Aberrant DNA repair reveals a vulnerability in histone H3.3-mutant brain tumors.

Pediatric high-grade gliomas (pHGG) are devastating and incurable brain tumors with recurrent mutations in histone H3.3. These mutations promote oncogenesis by dysregulating gene expression through alterations of histone modifications. We identify aberrant DNA repair as an independent mechanism, which fosters genome instability in H3.3 mutant pHGG, and opens new therapeutic options. The two most frequent H3.3 mutations in pHGG, K27M and G34R, drive aberrant repair of replication-associated damage by non-homologous end joining (NHEJ). Aberrant NHEJ is mediated by the DNA repair enzyme polynucleotide kinase 3'-phosphatase (PNKP), which shows increased association with mutant H3.3 at damaged replication forks. PNKP sustains the proliferation of cells bearing H3.3 mutations, thus conferring a molecular vulnerability, specific to mutant cells, with potential for therapeutic targeting.

Effect of simulated cataract on the accuracy of artificial intelligence in detecting diabetic retinopathy in color fundus photos.

PURPOSE: Artificial intelligence (AI) is often trained on images without ocular co-morbidities, limiting its generalizability. This study aims to evaluate the accuracy of a convolutional neural network (CNN) applied to color fundus photos (CFPs) with simulated cataracts (SCs) in detecting diabetic retinopathy (DR). METHODS: A database of 3662 CFPs (from Asia Pacific Tele-Ophthalmology Society (APTOS) 2019) was used. Using transfer learning, a CNN was trained to classify the training images as either DR or non-DR. The CNN was then applied to classify the testing images after an SC was applied, using varying degrees of Gaussian blur. RESULTS: Accuracy without SC was 97.0%, sensitivity (Sn) 95.7%, specificity (Sp) 98.3%. For mild SC, accuracy was 93.1%, Sn 91.8%, Sp 94.3%. For moderate SC, accuracy was 62.8%, Sn 31.4%, Sp 95.2%. For severe SC, accuracy was 53.5%, Sn 11.8%, Sp 96.5%. CONCLUSION: SCs significantly impaired AI accuracy. To prepare AI for clinical use, cataracts and other real-world clinical challenges affecting image quality must be accounted for.

Genomic sequence context differs between germline and somatic structural variants allowing for their differentiation in tumor samples without paired normals.

There is currently no method to distinguish between germline and somatic structural variants (SVs) in tumor samples that lack a matched normal sample. In this study, we analyzed several features of germline and somatic SVs from a cohort of 974 patients from The Cancer Genome Atlas (TCGA). We identified a total of 21 features that differed significantly between germline and somatic SVs. Several of the germline SV features were associated with each other, as were several of the somatic SV features. We also found that these associations differed between the germline and somatic classes, for example, we found that somatic inversions were more likely to be longer events than their germline counterparts. Using these features we trained a support vector machine (SVM) classifier on 555,849 TCGA SVs to computationally distinguish germline from somatic SVs in the absence of a matched normal. This classifier had an ROC curve AUC of 0.984 when tested on an independent test set of 277,925 TCGA SVs. In this dataset, we achieved a positive predictive value (PPV) of 0.81 for an SV called somatic by the classifier being truly somatic. We further tested the classifier on a separate set of 7,623 SVs from pediatric high-grade gliomas (pHGG). In this non-TCGA cohort, our classifier achieved a PPV of 0.828, showing robust performance across datasets.

Structural variants shape driver combinations and outcomes in pediatric high-grade glioma.

We analyzed the contributions of structural variants (SVs) to gliomagenesis across 179 pediatric high-grade gliomas (pHGGs). The most recurrent SVs targeted MYC isoforms and receptor tyrosine kinases (RTKs), including an SV amplifying a MYC enhancer in 12% of diffuse midline gliomas (DMG), indicating an underappreciated role for MYC in pHGG. SV signature analysis revealed that tumors with simple signatures were TP53 wild type (TP53WT) but showed alterations in TP53 pathway members PPM1D and MDM4. Complex signatures were associated with direct aberrations in TP53, CDKN2A and RB1 early in tumor evolution and with later-occurring extrachromosomal amplicons. All pHGGs exhibited at least one simple-SV signature, but complex-SV signatures were primarily restricted to subsets of H3.3K27M DMGs and hemispheric pHGGs. Importantly, DMGs with complex-SV signatures were associated with shorter overall survival independent of histone mutation and TP53 status. These data provide insight into the impact of SVs on gliomagenesis and the mechanisms that shape them.

FOXR2 Is an Epigenetically Regulated Pan-Cancer Oncogene That Activates ETS Transcriptional Circuits.

Forkhead box R2 (FOXR2) is a forkhead transcription factor located on the X chromosome whose expression is normally restricted to the testis. In this study, we performed a pan-cancer analysis of FOXR2 activation across more than 10,000 adult and pediatric cancer samples and found FOXR2 to be aberrantly upregulated in 70% of all cancer types and 8% of all individual tumors. The majority of tumors (78%) aberrantly expressed FOXR2 through a previously undescribed epigenetic mechanism that involves hypomethylation of a novel promoter, which was functionally validated as necessary for FOXR2 expression and proliferation in FOXR2-expressing cancer cells. FOXR2 promoted tumor growth across multiple cancer lineages and co-opted ETS family transcription circuits across cancers. Taken together, this study identifies FOXR2 as a potent and ubiquitous oncogene that is epigenetically activated across the majority of human cancers. The identification of hijacking of ETS transcription circuits by FOXR2 extends the mechanisms known to active ETS transcription factors and highlights how transcription factor families cooperate to enhance tumorigenesis. SIGNIFICANCE: This work identifies a novel promoter that drives aberrant FOXR2 expression and delineates FOXR2 as a pan-cancer oncogene that specifically activates ETS transcriptional circuits across human cancers. See related commentary by Liu and Northcott, p. 2977.

NFAT-dependent and -independent exhaustion circuits program maternal CD8 T cell hypofunction in pregnancy.

Pregnancy is a common immunization event, but the molecular mechanisms and immunological consequences provoked by pregnancy remain largely unknown. We used mouse models and human transplant registry data to reveal that pregnancy induced exhausted CD8 T cells (Preg-TEX), which associated with prolonged allograft survival. Maternal CD8 T cells shared features of exhaustion with CD8 T cells from cancer and chronic infection, including transcriptional down-regulation of ribosomal proteins and up-regulation of TOX and inhibitory receptors. Similar to other models of T cell exhaustion, NFAT-dependent elements of the exhaustion program were induced by fetal antigen in pregnancy, whereas NFAT-independent elements did not require fetal antigen. Despite using conserved molecular circuitry, Preg-TEX cells differed from TEX cells in chronic viral infection with respect to magnitude and dependency of T cell hypofunction on NFAT-independent signals. Altogether, these data reveal the molecular mechanisms and clinical consequences of maternal CD8 T cell hypofunction and identify pregnancy as a previously unappreciated context in which T cell exhaustion may occur.

Rare case of endogenous Klebsiella endophthalmitis associated with emphysematous prostatitis in a patient with diabetes, cirrhosis and COVID-19.

A 35-year-old Hispanic man presented with fever, chills, dysuria, diarrhoea, scleral icterus, tachycardia and tachypnea. He was found to be COVID-19 positive, CT of the pelvis revealed prostatic abscess, and urine culture grew Klebsiella pneumoniae Additionally, he was found to have diabetes and cirrhosis. During treatment, the patient developed vision loss, and was diagnosed with endogenous Klebsiella endophthalmitis. The patient was treated with intravenous antibiotics, pars plana vitrectomy, intravitreal antibiotics and cystoscopy/suprapubic catheter placement. On follow-up, the patient has had the suprapubic catheter removed, and successfully passed a voiding trial, but suffers permanent vision loss in both eyes.

Use of Adrenocorticotropic Hormone in Ophthalmology.

The ability of the adrenocorticotropic hormone (ACTH) to induce steroidogenesis and upregulate anti-inflammatory processes has long been known. More recently, however, extrasteroidal mechanisms, through which ACTH exerts anti-inflammatory processes, have been described. This has renewed hope that ACTH can combat inflammatory conditions even when resistant to steroids. This review article summarizes the literature on the use of ACTH in ocular disease. Unfortunately, much of the data regarding the clinical utility of ACTH are outdated, with many studies published in the 1950s and 1960s. Many of these older studies are inconsistent or incomplete with their reporting, making it difficult to ascertain the meaning of the outcomes. Despite the limitations, 2 important trends are evident. First, when used to treat an inflammatory disease, ACTH can be effective at decreasing or eliminating ocular inflammation, even in a refractory disease resistant to multiple treatment modalities. Second, adverse effects of ACTH are rare and are most likely to be reported with relatively high doses of ACTH therapy. Taken as a whole, these studies offer initial promising data that ACTH may be a safe and effective alternative in refractory ocular inflammatory disease. However, they highlight an important lack of prospective data to more rigorously understand the true safety and efficacy of this therapy.