PPAR and GST polymorphisms may predict changes in intellectual functioning in medulloblastoma survivors

Comparative Study of Gut Microbiome in Urban and Rural Eurasian Tree Sparrows

Gut microbiota play a significant role in various physiological functions, including digestion, nutritional metabolism, and host immune function. The composition of these gut microbes is largely influenced by habitats. This study examines the gut microbiota of the Eurasian tree sparrow (Passer montanus) inhabiting rural and urban environments to understand the effects of habitat variation on microbial composition. We captured 36 rural and 29 urban adult tree sparrows and observed minor differences in body mass but substantial differences in foraging microhabitats between the two groups. Fecal samples from adult males with similar body mass were selected for a gut microbiome analysis to mitigate potential confounding effects, resulting in 20 successfully sequenced samples. The analysis disclosed disparities in gut microbiota diversity and composition between rural and urban sparrows. The urban group demonstrated slightly higher alpha diversity and distinct dominant phyla and genera compared to the rural group. Additionally, differences in the relative abundance of potentially pathogenic bacteria were observed between the groups. Several potentially pathogenic bacteria (e.g., TM7, Staphylococcus, Helicobacter, and Shigella) were more abundant in the urban group, suggesting that tree sparrows may act as transmission vectors and develop stronger immune systems. This could potentially facilitate pathogen dissemination while also contributing to the natural cycling of nutrients and maintaining ecosystem health in urban environments. The beta diversity analysis confirmed structural differences in microbial communities, implicating habitat variation as a contributing factor. Furthermore, the LEfSe analysis emphasized significant differences in gut bacteria abundance (across two phyla, three classes, six orders, seven families, and eight genera) between urban and rural sparrows, with predicted functional differences in metabolic pathways. Notably, lipid metabolism was enriched in urban sparrows, indicating enhanced lipid synthesis and metabolism in urban habitats. In conclusion, this study underscores the profound influence of habitat on the gut microbiota composition and functional potential in tree sparrows. Our findings highlight that urbanization alters the gut microbes and, consequently, the physiological functions of bird species.

Comprehensive Analysis of the Mechanism of Anoikis in Hepatocellular Carcinoma

Background

Hepatocellular carcinoma (HCC), ranking as the second-leading cause of global mortality among malignancies, poses a substantial burden on public health worldwide. Anoikis, a type of programmed cell death, serves as a barrier against the dissemination of cancer cells to distant organs, thereby constraining the progression of cancer. Nevertheless, the mechanism of genes related to anoikis in HCC is yet to be elucidated.

Methods

This paper's data (TCGA-HCC) were retrieved from the database of the Cancer Genome Atlas (TCGA). Differential gene expression with prognostic implications for anoikis was identified by performing both the univariate Cox and differential expression analyses. Through unsupervised cluster analysis, we clustered the samples according to these DEGs. By employing the least absolute shrinkage and selection operator Cox regression analysis (CRA), a clinical predictive gene signature was generated from the DEGs. The Cell-Type Identification by Estimating Relative Subsets of RNA Transcripts (CIBERSORT) algorithm was used to determine the proportions of immune cell types. The external validation data (GSE76427) were procured from Gene Expression Omnibus (GEO) to verify the performance of the clinical prognosis gene signature. Western blotting and immunohistochemistry (IHC) analysis confirmed the expression of risk genes.

Results

In total, 23 prognostic DEGs were identified. Based on these 23 DEGs, the samples were categorized into four distinct subgroups (clusters 1, 2, 3, and 4). In addition, a clinical predictive gene signature was constructed utilizing ETV4, PBK, and SLC2A1. The gene signature efficiently distinguished individuals into two risk groups, specifically low and high, demonstrating markedly higher survival rates in the former group. Significant correlations were observed between the expression of these risk genes and a variety of immune cells. Moreover, the outcomes from the validation cohort analysis aligned consistently with those obtained from the training cohort analysis. The results of Western blotting and IHC showed that ETV4, PBK, and SLC2A1 were upregulated in HCC samples.

Conclusion

The outcomes of this paper underscore the effectiveness of the clinical prognostic gene signature, established utilizing anoikis-related genes, in accurately stratifying patients. This signature holds promise in advancing the development of personalized therapy for HCC.

Mechanisms of imbalanced testicular homeostasis in infancy due to aberrant histone acetylation in undifferentiated spermatogonia under different concentrations of Di(2-ethylhexyl) phthalate (DEHP) exposure

Di (2-ethylhexyl) phthalate (DEHP), identified as an endocrine-disrupting chemical, is associated with reproductive toxicity. This association is particularly noteworthy in newborns with incompletely developed metabolic functions, as exposure to DEHP can induce enduring damage to the reproductive system, potentially influencing adult reproductive health. In this study, we continuously administered 40 μg/kg and 80 μg/kg DEHP to postnatal day 5 (PD5) mice for ten days to simulate low and high doses of DEHP exposure during infancy. Utilizing single-cell RNA sequencing (scRNA-seq), our analysis revealed that varying concentrations of DEHP exposure during infancy induced distinct DNA damage response characteristics in testicular Undifferentiated spermatogonia (Undiff SPG). Specifically, DNA damage triggered mitochondrial dysfunction, leading to acetyl-CoA content alterations. Subsequently, this disruption caused aberrations in histone acetylation patterns, ultimately resulting in apoptosis of Undiff SPG in the 40 μg/kg DEHP group and autophagy in the 80 μg/kg DEHP group. Furthermore, we found that DEHP exposure impacts the development and functionality of Sertoli and Leydig cells through the focal adhesion and PPAR signaling pathways, respectively. We also revealed that Leydig cells regulate the metabolic environment of Undiff SPG via Ptn-Sdc4 and Mdk-Sdc4 after DEHP exposure. Finally, our study provided pioneering evidence that disruptions in testicular homeostasis induced by DEHP exposure during infancy endure into adulthood. In summary, this study elucidates the molecular mechanisms through which DEHP exposure during infancy influences the development of testicular cell populations.

Multiomics characterization of fatty acid metabolism for the clinical management of hepatocellular carcinoma

Hepatocellular carcinoma (HCC) is a prevalent malignancy and there is a lack of effective biomarkers for HCC diagnosis. Living organisms are complex, and different omics molecules interact with each other to implement various biological functions. Genomics and metabolomics, which are the top and bottom of systems biology, play an important role in HCC clinical management. Fatty acid metabolism is associated with malignancy, prognosis, and immune phenotype in cancer, which is a potential hallmark in malignant tumors. In this study, the genes and metabolites related to fatty acid metabolism were thoroughly investigated by a dynamic network construction algorithm named EWS-DDA for the early diagnosis and prognosis of HCC. Three gene ratios and eight metabolite ratios were identified by EWS-DDA as potential biomarkers for HCC clinical management. Further analysis using biological analysis, statistical analysis and document validation in the discovery and validation sets suggested that the selected potential biomarkers had great clinical prognostic value and helped to achieve effective early diagnosis of HCC. Experimental results suggested that in-depth evaluation of fatty acid metabolism from different omics viewpoints can facilitate the further understanding of pathological alterations associated with HCC characteristics, improving the performance of early diagnosis and clinical prognosis.

Genetic susceptibility to cognitive decline following craniospinal irradiation for pediatric central nervous system tumors

BACKGROUND

Survivors of pediatric central nervous system (CNS) tumors treated with craniospinal irradiation (CSI) exhibit long-term cognitive difficulties. Goals of this study were to evaluate longitudinal effects of candidate and novel genetic variants on cognitive decline following CSI.

METHODS

Intelligence quotient (IQ), working memory (WM), and processing speed (PS) were longitudinally collected from patients treated with CSI (n = 241). Genotype-by-time interactions were evaluated using mixed-effects linear regression to identify common variants (minor allele frequency > 1%) associated with cognitive performance change. Novel variants associated with cognitive decline (P < 5 × 10-5) in individuals of European ancestry (n = 163) were considered replicated if they demonstrated consistent genotype-by-time interactions (P < .05) in individuals of non-European ancestries (n = 78) and achieved genome-wide statistical significance (P < 5 × 10-8) in a meta-analysis across ancestry groups.

RESULTS

Participants were mostly males (65%) diagnosed with embryonal tumors (98%) at a median age of 8.3 years. Overall, 1150 neurocognitive evaluations were obtained (median = 5, range: 2-10 per participant). One of the five loci previously associated with cognitive outcomes in pediatric CNS tumors survivors demonstrated significant time-dependent IQ declines (PPARA rs6008197, P = .004). Two variants associated with IQ in the general population were associated with declines in IQ after Bonferroni correction (rs9348721, P = 1.7 × 10-5; rs31771, P = 7.8 × 10-4). In genome-wide analyses, we identified novel loci associated with accelerated declines in IQ (rs116595313, meta-P = 9.4 × 10-9), WM (rs17774009, meta-P = 4.2 × 10-9), and PS (rs77467524, meta-P = 1.5 × 10-8; rs17630683, meta-P = 2.0 × 10-8; rs73249323, meta-P = 3.1 × 10-8).

CONCLUSIONS

Inherited genetic variants involved in baseline cognitive functioning and novel susceptibility loci jointly influence the degree of treatment-associated cognitive decline in pediatric CNS tumor survivors.

An angiogenesis-related lncRNA signature predicts the immune microenvironment and prognosis of breast cancer

Both angiogenesis and lncRNAs play crucial roles in the development and progression of breast cancer. Considering the unknown association of angiogenesis and lncRNAs in breast cancer, we aim to identify angiogenesis-related lncRNAs (ARLs) and explore their prognostic value. Here, based on analysis of The Cancer Genome Atlas database, the correlation between ARL and the prognosis and immune infiltration landscape of breast cancer were investigated. Eight ARLs (MAFG-DT, AC097478.1, AL357054.4, AL118556.1, SNHG10, MED14OS, OTUD6B-AS1, and CYTOR) were selected to construct the risk model as a prognostic signature. The survival rate of the patients in the high-risk group was lower than that in the low-risk group. The ARL signature was an independent prognostic predictor, and areas under the curve of 1-, 3-, and 5-year survival were 0.745, 0.695, and 0.699, respectively. The prognostic ARLs were associated with the immune infiltration landscape and could indicate the immune status, immune response, tumor mutational burden, and drug sensitivity of patients with breast cancer. Furthermore, qRT-PCR of clinical samples revealed that OTUD6B-AS1 was correlated with prognostic pathological parameters. OTUD6B-AS1 promoted breast cancer cell proliferation, wound healing, migration, invasion, and human umbilical vein endothelial cells tube formation. Mechanistically, OTUD6B-AS1 regulated EMT- and angiogenesis-related molecules. Taken together, we constructed and verified a robust signature of eight ARLs for the prediction of survival in patients with breast cancer, and the characterization of the immune infiltration landscape. Our findings suggest that OTUD6B-AS1 could be a therapeutic target for patients with breast cancer.

Integrated analysis of multiple transcriptomic data identifies ST8SIA6‑AS1 and LINC01093 as potential biomarkers in HBV‑associated liver cancer

The mechanisms of long-non-coding RNAs (lncRNAs) in hepatitis B virus (HBV) infection-associated liver cancer remain largely unclear. Therefore, the aim of the present study was to investigate the regulatory mechanisms of lncRNAs in this disease. HBV-liver cancer related transcriptome expression profile data (GSE121248 and GSE55092) from the Gene Expression Omnibus database and survival prognosis information from The Cancer Genome Atlas (TCGA) database were obtained for analysis. The limma package was used to identify the overlapped differentially expressed RNAs (DERs), including DElncRNAs and DEmRNAs, in the GSE121248 and GSE55092 datasets. The screened optimized lncRNA signatures were used to develop a nomogram model based on the GSE121248 dataset, which was validated using the GSE55092 and TCGA datasets. A competitive endogenous RNA (ceRNA) network was constructed based on the screened prognosis-associated lncRNA signatures from TCGA dataset. In addition, the levels of specific lncRNAs were evaluated in HBV-infected human liver cancer tissues and cells, and Cell Counting Kit-8, ELISA and Transwell assays were performed to evaluate the effects of the lncRNAs in HBV-expressing liver cancer cells. A total of 535 overlapped DERs, including 30 DElncRNAs and 505 DEmRNAs, were identified in the GSE121248 and GSE55092 datasets. An optimized DElncRNA signature comprising 10 lncRNAs was used to establish a nomogram. ST8SIA6-AS1 and LINC01093 were identified as lncRNAs associated with HBV-liver cancer prognosis in TCGA dataset, and were applied to construct a ceRNA network. Reverse transcription-quantitative PCR analysis showed that ST8SIA6-AS1 was upregulated and LINC01093 was downregulated in HBV-infected human liver cancer tissues and HBV-expressing liver cancer cells compared with non-HBV-infected controls. ST8SIA6-AS1 knockdown and LINC01093 overexpression independently reduced the number of copies of HBV DNA, the levels of hepatitis B surface antigen and hepatitis B e antigen, as well as cell proliferation, migration and invasion. In summary, the present study identified ST8SIA6-AS1 and LINC01093 as two potential biomarkers that may be effective therapeutic targets for HBV-associated liver cancer.

A Systematic Review of Host Genomic Variation and Neuropsychological Outcomes for Pediatric Cancer Survivors

Pediatric survivors of brain tumors and acute lymphoblastic leukemia (ALL) are at risk for long-term deficits in their neuropsychological functioning. Researchers have begun examining associations between germline single nucleotide polymorphisms (SNPs), which interact with cancer treatment, and neuropsychological outcomes. This review synthesizes the impact of treatment-related toxicity from germline SNPs by neuropsychological domain (i.e., working memory, processing speed, psychological functioning) in pediatric survivors. By focusing on specific neuropsychological domains, this review will examine outcome measurement and critique methodology. Fourteen studies were identified and included in this review using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA). All studies were published in peer-reviewed journals in English by November 24th, 2021. Reviewed studies were not of sufficient quality for a meta-analysis due to varying measurement strategies, gaps in reported descriptive variables, and low power. All neuropsychological domains evaluated in this review had associations with SNPs, except fine motor and visual integration abilities. Only five SNPs had consistent neuropsychological findings in more than one study or cohort. Future research and replication studies should use validated measures of discrete skills that are central to empirically validated models of survivors' long-term outcomes (i.e., attention, working memory, processing speed). Researchers should examine SNPs across pathophysiological pathways to investigate additive genetic risk in pediatric cancer survivors. Two SNPs were identified that confer resiliency in neuropsychological functioning, and future work should investigate resiliency genotypes and their underlying biological mechanisms.

Prognostic and immune microenvironment analysis of cuproptosis-related LncRNAs in breast cancer

Breast cancer is the most common tumor and the leading cause of cancer death in women. Cuproptosis is a new type of cell death, which can induce proteotoxic stress and eventually lead to cell death. Therefore, regulating copper metabolism in tumor cells is a new therapeutic approach. Long non-coding RNAs play an important regulatory role in immune response. At present, cuproptosis-related lncRNAs in breast cancer have not been reported. Breast cancer RNA sequencing, genomic mutations, and clinical data were downloaded from The Cancer Genome Atlas (TCGA). Patients with breast cancer were randomly assigned to the train group or the test group. Co-expression network analysis, Cox regression method, and least absolute shrinkage and selection operator (LASSO) method were used to identify cuproptosis-related lncRNAs and to construct a risk prognostic model. The prediction performance of the model is verified and recognized. In addition, the nomogram was used to predict the prognosis of breast cancer patients. Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and immunoassay were used to detect the differences in biological function. Tumor mutation burden (TMB) was used to measure immunotherapy response. A total of 19 cuproptosis genes were obtained and a prognostic model based on 10 cuproptosis-related lncRNAs was constructed. Kaplan-Meier survival curves showed statistically significant overall survival (OS) between the high-risk and low-risk groups. Receiver operating characteristic curve (ROC) and principal component analysis (PCA) show that the model has accurate prediction ability. Compared with other clinical features, cuproptosis-related lncRNAs model has higher diagnostic efficiency. Univariate and multivariate Cox regression analysis showed that risk score was an independent prognostic factor for breast cancer patients. In addition, the nomogram model analysis showed that the tumor mutation burden was significantly different between the high-risk and low-risk groups. Of note, the additive effect of patients in the high-risk group and patients with high TMB resulted in reduced survival in breast cancer patients. Our study identified 10 cuproptosis-related lncRNAs, which may be promising biomarkers for predicting the survival prognosis of breast cancer.

Molecular mechanism of Cuscutae semen-radix rehmanniae praeparata in relieving reproductive injury of male rats induced with tripterygium wilfordii multiglycosides: A tandem mass tag-based proteomics analysis

Background: We determined the effects of Cuscutae semen (Cuscuta chinensis Lam. or Cuscuta australis R. Br.)-Radix rehmanniae praeparata (Rehjnannia glutinosa Libosch.) on the protein levels in testicular tissues of rats gavaged with tripterygium wilfordii multiglycosides (GTW) and elucidated the molecular mechanism underlying Cuscutae semen-Radix rehmanniae praeparata for relieving GTW-induced reproductive injury. Methods: A total of 21 male Sprague-Dawley rats were randomly divided into the control group, model group, and Cuscutae semen-Radix rehmanniae praeparata group based on their body weights. The control group was given 10 mLkg^-1 of 0.9% normal saline by gavage daily. The model group (GTW group) was administered with 12 mg kg^-1 GTW by gavage daily. Cuscutae semen-Radix rehmanniae praeparata group (the TSZSDH group) was administered with 1.56 gkg^-1 of Cuscutae semen-Radix rehmanniae praeparata granules daily according to their model group dosing. The serum levels of luteinizing hormone, follicle-stimulating hormone, estradiol, and testosterone were measured after 12 weeks of continuous gavage, and the pathological lesion of testicular tissues was observed. Differentially expressed proteins were evaluated by quantitative proteomics and verified by western blotting (WB) and Real-Time Quantitative Polymerase Chain Reaction (RT-qPCR). Results: Cuscutae semen-Radix rehmanniae praeparata can effectively relieve pathological lesions of GTW-induced testicular tissues. A total of 216 differentially expressed proteins were identified in the TSZSDH group and model group. High-throughput proteomics revealed that differentially expressed proteins are closely associated with the peroxisome proliferator-activated receptor (PPAR) signaling pathway, protein digestion and absorption, and protein glycan pathway in cancer. Cuscutae semen-Radix rehmanniae praeparata can significantly upregulate the protein expressions of Acsl1, Plin1, Dbil5, Plin4, Col12a1, Col1a1, Col5a3, Col1a2, Dcn, so as to play a protective role on testicular tissues. Acsl1, Plin1, and PPARγ on the PPAR signaling pathway were verified by WB and RT-qPCR experiments, which were found to be consistent with the results of proteomics analysis. Conclusion: Cuscutae semen and Radix rehmanniae praeparata may regulate the PPAR signaling pathway mediated Acsl1, Plin1 and PPARγ to reduce the testicular tissue damage of male rats caused by GTW.

Development and Validation of a Novel PPAR Signaling Pathway-Related Predictive Model to Predict Prognosis in Breast Cancer

This study is aimed at exploring the potential mechanism of the PPAR signaling pathway in breast cancer (BRCA) and constructing a novel prognostic-related risk model. We used various bioinformatics methods and databases to complete our exploration in this research. Based on TCGA database, we use multiple extension packages based on the R language for data conversion, processing, and statistics. We use LASSO regression analysis to establish a prognostic-related risk model in BRCA. And we combined the data of multiple online websites, including GEPIA, ImmuCellAI, TIMER, GDSC, and the Human Protein Atlas database to conduct a more in-depth exploration of the risk model. Based on the mRNA data in TCGA database, we conducted a preliminary screening of genes related to the PPAR signaling pathway through univariate Cox analysis, then used LASSO regression analysis to conduct a second screening, and successfully established a risk model consisting of ten genes in BRCA. The results of ROC curve analysis show that the risk model has good prediction accuracy. We can successfully divide breast cancer patients into high- and low-risk groups with significant prognostic differences (P = 1.92e - 05) based on this risk model. Combined with the clinical data in TCGA database, there is a correlation between the risk model and the patient's N, T, gender, and fustat. The results of multivariate Cox regression show that the risk score of this risk model can be used as an independent risk factor for BRCA patients. In particular, we draw a nomogram that can predict the 5-, 7-, and 10-year survival rates of BRCA patients. Subsequently, we conducted a series of pancancer analyses of CNV, SNV, OS, methylation, and immune infiltration for this risk model gene and used GDSC data to investigate drug sensitivity. Finally, to gain insight into the predictive value and protein expression of these risk model genes in breast cancer, we used GEO and HPA databases for validation. This study provides valuable clues for future research on the PPAR signaling pathway in BRCA.

Development and Validation of a Novel PPAR Signaling Pathway-Related Predictive Model to Predict Prognosis in Breast Cancer

This study is aimed at exploring the potential mechanism of the PPAR signaling pathway in breast cancer (BRCA) and constructing a novel prognostic-related risk model. We used various bioinformatics methods and databases to complete our exploration in this research. Based on TCGA database, we use multiple extension packages based on the R language for data conversion, processing, and statistics. We use LASSO regression analysis to establish a prognostic-related risk model in BRCA. And we combined the data of multiple online websites, including GEPIA, ImmuCellAI, TIMER, GDSC, and the Human Protein Atlas database to conduct a more in-depth exploration of the risk model. Based on the mRNA data in TCGA database, we conducted a preliminary screening of genes related to the PPAR signaling pathway through univariate Cox analysis, then used LASSO regression analysis to conduct a second screening, and successfully established a risk model consisting of ten genes in BRCA. The results of ROC curve analysis show that the risk model has good prediction accuracy. We can successfully divide breast cancer patients into high- and low-risk groups with significant prognostic differences (P = 1.92e - 05) based on this risk model. Combined with the clinical data in TCGA database, there is a correlation between the risk model and the patient's N, T, gender, and fustat. The results of multivariate Cox regression show that the risk score of this risk model can be used as an independent risk factor for BRCA patients. In particular, we draw a nomogram that can predict the 5-, 7-, and 10-year survival rates of BRCA patients. Subsequently, we conducted a series of pancancer analyses of CNV, SNV, OS, methylation, and immune infiltration for this risk model gene and used GDSC data to investigate drug sensitivity. Finally, to gain insight into the predictive value and protein expression of these risk model genes in breast cancer, we used GEO and HPA databases for validation. This study provides valuable clues for future research on the PPAR signaling pathway in BRCA.

Neuropsychological functioning in childhood cancer survivors following cranial radiotherapy - results from a long-term follow-up clinic

Treatment of malignant childhood posterior fossa tumors (CPFT) often includes surgical resection and craniospinal radiotherapy (CSI). Nasopharyngeal tumors in childhood (CNPHT) are often treated with surgery and radiotherapy (RT), leading to incidental brain irradiation. RT to the developing brain is associated with risks for cognitive impairments. We studied cognitive functioning, health-related quality of life (HRQOL), fatigue, and psychological distress, in adult survivors of CPFT and CNPHT, representing two groups, which had received high and low radiation dose-exposure to the brain, respectively. Cognitive tests were used to compare CPFT (n = 12) and CNPHT (n = 7) survivors to matched healthy controls (n = 28). HRQOL data was compared to the general population (GP) (n = 1415-1459). Average follow-up was 23 (CPFT) and 19 years (CNPHT). CPFT survivors had significant deficits in all cognitive domains. CNPHT survivors showed results below the control group but differed statistically only on one executive test. HRQOL-ratings indicated that both groups had similar self-reported cognitive problems. CPFT survivors reported more emotional problems and fatigue. Anxiety was seen in both CPFT and CNPHT survivors. This study confirmed long-term cognitive sequelae after RT in adult survivors of CPFT,and possible RT-induced cognitive deficits in adult CNPHT survivors.

Magnetic Resonance Imaging Findings Are Associated with Long-Term Global Neurological Function or Death after Traumatic Brain Injury in Critically Ill Children

The identification of children with traumatic brain injury (TBI) who are at risk of death or poor global neurological functional outcome remains a challenge. Magnetic resonance imaging (MRI) can detect several brain pathologies that are a result of TBI; however, the types and locations of pathology that are the most predictive remain to be determined. Forty-two critically ill children with TBI were recruited prospectively from pediatric intensive care units at five Canadian children's hospitals. Pathologies detected on subacute phase MRIs included cerebral hematoma, herniation, cerebral laceration, cerebral edema, midline shift, and the presence and location of cerebral contusion or diffuse axonal injury (DAI) in 28 regions of interest were assessed. Global functional outcome or death more than 12 months post-injury was assessed using the Pediatric Cerebral Performance Category score. Linear modeling was employed to evaluate the utility of an MRI composite score for predicting long-term global neurological function or death after injury, and nonlinear Random Forest modeling was used to identify which MRI features have the most predictive utility. A linear predictive model of favorable versus unfavorable long-term outcomes was significantly improved when an MRI composite score was added to clinical variables. Nonlinear Random Forest modeling identified five MRI variables as stable predictors of poor outcomes: presence of herniation, DAI in the parietal lobe, DAI in the subcortical white matter, DAI in the posterior corpus callosum, and cerebral contusion in the anterior temporal lobe. Clinical MRI has prognostic value to identify children with TBI at risk of long-term unfavorable outcomes.

Identification of a Potential PPAR-Related Multigene Signature Predicting Prognosis of Patients with Hepatocellular Carcinoma

Peroxisome proliferator-activated receptors (PPARs) and part of their target genes have been reported to be related to the progression of hepatocellular carcinoma (HCC). The prognosis of HCC is not optimistic, and more accurate prognostic markers are needed. This study focused on discovering potential prognostic markers from the PPAR-related gene set. The mRNA data and clinical information of HCC were collected from TCGA and GEO platforms. Univariate Cox and lasso Cox regression analyses were used to screen prognostic genes of HCC. Three genes (MMP1, HMGCS2, and SLC27A5) involved in the PPAR signaling pathway were selected as the prognostic signature of HCC. A formula was established based on the expression values and multivariate Cox regression coefficients of selected genes, that was, risk score = 0.1488∗expression value of MMP1 + (−0.0393)∗expression value of HMGCS2 + (−0.0479)∗expression value of SLC27A5. The prognostic ability of the three-gene signature was assessed in the TCGA HCC dataset and verified in three GEO sets (GSE14520, GSE36376, and GSE76427). The results showed that the risk score based on our signature was a risk factor with a HR (hazard ratio) of 2.72 (95%CI (Confidence Interval) = 1.87 ~ 3.95, p < 0.001) for HCC survival. The signature could significantly (p < 0.0001) distinguish high-risk and low-risk patients with poor prognosis for HCC. In addition, we further explored the independence and applicability of the signature with other clinical indicators through multivariate Cox analysis (p < 0.001) and nomogram analysis (C‐index = 0.709). The above results indicate that the combination of MMP1, HMGCS2, and SLC27A5 selected from the PPAR signaling pathway could effectively, independently, and applicatively predict the prognosis of HCC. Our research provided new insights to the prognosis of HCC.

Mapping of long-term cognitive and motor deficits in pediatric cerebellar brain tumor survivors into a cerebellar white matter atlas

PURPOSE

Diaschisis of cerebrocerebellar loops contributes to cognitive and motor deficits in pediatric cerebellar brain tumor survivors. We used a cerebellar white matter atlas and hypothesized that lesion symptom mapping may reveal the critical lesions of cerebellar tracts.

METHODS

We examined 31 long-term survivors of pediatric posterior fossa tumors (13 pilocytic astrocytoma, 18 medulloblastoma). Patients underwent neuronal imaging, examination for ataxia, fine motor and cognitive function, planning abilities, and executive function. Individual consolidated cerebellar lesions were drawn manually onto patients' individual MRI and normalized into Montreal Neurologic Institute (MNI) space for further analysis with voxel-based lesion symptom mapping.

RESULTS

Lesion symptom mapping linked deficits of motor function to the superior cerebellar peduncle (SCP), deep cerebellar nuclei (interposed nucleus (IN), fastigial nucleus (FN), ventromedial dentate nucleus (DN)), and inferior vermis (VIIIa, VIIIb, IX, X). Statistical maps of deficits of intelligence and executive function mapped with minor variations to the same cerebellar structures.

CONCLUSION

We identified lesions to the SCP next to deep cerebellar nuclei as critical for limiting both motor and cognitive function in pediatric cerebellar tumor survivors. Future strategies safeguarding motor and cognitive function will have to identify patients preoperatively at risk for damage to these critical structures and adapt multimodal therapeutic options accordingly.

The role of cerebellum in the child neuropsychological functioning

This chapter proposes a review of neuropsychologic and behavior findings in pediatric pathologies of the cerebellum, including cerebellar malformations, pediatric ataxias, cerebellar tumors, and other acquired cerebellar injuries during childhood. The chapter also contains reviews of the cerebellar mutism/posterior fossa syndrome, reported cognitive associations with the development of the cerebellum in typically developing children and subjects born preterm, and the role of the cerebellum in neurodevelopmental disorders such as autism spectrum disorders and developmental dyslexia. Cognitive findings in pediatric cerebellar disorders are considered in the context of known cerebellocerebral connections, internal cellular organization of the cerebellum, the idea of a universal cerebellar transform and computational internal models, and the role of the cerebellum in specific cognitive and motor functions, such as working memory, language, timing, or control of eye movements. The chapter closes with a discussion of the strengths and weaknesses of the cognitive affective syndrome as it has been described in children and some conclusions and perspectives.

Neurocognitive functioning and health-related quality of life in adult medulloblastoma patients: long-term outcomes of the NOA-07 study

Background

Combined radiochemotherapy followed by maintenance chemotherapy with cisplatin, lomustine and vincristine within the NOA-07 study resulted in considerable short-term toxicity in adult medulloblastoma patients. Here we investigated the long-term impact of this treatment, focusing on neurocognitive functioning and health-related quality of life (HRQoL).

Methods

Neurocognitive functioning and HRQoL scores over time were determined, and differences between the post-treatment and follow-up assessments were calculated up to 18 months for neurocognition and 60 months for HRQoL.

Results

28/30 patients were analyzed. The three preselected HRQoL scales (role, social and cognitive functioning) showed improved scores, to a clinically relevant extent (≥ 10 points), compared to post-treatment levels up to 30 months, but decreased afterwards. Z-scores for verbal working memory were worse during follow-up compared to post-treatment scores and remained impaired during 18 months follow-up (i.e. z-score below − 1 standard deviation). Attention was impaired post-treatment, and remained impaired to a clinically relevant extent during follow-up. Coordination/processing speed and lexical verbal fluency improved compared to post-treatment scores, and remained within the normal range thereafter. Other tests of verbal fluency were stable over time, with z-scores within the normal range.

Conclusions

This long-term follow-up study showed that the NOA-07 treatment regimen was not associated with a deterioration in HRQoL in the post-treatment period. Verbal working memory deteriorated, while other neurocognitive domains did not seem to be impacted negatively by the treatment.

Electronic supplementary material

The online version of this article (10.1007/s11060-020-03502-y) contains supplementary material, which is available to authorized users.

GSTP1 polymorphisms sex-specific association with verbal intelligence in survivors of pediatric medulloblastoma tumors

Glutathione S-transferase (GST) single nucleotide polymorphisms (SNPs) have been associated with a lower intellectual quotient (IQ) in medulloblastoma survivors. We investigated the association of GSTP1 polymorphisms with intellectual, neurocognitive skills (e.g., attention span, working memory, and processing speed), and adaptive outcomes for long-term pediatric medulloblastoma survivors. We hypothesized that genetic risk and sex-specific risk would contribute to significantly lower performances across all measures. Eighteen long-term pediatric medulloblastoma survivors completed the Wechsler Abbreviated Scale Intelligence, California Verbal Learning Test-II, Auditory Consonant Trigrams, and Oral Symbol Digit Modality Test. Informants were interviewed with the Scales of Independent Behavior-Revised (SIB-R). After controlling for the false discovery rate, females with a polymorphism performed significantly worse than females without a polymorphism on verbal IQ (p = .005) and SIB-R (p = .012). There was a significant interaction between sex and polymorphism status for verbal IQ (b = -1.8, SE = 0.827, CI: -3.58, -.036). The main effect of this interaction was significant for females (p = .004) and not for males (p = .557). We found large effect sizes between males with the polymorphism and females with the polymorphism across measures of attention span (g = .877), working memory (g = 1.12), and processing speed (g = 1.53). Female medulloblastoma survivors with a GSTP1 polymorphism may have increased vulnerability to deficits in core cognitive skills, IQ, and everyday functional outcomes. Sex-specific genetic risk contributes to the variability in long-term verbal intelligence for medulloblastoma survivors.

Late effects of pediatric brain tumors

PURPOSE OF REVIEW

Adverse late effects of pediatric brain tumors can be numerous and complex and potentially alter the life trajectories of survivors in a multitude of ways. We review these inter-related late effects that compromise neurocognitive function, general health, social and psychological adjustment, and overall adaptive and vocational outcomes, and threaten to undermine the ability of survivors to transition independently into adulthood and effectively manage their care. Intervention/prevention strategies and advances in treatment that may reduce such late effects are discussed.

RECENT FINDINGS

Studies of neuropsychological late effects have revealed specific deficits in core cognitive functions of attention, working memory and processing speed, with many survivors demonstrating decline in working memory and processing speed over time, irrespective of tumor type or treatment. This in turn affects the ongoing development of higher order neurocognitive skills. Research also highlights the increasing burden of health-related, neuropsychological and psychosocial late effects into adulthood and impact across life outcomes.

SUMMARY

Pediatric brain tumor survivors require coordinated interdisciplinary care, ongoing evaluation and management of late effects, and timely interventions focused on mitigating the impact of late effects. The transition to adulthood can be especially vulnerable and addressing barriers to care is of paramount importance.

PPAR signaling pathway in the first trimester placenta from in vitro fertilization and embryo transfer

Placenta is a temporary critical organ related to fetal development and pregnancy outcomes. And epidemiologic data demonstrate an increased risk of placental abnormality after in vitro fertilization and embryo transfer (IVF-ET). This study aims to explore the molecular mechanism for PPAR signaling pathway in placenta subjected to IVF-ET in the first trimester. Four first trimester placenta samples from double chorionic twins to single reduction in IVF-ET only because of oviducts factors. The other four control placenta samples from double chorionic twin were derived from those unplanned spontaneously conceived pregnancy after the legal termination. Affymetrix HG-U133 Plus 2.0 Array was performed to evaluate the global gene expressions. We confirmed microarray results from 10 significant differential genes using RT-qPCR. And 10 deregulated gene products were stained in the first trimester placenta by immunohistochemistry. These differentially expressed genes in IVF-ET placentas were submitted to functional annotation of clustering tools of bioinformatics resources and gene ontology enrichment analysis. Schematic representation of placental PPAR signaling pathway was labelled by Kyoto Encyclopedia of Genes and Genomes (KEGG). Analysis results of early placental PPAR signaling pathway gene expression from 8 women demonstrated 34 genes with a significant change in expression between IVF-ET and control group, 25 up-regulated; 9 down-regulated. KEGG pathway analysis indicated that IVF-ET manipulation extensively over-activated PPAR signaling pathway. Immune tolerance, trophoblast invasion, syncytia formation, lipid and glucose metabolism, inflammatory response and other complex biological functions were disturbed. RT-qPCR results and proteins staining intensity were consisted with microarray. Placental gene expressions and functions in PPAR signaling pathway were affected by IVF-ET treatment in the first trimester, which may offer a potential mechanism for the pathogenesis of various adverse outcomes during the perinatal period.

Host Genome Variation is Associated with Neurocognitive Outcome in Survivors of Pediatric Medulloblastoma

Host genome analysis is a promising source of predictive information for long-term morbidity in cancer survivors. However, studies on genetic predictors of long-term outcome, particularly neurocognitive function following chemoradiation in pediatric oncology, are limited. Here, we evaluated variation in host genome of long-term survivors of medulloblastoma and its association with neurocognitive outcome. Whole-genome sequencing was conducted on peripheral blood of long-term survivors of pediatric medulloblastoma who also completed neuropsychological testing. Cognitively impaired and less impaired survivors did not differ in exposure to chemoradiation therapy or age at treatment. Unsupervised consensus clustering yielded two distinct variant clusters that were significantly associated with neurocognitive outcome. Interestingly, 34 of the 36 significant variants were found in noncoding DNA regions with unknown regulatory function. A separate unsupervised cluster analysis of variants within DNA repair genes identified discrete variant groups that were not associated with neurocognitive outcome, suggesting that variations in genes corresponding to a single functional group may be insufficient to predict long-term outcome alone. These findings are supportive of the presence of a genetic diathesis for treatment-related neurocognitive morbidity in medulloblastoma that may be driven by variation in noncoding regulatory elements.