Digital Spatial Profiling for Characterization of the Microenvironment in Adult-Type Diffusely Infiltrating Glioma.

Diffusely infiltrating gliomas are associated with high morbidity and mortality due to the infiltrative nature of tumor spread. They are morphologically complex tumors, with a high degree of proteomic variability across both the tumor itself and its heterogenous microenvironment. The malignant potential of these tumors is enhanced by the dysregulation of proteins involved in several key pathways, including processes that maintain cellular stability and preserve the structural integrity of the microenvironment. Although there have been numerous bulk and single-cell glioma analyses, there is a relative paucity of spatial stratification of these proteomic data. Understanding differences in spatial distribution of tumorigenic factors and immune cell populations between the intrinsic tumor, invasive edge, and microenvironment offers valuable insight into the mechanisms underlying tumor proliferation and propagation. Digital spatial profiling (DSP) represents a powerful technology that can form the foundation for these important multilayer analyses. DSP is a method that efficiently quantifies protein expression within user-specified spatial regions in a tissue specimen. DSP is ideal for studying the differential expression of multiple proteins within and across regions of distinction, enabling multiple levels of quantitative and qualitative analysis. The DSP protocol is systematic and user-friendly, allowing for customized spatial analysis of proteomic data. In this experiment, tissue microarrays are constructed from archived glioblastoma core biopsies. Next, a panel of antibodies is selected, targeting proteins of interest within the sample. The antibodies, which are preconjugated to UV-photocleavable DNA oligonucleotides, are then incubated with the tissue sample overnight. Under fluorescence microscopy visualization of the antibodies, regions of interest (ROIs) within which to quantify protein expression are defined with the samples. UV light is then directed at each ROI, cleaving the DNA oligonucleotides. The oligonucleotides are microaspirated and counted within each ROI, quantifying the corresponding protein on a spatial basis.

Clinical management of brain tumors in pregnancy.

PURPOSE OF REVIEW: We review the diagnostic tools, treatment options, and clinical management for brain tumors diagnosed in pregnancy with consideration for management approaches that are best suited to preserve maternal and fetal health. RECENT FINDINGS: Women of child-bearing age are at risk of developing brain tumors and are at increased risk compared with male counterparts for tumors that are hormonally driven. Brain tumors are rare neoplasms, and diagnosis of brain tumors in pregnancy is uncommon, such that management guidelines and treatment recommendations are lacking for most tumor types. We discuss the standard treatment options for brain tumors and the relative risks and safety when these treatments are considered during pregnancy. We review the neoplasms most commonly affecting pregnant women and the existing literature and guidelines. SUMMARY: Pregnancy is a unique phase of life in which hormonal, immunologic, and vascular changes may impact tumor growth and presentation. Treatment decisions should consider the symptoms and stability of the pregnant patients, the gestational age and health of the fetus, and the location and behavior of the neoplasm.

Venetoclax: A Novel Therapeutic Agent for CLL with CNS Involvement.

Chronic lymphocytic leukemia (CLL) involves the proliferation of a clonal population of B cells within the bone marrow that classically spreads to the blood and lymphatic system. Central nervous system (CNS) manifestations of CLL occur rarely, and no gold standard treatment regimen has been designated to date. We report a case of CLL with CNS involvement in a 68-year-old woman who presented with a severe headache 4 years after initial diagnosis. She was started on ibrutinib, which failed to clear her CSF of malignancy. Venetoclax was then added, and this was successful in clearing her CSF. For its CNS penetration and efficacy in achieving CSF remission of CLL, we propose that venetoclax be considered as a treatment option for CLL meningitis.

ACTA2 leukovasculopathy: A rare pediatric white matter disorder.

A 3-year-old girl presented with ataxia, dilated pupils, and behavioral change prompting work up for stroke. Her medical history included chronic mydriasis and patent ductus arteriosus requiring aortoplasty. Magnetic resonance imaging of the brain demonstrated confluent white matter signal abnormality concerning for leukodystrophy. Magnetic resonance angiography revealed a cerebral vessel arteriopathy with a "broomstick appearance" and other neuroradiographic findings consistent with ACTA2 mutation. Pathogenic Arg179His ACTA2 mutation was confirmed in the patient. ACTA2-related leukovasculopathy should be considered during workup of patients with abnormal white matter (eg, leukodystrophies), childhood stroke, and arteriopathies. Recognizing the combination of commonly associated physical and medical conditions associated with radiographic features of this neurogenetic condition will prompt appropriate care and screening for comorbidities associated with this disorder.

Effect of fragmentation of cancer care on treatment use and survival in hepatocellular carcinoma.

BACKGROUND: Fragmented cancer care (FC), or care received from multiple institutions, increases systemic health care costs and potentiates cancer care disparities. There is a paucity of data on mechanisms contributing to FC and the resulting effect on patient outcomes. This study characterized patient- and hospital-level factors associated with FC, time to treatment (TTT), and overall survival (OS) in patients with hepatocellular carcinoma (HCC). METHODS: Patients newly diagnosed with HCC from 2004 to 2015 and receiving treatment were identified in the Texas Cancer Registry. Patient- and hospital-level factors were compared across 2 cohorts: an FC treatment group and a nonfragmented cancer care (NFC) treatment group. Covariate-adjusted treatment use and OS were compared between the 2 treatment groups. RESULTS: Among 4329 patients with HCC, 1185 (27.4%) received FC, and 3144 (72.6%) received NFC. Compared with NFC patients, FC patients had larger tumors (median size ≥4 cm, 52.6% vs 35.2%; P < .001), and a higher proportion had a regional/metastatic stage (35.9% vs 26.7%; P < .001). Among patients with localized disease, FC was associated with decreased odds of curative therapy (odds ratio, 0.83; 95% confidence interval [CI], 0.7-0.9). FC was associated with worse OS (hazard ratio [HR], 1.14; 95% CI, 1.05-1.24) and increased TTT (HR, 0.76; 95% CI, 0.7-0.8). In the subset of patients with localized-stage HCC who received curative therapy, FC was associated with worse OS (median survival, 67 vs 43 months; HR, 1.2; 95% CI, 1.0-1.4) and increased TTT (HR, 0.74; 95% CI, 0.7-0.8). CONCLUSIONS: FC patients were less likely to undergo curative therapy when they were diagnosed at an early stage. After covariate adjustment, newly diagnosed patients with HCC receiving FC had worse OS and increased TTT.

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

BACKGROUND: Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects like ENCODE and Illumina Body Map 2.0. RESULTS: We aligned 21,504 Illumina-sequenced human RNA-seq samples from the Sequence Read Archive (SRA) to the human genome and compared detected exon-exon junctions with junctions in several recent gene annotations. We found 56,861 junctions (18.6%) in at least 1000 samples that were not annotated, and their expression associated with tissue type. Junctions well expressed in individual samples tended to be annotated. Newer samples contributed few novel well-supported junctions, with the vast majority of detected junctions present in samples before 2013. We compiled junction data into a resource called intropolis available at http://intropolis.rail.bio . We used this resource to search for a recently validated isoform of the ALK gene and characterized the potential functional implications of unannotated junctions with publicly available TRAP-seq data. CONCLUSIONS: Considering only the variation contained in annotation may suffice if an investigator is interested only in well-expressed transcript isoforms. However, genes that are not generally well expressed and nonetheless present in a small but significant number of samples in the SRA are likelier to be incompletely annotated. The rate at which evidence for novel junctions has been added to the SRA has tapered dramatically, even to the point of an asymptote. Now is perhaps an appropriate time to update incomplete annotations to include splicing present in the now-stable snapshot provided by the SRA.

Persistent behavioral effects following early life exposure to retinoic acid or valproic acid in zebrafish.

BACKGROUND: Moderate to severe dysregulation in retinoid signaling during early development is associated with a constellation of physical malformations and/or neural tube defects, including spina bifida. It is thought that more subtle dysregulation of this system, which might be achievable via dietary (i.e. hypervitaminosis A) or pharmacological (i.e. valproic acid) exposure in humans, will manifest on behavioral domains including sociability, without overt physical abnormalities. METHODS: During early life, zebrafish were exposed to low doses of two chemicals that disrupt retinoid signaling. From 0 to 5dpf, larvae were reared in aqueous solutions containing retinoic acid (0, 0.02, 0.2 or 2nM) or valproic acid (0, 0.5, 5.0 or 50µM). One cohort of zebrafish was assessed using a locomotor activity screen at 6-dpf; another was reared to adulthood and assessed using a neurobehavioral test battery (startle habituation, novel tank exploration, shoaling, and predator escape/avoidance). RESULTS: There was no significant increase in the incidence of physical malformation among exposed fish compared to controls. Both retinoic acid and valproic acid exposures during development disrupted larval activity with persisting behavioral alterations later in life, primarily manifesting as decreased social affiliation. CONCLUSIONS: Social behavior and some aspects of motor function were altered in exposed fish; the importance of examining emotional or psychological consequences of early life exposure to retinoid acting chemicals is discussed.