Comparison Of Expression Profiles Research Articles

Comparative proteomic analysis of astrocytoma tissues from patients with and without seizures

Astrocytoma is a common type of glioma and a frequent cause of brain tumour-related epilepsy. Although the link between glioma and epilepsy is well established, the precise mechanisms underlying epileptogenesis in astrocytoma remain poorly understood. In this study, we performed proteomic analysis of astrocytoma tissue from patients with and without seizures using mass spectrometry-based techniques. We detected 131 differentially expressed proteins (42 upregulated and 89 downregulated). Proteins upregulated in patients with seizures were mostly related to an increase in energy metabolism. Moreover, glial fibrillary acidic protein, which is involved in maintaining normal axonal structures, was abnormally highly expressed in patients with seizures. Proteins downregulated in patients with seizures included those involved in trans-synaptic signalling and gamma-aminobutyric acid synaptic transmission. Interestingly, comparison of protein expression profiles from our cohort with those from a previous study of patients with epilepsy due to other causes showed that the collapsin response mediator protein family of axonal growth regulators was highly expressed only in patients with seizures due to astrocytomas. Further studies of the proteins identified here are required to determine their potential as biomarkers and therapeutic targets.

Comparative analysis of the WRKY gene family between Chimonanthus praecox and C. salicifolius.

Gene duplications provide evolutionary potentials for generating novel functions. Chimonanthus praecox and C. salicifolius are closely related species from Calycantaceae, Magnoliids. In this study, we compared the WRKY gene family from C. praecox and C. salicifolius, and predicted the potential gene function through gene expression patterns to explore the evolution of orthologous and paralogous gene pairs. A total of 73 and 85 WRKY genes were identified and analyzed from the whole genome sequencing of C. praecox and C. salicifolius. Based on the phylogenetic analysis, CpWRKY and CsWRKY genes were clustered into three groups (Group I、II、III) and 5 subgroups (Group IIa、IIb、IIc、IId、IIe). In C. praecox and C. salicifolius, we identified thirty-six and fifty-four pairs of WRKY segmental duplicated genes, respectively, along with two and three pairs of tandem duplicates, indicating that segmental duplication plays a crucial role in the evolution of Chimonanthus WRKY gene family. Most WRKY duplication gene pairs originated from segmental duplications before the first whole genome duplication (WGD), highlighting this period as a significant source of genetic diversity and functionality for the WRKY family. The analysis of WRKY gene expression levels suggests that CsWRKY18 and CsWRKY68 may promote the growth of the roots in C. salicifolius. Comparisons of expression profiles between species revealed that five orthologous gene pairs presented identical expression trends, indicating functional conservation and absence of neo-functionalization or sub-functionalization. However, most orthologous gene pairs exhibit differences in expression patterns, suggesting that they have undergone functional divergence. This functional differentiation may be due to the different selective pressures faced by C. praecox and C. salicifolius during their speciation processes. This study provided detailed information on the WRKY gene family from C. praecox and C. salicifolius, and a new insight for studying gene duplication and function evolution.

IRX-related homeobox gene MKX is a novel oncogene in acute myeloid leukemia.

Homeobox genes encode transcription factors which organize differentiation processes in all tissue types including the hematopoietic compartment. Recently, we have reported physiological expression of TALE-class homeobox gene IRX1 in early myelopoiesis restricted to the megakaryocyte-erythroid-progenitor stage and in early B-cell development to the pro-B-cell stage. In contrast, sister homeobox genes IRX2, IRX3 and IRX5 are aberrantly activated in the corresponding malignancies acute myeloid leukemia (AML) and B-cell progenitor acute lymphoid leukemia. Here, we examined the role of IRX-related homeobox gene MKX (also termed IRXL1 or mohawk) in normal and malignant hematopoiesis. Screening of public datasets revealed silent MKX in normal myelopoiesis and B-cell differentiation, and aberrant expression in subsets of AML and multiple myeloma (MM) cell lines and patients. To investigate its dysregulation and oncogenic function we used AML cell line OCI-AML3 as model which strongly expressed MKX at both RNA and protein levels. We found that IRX5, JUNB and NFkB activated MKX in this cell line, while downregulated GATA2 and STAT5 inhibited its expression. MKX downstream analysis was conducted by siRNA-mediated knockdown and RNA-sequencing in OCI-AML3, and by comparative expression profiling analysis of a public dataset from MM patients. Analysis of these data revealed activation of CCL2 which in turn promoted proliferation. Furthermore, MKX upregulated SESN3 and downregulated BCL2L11, which may together underlie decreased etoposide-induced apoptosis. Finally, myeloid differentiation genes CEBPD and GATA2 were respectively up- and downregulated by MKX. Taken together, our study identified MKX as novel aberrantly expressed homeobox gene in AML and MM, highlighting the function of IRX1 in normal myelopoiesis and B-cell development, and of IRX-related genes in corresponding malignancies. Our data merit further investigation of MKX and its deregulated target genes to serve as novel markers and/or potential therapeutic targets in AML patient subsets.

Identification of Pappa and Sall3 as Gli3 direct target genes acting downstream of cilia signaling in corticogenesis

Abstract The cerebral cortex is critical for advanced cognitive functions and relies on a vast network of neurons to carry out its highly intricate neural tasks. Generating cortical neurons in accurate numbers hinges on cell signaling orchestrated by primary cilia to coordinate the proliferation and differentiation of cortical stem cells. While recent research has shed light on multiple ciliary roles in corticogenesis, specific mechanisms downstream of cilia signaling remain largely unexplored. We previously showed that an excess of early-born cortical neurons in mice mutant for the ciliary gene Inpp5e was rescued by re-introducing Gli3 repressor. By comparing expression profiles between Inpp5e and Gli3 mutants, we here identified novel Gli3 target genes. This approach highlighted the transcription factor gene Sall3 and Pappalysin1 (Pappa), a metalloproteinase involved in IGF signaling, as upregulated genes in both mutants. Further examination revealed that Gli3 directly binds to Sall3 and Pappa enhancers and suppresses their activity in the dorsal telencephalon. Collectively, our analyses provide important mechanistic insights into how primary cilia govern the behavior of neural stem cells, ultimately ensuring the production of adequate numbers of neurons during corticogenesis.

Circulating Micro-RNAs Predict the Risk of Recurrence in Triple-Negative Breast Cancer.

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with a high tendency for developing a recurrent disease. Circulating micro-RNAs (cmiRNAs) obtained through liquid biopsy are potential prognostic biomarkers for the assessment of TNBC recurrence risk. In this study, we sequenced cmiRNAs from the serum samples of 14 recurrent and 19 non-recurrent TNBC cases and compared expression profiles in relation to recurrence status, survival data and miRNA expression in matched tumor samples. Differential expression analysis between recurrent and non-recurrent cases identified ten differentially expressed (DE) cmiRNAs, of which cmiRNAs miR-21-5p (p = 0.030, HR = 1.87, 95% CI 1.06-3.30), miR-16-5p (p = 0.032, HR = 0.53, 95% CI 0.30-0.95), and miR-26b-5p (p = 0.023, HR = 0.52, 95% CI 0.29-0.91) were associated with recurrence-free survival in multivariable survival analysis. Expression profiles of matched tumor and serum samples were shown to correlate with each other. DE cmiRNAs were associated with common cancer-related signaling pathways and improved the overall predictive performance of the logistic regression model assessing the recurrence risk. Our results indicate that recurrent and non-recurrent TNBC differ in their cmiRNA expression profiles, and that three specific cmiRNAs can be used to assess the risk of recurrence in TNBC.

Genome-wide characterization and comparative expression profiling of dual-specificity phosphatase genes in yellow catfish (Pelteobagrus fulvidraco) after infection with exogenous Aeromonas hydrophila.

Dual-specificity phosphatases (DUSPs) are crucial regulators in many mammals, managing dephosphorylation and inactivation of mitogen-activated protein kinases (MAPKs) and playing essential roles in immune responses. However, their presence and functions in teleosts, like the yellow catfish (Pelteobagrus fulvidraco), remain unexplored. In this study, eight pfDusp genes (pfDusp1-7 and pfDusp10) were identified in yellow catfish. We characterized their molecular features, conserved protein sequences, and chromosomal localization through genome-wide analyses, and we examined their expression patterns in immune responses. Our findings reveal two conserved motifs, Leu-Phe-Leu-Gly and Ala-Tyr-Leu-Met, within the DSPc domain of DUSP proteins. The genes were mapped across seven chromosomes without evidence of duplication. Comparative analysis showed high conservation of Dusp genes across vertebrates, with evolutionary analysis suggesting Dusp3 as a potential intermediate form. Dusp transcripts were significantly upregulated in the kidney post-A. hydrophila infection. These results suggest the involvement of Dusp genes in the immune response of yellow catfish to bacterial pathogens, providing insights into their evolutionary significance and potential applications in aquaculture and molecular breeding.

CNSC-58. BIOPROCESSING OF VIABLE SURGICAL PEDIATRIC BRAIN TUMOR SPECIMENS FOR GENOME-GUIDED PERSONALIZED DRUG TESTING

Abstract Novel treatment approaches are urgently needed for pediatric central nervous system (CNS) tumors as they are the leading cause of cancer-related deaths in children. A lack of research materials impedes progress towards developing such therapies. Although various brain cancer biobanks exist, these rarely store viable patient-derived tissue and cells for live cell analyses, including cell fate assays and testing for drug sensitivities. We propose that a biorepository of viable cell dissociates and tissue broadly representing CNS tumor entities overcomes these limitations. From a combination of molecular diagnoses and histopathologic assessment of over 120 samples collected, we generated a biorepository of roughly 35 distinct entities of pediatric CNS tumors in our Stanford neuro-bioprocessing cohort. Based on the Central Brain Tumor Registry of the United States, the proportion of subtypes represented in our cohort match that of the general population with exceptions. We established a standardized bioprocessing pipeline that can be used as a template for tissue collection and model development in the broader disease context and for multiple downstream applications. Our emphasis on cryostorage of viable cells and tissue facilitates ad hoc live cell analyses. In addition to gaining a better understanding of tumor pathophysiology, we attempted a rapid bed-to-bench-to-bedside approach using comparative RNA expression profile analyses in an individual patient’s pilocytic astrocytoma. Novel drug targets were identified by analyzing RNA transcripts that are highly expressed (outliers) compared with a compendium of 12,747 brain and non-brain tumor samples. We validated outliers as drug targets using acute cell isolates, and identified a novel target in recurrent low-grade glioma. These studies illustrate that biobanking of viable patient-derived material enables developing personalized therapies with the goal of improving patient outcomes. As demonstrated here, patient-derived acute cell isolates facilitate identifying drug vulnerability, creating an opportunity for more personalized treatment of patients with CNS tumors.

Gene expression profile comparison of primary and pulmonary metastatic lesions in a dog with appendicular osteosarcoma and hypertrophic osteopathy

Hypertrophic osteopathy (HO) is a paraneoplastic syndrome, and the most notable cause in dogs is pulmonary metastatic osteosarcoma (OSA). Although many molecular factors in canine OSA have been shown in metastasis, little is known about the gene expression profile of HO secondary to metastatic OSA. Therefore, the purpose of this study was to compare the gene expression profiles between primary and metastatic OSA lesions from the same dog and to look for gene expression changes that can elucidate the molecular mechanism of metastases and HO. Tumoral samples were obtained from a 2-year-old, intact male, Labrador retriever. At the first visit, the patient presented with an appendicular OSA as the primary lesion. About 10 months later, the dog developed HO due to a single pulmonary metastasis. Using these primary and metastatic samples from the same dog, as well as normal canine osteoblasts, we investigated the gene expression profiling using the NanoString nCounter® Canine IO panel. A total of 180 differentially expressed genes were identified between malignant OSA cells and non-malignant canine osteoblasts. Furthermore, 5 genes (CCL17, VEGFC, C3, C4BPA, and FOS) were differentially expressed in comparison between primary and metastatic OSA samples. CCL17 and VEGFC were upregulated in the primary lesion compared to the metastatic lesion, while C3, C4BPA, and FOS were downregulated in the primary lesion relative to the metastatic lesion. Given that the metastatic lesion was relevant to the development of HO, the different gene expression profiles may be relevant to understanding the pathophysiology of HO.

Potential Roles of the GRF Transcription Factors in Sorghum Internodes during Post-Reproductive Stages.

Growth-regulating factor (GRF) is a plant-specific family of transcription factors crucial for meristem development and plant growth. Sorghum (Sorghum bicolor L. Moench) is a cereal species widely used for food, feed and fuel. While sorghum stems are important biomass components, the regulation of stem development and the carbohydrate composition of the stem tissues remain largely unknown. Here, we identified 11 SbGRF-encoding genes and found the SbGRF expansion driven by whole-genome duplication events. By comparative analyses of GRFs between rice and sorghum, we demonstrated the divergence of whole-genome duplication (WGD)-derived OsGRFs and SbGRFs. A comparison of SbGRFs' expression profiles supports that the WGD-duplicated OsGRFs and SbGRFs experienced distinct evolutionary trajectories, possibly leading to diverged functions. RNA-seq analysis of the internode tissues identified several SbGRFs involved in internode elongation, maturation and cell wall metabolism. We constructed co-expression networks with the RNA-seq data of sorghum internodes. Network analysis discovered that SbGRF1, 5 and 7 could be involved in the down-regulation of the biosynthesis of cell wall components, while SbGRF4, 6, 8 and 9 could be associated with the regulation of cell wall loosening, reassembly and/or starch biosynthesis. In summary, our genome-wide analysis of SbGRFs reveals the distinct evolutionary trajectories of WGD-derived SbGRF pairs. Importantly, expression analyses highlight previously unknown functions of several SbGRFs in internode elongation, maturation and the potential involvement in the metabolism of the cell wall and starch during post-anthesis stages.

Cross-species imputation and comparison of single-cell transcriptomic profiles.

Cross-species comparison and prediction of gene expression profiles are important to understand regulatory changes during evolution and to transfer knowledge learned from model organisms to humans. Single-cell RNA-seq (scRNA-seq) profiles enable us to capture gene expression profiles with respect to variations among individual cells; however, cross-species comparison of scRNA-seq profiles is challenging because of data sparsity, batch effects, and the lack of one-to-one cell matching across species. Moreover, single-cell profiles are challenging to obtain in certain biological contexts, limiting the scope of hypothesis generation. Here we developed Icebear, a neural network framework that decomposes single-cell measurements into factors representing cell identity, species, and batch factors. Icebear enables accurate prediction of single-cell gene expression profiles across species, thereby providing high-resolution cell type and disease profiles in under-characterized contexts. Icebear also facilitates direct cross-species comparison of single-cell expression profiles for conserved genes that are located on the X chromosome in eutherian mammals but on autosomes in chicken. This comparison, for the first time, revealed evolutionary and diverse adaptations of X-chromosome upregulation in mammals.

Mitochondrial proteome analysis reveals that an augmented cytochrome c oxidase assembly and activity potentiates respiratory capacity in sarcoma

Mitochondrial oxidative phosphorylation (OXPHOS) is an obligatory process in sarcoma. Despite that, the metabolic programming of sarcoma mitochondria is still unknown. To obtain a comprehensive metabolic insight of mitochondria, we developed a mouse fibrosarcoma model by injecting 3-methylcholanthrene and compared mitochondrial proteomes between sarcoma and its contralateral normal muscle using mass spectrometry. Our study identified ∼449 proteins listed in the SwissProt databases, and all the data sets are available via ProteomeXchange with the identifier PXD044903. In sarcoma, 49 mitochondrial proteins were found differentially expressed, including 36 proteins up-regulated and 13 proteins down-regulated, with the significance of p-value <0.05 and the log2[fold change] > 1 and < −1 as compared to normal muscle. Our data revealed that various anaplerotic reactions actively replenish the TCA cycle in sarcoma. The comparative expression profile and Western blotting analysis of OXPHOS subunits showed that complex-IV subunits, MT-CO3 and COX6A1, were significantly up-regulated in sarcoma vs. normal muscle. Further, biochemical and physiological assays confirmed enhanced complex-IV specific enzymatic and supercomplex activities with a concomitant increase of oxygen consumption rate in sarcoma mitochondria compared to normal muscle. Validation with human post-operative sarcoma tissues also confirms an increased MT-CO3 expression compared to normal tissue counterparts. Thus, our data comprehensively analyses the mitochondrial proteome and identifies augmented complex-IV assembly and activity in sarcoma.

Comprehensive molecular characterization of TFE3-rearranged renal cell carcinoma

TFE3-rearranged renal cell cancer (tRCC) is a rare form of RCC that involves chromosomal translocation of the Xp11.2 TFE3 gene. Despite its early onset and poor prognosis, the molecular mechanisms of the pathogenesis of tRCC remain elusive. This study aimed to identify novel therapeutic targets for patients with primary and recurrent tRCC. We collected 19 TFE3-positive RCC tissues that were diagnosed by immunohistochemistry and subjected them to genetic characterization to examine their genomic and transcriptomic features. Tumor-specific signatures were extracted using whole exome sequencing (WES) and RNA sequencing (RNA-seq) data, and the functional consequences were analyzed in a cell line with TFE3 translocation. Both a low burden of somatic single nucleotide variants (SNVs) and a positive correlation between the number of somatic variants and age of onset were observed. Transcriptome analysis revealed that four samples (21.1%) lacked the expected fusion event and clustered with the genomic profiles of clear cell RCC (ccRCC) tissues. The fusion event also demonstrated an enrichment of upregulated genes associated with mitochondrial respiration compared with ccRCC expression profiles. Comparison of the RNA expression profile with the TFE3 ChIP-seq pattern data indicated that PPARGC1A is a metabolic regulator of the oncogenic process. Cell proliferation was reduced when PPARGC1A and its related metabolic pathways were repressed by its inhibitor SR-18292. In conclusion, we demonstrate that PPARGC1A-mediated mitochondrial respiration can be considered a potential therapeutic target in tRCC. This study identifies an uncharacterized genetic profile of an RCC subtype with unique clinical features and provides therapeutic options specific to tRCC.

Comparison of the gene expression profiles of endometrial and trophoblastic cells in women with recurrent miscarriage: A bioinformatics approach.

Recurrent miscarriage (RM) remains unsolved in 50% of patients and causes physical and psychological problems in women without specific risk factors for miscarriage. For a successful pregnancy, acceptance of the endometrium and invasion of trophoblast cells into the endometrium is necessary. This study aimed to use computational analysis to identify key genes and related pathways in endometrial and trophoblast cells derived from RM samples. In this bioinformatics study, we explored the differential expression of genes in endometrial and trophoblast cells by analyzing the GSE165004 and GSE76862 datasets, respectively with the limma package in R software. Subsequently, overlapped genes between 2 datasets were selected, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were performed. The overlapped genes were integrated to construct a protein-protein interaction network and hub genes selection. We observed 41 overlapped genes between endometrial and trophoblast cells, and future analysis was accomplished in overlapped and nonoverlapped genes. Kyoto Encyclopedia of Genes and Genomes analysis indicated that overlapped genes were significantly enriched in the complement and coagulation cascades, pluripotency of stem cells, and synthesis and degradation of ketone bodies. Gene ontology analysis suggested that the genes were enriched in the cell cycle, apoptosis, and cell division. The top 10 genes included: IRS1, FGF2, MAPK6, MAPK1, MAPK3, MAPK8, MAPK9, PLK1, PRKACA, and PRKCA were identified from the PPI network. This study identified the key genes and potential molecular pathways underlying the development of RM. This could provide novel insights to determine the possible mechanisms and interventional strategies associated with miscarriage.

Maternal obesity and offspring neurodevelopment are associated with hypoxic gene expression in term human placenta.

One third of women in the United States are affected by obesity during pregnancy. Maternal obesity (MO) is associated with an increased risk of neurodevelopmental and metabolic disorders in the offspring. The placenta, located at the maternal-fetal interface, is a key organ determining fetal development and likely contributes to programming of long-term offspring health. We profiled the term placental transcriptome in humans (pre-pregnancy BMI 35+ [MO condition] or 18.5-25 [lean condition]) using single-nucleus RNA-seq to compare expression profiles in MO versus lean conditions, and to reveal potential mechanisms underlying offspring disease risk. We recovered 62,864 nuclei of high quality from 10 samples each from the maternal-facing and fetal-facing sides of the placenta. On both sides in several cell types, MO was associated with upregulation of hypoxia response genes. On the maternal-facing side only, hypoxia gene expression was associated with offspring neurodevelopmental measures, in Gen3G, an independent pregnancy cohort with bulk placental tissue RNA-seq. We leveraged Gen3G to determine genes that correlated with impaired neurodevelopment and found these genes to be most highly expressed in extravillous trophoblasts (EVTs). EVTs further showed the strongest correlation between neurodevelopment impairment gene scores (NDIGSs) and the hypoxia gene score. We reanalyzed gene expression of cultured EVTs, and found increased NDIGSs associated with exposure to hypoxia. Among EVTs, accounting for the hypoxia gene score attenuated 44% of the association between BMI and NDIGSs. These data suggest that hypoxia in EVTs may be a key process in the neurodevelopmental programming of fetal exposure to MO.

Comparative expression profile of selected genes in Venturia inaequalis Cooke (Wint.) infecting apple fruits and leaves

Scab is a noxious fungal disease of apples (Malus domestica Borkh) in all apple producing regions caused by a host-specific phytopathogen Venturia inaequalis Cooke (Wint.). Its symptoms include black or brown lesions on leaves as well as on fruits, and causes fruit deformation. In this study, V. inaequalis was isolated from infected fruit samples and expression level of selected pathogenesis related genes in scab infected fruits and leaves was studied. The isolated fungus formed a brown coloured mat-like colony having septate mycelium and produced acute ovoid shaped conidia. Molecular characterization of the fungus was done by amplification and sequencing of internal transcribed spacer (ITS) and Cytochrome (CYP51A1) regions of the isolate. The Sanger sequencing of amplicons and sequence analysis using BLAST tool of the NCBI against GenBank database confirmed that the obtained sequence of ITS and CYP51A1 regions had 99.6 % and 98 % sequence identity with the reference V. inaequalis, respectively. The isolated strain of V. inaequalis was submitted in the fungal repository of Microbial Type Culture Collection (MTCC), India. The phylogenetic analysis of ITS region of the isolate revealed that the isolated strain of V. inaequalis was more closely related to Fusicladium eriobotryae compared to other Venturia species. The expression levels of pathogenesis related genes viz. CIN1, CE5 and VICE16 were higher in infected leaves as compared to infected fruits. Whereas expression of VICE12 and GH28 were higher in infected fruits compared to infected leaves. VICE4 gene showed equal level of expression during infection in both fruits and leaves, which was also maximum as compared to the control treatment. The transcript analysis of aforementioned genes of V. inaequalis gives the insights of the pathogen's expression profile during pathogenesis in fruits and leaves. This expression analysis can form a basis selecting pathogenesis related genes as targets for developing dsRNA expressing constructs with an aim to reduce RNAi mediated silencing of specific genes, in a futuristic biotechnological based solution to deal with apple scab disease.

ATRT-09. MULTI-OMICS SEQUENCING OF ATYPICAL TERATOID RHABDOID TUMORS UNVEILS A SHARED GROUND-STATE POPULATION PROMOTING SUBGROUP-SPECIFIC DIFFERENTIATION TRAJECTORIES

Abstract BACKGROUND Atypical teratoid rhabdoid tumors (ATRTs) remain a significant clinical challenge in pediatric neurooncology. Despite the simplicity of the genomic profile, mostly characterized by the functional loss of SMARCB1 and in rare cases SMARCA4, ATRTs are molecularly and epigenetically diverse, with three main molecular subgroups identified: ATRT-TYR, ATRT-SHH and ATRT-MYC. METHODS To address the lack of effective mechanism-of-action based treatments and comprehend the biology of these subgroups, we conducted 10X single-nucleus transcriptome (n = 12) and multiome (transcriptome + ATAC) (n = 7) sequencing on tumor samples (ATRT-TYR = 6, ATRT-SHH = 9, ATRT-MYC = 4). Validation datasets included 10X single-cell transcriptomics (n = 1), 10X single-nucleus transcriptomics of cell lines (n = 5), and single-cell (n = 3) and single-nucleus (n = 9) SMART-seq transcriptomics. Separation of malignant cells from tumor microenvironment (TME) cells was achieved by comparison of expression profiles against literature-based marker genesets of normal cell types. Tumor cell populations were characterized based on enrichment in fetal cell types and recurrent tumor programs across cancer types, coupled with non-negative matrix factorization (NMF) and differential expression analyses. RESULTS ATRT-TYR exhibited choroid plexus-like and cilia-like cell populations, ATRT-SHH displayed radial glia-like, OPC-like and NPC-like cell populations and ATRT-MYC mainly demonstrated a mesenchymal-like cell population. Each subgroup represented unique differentiation trajectories. However, we identified a population of intermediate neuronal precursor-like cells (IPC-like) shared across all subgroups, expressing markers of pluripotent stem cells and cell cycle. RNA + ATAC transcription factor (TF) enrichment analysis for IPC-like cells revealed TFs linked to each subgroup’s differentiation trajectory, suggesting IPC-like cells as a putative ground-state tumor cell population driving differentiation of each subgroup. Functional validation of these findings in ATRT organoid models is currently ongoing. CONCLUSIONS This study elucidates defined ATRT subgroup-specific differentiation trajectories that may provide guidance for the development of subgroup-based therapies.

The astrocyte-enriched gene deathstar plays a crucial role in the development, locomotion, and lifespan of D. melanogaster

ABSTRACT The Drosophila melanogaster brain is a complex organ with various cell types, orchestrating the development, physiology, and behaviors of the fly. While each cell type in Drosophila brain is known to express a unique gene set, their complete genetic profile is still unknown. Advances in the RNA sequencing techniques at single-cell resolution facilitate identifying novel cell type markers and/or re-examining the specificity of the available ones. In this study, exploiting a single-cell RNA sequencing data of Drosophila optic lobe, we categorized the cells based on their expression pattern for known markers, then the genes with enriched expression in astrocytes were identified. CG11000 was identified as a gene with a comparable expression profile to the Eaat1 gene, an astrocyte marker, in every individual cell inside the Drosophila optic lobe and midbrain, as well as in the entire Drosophila brain throughout its development. Consistent with our bioinformatics data, immunostaining of the brains dissected from transgenic adult flies showed co-expression of CG11000 with Eaat1 in a set of single cells corresponding to the astrocytes in the Drosophila brain. Physiologically, inhibiting CG11000 through RNA interference disrupted the normal development of male D. melanogaster, while having no impact on females. Expression suppression of CG11000 in adult flies led to decreased locomotion activity and also shortened lifespan specifically in astrocytes, indicating the gene’s significance in astrocytes. We designated this gene as ‘deathstar’ due to its crucial role in maintaining the star-like shape of glial cells, astrocytes, throughout their development into adult stage.

Identification and Characterization of Metastasis-Initiating Cells in ESCC in a Multi-Timepoint Pulmonary Metastasis Mouse Model.

Metastasis is the biggest obstacle to esophageal squamous cell carcinoma (ESCC) treatment. Single-cell RNA sequencing analyses are applied to investigate lung metastatic ESCC cells isolated from pulmonary metastasis mouse model at multiple timepoints to characterize early metastatic microenvironment. A small population of parental KYSE30 cell line (Cluster S) resembling metastasis-initiating cells (MICs) is identified because they survive and colonize at lung metastatic sites. Differential expression profile comparisons between Cluster S and other subpopulations identified a panel of 7 metastasis-initiating signature genes (MIS), including CD44 and TACSTD2, to represent MICs in ESCC. Functional studies demonstrated MICs (CD44high) exhibited significantly enhanced cell survival (resistances to oxidative stress and apoptosis), migration, invasion, stemness, and in vivo lung metastasis capabilities, while bioinformatics analyses revealed enhanced organ development, stress responses, and neuron development, potentially remodel early metastasis microenvironment. Meanwhile, early metastasizing cells demonstrate quasi-epithelial-mesenchymal phenotype to support both invasion and anchorage. Multiplex immunohistochemistry (mIHC) staining of 4 MISs (CD44, S100A14, RHOD, and TACSTD2) in ESCC clinical samples demonstrated differential MIS expression scores (dMISs) predict lymph node metastasis, overall survival, and risk of carcinothrombosis.

Phosphoenolpyruvate carboxykinase-1 targeted siRNA promotes wound healing in type 2 diabetic mice by restoring glucose homeostasis

It is well-accepted that the liver plays a vital role in the metabolism of glucose and its homeostasis. Dysregulated hepatic glucose production and utilization, leads to type 2 diabetes (T2DM). In the current study, RNA sequencing and qRT-PCR analysis of nanoformulation-treated T2DM mice (TGthr group) revealed beneficial crosstalk of PCK-1 silencing with other pathways involved in T2DM. The comparison of precise genetic expression profiles of the different experimental groups showed significantly improved hepatic glucose, fatty acid metabolism and several other T2DM-associated crucial markers after the nanoformulation treatment. As a result of these improvements, we observed a significant acceleration in wound healing and improved insulin signaling in vascular endothelial cells in the TGthr group as compared to the T2DM group. Enhanced phosphorylation of PI3K/Akt pathway proteins in the TGthr group resulted in increased angiogenesis as observed by the increased expression of endothelial cell markers (CD31, CD34) thereby improving endothelial dysfunctions in the TGthr group. Additionally, therapeutic nanoformulation has been observed to improve the inflammatory cytokine profile in the TGthr group. Overall, our results demonstrated that the synthesized therapeutic nanoformulation referred to as GPR8:PCK-1siRNA holds the potential in ameliorating hyperglycemia-associated complications such as delayed wound healing in diabetes.

Comparison of Novel Proteomic Expression Profiles for Radiation Exposure in Male and Female C57BL6 Mice.

There is a need for point-of-care diagnostics for future mass casualty events involving radiation exposure. The development of radiation exposure and dose prediction algorithms for biodosimetry is needed for screening of large populations during these scenarios, and exploration of the potential effects which sex, age, genetic heterogeneity, and physiological comorbidities may have on the utility of biodosimetry diagnostics is needed. In the current study, proteomic profiling was used to examine sex-specific differences in age-matched C57BL6 mice on the blood proteome after radiation exposure, and the usefulness of development and application of biodosimetry algorithms using both male and female samples. Male and female mice between 9-11 weeks of age received a dose of total-body irradiation (TBI) of either 2, 4 or 8 Gy and plasma was collected at days 1, 3 and 7 postirradiation. Plasma was then screened using the SomaScan v4.1 assay for ∼7,000 protein analytes. A subset panel of protein biomarkers demonstrated significant (FDR < 0.05 and |logFC| > 0.2) changes in expression after radiation exposure. All proteins were used for feature selection to build predictive models of radiation exposure using different sample and sex-specific cohorts. Both binary (prediction of any radiation exposure) and multidose (prediction of specific radiation dose) model series were developed using either female and male samples combined or only female or only male samples. The binary series (models 1, 2 and 3) and multidose series (models 4, 5 and 6) included female/male combined, female only and male only respectively. Detectable values were obtained for all ∼7,000 proteins included in the SomaScan assay for all samples. Each model algorithm built using a unique sample cohort was validated with a training set of samples and tested with a separate new sample series. Overall predictive accuracies in the binary model series was ∼100% at the model training level, and when tested with fresh samples, 97.9% for model 1 (female and male) and 100% for model 2 (female only) and model 3 (male only). When sex-specific models 2 and 3 were tested with the opposite sex, the overall predictive accuracy rate dropped to 62.5% for model 2 and remained 100% for model 3. The overall predictive accuracy rate in the multidose model series was 100% for all models at the model training level and, when tested with fresh samples, 83.3%, 75% and 83.3% for Multidose models 4-6, respectively. When sex-specific model 5 (female only) and model 6 (male only) were tested with the opposite sex, the overall predictive accuracy rate dropped to 52.1% and 68.8%, respectively. These models represent novel predictive panels of radiation-responsive proteomic biomarkers and illustrate the utility and necessity of considering sex-specific differences in development of radiation biodosimetry prediction algorithms. As sex-specific differences were observed in this study, and as use of point-of-care radiation diagnostics in future mass casualty settings will necessarily include persons of both sexes, consideration of sex-specific variation is essential to ensure these diagnostic tools have practical utility in the field.