Genomic analysis of human brain metastases treated with stereotactic radiosurgery reveals unique signature based on treatment failure

Stereotactic radiosurgery (SRS) has been shown to be efficacious for the treatment of limited brain metastasis (BM); however, the effects of SRS on human brain metastases have yet to be studied. We performed genomic analysis on resected brain metastases from patients whose resected lesion was previously treated with SRS. Our analyses demonstrated for the first time that patients possess a distinct genomic signature based on type of treatment failure including local failure, leptomeningeal spread, and radio-necrosis. Examination of the center and peripheral edge of the tumors treated with SRS indicated differential DNA damage distribution and an enrichment for tumor suppressor mutations and DNA damage repair pathways along the peripheral edge. Furthermore, the two clinical modalities used to deliver SRS, LINAC and GK, demonstrated differential effects on the tumor landscape even between controlled primary sites. Our study provides, in human, biological evidence of differential effects of SRS across BM's.

SpatialView: an interactive web application for visualization of multiple samples in spatial transcriptomics experiments

MOTIVATION

Spatial transcriptomics (ST) experiments provide spatially localized measurements of genome-wide gene expression allowing for an unprecedented opportunity to investigate cellular heterogeneity and organization within a tissue. Statistical and computational frameworks exist that implement robust methods for pre-processing and analyzing data in ST experiments. However, the lack of an interactive suite of tools for visualizing ST data and results currently limits the full potential of ST experiments.

RESULTS

To fill the gap, we developed SpatialView, an open-source web browser-based interactive application for visualizing data and results from multiple 10× Genomics Visium ST experiments. We anticipate SpatialView will be useful to a broad array of clinical and basic science investigators utilizing ST to study disease.

AVAILABILITY AND IMPLEMENTATION

SpatialView is available at https://github.com/kendziorski-lab/SpatialView (and https://doi.org/10.5281/zenodo.10223907); a demo application is available at https://www.biostat.wisc.edu/˜kendzior/spatialviewdemo/.

Rhinovirus infection of airway epithelial cells uncovers the non-ciliated subset as a likely driver of genetic susceptibility to childhood-onset asthma

Asthma is a complex disease caused by genetic and environmental factors. Epidemiological studies have shown that in children, wheezing during rhinovirus infection (a cause of the common cold) is associated with asthma development during childhood. This has led scientists to hypothesize there could be a causal relationship between rhinovirus infection and asthma or that RV-induced wheezing identifies individuals at increased risk for asthma development. However, not all children who wheeze when they have a cold develop asthma. Genome-wide association studies (GWAS) have identified hundreds of genetic variants contributing to asthma susceptibility, with the vast majority of likely causal variants being non-coding. Integrative analyses with transcriptomic and epigenomic datasets have indicated that T cells drive asthma risk, which has been supported by mouse studies. However, the datasets ascertained in these integrative analyses lack airway epithelial cells. Furthermore, large-scale transcriptomic T cell studies have not identified the regulatory effects of most non-coding risk variants in asthma GWAS, indicating there could be additional cell types harboring these "missing regulatory effects". Given that airway epithelial cells are the first line of defense against rhinovirus, we hypothesized they could be mediators of genetic susceptibility to asthma. Here we integrate GWAS data with transcriptomic datasets of airway epithelial cells subject to stimuli that could induce activation states relevant to asthma. We demonstrate that epithelial cultures infected with rhinovirus significantly upregulate childhood-onset asthma-associated genes. We show that this upregulation occurs specifically in non-ciliated epithelial cells. This enrichment for genes in asthma risk loci, or 'asthma heritability enrichment' is also significant for epithelial genes upregulated with influenza infection, but not with SARS-CoV-2 infection or cytokine activation. Additionally, cells from patients with asthma showed a stronger heritability enrichment compared to cells from healthy individuals. Overall, our results suggest that rhinovirus infection is an environmental factor that interacts with genetic risk factors through non-ciliated airway epithelial cells to drive childhood-onset asthma.

Targeted inhibition of BET proteins in HPV-16 associated head and neck squamous cell carcinoma reveals heterogeneous transcription response

Integrated human papillomavirus (HPV-16) associated head and neck squamous cell carcinoma (HNSCC) tumors have worse survival outcomes compared to episomal HPV-16 HNSCC tumors. Therefore, there is a need to differentiate treatment for HPV-16 integrated HNSCC from other viral forms. We analyzed TCGA data and found that HPV+ HNSCC expressed higher transcript levels of the bromodomain and extra terminal domain (BET) family of transcriptional coregulators. However, the mechanism of BET protein-mediated transcription of viral-cellular genes in the integrated viral-HNSCC genomes needs to be better understood. We show that BET inhibition downregulates E6 significantly independent of the viral transcription factor, E2, and there was overall heterogeneity in the downregulation of viral transcription in response to the effects of BET inhibition across HPV-associated cell lines. Chemical BET inhibition was phenocopied with the knockdown of BRD4 and mirrored downregulation of viral E6 and E7 expression. Strikingly, there was heterogeneity in the reactivation of p53 levels despite E6 downregulation, while E7 downregulation did not alter Rb levels significantly. We identified that BET inhibition directly downregulated c-Myc and E2F expression and induced CDKN1A expression. Overall, our studies show that BET inhibition provokes a G1-cell cycle arrest with apoptotic activity and suggests that BET inhibition regulates both viral and cellular gene expression in HPV-associated HNSCC.

Rhinovirus C causes heterogeneous infection and gene expression in airway epithelial cell subsets

Rhinoviruses infect ciliated airway epithelial cells, and rhinoviruses' nonstructural proteins quickly inhibit and divert cellular processes for viral replication. However, the epithelium can mount a robust innate antiviral immune response. Therefore, we hypothesized that uninfected cells contribute significantly to the antiviral immune response in the airway epithelium. Using single-cell RNA sequencing, we demonstrate that both infected and uninfected cells upregulate antiviral genes (e.g. MX1, IFIT2, IFIH1, and OAS3) with nearly identical kinetics, whereas uninfected non-ciliated cells are the primary source of proinflammatory chemokines. Furthermore, we identified a subset of highly infectable ciliated epithelial cells with minimal interferon responses and determined that interferon responses originate from distinct subsets of ciliated cells with moderate viral replication. These findings suggest that the composition of ciliated airway epithelial cells and coordinated responses of infected and uninfected cells could determine the risk of more severe viral respiratory illnesses in children with asthma, chronic obstructive pulmonary disease, and genetically susceptible individuals.

SpatialCorr identifies gene sets with spatially varying correlation structure

Recent advances in spatially resolved transcriptomics technologies enable both the measurement of genome-wide gene expression profiles and their mapping to spatial locations within a tissue. A first step in spatial transcriptomics data analysis is identifying genes with expression that varies spatially, and robust statistical methods exist to address this challenge. While useful, these methods do not detect spatial changes in the coordinated expression within a group of genes. To this end, we present SpatialCorr, a method for identifying sets of genes with spatially varying correlation structure. Given a collection of gene sets pre-defined by a user, SpatialCorr tests for spatially induced differences in the correlation of each gene set within tissue regions, as well as between and among regions. An application to cutaneous squamous cell carcinoma demonstrates the power of the approach for revealing biological insights not identified using existing methods.

Abstract 1503: Augmenting genomic instability in HPV head and neck cancer tumors through combination bromodomain and extra-terminal (BET) proteins inhibition and radiation treatments

Integration of human papillomavirus (HPV)16 genomes into host head and neck squamous cell carcinoma (HNSCC) DNA is an essential driver for cancer progression. Currently, there are no treatment strategies based on HPV integration status. We postulate that a conceptual advance in the treatment of HPV HNSCC cancer can be formalized by targeting transcriptional co-regulator - bromodomain and extra-terminal (BET) proteins which mediate viral and host transcription. HPV maintenance in the host environment is dependent on BET protein-BRD4. An additional function of BET proteins in regulating transcription of tumor suppressors and DNA damage repair (DDR) genes. Given that patient populations have viral integrations into their genomes and its maintenance depends on cellular Brd4, displacing Brd4 through novel second-generation BET inhibitors can abrogate HPV transcription. Through chemical and knockdown studies of BET proteins in integrated viral HNSCC cells, we show viral oncogenes E6 and E7 are directly regulated by Brd4, reactivate tumor suppressors p53, release E2F1-Rb cell cycle brake to induce G1 cell cycle arrest, and significantly converge towards downregulation of DDR pathways in disrupted viral genomes. In contrast, non-disrupted viral genomes diverge from DDR pathways towards downregulation of interferon signaling pathways. As a result of the intrinsic genomic instability caused by the downregulation of components of the DDR machinery, the addition of external beam radiation further delayed DNA repair kinetics quantified through H2AX foci formation in cells harboring disrupted viral genomes. Taken together, targeting BET proteins is not a viable monotherapy but creates genomic instability, which, when combined with radiation, has the potential to eradicate HPV-associated tumors.

Citation Format: Aakarsha Rao, Zijian Ni, Albert Wang, Dhruthi Suresh, Chitrasen Mohanty, Christina Kendziorski, Gopal Iyer. Augmenting genomic instability in HPV head and neck cancer tumors through combination bromodomain and extra-terminal (BET) proteins inhibition and radiation treatments [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1503.

Myofascial release versus other soft tissue release techniques along superficial back line structures for improving flexibility in asymptomatic adults: A systematic review with meta-analysis

OBJECTIVE

Our review is aimed to find out the efficacy of Myofascial Release Technique (MFRT) based on the Randomised Controlled Trials, on flexibility when given along superficial back line (SBL) structures and to compare it with other soft tissue release techniques.

DATA SOURCES

A systematic literature search on MEDLINE (Pubmed), Google Scholar, Science direct, Cochrane Library, Physiotherapy Evidence Database (PEDro) and Clinical Trial Database in English; up to April 2020 was undertaken.

STUDY SELECTION

PRISMA (The Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols) was used for screening the relevant citations and reviewing the relevant studies. The literature searched total of 6,938 articles, however, only 68 were screened for eligibility. In the further screening, 16 studies fulfilled the inclusion criteria for our systematic review.

DATA EXTRACTION

Data were extracted into a table containing sample size, mean age of subjects, types of intervention, area to be treated, outcome measures used, and results of the accepted studies.

DATA SYNTHESIS

16 randomized controlled trials and cross-over trials were found to be eligible for our review. Quality assessment of the RCTs was done with the PEDro scoring method. Randomised clinical trials that studied the comparative effect of Myofascial Release (MFRT) technique with different MFRT techniques, control/sham, and other soft tissue release techniques like stretching, were included. Results of this analysis showed little evidence proving the additional effectiveness of MFRT treatment compared to other soft tissue release techniques for improving flexibility so as to consider it as the preferred treatment. Methodological aspects of selected studies for further research are suggested. Study was registered in the PROSPERO database (CRD42020179118).

CONCLUSION

MFRT appears to be a good technique for improving flexibility. However, in comparison with other soft tissue release techniques, this therapy becomes less successful. More research is needed regarding its effectiveness.

Novel immortalized human vocal fold epithelial cell line: In vitro tool for mucosal biology

Study of vocal fold (VF) mucosal biology requires essential human vocal fold epithelial cell (hVFE) lines for use in appropriate model systems. We steadily transfected a retroviral construct containing human telomerase reverse transcriptase (hTERT) into primary normal hVFE to establish a continuously replicating hVFE cell line. Immortalized hVFE across passages have cobblestone morphology, express epithelial markers cytokeratin 4, 13 and 14, induced hTERT gene and protein expression, have similar RNAseq profiling, and can continuously grow for more than 8 months. DNA fingerprinting and karyotype analysis demonstrated that immortalized hVFE were consistent with the presence of a single cell line. Validation of the hVFE, in a three‐dimensional in vitro VF mucosal construct revealed a multilayered epithelial structure with VF epithelial cell markers. Wound scratch assay revealed higher migration capability of the immortalized hVFE on the surface of collagen‐fibronectin and collagen gel containing human vocal fold fibroblasts (hVFF). Collectively, our report demonstrates the first immortalized hVFE from true VFs providing a novel and invaluable tool for the study of epithelial cell‐fibroblast interactions that dictate disease and health of this specialized tissue.

Normalization by distributional resampling of high throughput single-cell RNA-sequencing data

Motivation

Normalization to remove technical or experimental artifacts is critical in the analysis of single-cell RNA-sequencing experiments, even those for which unique molecular identifiers are available. The majority of methods for normalizing single-cell RNA-sequencing data adjust average expression for library size (LS), allowing the variance and other properties of the gene-specific expression distribution to be non-constant in LS. This often results in reduced power and increased false discoveries in downstream analyses, a problem which is exacerbated by the high proportion of zeros present in most datasets.

Results

To address this, we present Dino, a normalization method based on a flexible negative-binomial mixture model of gene expression. As demonstrated in both simulated and case study datasets, by normalizing the entire gene expression distribution, Dino is robust to shallow sequencing, sample heterogeneity and varying zero proportions, leading to improved performance in downstream analyses in a number of settings.

Availability and implementation

The R package, Dino, is available on GitHub at https://github.com/JBrownBiostat/Dino. The Dino package is further archived and freely available on Zenodo at https://doi.org/10.5281/zenodo.4897558.

Supplementary information

Supplementary data are available at Bioinformatics online.

Oxidative stress in children with severe malaria

Fifty cases of severe malaria were studied for their oxidant and antioxidant status. Severe anemia (54%) was the most common presentation followed by hyperpyrexia, cerebral malaria and jaundice. Plasma malondialdehyde, protein carbonyl, nitrite, ascorbic acid and copper levels were significantly raised in cases as compared with controls (p < 0.001). Plasma ceruloplasmin, glutathione and superoxide dismutase levels were significantly decreased in children with severe malaria (p < 0.001). Plasma zinc was increased in cases but difference is not statistically significant. Significantly decreased level of nitrites and increased value of glutathione was found in patients with hemoglobinuria and jaundice, respectively. The significantly elevated malondialdehyde and protein carbonyl levels reflect the increased oxidative stress, whereas decreased levels of glutathione and superoxide dismutase point toward utilization of the antioxidants in severe malaria. Thus, changes in oxidants and antioxidants observed suggest the production of reactive oxygen species and their possible role in pathogenesis of severe malaria.

Cysticercal encephalitis with cortical blindness

The authors report a 6-year-old boy, who had presented with low-grade fever, altered sensorium, headache and seizure for 5 days. On examination, he had features of raised intracranial pressure with left VI cranial-nerve palsy and bilateral extensor plantar response. CT scan showed multiple calcifications in cerebral cortex. MRI cranium showed multiple cysts involving whole of the brain. He was diagnosed as having cysticercal encephalitis, based on immunological and imaging study. He was managed with 20% mannitol, phenytoin and albendazole, and regained consciousness 7 days later, but had residual neurological deficit as left-lower-limb monoparesis and visual acuity of just projection of rays (PR+) and perception of light (PL+).

Parenteral immunization of fish, Labeo rohita with Poly D, L-lactide-co-glycolic acid (PLGA) encapsulated antigen microparticles promotes innate and adaptive immune responses

Immunogenicity of different antigen preparations of outer membrane proteins (OMP) of Aeromonas hydrophila such as Poly d, l-lactide-co-glycolic acid (PLGA) microparticles, oil emulsion, neat OMP and bacterial whole cells were compared through intra-peritoneal injection in fish, Labeo rohita. Among these preparations, PLGA encapsulated antigen stimulated both innate and adaptive immune parameters and the immunogenicity exhibited by PLGA microparticles was significantly higher (p < 0.05) at both 21 and 42 days post-immunization suggesting that the above delivery system would be a novel antigen carrier for parenteral immunization in fish, Labeo rohita.

Maternal anthropometry as predictors of low birth weight

The usefulness of maternal anthropometric parameters i.e. maternal weight (MWt), maternal height (MHt), maternal mid-arm circumference (MMAC) and maternal body mass index (MBMI) as predictors of low birth weight (LBW) was studied in 395 singleton pregnancies. The maternal anthropometric parameters were measured in the first trimester of pregnancy and were plotted against the birth weight of the newborns. Significant positive correlations were observed among MWt and birth weight (r=0.38), MHt and birth weight (r=0.25), MMAC and birth weight (r=0.30) and MBMI and birth weight (r=0.30). The most sensitive being MWt (t=7.796), followed by MMAC (t=5.759), MHt (t=4.706) and MBMI (t=5.89). For prediction of LBW, the critical limits of MWt, MHt, MMAC and MBMI were 45 kg, 152 cm, 22.5 cm, 20 kg/m2 respectively. From these observations, the use of colour-coded weighing machines, height rods and tapes may be devised for use by peripheral health workers and traditional birth attendants for detection of mothers at risk of delivering low birth weight babies (Table 5). Mothers who have anthropometric parameters in the 'red zone' are at risk of delivery LBW infants.

Effect of amniotic sac puncture on parturition in rat

Pregnant Charles Foster rats were subjected to amniotic sac puncture on day 15 of gestation and the effect was observed on parturition. All the control rats as expected delivered on day 22 of gestation. In the group where all the sacs were punctured, only 12.5% rats delivered on day 22 while rest either failed to deliver (62.5%) or died (25%). In the group with unpunctured sacs at vaginal ends, 75% rats delivered on day 21 while 25% on day 22. In the group with unpunctured sacs at ovarian ends, 75% rats delivered on day 23 and rest 25% failed to deliver. The resorption rates ranged between 61 to 94% in different groups. Malformations were observed only in one pup. The results suggest that amniotic sac puncture interferes with parturition in the form of either failure or delayed parturition. Nonpatency of the birth canal due to puncture induced fetal deaths and tissue adhesions were presumed to be the contributing factors.

Parturient abdominal circumference as a predictor of low birthweight

The usefulness of parturient abdominal circumference as a predictor of low birthweight (LBW) was studied in 151 singleton pregnancies. The abdominal circumference was measured in early labour and was plotted against the birthweight of the newborns. A significant positive correlation was observed between the two parameters (r = +0.507). For the prediction of LBW, the critical limit of the abdominal circumference was 86 cm, which means that an abdominal circumference of more than 86 cm is reasonably safe while lesser values predict a higher chance of a LBW infant. From these observations, the use of a colour-coded tape by peripheral health workers and traditional birth attendants is suggested: red for abdominal circumference <82 cm, yellow for abdominal circumference 82-86 cm, and green for abdominal circumference >86 cm. Mothers who have an abdominal circumference in the 'red zone' are at risk of delivering LBW infants.

Acardiac anomaly spectrum

BACKGROUND

Acardiac anomaly spectrum is a rare congenital malformation found in monozygotic twin pregnancy. Besides the absence of heart, the condition is associated with variable grades of developmental disruption. Thus, no two cases are similar.

METHODS

This case report is based on physical examination and autopsy findings.

RESULTS

The twin had acardia and partial development of head and face. There was complete absence of upper extremities.

CONCLUSIONS

The twin reversed arterial perfusion (TRAP) theory is the most accepted etiology of the disorder. Normally, the cephalic pole is the most severely affected, being most distal to the retrograde perfusion. In acardia, partial development of head, face, and brain is usually associated with the development of the upper extremities. However, in the present case, there was extensive cephalic development in the absence of upper extremity development.

Effect of intraamniotic vitamin A on palatal closure of fetal rats

On day 15 of gestation, intraamniotic vitamin A in a dose of 150 IU was administered to the fetal rats to examine its effect on palatal closure. Fetuses subjected to only amniocentesis acted as control for the study. The fetuses were recovered on day 19, 20 and 21, respectively. Vitamin A resulted in poor development of palatine shelves. There was no clear demarcation of the base and the free margins of the shelves were either rounded or blunted with poor attempt towards closure. In the vitamin A group, the incidence of cleft palate were similar in all three days while there was a gradual decline with increasing gestational age in the amniocentesis group. The results suggest that unlike amniocentesis, in vitamin A treated fetuses, there was no attempt towards a delayed closure of the palate.

New observations on carrying angle

Based on experiments on fresh cadaveric and accidentally amputated 8 upper limbs of children, study of ulnae for presence and absence of non articular strip on the trochlear notch, measurements of carrying angle, length of forearm bones, pronation-supination, height and weight in 2250 infants, children and adults of various age groups and clinical observations on 800 cases of injuries around elbow many new facts have been observed about the development of the carrying angle and its significance in the etiopathogenesis of various types of fractures seen around the elbow. The carrying angle develops in response to pronation of the forearm and is dependent on length of the forearm bones. Lesser the length of forearm bones greater is the carrying angle. So the carrying angle is more in shorter persons as compared to taller persons. It is abduction at the shoulder and not the carrying angle which keeps the swinging upper limbs away from the side of the pelvis during walking. Carrying angle is not a secondary sex character. The type of fracture a child sustains after fall on outstretched hand is also determined by the value of the carrying angle. A new type of fracture hitherto undescribed in the literature, T-Y fracture of the distal humeral epiphysis is also reported.

Parturient fundal height as a predictor of low birth weight

The usefulness of parturient fundal height as a predictor of low birth weight (LBW) was studied in 151 singleton pregnancies. The symphysis to fundus (S-F) distance was measured in early labour and was plotted against the birth weight of the newborns. A significant positive correlation was observed between the two parameters (r = +0.740). For the prediction of LBW, the critical limit of the fundal height was 31 cm, meaning that a S-F distance of more than 31 cm is reasonably safe while lesser values predict a higher chance of a LBW infant. From these observations, the use of a colour-coded tape by peripheral health workers and traditional birth attendants is suggested: red for S-F < 28 cm, yellow for S-F = 28-31 cm, and green for S-F > 31 cm. Mothers who have a fundal height in the 'red zone' are at risk of delivering LBW infants.