cells were treated with hydrogen peroxide

status: Public on Jun 16 2024

city: Guiyang

first: Dong

middle: mei

last: ling

state: Guizhou

address: Guizhou Medical University

department: School of Basic Medical Sciences

institute: Guizhou Medical University

summary: RNA sequencing(seq-RNA) was used to analyze the underlying mechanism of immature dendritic cells (imDCs) response to extracellular reactive oxygen species (ROS). The oxidative stress model of imDCswas constructed by simulating ROS with H2O2. The final H2O2 concentration was determined by CCK8 and Annexin V-FITC/ PI double staining methods. The free migration of imDCs was analyzed by cell real-time imaging. Total RNA was extracted and transcriptome sequencing was performed. Go and KEGG enrichment analysis of differential expressed genes(DEGs) was performed. Transcripts related to metabolism and skeleton regulation were screened according to the changes of differential gene expression ≥1 and FDR≤0.05. The result showed that there were no significant changes in cell viability and apoptosis of imDCs when H2O2 concentration was less than 100 μmol/L. The free migrate ability of imDCs was enhanced in ROS environment. RNA-seq data showed that 282 differentially expressed genes between the control group and the H2O2 treatment group. Among them, 225 differentially expressed genes were down-regulated, and 57 were up-regulated. GO and KEGG enrichment analysis found that these genes were involved in metabolism, cell cycle and cytoskeleton related signaling pathway. Gsta1, Gsta3，Cstdc5，Cstdc5 and Prdx1 involved in response to xenobtiotic metabolism were up-regulated. S100a8, Tm4sf19 and Ppbp involved in skeleton regulation were also up-regulated. While Nusap1, Stmn1, Kif20 and Prc1 were down-regulated. This study suggested that the activation of antioxidant system, cytoskeletal remodeling and cell cycle arrest may be involved in regulating the migration ability of imDCs in response to extracellular ROS.

first: Mingling

last: Dong

first: Yun

last: Wang

first: Zhu

last: Zeng


title: TFEB safeguards trophoblast syncytialization in humans and mice (ChIP-Seq)

city: Xiamen

first: wanshan

last: zheng

state: Fujian

address: Xiang'an Road

department: School of Medicine,

institute: Xiamen University

summary: Nutrient sensing and adaptation in the placenta are essential for pregnancy viability and proper fetal growth. Our recent research demonstrates that the placenta adapts to nutrient insufficiency through mTOR inhibition-mediated trophoblast differentiation toward syncytiotrophoblasts (STBs), a highly specialized multinucleated trophoblast subtype directing extensive maternal-fetal interactions. However, the underlying mechanism remains elusive. Here, we unravel the indispensable role of the mTORC1 downstream transcriptional factor TFEB in STB formation both in vitro and in vivo. Endogenous TFEB deficiency significantly impaired STB differentiation in trophoblast cells and placenta organoids. Mechanistically, TFEB conferred direct transcriptional regulation of the fusogen ERVFRD-1 in human trophoblasts and thereby profoundly promoted STB formation, independent of its canonical function as a master regulator of the autophagy-lysosomal pathway. In line with the in vitro findings, systemic or trophoblast-specific deletion of Tfeb compromised STB formation and placental vascular construction, leading to severe embryonic lethality. Moreover, TFEB directs the trophoblast syncytialization response driven by mTORC1 signaling. Importantly, TFEB expression positively correlates with the reinforced trophoblast syncytialization in human fetal growth restriction (FGR) placentas exhibiting suppressed mTORC1 activity. Our findings substantiate that the TFEB-fusogen axis ensures proper STB formation during placenta development and under nutrient stress, shedding light on TFEB as a mechanistic link between nutrient-sensing machinery and trophoblast differentiation.

overall_design: To investigate the function of TFEB in the regulation of trophoblast syncytialization in human and mice, we established Tfeb ko mice. We then performed gene expression profiling analysis using data obtained from RNA-seq of control or Tfeb KO mice from placenta in E9.5 and E11.5.

first: Wanshan

last: Zheng

first: Yue

last: Zhang


title: TFEB safeguards trophoblast syncytialization in humans and mice

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

sample_organism:
Homo sapiens
Mus musculus

platform_organism:
Homo sapiens
Mus musculus


title: TFEB safeguards trophoblast syncytialization in humans and mice (mouse RNA-Seq)


title: TFEB safeguards trophoblast syncytialization in humans and mice (human RNA-Seq)

overall_design: To investigate the function of TFEB in the regulation of trophoblast syncytialization in human and mice, we established BeWo cell lines in which TFEB has been knockout by CRISPR-Cas9 genome editing technology.We then performed gene expression profiling analysis using data obtained from RNA-seq of control or TFEB KO BeWo cell lines treated with DMSO or FSK at 12h or 24h.


title: Early-responsive molecular signatures associated with halophytic adaptation in Sesuvium portulacastrum (L.)

city: Bearsden

first: Pawel

last: Herzyk

address: Wolfson Wohl Cancer Research Centre, Garscube Estate

department: College of Medical, Veterinary and Life Sciences

country: United Kingdom

institute: University of Glasgow

summary: Sesuvium portulacastrum (L.) is a halophyte, adapted to grow naturally under high-saline environments. Under control conditions, an inverse correlation was seen between Na and K accumulation, suggesting its facultative nature and ability to use Na-K interchangeably. No significant growth reduction was seen in seedlings upto 250 mM NaCl, except for youngest leaf-curling. Significantly higher accumulation of proline (4.3/1.8-folds), glycine betaine (1.4/1.4-folds) and selected amino-acids (1.4-4.2/1.4-2.3-folds) were seen in root/shoot of seedlings within 8 h stress duration. Inspite of having higher Na-accumulation, significantly lower number of differentially expressed genes (DEGs) were identified at 24 h than 8 h stress duration, indicating transcriptional restoration. As initial hours after NaCl stress are dominated by osmotic-component, 8h-specific DEGs, which are mainly transporters and transcription factors, reflect plant’s response towards NaCl-induced osmotic challenge. Most of the growth-related pathways including photosynthesis and ribosome-associated biogenesis gets suppressed, to support the activation of stress defence. Overexpression of SpRAB18 (an ABA-responsive dehydrin), one of the top-ranked DEGs, was found to impart salt-tolerance in soybean, indicating gene-function level conservation between halophyte and glycophyte. An open-access transcriptome database “SesuviumKB” (https:/ /cb.imsc.res.in/sesuviumkb) was developed to enable wide-scale gene function studies in S. portulacastrum, that could pave the way to engineer salt-tolerance in crops.

overall_design:
To increase our understanding of the mechanism of salinity tolerance in halophytes we investigated responses to NaCl stress in a halophyte Sesuvium portulacastrum (L.) in root and shoot tissues.
We performed an experiment where NaCl stress was applied to 15 days old hydroponically grown seedlings for 8 hours and 24 hours and samples were collected prior to the stress at T0 and after the stress at T8 and T24 time points.
Transcript expression profiles were generated at each of the three time points T0, T8 and T24 for samples generated from shoot and root tissues, separately. Each of the conditions had three biological replicates.

first: Jayant

last: Kulkarni

first: Sripati

last: Sahoo

first: Vitthal

middle: T

last: Barvkar

first: Sanjukta

last: Kumar

first: Janani

last: Ravichandran

first: Areejit

last: Samal

first: Anna

last: Amtmann

first: Mahesh

last: Borde

first: Penna

last: Suprasanna

first: Ashish

middle: K

last: Srivastava


title: Mass spectrometry-based proteomic landscape of rice reveals a post-transcriptional regulatory role of N6-methyladenosine

city: Beijing

first: Zhe

last: Liang

address: No12 Zhongguancun South Street

department: Biotechnology Research Institute

institute: Chinese Academy of Agricultural Sciences

type: Methylation profiling by high throughput sequencing

summary: Rice is one of the most important staple food and model species in plant biology, yet its quantitative proteomes are largely uncharacterized. Here we quantify the relative protein levels of over 15,000 genes across major rice tissues using a tandem mass tag strategy followed by intensive fractionation and mass spectrometry. We identify tissue-specific and -enriched proteins that are linked to the functional specificity of individual tissues. Proteogenomic comparison of rice and Arabidopsis reveals conserved proteome expression, which differs from mammals in that there is a strong separation of species rather than tissues. Notably, profiling of N6-methyladenosine (m6A) across the rice major tissues shows that m6A at untranslated regions is negatively correlated with protein abundance and contributes to the discordance between RNA and protein levels. We also demonstrate that our data are valuable for identifying novel genes required for regulating m6A methylation. Taken together, this study provides a paradigm for further research into rice proteogenome.

overall_design:
m6A profile from 14 tissues of rice
m6A-seq2 of rice wild type and med18 plants. 3 biological replicates.


title: Perturbation of TET2 condensation induces genome-wide promiscuous DNA hypomethylation and curtails leukemia cell growth

city: Houston

first: Jia

last: Li

state: Texas

address: 2121 W HOLCOMBE BLVD

department: CEDP

institute: Guangzhou Medical University

summary: The Ten-Eleven Translocation (TET)-mediated DNA modification pathway is intimately involved in transcriptional regulation. As the major catalytic product of TET enzymes, 5-hydroxymethylcytosine (5hmC) is enriched at selected enhancers in a tissue specific manner, with the underlying mechanism yet to be clarified. Here, we report a low complexity insert (LCI) domain within the TET2 catalytic domain that facilitates TET2 condensation and enables its precise chromatin binding, which leads to DNA demethylation at specific genomic regions. Perturbation of TET2 condensation results in promiscuous DNA demethylation that accounts for large-scale topological changes in the genome, which alter the expression of genes that associated with patient survival and ultimately suppresses leukemia cell growth both in vitro and in vivo. Our study illuminates a previously neglected liquid-like condensation property of TET2 in gene regulation and explores the potential of targeting biomolecular condensation of epigenetic enzymes for effective cancer intervention.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for MOLM13 cells expressing human TET2 CD and TET2-CDΔLCI .DNA from mESC or MOLM13 cells expressing TET2-CD and TET2-CDΔLCI were extracted and subjected to WGBS. We generated mouse embryonic stem cells (mESCs) that stably expressed DamID only, TET2CD-Dam or TET2CDΔLCI-Dam. DNA from mESC or MOLM13 cells expressing TET2-CD and TET2-CDΔLCI were extracted and subjected to CMS-IP. Mouse stem cells (mESCs) 5hmC mapping (CMSIP).

first: Lei

last: Guo

first: Xue

last: Hu

first: Yi-Tsang

last: Lee

first: Guokai

last: Pan

first: Yubin

last: Zhou

first: Peter

last: Davis

first: Margaret

last: Goodell

first: Yun

last: Huang


title: miRNA signatures derived from plasma small extracellular vesicle as predictors for organo-tropic metastasis of gastric cancer

first: Lin

last: Shen

state: Beijing

address: Peking University Cancer Hospital & Institute, 52 Fucheng Rd, Haidian District

summary: Metastasis is a major problem of gastric cancer. In this study, small extracellular vesicle (sEV)-derived miRNAs were sequenced to screen biomarkers for GC’s organo-tropic metastasis. Plasma from 40 treatment-naïve gastric cancer patients including 10 no metastasis (M0) and 30 distant metastasis (M1) were assessed by sEV-miRNA-sequencing. sEV miRNAs with diverse expression profiles across different metastatic patterns were combined into sigantures to characterize and predict gastric cancer metastasis.

overall_design: Small extracellular miRNAs from 40 gastric cancer plasma samples were sequenced with Illumina NovaSeq platform.

first: Cheng

last: Zhang


title: Effects of hair keratin on cell cycle regulation of human periodontal ligament cells in histidine-tryptophan-ketoglutarate-based storage media

status: Public on Jun 15 2024

city: Seoul

first: Yong Kwon

last: Chae

address: Kyungheedaero 26

country: South Korea

institute: Kyung Hee University Dental Hospital

summary: In this study, the effect of a storage medium (hK-HTCM) in which hair keratin was dissolved in a 1:1 mixed solution of Histidine-Tryptophan-Ketoglutarate and Culture media solution (HTCM) was evaluated on the viability and proliferation of human periodontal ligament cells. There was no difference in cytotoxicity between 0.1% and 0.25% hK-HTCM against 0% hK-HTCM and human periodontal ligament cells. Human periodontal ligament cells were cultured in 0.1% and 0.25% hK-HTCM for 48 hours, and after removing hair keratin from the culture medium, the cells resumed proliferation. When exposed to 0.25% hK-HTCM, human periodontal ligament cells showed differential expression of genes related to cell cycle and cell division regulation. On the other hand, differential expression of genes related to phosphorylation and ubiquitination related to cell cycle resumption was observed in human periodontal ligament cells after removal of 0.25% hK-HTCM. 0.25% hK-HTCM showed the ability to regulate the cell cycle of human periodontal ligament cells without showing cytotoxicity, and its potential to be used as a long-term storage medium for avulsed teeth was confirmed.

overall_design: Quantseq 3' mRNA sequencing was performed on cells before exposure to optimal hK-HTCM, 48 hours after exposure, and 48 hours after washing and medium exchange to identify differentially expressed genes and use bioinformatics methods to identify differentially expressed genes. were analyzed to interpret the biological changes that occurred.

first: Yong

first: Mi

middle: S

last: Kim

first: Ok

middle: H

last: Nam

first: Hyo-Seol

first: Yu-Shik

last: Hwang

first: Sung

last: Choi


title: Systems genetics uncover new loci containing functional gene candidates in Mycobacterium tuberculosis-infected Diversity Outbred mice

city: Boston

first: Boston University

last: Microarray and Sequencing Resource

state: MA

address: 72 East Concord Street, E631

department: Microarray and Sequencing Resource

institute: Boston University

summary: Mycobacterium tuberculosis infects two billion people across the globe, and results in 8-9 million new tuberculosis (TB) cases and 1-1.5 million deaths each year. Most patients have no known genetic basis that predisposes them to disease. Here, we investigate the complex genetic basis of pulmonary TB by modelling human genetic diversity with the Diversity Outbred mouse population. When infected with M. tuberculosis, one-third develop early onset, rapidly progressive, necrotizing granulomas and succumb within 60 days. The remaining develop non-necrotizing granulomas and survive longer than 60 days. Genetic mapping using immune and inflammatory mediators; and clinical, microbiological, and granuloma correlates of disease identified five new loci on mouse chromosomes 1, 2, 4, 16; and three known loci on chromosomes 3 and 17. Further, multiple positively correlated traits shared loci on chromosomes 1, 16, and 17 and had similar patterns of allele effects, suggesting these loci contain critical genetic regulators of inflammatory responses to M. tuberculosis. To narrow the list of candidate genes, we used a machine learning strategy that integrated gene expression signatures from lungs of M. tuberculosis-infected Diversity Outbred mice with gene interaction networks to generate scores representing functional relationships. The scores were used to rank candidates for each mapped trait, resulting in 11 candidate genes: Ncf2, Fam20b, S100a8, S100a9, Itgb5, Fstl1, Zbtb20, Ddr1, Ier3, Vegfa, and Zfp318. Although all candidates have roles in infection, inflammation, cell migration, extracellular matrix remodeling, or intracellular signaling, and all contain single nucleotide polymorphisms (SNPs), SNPs in only four genes (S100a8, Itgb5, Fstl1, Zfp318) are predicted to have deleterious effects on protein functions. We performed methodological and candidate validations to (i) assess biological relevance of predicted allele effects by showing that Diversity Outbred mice carrying PWH/PhJ alleles at the H-2 locus on chromosome 17 QTL have shorter survival; (ii) confirm accuracy of predicted allele effects by quantifying S100A8 protein in inbred founder strains; and (iii) infection of C57BL/6 mice deficient for the S100a8 gene. Overall, this body of work demonstrates that systems genetics using Diversity Outbred mice can identify new (and known) QTLs and functionally relevant gene candidates that may be major regulators of complex host-pathogens interactions contributing to granuloma necrosis and acute inflammation in pulmonary TB.

overall_design:
Animals were infected with aerosolized M. tuberculosis (an average of 16 bacilli) and maintained until sacrifice due to morbidity or until the end of the experiment (day ~160) and one lung lobe was homogenized and used for gene expression profiling by microarray.
Please note that the records represent the re-analyzed GSE266564 samples using a different Platform annotation (GPL34456).

first: Daniel

last: Gatti

first: Gillian

last: Beamer


title: Perivascular and peribronchiolar granuloma-associated lymphoid tissue and B-cell gene expression pathways identify asymptomatic Mycobacterium tuberculosis lung infection in Diversity Outbred mice


title: Perivascular and peribronchiolar granuloma-associated lymphoid tissue and B-cell gene expression pathways identify asymptomatic Mycobacterium tuberculosis lung infection in Diversity Outbred mice (dataset 1)

summary: Humans are highly genetically diverse, and most are resistant to Mycobacterium tuberculosis. However, lung tissue from genetically resistant humans is not readily available to identify potential mechanisms of resistance. To address this, we model M. tuberculosis infection in Diversity Outbred mice. Like humans, Diversity Outbred mice also exhibit genetically determined susceptibility to M. tuberculosis infection: Progressors who succumb within 60 days of a low dose aerosol infection due to acute necrotizing granulomas, and Controllers who maintain asymptomatic infection for at least 60 days, and then develop chronic pulmonary TB with occasional necrosis and cavitation, over months to greater than 1 year. Here, we identified specific regions of granuloma-associated lymphoid tissue (GrALT) and B-cell gene expression pathways as key features of asymptomatic lung infection using cytokine, antibody, granuloma image, and gene expression datasets. Cytokines and anti-M. tuberculosis cell wall antibodies discriminated acute vs chronic pulmonary TB but not asymptomatic lung infection. To find unique features of asymptomatic lung infection, we trained a weakly supervised, deep-learning neural network on lung histology images. The neural network accurately produced an interpretable imaging biomarker: perivascular and bronchiolar lymphocytic cuffs, a type of GrALT. We expected CD4 T cell genes would be highly expressed in asymptomatic lung infection. However, the significantly different, highly expressed genes in lungs of asymptomatically infected Diversity Outbred mice corresponded to B-cell activation, proliferation, and antigen-receptor signaling, including Fcrl1, Cd79, Pax5, Cr2, and Ms4a1. Overall, our results suggest that genetically controlled B-cell responses are important for establishing asymptomatic M. tuberculosis lung infection.

overall_design: Animals were infected with aerosolized M. tuberculosis (an average of 16 bacilli) and maintained until sacrifice due to morbidity or until the end of the experiment (day ~160) and one lung lobe was homogenized and used for gene expression profiling by microarray.

first: Deniz

last: Koyuncu


title: Two transcriptionally and functionally distinct waves of pro-inflammatory versus pro-repair neutrophils during acute liver injury

city: Montreal

first: Naglaa

last: Shoukry

state: QC

address: Tour Viger, Local 09.414, 900 rue St-Denis

country: Canada

institute: CRCHUM

summary: We used the CCl 4 -induced ALI model and employed flow cytometry, microscopy imaging and qRT-PCR to examine intrahepatic neutrophil subpopulations during the necroinflammatory and early and late repair phases of the wound healing response. We also analyzed intrahepatic neutrophils for their transcriptional profiles using RNA-seq. Finally, we evaluated their protein translation, mitochondrial function and cell metabolism using the Seahorse Mito Stress Test. We detected two temporarily distinct waves of neutrophils during (i) necroinflammation (at 24 hrs post-injury) and (ii) late repair (at 72 hrs). Early neutrophils were characterized by: (i) up-regulation of inflammatory cytokines (e.g., IL-12a), (ii) activation of the non-canonical NF-κB pathway, (iii) reduction of protein translation and (iv) decreased oxidative phosphorylation. In contrast, late neutrophils exhibited an enrichment of several genes and pathways associated with tissue repair and angiogenesis. In addition, early neutrophils, identified as pro-inflammatory, show strong expression for CXCR5, while second wave neutrophils, identified as angiogenic highly expressed CXCR4. Finally, our data demonstrated that neutrophils expressing CXCR5 express a short isoform of this protein, truncated by 55 aa at the N-terminal end.

overall_design: Gene expression analyses of different liver neutrophil populations at time points (24h- and 72h post CCl 4) compared with splenic neutrophils (control)

first: Yousef

last: Maali

first: Manuel

middle: F

last: Molina

first: Omar

last: Khedr

first: Mohamed

last: Abdelnabi

first: Jessica

last: Dion

first: Ghada

last: Hassan


title: Perivascular and peribronchiolar granuloma-associated lymphoid tissue and B-cell gene expression pathways identify asymptomatic Mycobacterium tuberculosis lung infection in Diversity Outbred mice (dataset 2)

overall_design: Animals were infected with aerosolized M. tuberculosis (an average of 28 bacilli) and maintained until sacrifice due to morbidity or until the end of the experiment (day 56) and one lung lobe was homogenized and used for gene expression profiling by microarray.


title: miRNA expression profiles of exosomes from polarized bone marrow derived macrophages

city: Taipa, Macau

first: Ruohan

last: Lou

address: Avenida da Universidade

country: Macau

institute: University of Macau

summary: Unprogrammed macrophage polarization, is associated with diabetic wound ulcers. Nevertheless, development of corresponding drugs is still a challenge. Here, exosomes are isolated from naive bone marrow-derived macrophages (BMDMs) (M0-Exos), inflammatory BMDMs (M1-Exos), and anti-inflammatory BMDMs (M2-Exos), with the aim of pinpointing the exosomes functionality and identify global miRNAs expression profiles.

overall_design: Expression profile analysis of exosomal microRNA data from M1(pro-inflammatory macrophages), M2 (anti-inflammatory macrophages) and M0 (unpolarized macrophages).

first: Ligen

last: Lin


title: Bioengineered human colon organoids with in vivo-like complexity and function

first: Nicolas

last: Broguiere

address: AI 1208 Station 15

department: Sciences de la vie

institute: EPFL

summary: Human intestinal organoids offer remarkable prospects for modeling intestinal homeostasis and disease. Although it is now possible to recreate many physiological features of the human gut in vitro, current approaches to generate organoids produce closed cystic structures with limited cell-type variability, hampering their relevance and applicability. Here we integrated organoid and organ-on-a-chip technology to develop a primary human stem–cell-derived organoid model, called human ‘mini-colons’ which show remarkable cell-type diversity, tissue architecture and function.

overall_design: Human mini-colons were maintained in culture for 14 and 21 days, and control organoids cultured in matrigel or matrigel + 20% collagen, were dissociated to single cells and analyzed by scRNAseq in three biological rep (multiplexed with hashtags) and two technical replicates (different lanes of 10XG chip).

first: Olga

last: Mitrofanova

first: Mikhail

last: Nikolaev

first: Matthias

last: Lutolf


title: Comparative gene expression profiling analysis of RNA-seq data from spleens of NOD and NOD.Lc7 mice

city: Montréal

first: Capucine

last: Bourel

address: 2900 Bd Edouard-Montpetit

institute: Université de Montréal

summary: RNA sequencing to compare gene expression between NOD.g7 and NOD.L7 mice  in order to identify a gene that may influence pre-mNK cell number

overall_design: RNA-seq on spleen cells from NOD.g7 and NOD.L7

first: Fanny

last: Guimont-Desrochers

first: Sylvie

last: Lesage


title: Alkynyl nicotinamides show antileukemic activity in drug-resistant acute myeloid leukemia

city: Indianapolis

first: Baskar

last: Ramdas

state: Indiana

address: 1044 West Walnut Street

department: Wells Center for Pediatric Research

institute: Indiana University

summary: We identified novel nicotinamide-based FLT3 inhibitors ( HSN748) that specifically target FLT3-ITD at sub-nanomolar concentrations and are effective against drug-resistant secondary mutations. In the current study, we evaluated these compounds’ antileukemic activity against FLT3-ITD and gatekeeper mutations in drug-resistant AML, relapsed/refractory AMLs with FLT3 mutations

overall_design:
We  performed gene expression profiling analysis using data obtained from RNA-seq data from  MOLM14 cells
Comparative gene expression profiling analysis of RNA-seq data for MOLM14 cells treated with DMSO and HSN748

first: Reuben

last: Kapur

first: Sheng

last: Liu

first: Jun

last: Wan


title: Harmful algal bloom toxin microcystin-LR interferes with PP1-mediated PI3K/AKT/FOXO1 signaling in granulosa cells to disrupt ovarian follicle maturation and ovulation

city: Piscataway

first: Yingzheng

last: Wang

state: New Jersey

address: 170 Frelinghuysen Rd, Rm 406

department: Pharmacology and Toxicology

institute: Rutgers University

summary: Harmful algal blooms (HABs) arise from the rapid growth of algae in both marine and freshwater ecosystems due to the continuous global temperature rise and anthropogenic eutrophication. Humans are at a great risk of exposure to toxins released from HABs through drinking water, food, and recreational activities, making HAB toxins contaminants of emerging concern (CECs). The impact of HAB toxins on women’s reproductive health, however, remains poorly understood. Here, we investigated the effects of microcystin-LR (MC-LR), the most common HAB toxin, on the ovary, the female gonad, and associated ovarian functions. The results of a chronic daily oral mouse exposure model and an acute exposure using the mouse superovulation model revealed that MC-LR accumulated in the ovary and environmentally-relevant exposure to MC-LR perturbed follicle-stimulating hormone (FSH)-dependent follicle maturation to disrupt ovulation and luteinization. Using an ex vivo mouse follicle maturation and ovulation assay and in vitro culture of human primary granulosa cells, mechanistic studies such as the single-follicle RNA sequencing analysis and others elucidated that MC-LR inhibited protein phosphatase 1 (PP1) and interfered with PP1-mediated PI3K/AKT/FOXO1 signaling in granulosa cells, which suppressed follicle maturation, ovulation, luteinization, and progesterone secretion. Together, our study demonstrates that environmentally-relevant exposure to MC-LR acts a PP1 inhibitor to interfere with the PI3K/AKT/FOXO1 signaling in granulosa cells, which disrupts follicle maturation and results in adverse female reproductive outcomes. As a newly identified ovarian endocrine disrupting chemical (EDC), exposure to MC-LR poses a serious threat to women’s reproductive health and fertility.

overall_design: Ovaries were removed from 16-day-old CD-1 female mice and multilayered secondary follicles were enzymatically isolated using enzymatic solution. Next, morphologically normal follicles with diameters of 130 to 160 µm were selected, encapsulated with alginate hydrogel for eIVFG. To investigate the effects of MC-LR on the whole follicular transcriptome, antral follicles treated vehicle or 10 µM MC-LR were collected from day 6 of eIVFG for single-follicle RNA sequencing.

first: Shuo

last: Xiao


title: The role of RPA1 in T cells [thymus]

first: Jia

last: Song

state: China

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

institute: Peking University

summary: As a single strand DNA binding protein, RPA1 participates in various cellular processes including DNA replication and DNA repair. However, the role of RPA1 in T cells is largely unknown. We generated a mouse model in which RPA1 was specifically deleted in T cells. Through single cell RNA sequencing, we reveal the immune landscape in RPA1 conditional knockout mice.

overall_design: Study of immune cells in thymus from WT or RPA1 conditional knockout mice using 10x scRNA-seq technologies.

first: Dan

last: Lu

first: Xin

last: Zhang


title: The role of RPA1 in T cell

summary: As a single strand DNA binding protein, RPA1 participates various cellular processes including DNA replication and DNA repair.However, the role of RPA1 in T cell is largely unknown. We generate a mice model in which RPA1 was specifically deleted in T cell. Through single cell RNA sequencing, we reveal the immune landscape in RPA1 conditional knockout mice.

overall_design: Study of immune cells in lymph nodes from WT or RPA1 conditional knockout mice using 10x scRNA-seq technologies.


title: The AKT2/SIRT5/TFEB pathway as a potential therapeutic target in non-neovascular AMD

status: Public on Jun 14 2024

city: Pittsburgh

first: Dhivyaa

last: Rajasundaram

address: 4401 Penn Avenue

department: Pediatrics

institute: University of Pittsburgh

summary: Non-neovascular or dry age-related macular degeneration (AMD) is a multi-factorial disease with degeneration of the aging retinal-pigmented epithelium (RPE) as a central pathogenic driver. Lysosomes play a crucial role in RPE health due to their involvement in phagocytosis and autophagy, which are regulated by transcription factor EB/E3 (TFEB/E3). Disruption in these processes can accelerate aging disorders, like AMD. Here we tried to ascertain if upregulation of AKT2 in the RPE cells triggers abnormalities lysosomal/autophagy processes and mitochondrial function culminating into an early AMD-like phenotype using mouse and in vitro "disease in a dish" models as tools.

overall_design: Understanding changes in autophagy genes in RPE cells from WT and Akt2 KI mice

first: Debasish

last: Sinha

first: Sayan

last: Ghosh


title: The role of RPA1 in T cells [spleen]

overall_design: Study of immune cells in spleen from WT or RPA1 conditional knockout mice using 10x scRNA-seq technologies.


title: Adiponectin regulated by IAA in Paneth cells controls renewal and differentiation of gut stem cells to maintain homeostasis of epithelial cells

city: Tianjin

first: Yun Huan

last: Gao

address: 94 Weijin Road, Nankai District, Tianjin

institute: Nankai University

summary: We here demonstrate that adiponectin in Paneth cells can suppress renewal and differentiation of gut stem cells through adiponectin receptor 1 (AdipR1). Crypt cells (mainly stem and transit amplifying (TA) cells) in Adipfl/flpVilli-CreT (gut epithelial cell adiponectin conditioned knockout) mice exhibited stronger ability of renewal and differentiation. ScRNA-seq found that there had much more enrichment intestinal stem and TA cells in Adipfl/flpVilli-CreT mice. The renewal and development of gut epithelial cells in irradiated or DSS (dextran sulfate sodium) treated Adipfl/flpVilli-CreT mice was faster than control Adipfl/flp mice. In vitro culture gut organoid of Adipfl/flpVilli-CreT mice exhibited faster growth than those from Adipfl/flp mice. The gut epithelial cells in AdipR1 knockout (KO) mice had much longer crypts than control mice. Interestingly, indole-3-acetic acid (IAA) from gut microbiota could control the expression of adiponectin to promote the renewal and proliferation of gut stem cells. In vitro culture organoid also showed faster development after exposing to IAA. Thus, adiponectin, which is regulated by gut microbiota derived IAA controls the renewal and differentiation of gut stem cells to maintain the homeostasis of epithelial cells.

overall_design: To further illustrate the function of adiponectin from gut Paneth cells, we again generated in vitro gut organoids from the intestines of Adipfl/flpVilli-CreT mice (Adip KO) and from control Adipfl/fl mice(WT).

first: Xiaomin

last: Su

first: Juanjuan

first: Rongcun

last: Yang


title: Regulation of intracellular pH by SLC4A7 tunes mTORC1 function to promote plasma cell differentiation

city: New York

first: Anthony

last: Tao

state: NY

address: 550 1st Ave Smilow 506

department: Pathology

institute: New York University Grossman School of Medicine

summary: B cells differentiate into antibody-producing plasma cells, which are critical for humoral immunity, autoimmunity, and vaccine responses. Despite the importance of environmental stressors on regulating humoral immune responses, the influence of pH on PC differentiation has not been described. Here, we identified SLC4A7, a sodium/bicarbonate cotransporter, as a selective regulator of PC differentiation. SLC4A7 deletion impaired the formation of PCs and humoral immunity to influenza A virus infection in mice. Mechanistically, we find that SLC4A7 prevents acidification of intracellular pH and thus maintains lysosomal function and mTORC1 activity. Loss of SLC4A7 suppresses PC differentiation under conditions of extracellular acidosis in vitro and in a mouse model of metabolic acidosis. Here we reveal a novel relationship between the regulation of intracellular pH by SLC4A7  and mTORC1-dependent PC differentiation and humoral immunity.

overall_design: To investigate the pathways dysregulated downstream of SLC4A7 deletion, we sorted in vitro-differentiated CD138+ plasma cells (PCs) and CD138- non-PCs from Slc4a7-KO and WT murine B cells. B cells were stimualted with NIH3T3 feeder cells expressing CD40L and BAFF, in the presence of IL-4.

first: Ke

last: Hu

first: Stefan

last: Feske


title: single-cell RNA-seq experiment to study mouse stomach metaplastic organoids

city: Nashville

first: Ken

last: Lau

state: TN

address: 2215 Garland Ave. MRBIV10475

department: Cell and Developmental Biology

institute: Vanderbilt University

summary: Created scRNA seq datasets for mouse stomach metaplastic organoids

overall_design: Compared metaplastic organoids with dysplastic organoids

first: Alan

middle: J

last: Simmons

first: Eunyoung

last: Choi


title: U937 cells: Control treated LPS vs. Co-cultured Panc-1 cells

city: Tainan

first: Chang-Jung

last: Chen

address: Sheng-Li Road

country: Taiwan

institute: National Cheng Kung University Medical College

summary: We collected U937 cells after 72 h of LPS treatment or 72 h of co-culture with PANC-1 cells for microarray analysis. The gene microarray data were analyzed using the Agilent Human whole genome oligo 4*44k chip (array kit serial number: US00082833) and Agilent’s gene expression microarray software, including Feature Extraction and GeneSpring GX. Feature Extraction software extracts data from microarray images and provides workflows for analysis. GeneSpring GX offers statistical tools for data analysis and visualization (Welgene Biotech), and the genes of interest were drawn as a heatmap.

overall_design: Two-condition experiment, U937 treated LPS vs. U937 cocultured Panc-1 cells. Biological replicates: 1 control replicates, 1 coculture replicates.


title: The effects of stepped structures of  hydroxyapatite surface on the mRNA expression profile of immature dendritic cells

city: Guiyang

first: Ｗang

last: Yun

state: Guizhou province

address: School of Basic Medicine

institute: Guizhou Medical University

summary: Hydroxyapatite (HA) has significant clinical promise for the repair of bone defects and the modification of implant material interfaces. However, after implantation, there are potential risks of chronic inflammation. Dendritic cells (DCs) are key cells in regulating chronic inflammatory responses, and their phenotype and functions are influenced by the surface structure of materials. Therefore, in order to provide some theoretical guidance for the optimal design of HA surface structures, this study tried to construct stepped structures on HA surfaces and investigate the effects of stepped structures on the cytoskeletal, cellular morphology, and mRNA expression profile of immature dendritic cells (imDCs). HA dishes with stepped structures were prepared utilizing the principle of oriented attachment growth, and subsequently used to construct in vitro cell culture models. The imDCs were observed by immunofluorescence staining to characterize their cytoskeleton structures and cellular morphology. Besides, transcriptome sequencing was used to examine the changes in the mRNA expression profile of imDCs. The results indicated that the stepped structures exposed on HA surfaces would increase the spread area of imDCs and affect the cell adhesion morphology. In addition, the results of the transcriptome sequencing revealed significant alterations in the mRNA expression profile, with differentially expressed genes (DEGs) predominantly enriched in the pathways associated with the focal adhesion signal pathway, the chemokine signal pathway, and the IL-17 signal pathway. Thus, the stepped structures could modulatethe cellular morphology and the immunological functions of imDCs by modulating the aforementioned signal pathways, including the focal adhesion pathway, the chemokine signaling pathway, and the IL-17 signaling pathway, thereby affecting the immune response process.

overall_design: ImDCs cultured on tissue culture plates（Control）and the surfaces of HA dishes (Nano and Meso) for 24 h were used as sequencing samples. The HA dishs with stepped structures were labled as "Meso," while the HA dishs  without  stepped structure were labled as Nano. The sequencing samples were sent to the BGI sequencing company for transcriptome sequencing. Total RNA of imDCs cutured on  tissue culture plates and the different HA dishes was extracted and transcriptome sequencing was performed. Go and KEGG enrichment analysis of differential expressed genes (DEGs) was performed. Transcripts related to Cellular immunological function were screened according to the changes of differential gene expression ≥1 and FDR≤0.05. In addition, signaling pathways linked to the immune response were  explored.

first: Fang

last: Wang

first: Jin

first: Zhu

last: Zeng


title: A system for functional studies of the major virulence factor of malaria parasites

city: Hamburg

first: Johannes

last: Allweier

address: Bernhard-Nocht-Straße 74

institute: Bernhard Nocht Institute for Tropical Medicine

summary: The major virulence factor of Plasmodium falciparum parasites, PfEMP1 is expressed by a multigene family, termed var genes. Here selection linked integration (SLI) was utilized to modify var genes in P. falciparum parasites to select for parasite populations expressing a single var gene. Bulk RNA was isolated from ring stage parasites of these SLI parasite populations and analyzed with next generation sequencing. The proportion of exon 2 transcripts of var genes normalized to transcripts per million was determined per cell line to confirm the predominant expression of the desired var gene.

overall_design: RNA-seq samples of Plasmodium falciparum infected human erythorcyes

first: Jakob

last: Cronshagen

first: Paolo

last: Mesén-Ramírez

first: Jan

last: Stäcker

first: Anna

last: Viktoria Vaaben

first: Gala

last: Ramón-Zamorano

first: Isabel

last: Naranjo

first: Susann

last: Ofori

first: Pascal

last: Jansen

first: Joëlle

last: Hornebeck

first: Florian

last: Kieferle

first: Elicia

last: Martin

first: Agnes

last: Murk

first: Carolina

last: Castro-Peña

first: Richárd

last: Bártfai

first: Thomas

last: Lavstsen

first: Iris

last: Bruchhaus

first: Tobias

last: Spielmann


title: Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity [scRNA-Seq]

city: Seattle

first: Christopher

last: Yin

state: WA

address: 3946 W Stevens Wy NE

department: Electrical & Computer Engineering

institute: University of Washington

summary: An important and largely unsolved problem in synthetic biology is how to target gene expression to specific cell types. Here, we apply iterative deep learning to design synthetic enhancers with strong differential activity between two human cell lines. We initially train models on published datasets of enhancer activity and chromatin accessibility and use them to guide the design of synthetic enhancers that maximize predicted specificity. We experimentally validate these sequences, use the measurements to re-optimize the predictor, and design a second generation of enhancers with improved specificity. Our design methods embed relevant transcription factor binding site (TFBS) motifs with higher frequencies than comparable endogenous enhancers while using a more selective motif vocabulary, and we show that enhancer activity is correlated with transcription factor expression at the single cell level. Finally, we characterize causal features of top enhancers via perturbation experiments and show enhancers as short as 50bp can maintain specificity.

overall_design: We transfected a library of synthetic enhancers (R1-MPRA) into two different human cell lines, HepG2 and K562. We quantified enhancer strength at the single cell level and correlate enhancer activity with transcriptome analysis.

first: Yin

last: Christopher

first: Castillo-Hair

last: Sebastian

first: Byeon

last: Gun Woo

first: Bromley

last: Peter

first: Meuleman

last: Wouter

first: Seelig

last: Georg


title: Iterative deep learning-design of human enhancers exploits condensed sequence grammar to achieve cell type-specificity [RNA-Seq]

sample_organism:
Homo sapiens
synthetic construct

platform_organism:
Homo sapiens
synthetic construct

overall_design: We designed 3 plasmid libraries (R1-MPRA, R1-DHS, R2) of synthetic candidate enhancer sequences placed upstream of a minimal promoter (minP) and unique barcode sequence, and transfected them into two different human cell lines, HepG2 and K562. We quantified enhancer strength by sequencing the mRNA of transfected cells as well as the DNA of the plasmid libraries, and calculated a ratio of RNA barcode counts to DNA barcode counts. Two biological replicates of each cell line measurement were obtained.


title: Diacylglycerol Kinase Delta Improves Glucose Clearance and Protects Against the Development of Obesity

city: Stockholm

last: Nylén

address: Karolinska University Hospital

country: Sweden

institute: Karolinska Institutet

summary: Background and aim: Diacylglycerol kinase (DGK) isoforms catalyze an enzymatic reaction that removes diacylglycerol (DAG) and thereby terminates protein kinase C (PKC) signaling by converting DAG to phosphatidic acid (PA). We have reported that downregulation of DGKδ (type II isozyme) causes peripheral insulin resistance, metabolic inflexibility, and obesity. Our aim was to determine whether overexpression of DGKδ protects against the development of metabolic impairments and obesity.  Methods: We generated a transgenic mouse model overexpressing the human DGKδ2 isoform under the myosin light change promoter (DGKδ TG). We performed deep metabolic phenotyping of DGKδ TG and wild-type mice fed chow or high-fat diet. Mice were also given free access to running wheels to examine the effects of DGKδ overexpression on exercise-induced metabolic outcomes.   Results: DGKδ TG mice were leaner than wild-type littermates, with improved glucose tolerance, increased glycogen storage in skeletal muscle, and enhanced glucose uptake in white adipose tissue. Moreover, DGKδ TG mice were protected against high fat diet (HFD)-induced glucose intolerance and obesity. DGKδ TG mice had reduced epididymal fat pad weight, and enhanced lipolysis. Strikingly, DGKδ overexpression recapitulates the beneficial effects exercise on metabolic outcomes. DGKδ overexpression and exercise have a synergistic effect on body weight reduction. Microarray analysis of skeletal muscle confirmed an overlap between genes associated with exercise and DGKδ overexpression. Gene ontology signatures of exercise and DGKδ overexpression were related to lipid storage, extracellular matrix, and glycogen biosynthesis pathways.  Conclusion: We identify a role for DGKδ in glucose and energy homeostasis. Overexpression of DGKδ induces adaptive changes in both skeletal muscle and adipose tissue, resulting in protection against high fat diet-induced obesity. DGKδ overexpression recapitulates exercise-induced adaptations on energy homeostasis and skeletal muscle gene expression profiles.

overall_design: wild-type sedentary (WT; n=5), MLC_DGKδ2 transgenic sedentary mice (TG; n=6), wild-type exercised (WT exercised; n=5) and MLC_DGKδ2 transgenic exercised mice (TG exercised; n=5)

first: Lake

middle: Q

last: Jiang

first: Mladen

last: Savikj

first: Nicolas

last: Pillon

first: Juleen

middle: R

last: Zierath


title: Effect of overexpression of miR-423-5p on gene expression of endothelial cells.

city: Shanghai

first: feng

last: Long

state: --- Select One

address: Department of Orthopedics, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, China

institute: fudan university

summary: To investigate machanism of miR-423-5p regulating the angiogenic ability of bEnd.3 cells, we transfected miR-423-5p mimic to overexpress miR-423-5p in bEnd.3 cells. Then we performed high throughput sequencing of miR-423-5p mimic-transfected and control bEnd.3 cells to evaluate different gene expressions between miR-210-3p-overexpressing and control.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for control and miR-423-5p overexpressed bEnd.3 cells.

first: Feng

first: Hailong

last: Li

first: Xujun

last: Chen

first: Yiqun

last: He

first: Youhai

last: Dong


title: PRKDC Induces Chemoresistance in Osteosarcoma by Recruiting GDE2 to Stabilize GNAS and Activate AKT

city: changsha

first: ruijiang

last: Zeng

address: No.139 Renmin Road Central

institute: The Second Xiangya Hospital of Central South University

summary: Chemoresistance is one of the major causes of poor prognosis in osteosarcoma. Thus far, the therapeutic alternative for osteosarcoma is quite limited, thereby increasing sensitivity of the currently used drugs is an effective way to improve outcome of patients. In this study, through a Kinome-wide CRISPR screen, we identified PRKDC as a critical determinant of Doxorubicin (DOX) sensitivity in osteosarcoma. Clinical sample analysis and functional experiments demonstrated that PRKDC is hyperactivated in osteosarcoma and that knockdown of PRKDC significantly increased sensitivity of osteosarcoma to DOX. Mechanistically, PRKDC could recruit and bind with GDE2 to augment the stability of GNAS. The increased GNAS protein subsequently activate Akt S473 and T308 phosphorylation and mediated DOX sensitivity. We also showed that the PRKDC inhibitor AZD7648 and DOX could synergize with each other and intensely suppressed the growth of osteosarcoma in mice xenograft models and human organoids. In conclusion, these results revealed a novel PRKDC-GDE2-GNAS-Akt regulatory axis in DOX sensitivity and provided targetable candidates for improving therapeutic efficacy of DOX in osteosarcoma.

overall_design: Comparative gene expression profiling analysis of RNA-seq data for the HOS cells. siPRKDC vs. siNC, AZD7648 vs. DMSO

first: WenChao

last: Zhang

first: Huaiyuan

last: Liang

first: Ruijiang

last: zeng


title: Blood miRNA as biomarkers of epilepsy (CTRL vs. SE)

city: Warsaw

first: Kinga

last: Szydlowska

state: Select State

address: Pasteura 3

country: Poland

institute: Nencki Institute of Experimental Biolo

summary:
Epilepsy frequently develops as a result of brain insult, for example brain injury or stroke. Currently there are no tools allowing us to predict which trauma patients will eventually develop epilepsy. There is evidence that microRNAs levels are altered in the blood, making them attractive candidates for peripheral biomarkers of epilepsy.
We analyzed miRNA levels in blood samples using Affymetrix microarrays 4.1 and performed comparative analysis of samples. We performed 3 comparisons: i) control animals vs. Status epilepticus animals, ii) animals which developed first spontaneous seizure around 7 days post stimulation (EARLY), or later after 21days post stimulation (LATE), iii) animals that had high or low number of seizures as determined by seizures number (EARLY vs. LATE).

overall_design: We draw the blood from rats after electrical stimulation of amygdala, which induces status epilepticus, at 3 timepoints: 2 days, 9 days and 8 months. Laterr RNA was isolated from all the samples at the same time and microarray 4.1 were used in agreement with the producer's protocol, to test levels of each miRNA.

first: Katarzyna

last: Lukasiuk


title: Blood miRNA as biomarkers of epilepsy (HIGH vs. LOW)


title: Blood miRNA as biomarkers of epilepsy

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

overall_design: Refer to individual Series


title: effect of slc11a2 deletion on placental gene expression

city: BOSTON

first: CHANG

last: CAO

address: 185 CAMBRIDGE ST.

department: CENTER FOR GENOMIC MEDICINE

institute: Mass General Brigham

summary:
To investigate the function of slc11a2, we deleted slc11a2 gene in mouse placenta using cre.
We performed RNA-sequencing on 14 knockout and 6 control placentas.

overall_design: Compare gene expression in slc11a2 knockout (KO) and the control (C) placentas.

first: Chang

last: Cao

first: Mark

middle: D

last: Fleming


title: RNA-seq of Peripheral Blood Cells Identifies Molecular Network Linked to Lymphocyte Subset Aberrations and Active Lupus Nephritis in SLE

city: Taipei

first: Jyh-Hong

last: Lee

address: 8 Chung-Shan South Road

institute: National Taiwan University Hospital

summary:
We aimed to investigate whether  differentially expressed genes  are related to lupus nephritis (LN)
We then performed gene expression profiling analysis using data obtained from RNA-seq of peripheral blood cell from LN patients

overall_design: Comparative gene expression profiling analysis of mRNA RNA-seq data between active LN and inactive LN


title: PLETHORA transcription factors promote early embryo development through induction of meristematic potential

city: Wageningen

first: Merijn

last: Kerstens

address: Droevendaalsesteeg 1

department: Plant Developmental Biology

country: Netherlands

institute: Wageningen University & Research

summary: Given that PLTs are key transcription factors in meristems, we hypothesized that loss of activity fails to confer meristematic properties or 'stemness' to the first embryonic cells, leading to developmental arrest. We asked to what degree downstream PLT targets in meristems overlap with those in early embryos. We selected direct PLT target genes by overlaying existing PLT ChIP-seq and DAP-seq datasets. We extended this set with an additional PLT3-DAP experiment on young roots, because previous PLT-DAP data have only low read counts and used leaf material in which PLTs are typically not strongly expressed.

overall_design: DAP-seq was performed on gDNA extracted from 5 dpg Col-0 roots. Two DAP experiments were performed on the same gDNA sample: a 3xFLAG-PLT3 DAP and a 3xFLAG-EGFP DAP (negative control).

first: Carla

last: Galinha

first: Hugo

last: Hofhuis

first: Michael

last: Nodine

first: Renan

last: Pardal

first: Ben

last: Scheres

first: Viola

last: Willemsen


title: YTHDC1 promotes stemness maintenance and malignant progression in head and neck squamous cell carcinoma

city: shenzhen

first: junquan

last: weng

address: Dongmen North Road

institute: Shenzhen People's Hospital

summary: RNA sequencing was used to detect differential expressed genes (DEGs) between SCC9-sphere and SCC9 cell line and to uncover molecular pathways and target molecules associated with cancer stem cells.

overall_design: We then performed gene expression profiling analysis using data obtained from RNA-seq of two biological replicates of the SCC9 cell line and SCC9 sphere for RNA-sequencing profiling.

first: Junquan

last: Weng

first: Huijuan

last: Liu

first: Hui


title: Transcriptomic analysis of Hsp90 inhibitor (Hsp90i)-treated HIV-infected pediatric tonsillar mononuclear cells

city: Durham

first: Ria

last: Goswami

state: NC

address: 2 Genome Ct. MSRBII

department: Duke Human Vaccine Institute

institute: Duke University

summary:
Purpose: Hsp90 is a host chaperone protein that regulates cellular homeostasis by interacting with a diverse clientele of cellular proteins. Several of these proteins are involved in cellular pathways that play crucial roles in facilitating HIV replication. Identification of key cellular genes that are utilized by HIV for their replication, and whose expression is altered by Hsp90i, will lead to the development of targeted HIV therapeutics, which will ultimately be utilized for HIV cure. Here we characterized the key cellular genes altered upon Hsp90i treatment of HIV-infected pediatric tonsillar mononuclear cells.
Methods: Discarded tonsil tissues from 8 independent donors <15 years of age were obtained through Duke University School of Medicine Biorepository and Precision Pathology Center (BRPC), during routine tonsillectomy.  Tonsil tissues were washed and minced in RPMI 1640 (Gibco), containing 1X antibiotic/antimycotic mixture (Gibco), 50μg/ml Gentamicin (Gibco), 10μg/ml Cephalothin (Sigma-Aldrich) and 5μg/ml Fluconazole (Sigma-Aldrich), and tonsillar mononuclear cells (TMCs) were isolated by filtering tonsillar tissue pieces through a 70-μm mesh filter, followed by density gradient centrifugation using Ficoll-Paque PLUS (GE Healthcare, Waukesha, WI). 5x105 TMCs were infected with 250ng p24 equivalent of the cell-free CCR5-tropic HIV-JRFL virus. After 24hr, virus- infected cells were treated with either 0.1% DMSO or 0.1μM Hsp90i, daily. After 96hrs, total cellular RNA was extracted from TMCs using RNAeasy Mini kit (Qiagen). Total RNA quality and quantity was assessed using the Agilent Bionalyzer 2100 and the Qubit fluorometer, respectively. Poly(A) mRNA capture and construction of stranded mRNA-seq libraries from intact total RNA (RIN >7) was achieved using the commercially available KAPA Stranded mRNA-Seq Kit. In brief, mRNA transcripts were first captured from 200ng of total RNA using magnetic oligo-dT beads, fragmented using heat and magnesium, and reverse transcribed to produce dscDNA. Illumina sequencing adapters were then ligated to the dscDNA fragments and amplified to produce the final RNA-seq library. Libraries were indexed using dual molecular indices allowing for multiple libraries to be pooled and sequenced on the same sequencing lane on a HiSeq 4000 Illumina sequencing platform. Before pooling and sequencing, fragment length distribution and library quality was assessed on a 2100 Bioanalyzer using the High Sensitivity DNA Kit (Agilent Technologies).  All libraries were then pooled in equimolar ratio and sequenced. Multiplexing 8 libraries on one lane of an Illumina HiSeq 4000 flow cell yielded about 43 million 50bp sequences per sample. Once generated, sequence data was de-multiplexed and Fastq files generated using Bcl2Fastq conversion software provided by Illumina.
Conclusion: This study identified differentially expressed genes between DMSO-treated and Hsp90i-treated HIV-infected pediatric tonsillar mononuclear cells.

overall_design: Bulk RNA-seq analysis of HIV-infected human pediatric tonsillar mononuclear cells from 8 independent donors treated with  0.1μM Hsp90i or 0.1% DMSO (drug-vehicle)

first: Veronica

last: Russell

first: Timothy

last: Haystead

first: Sallie

last: Permar


title: Blood miRNA as biomarkers of epilepsy (EARLY vs. LATE)

first: Kinga

last: Szydlowska

first: Katarzyna

last: Lukasiuk


title: 8-Oxoguanine DNA glycosylase 1 hijacked by nucleoprotein conceals guanine oxidation in respiratory syncytial virus RNA

status: Public on Jun 13 2024

city: Galveston

first: Haiping

last: Hao

address: 301 University Blvd

institute: UTMB NGS Core

summary: Respiratory Syncytial Virus (RSV), alongside other prominent respiratory RNA viruses such as influenza and SARS-CoV-2, significantly contributes to the global incidence of respiratory tract infections. These pathogens prompt the production of reactive oxygen species (ROS), which play a crucial role in the onset and progression of respiratory diseases. However, the strategies by which viral RNA manages ROS-induced base oxidation are not well understood. Here we uncover that 8-oxo-7,8-dihydroguanine (8-oxoGua) is not merely an incidental byproduct of ROS activity but serves as a strategic adaptation of RSV RNA during replication within host cells. Through RNA immunoprecipitation and next-generation sequencing, we discovered that 8-oxoguanine DNA glycosylase 1 (OGG1) binding sites are predominantly found in the RSV antigenome, especially within guanine-rich areas. Further investigation revealed that viral ribonucleoprotein complexes specifically hijack OGG1. Crucially, our findings show that inhibiting OGG1's ability to recognize 8-oxoGua leads to a substantial reduction in RSV progeny production. Our results underscore the viral replication machinery's adaptation to oxidative challenges, pointing to the inhibition of OGG1's reading function as a potential novel strategy for antiviral intervention.

overall_design: RSV nucleocapsid immunoprecipitation RNA-sequencing (RNA-seq) for OGG1 in Human Small Airway Epithelial Cells (hSAECs).

first: Lang

last: Pan

first: Istvan

last: Boldogh


title: A tagged histone variant exploits cancer-specific pathway in human cells

city: Bethesda

first: Songjoon

last: Baek

state: MD

address: 41 Library Drive

department: CCR

institute: NCI / NIH

summary: Little is knownThe use of tags is ubiquitous in scientific research, has allowed researchers the capability to make great strides in scientific discoveries that have left lasting impact in many disciplines. Here, we investigate the aberrant functional roles associated with C-terminally TAP-tagged CENP-A (CpA-TAP) when compared to centromeric native CENP-A (CpA).

overall_design: ChIPseq of native CpA or CpA-TAP in control or transfected HeLa cells, in a DAXX knock-out (KO) cell line, and double DAXX KO + HIRA knock-down. ChIPseq was replicated for GFP-CpA expressing HeLa cells.

first: Minh

last: Bui

first: Yamini

last: Dalal


title: Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma

city: Tübingen

first: Daniel

middle: J.

last: Merk

address: Otfried-Müller-Str. 27

institute: Hertie-Institute for Clinical Brain Research

type: Methylation profiling by genome tiling array


title: B cell characteristics define HCV reinfection outcome

city: Sydney

first: Rowena

last: Bull

state: NSW

address: Wallace Wurth Building (C27)

country: Australia

institute: University of New South Wales

summary: In individuals highly exposed to hepatitis C virus (HCV), reinfection is common, suggesting that natural development of sterilising immunity is difficult. In those that are reinfected, some will develop a persistent infection, while a small proportion repeatedly clear the virus, suggesting natural protection is possible. The aim of this study was to characterise immune responses associated with rapid natural clearance of HCV reinfection. Broad neutralising antibodies (BnAbs) and Envelope 2 (E2)-specific memory B cell (MBCs) responses were examined longitudinally in 15 subjects with varied reinfection outcomes. BnAb responses were associated with MBC recall, but not with reinfection clearance. Strong evidence of antigen imprinting was found, and the B cell receptor repertoire showed a high level of clonality with ongoing somatic hypermutation of many clones over subsequent reinfection events. Single cell transcriptomic analyses showed that cleared reinfections featured an activated transcriptomic profile in HCV-specific B cells that rapidly expanded upon reinfection. MBC quality, but not necessarily breadth of nAb responses, is important for protection against antigenically diverse variants, which is encouraging for HCV vaccine development.

overall_design: Single cell RNA sequecing data from E2+IgG+ memory B cells from HCV reinfection cohort isolated at multiple timepoints after flow cytometry experiments

first: Alexander

last: Underwood

first: Money

last: Gupta

first: Bing-Ru

last: Wu

first: Auda

middle: A

last: Eltahla

first: Irene

last: Boo

first: Jing

last: Wang

first: David

last: Agapiou

first: Arunasingam

last: Abayasingam

first: Arnold

last: Reynaldi

first: Elizabeth

last: Keoshkerian

first: Yanran

last: Zhao

first: Nicholas

last: Brasher

first: Melanie

last: Walker

first: Jens

last: Bukh

first: Lisa

last: Maher

first: Tom

last: Gordon

first: Miles

last: Davenport

first: Fabio

last: Luciani

first: Heidi

middle: E

last: Drummer

first: Andrew

last: Llyod


title: Identification of Lineage-specific Transcriptional Factor–defined Molecular Subtypes in Small Cell Bladder Cancer

city: Baltimore

first: Woonyoung

last: Choi

state: Maryland

address: 1550 Orleans Street

department: Urology

institute: Johns Hopkins University

summary: Three subtypes of small cell/neuroendocrine bladder cancers (SCBCs) were identified: ASCL1, NEUROD1, and POU2F3. These subtypes are with neuroendocrine (NE) level, immune signature, and antibody-drug conjugate (ADC) target implications.

overall_design: A total of 44 small cell/neuroendocrine bladder cancer (SCBC) tissue samples were collected.

first: Mingxiao

last: Feng


title: Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma [Methylation array]

first: Daniel

last: Merk

summary: Sonic hedgehog subgroup of medulloblastoma (SHH-MB) is characterized by aberrant activation of the SHH signaling pathway. An inhibition of the positive SHH regulator Smoothened (SMO) has demonstrated promising clinical efficacy. Yet, primary and acquired resistance to SMO inhibitors limit their efficacy. An understanding of underlying molecular mechanisms of resistance to therapy is warranted to bridge this unmet need. Here, we make use of genome-wide CRISPR-Cas9 knockout screens in SMB21 and DAOY cells, in order to unravel genetic dependencies and drug-related genetic interactors that could serve as alternative therapeutic targets for SHH-MB. Our screens reinforce SMB21 cells as a faithful model system for SHH-MB, as opposed to DAOY cells, and identify members of the epigenetic machinery including DNA methyltransferase 1 (DNMT1) as druggable targets in SHH-dependent tumors. We show that Dnmt1 plays a crucial role in normal murine cerebellar development and is required for SHH-MB growth in vivo. Additionally, DNMT1 pharmacological inhibition alone and in combination with SMO inhibition effectively inhibits tumor growth in murine and human SHH-MB cell models and prolongs survival of SHH-MB mouse models by inhibiting SHH signaling output downstream of SMO. In conclusion, our data highlight the potential of inhibiting epigenetic regulators as a novel therapeutic avenue in SMO-inhibitor sensitive as well as resistant SHH-MBs.

overall_design: Murine cell line models of Sonic hedgehog medulloblastoma (SMB21 and SMB55) were treated with 3µM 5-azacytidine for 24 hours or corresponding concentration of DMOS solvent.


title: Notch induces transcription by stimulating release of paused RNA Pol II without increasing chromatin accessibility [TT-seq]

city: Boston

first: Julia

middle: M

last: Rogers

state: Massachusetts

address: 45 Shattuck Street

department: BCMP

institute: Harvard Medical School

summary: Notch proteins undergo ligand-induced proteolysis to release a nuclear effector that influences a wide range of cell fate decisions by regulating gene activity. However, despite years of study, how Notch induces the transcription of its target genes remains unclear. Here, we comprehensively examined the response to human Notch1 across a time course of activation, using genomic assays of nascent RNA and chromatin accessibility. These data revealed that Notch induces target gene transcription primarily by releasing paused RNA polymerase II (RNAPII), in contrast to prevailing models suggesting that Notch acts by promoting chromatin accessibility. Indeed, we found that open chromatin is established at Notch-responsive regulatory elements prior to Notch signaling, through SWI/SNF-mediated remodeling. Notch activation, however, elicited no further chromatin opening at these loci. Together, these studies reveal that the nuclear response to Notch signaling is dictated by the pre-existing chromatin state and RNAPII distribution at the time of signal activation.

overall_design: To determine which genes are induced by Notch signaling in SC2 cells, and how SWI/SNF inhibition affects gene expression in the Notch response, Notch signaling was induced in SC2 cells by GSI washout. Cells were harvested at 1 and 4 hours post Notch activation, and immediately after mock GSI washout, and harvested for TT-seq sample preparation. Mock washout control samples were also harvested at 1 and 4 hours. For each of these time points, cells were either treated with SWI/SNF inhibitor (1 µM BRM014) or 0.01% DMSO at the time of washout or mock-washout. There are 10total conditions, and two replicates of the full experiment.

first: Claudia

last: Mimoso

first: Benjamin

last: Martin

first: Karen

last: Adelman

first: Stephen

last: Blacklow


title: Notch induces transcription by stimulating release of paused RNA Pol II without increasing chromatin accessibility [PRO-seq]

overall_design: To determine how Notch signaling affects the behavior of RNA Polymerase II, Notch signaling was induced in SC2 cells by GSI washout. Cells were harvested at 15m, 30m, 45m, 1h, 90m, 2h, 3h, and 4h post Notch activation, and harvested for PRO-seq sample preparation. A reference condition was harvested immediately after mock GSI washout, and harvested for PRO-seq sample preparation.  There are 9 total conditions, with two replicates of the full experiment, and 3 replicates of the reference condition.


title: Notch induces transcription by stimulating release of paused RNA Pol II without increasing chromatin accessibility [ChIP-seq]

overall_design: Notch signaling was induced in SC2 cells by GSI washout, and cells were harvested at 15m, 30m, 45m, 1h, 90m, 2h, and 4h after Notch induction, and chromatin was prepared from these samples. Chromatin was also prepared from cells harvested at 0h, immediately post mock GSI washout, as a reference condition. ChIP-seq was performed for the H3K27ac chromatin mark. There are 10total conditions, and two replicates of the full experiment.


title: Genome-wide CRISPR-Cas9 knockout screens identify DNMT1 as a druggable dependency in sonic hedgehog medulloblastoma [RNA-seq]

overall_design: A murine cell line models of Sonic hedgehog medulloblastoma (SMB21) was treated with 3µM 5-azacytidine for 2 hours, 24 hours, or corresponding concentration of DMSO solvent.


title: Notch induces transcription by stimulating release of paused RNA Pol II without increasing chromatin accessibility.


title: Human Platelet Lysate-Cultured Adipose-Derived Stem Cell Sheets Promote Angiogenesis and Accelerate Wound Healing via CCL5 Modulation

first: Yueh Chen

last: Chen

address: No.7, Chung Shan S. Rd.（Zhongshan S. Rd.）, Zhongzheng Dist.

department: Surgery

summary: To further differentiate the gene expression of HPL-cultured or FBS-cultured ASC sheets, we have employed microarray analysis. ASCs were isolated from the subcutaneous fat tissue of four non-diabetic, non-smoking female donors with an average age of 45 y (32–57 y) and an average body mass index of 24.6 (21.0–26.6). Significantly up-regulated or down-regulated genes are highlighted in the HPL-cultured ASC sheets. Pathway enrichment analysis showcasing the top 10 hallmark gene-sets from MSigDB significantly enriched in up-regulated (top) or down-regulated (bottom) genes. The heatmap represented the expression patterns of angiogenesis-related genes between the HPL-cultured and FBS-cultured ASC sheets.

overall_design: Adipose-derived stem cells (ASCs) were cultured with 5%HPL or 10% FBS for 7 day-sheet fabrication. Angiogenesis-related genes induced in HPL-cultured ASC sheets or the FBS counterpart were investigated.