Detailed Image Data Quality and Cleaning Practices for Artificial Intelligence Tools for Breast Cancer

Standardizing image-data preparation practices to improve accuracy/consistency of AI diagnostic tools.

Modeling gamma knife radiosurgical toxicity for multiple brain metastases

BACKGROUND AND PURPOSE

Radiation oncology protocols for single fraction radiosurgery recommend setting dosing criteria based on assumed risk of radionecrosis, which can be predicted by the 12 Gy normal brain volume (V12). In this study, we show that tumor surface area (SA) and a simple power-law model using only preplan variables can estimate and minimize radiosurgical toxicity.

MATERIALS AND METHODS

A 245-patient cohort with 1217 brain metastases treated with single or distributed Gamma Knife sessions was reviewed retrospectively. Univariate and multivariable linear regression models and power-law models determined which modeling parameters best predicted V12. The V12 power-law model, represented by a product of normalized Rx dose Rxn, and tumor longest axial dimension LAD (V12 ∼ Rxn1.5*LAD2), was independently validated using a secondary 63-patient cohort with 302 brain metastases.

RESULTS

Surface area was the best univariate linear predictor of V12 (adjR2 = 0.770), followed by longest axial dimension (adjR2 = 0.755) and volume (adjR2 = 0.745). The power-law model accounted for 90% variance in V12 for 1217 metastatic lesions (adjR2 = 0.906) and 245 patients (adjR2 = 0.896). The average difference ΔV12 between predicted and measured V12s was (0.28 ± 0.55) cm3 per lesion and (1.0 ± 1.2) cm3 per patient. The power-law predictive capability was validated using a secondary 63-patient dataset (adjR2 = 0.867) with 302 brain metastases (adjR2 = 0.825).

CONCLUSION

Surface area was the most accurate univariate predictor of V12 for metastatic lesions. We developed a preplan model for brain metastases that can help better estimate radionecrosis risk, determine prescription doses given a target V12, and provide safe dose escalation strategies without the use of any planning software.

Five-Fraction Stereotactic Radiation for Head and Neck Paragangliomas

PURPOSE/OBJECTIVE(S)

Paragangliomas of the head and neck (HN) are benign, slow-growing neoplasms that are rarely functional. Treatment is often indicated for patients presenting with mass effect, cranial neuropathies, or pulsatile tinnitus. Radiotherapy, traditionally conventionally fractionated, is often used for primary, post-operative, and salvage therapy, given its excellent control rates and reduced risks to adjacent neurovascular structures. Stereotactic ablative radiation (SAbR) offers shorter treatment time, and modern techniques eliminate margins to improve organ-at-risk avoidance. SAbR may offer additional radiobiological sparing of normal structures over single-fraction SAbR. We aimed to evaluate tumor and symptom response, acute and late toxicity rates, and recurrence patterns in HN paraganglioma patients treated with 25 Gy in 5 fractions.

MATERIALS/METHODS

Retrospective chart review collected baseline patient and tumor information, treatment and dosimetry details, acute and long-term toxicity grades (per the CTCAE v. 5.0), symptom and tumor response, and survival. Local control was defined as the absence of local enlargement (per RECIST v. 1.1) or marginal failure and was estimated using the Kaplan-Meier method.

RESULTS

Between December 2009-March 2020, 39 patients received 25 Gy in 5 fractions to 43 HN paragangliomas, of which 17 were treated in 11 patients with hereditary paraganglioma-pheochromocytoma syndrome. Fifteen targets were post-operative recurrent or residual tumors. There were 27 jugulotympanic tumors, 4 jugular, 1 tympanic, 8 vagal, 5 carotid body, and 2 jugulotympanic or vagal. Median follow-up time was 3.3 years (range 0-11.4 years), and 21 targets had at least 4 years of follow-up. Tumor volume decreased by a median of 37%. Three-year local control was 100%. One patient, known to harbor an SDHD mutation, had 2 out-of-field recurrences within the post-operative bed at 7.1 years. Two patients experienced 2 marginal recurrences within the post-operative bed at 6.1 and 8.4 years: one had an SDHB mutation and developed metastatic disease, and the other did not have genetic testing. The most common grade 1-2 acute toxicities were headache and fatigue; the most common grade 1-2 late toxicities were dysphagia and otalgia. There were no grade >2 acute toxicities. A late grade 3 aspiration event was seen in 1 patient who presented with paralyzed vocal cord requiring multiple medialization laryngoplasties. Within 6 months of SAbR, 18% of symptoms or toxicities improved or resolved; 34% improved or resolved more than 6 months after SAbR.

CONCLUSION

This is the largest series of HN paragangliomas treated with SAbR, detailing a 10-year experience with a 5-fraction regimen that is well-tolerated and achieves excellent local control. Post-SAbR recurrences occurred outside of the radiation field but within the post-operative bed, suggesting that some post-operative patients may benefit from expanded radiation volumes or close surveillance for salvage therapy.

Modeling Gamma Knife Radiosurgical Toxicity for Multiple Brain Metastases

PURPOSE/OBJECTIVE(S)

Dosing for single fraction radiosurgery has traditionally relied on tumor measurements from a single maximum diameter. Most protocols recommend setting dosing criteria based on assumed risk of radionecrosis roughly correlating with tumor size. However, the risk of radionecrosis after radiosurgery is best modeled by a function of dose and volume treated, with the largest body of evidence supporting the use of brain tissue receiving ≥12 Gy in one fraction (V12, i.e., > 10.9 cm3). Here we show that tumor surface area (SA) and second order dimensions are superior predictors for Gamma Knife radiosurgical toxicity and can be used to estimate V12.

MATERIALS/METHODS

A total of 1217 brain metastases from 245 patients treated with a prescribed dose from 13 to 27 Gy in one fraction were retrospectively reviewed. Eight independent modeling parameters were considered; 3 geometric tumor characteristics: SA, volume (V), and largest axial dimension (LAD) and 5 treatment planning variables: prescription dose (Rx), coverage, selectivity, gradient index, and number of shots. Linear regression and power-law formulations were performed to determine which parameters were the most accurate predictors of V12. The power model is dependent on a conceptualized "pseudo surface area" (PSA), defined as the surface area of a sphere with a diameter of LAD of a lesion (PSA = π*LAD2). At the aggregate patient level, the model predicts total brain V12 by summing the V12 values for each singular lesion only by using LAD and Rx as input variables.

RESULTS

Tumor SA was the best univariate linear predictor of V12 (adjR2 = 0.770), followed by LAD (adjR2 = 0.755) and V (adjR2 = 0.745). The SA predictive model improves for lesions that have high sphericity > 0.85 (adjR2 = 0.837), with a measure of 1 indicating a perfect sphere. Using bivariable regression analysis, we formulated a single term power model that even more accurately predicts for V12 (V12 = 0.0137 * Rx1.5 * LAD2, adjR2 = 0.906) and is proportional to PSA. At the patient level, this model also accurately predicts for total brain V12 (adjR2 = 0.896) and V12 > 10.9 cm3 (Sensitivity = 99.1%, Specificity = 90.5%).

CONCLUSION

Conceptually, SA univariately predicts for V12 more accurately than other tumor physical dimensions or treatment planning parameters, while the best bivariable power model involves PSA. We provide a preplan model for brain metastases that can help better estimate radionecrosis risk, determine prescription doses given a target V12, and provide safe dose escalation strategies without the use of any planning software.

Impact of CDKN2A/B, MTAP, and TERT Genetic Alterations on Survival in IDH Wild Type Glioblastomas

PURPOSE

Poor outcomes in IDH wild-type (IDHwt) glioblastomas indicate the need to determine which genetic alterations can indicate poor survival and guidance of patient specific treatment options. We sought to identify the genetic alterations in these patients that predict for survival when adjusting particularly for treatments and other genetic alterations.

METHODS

A cohort of 167 patients with pathologically confirmed IDHwt glioblastomas treated at our institution was retrospectively reviewed. Next generation sequencing was performed for each patient to determine tumor genetic alterations. Multivariable cox proportional hazards analysis for overall survival (OS) was performed to control for patient variables.

RESULTS

CDKN2A, CDKN2B, and MTAP deletion predict for worse OS independently of other genetic alterations and patient characteristics (hazard ratio [HR] 2.192, p = 0.0017). Patients with CDKN2A copy loss (HR 2.963, p = 0.0037) or TERT mutated (HR 2.815, p = 0.0008) glioblastomas exhibited significant associations between radiation dose and OS, while CDKN2A and TERT wild type patients did not. CDKN2A deleted patients with NF1 mutations had worse OS (HR 1.990, p = 0.0540), while CDKN2A wild type patients had improved OS (HR 0.229, p = 0.0723). Patients with TERT mutated glioblastomas who were treated with radiation doses < 45 Gy (HR 3.019, p = 0.0010) but not those treated with ≥ 45 Gy exhibited worse OS compared to those without TERT mutations.

CONCLUSION

In IDHwt glioblastomas, CDKN2A, CDKN2B, and MTAP predict for poor prognosis. TERT and CDKN2A mutations are associated with worse survival only when treated with lower radiation doses, thus potentially providing a genetic marker that can inform clinicians on proper dose-fractionation schemes.

Socioeconomic and demographic determinants of radiation treatment and outcomes in glioblastoma patients

Introduction

Poor outcomes in glioblastoma patients, despite advancing treatment paradigms, indicate a need to determine non-physiologic prognostic indicators of patient outcome. The impact of specific socioeconomic and demographic patient factors on outcomes is unclear. We sought to identify socioeconomic and demographic patient characteristics associated with patient survival and tumor progression, and to characterize treatment options and healthcare utilization.

Methods

A cohort of 169 patients with pathologically confirmed glioblastomas treated at our institution was retrospectively reviewed. Multivariable cox proportional hazards analysis for overall survival (OS) and cumulative incidence of progression was performed. Differences in treatment regimen, patient characteristics, and neuro-oncology office use between different age and depressive disorder history patient subgroups were calculated two-sample t-tests, Fisher's exact tests, or linear regression analysis.

Results

The median age of all patients at the time of initiation of radiation therapy was 60.5 years. The median OS of the cohort was 13.1 months. Multivariable analysis identified age (Hazard Ratio 1.02, 95% CI 1.00–1.04) and total resection (Hazard Ratio 0.52, 95% CI 0.33–0.82) as significant predictors of OS. Increased number of radiation fractions (Hazard Ratio 0.90, 95% CI 0.82–0.98), depressive disorder history (Hazard Ratio 0.59, 95% CI 0.37–0.95), and total resection (Hazard Ratio 0.52, 95% CI 0.31–0.88) were associated with decreased incidence of progression. Notably, patients with depressive disorder history were observed to have more neuro-oncology physician office visits over time (median 12 vs. 16 visits, p = 0.0121). Patients older than 60 years and those with Medicare (vs. private) insurance were less likely to receive as many radiation fractions (p = 0.0014) or receive temozolomide concurrently with radiation (Odds Ratio 0.46, p = 0.0139).

Conclusion

Older glioblastoma patients were less likely to receive as diverse of a treatment regimen as their younger counterparts, which may be partially driven by insurance type. Patients with depressive disorder history exhibited reduced incidence of progression, which may be due to more frequent health care contact during neuro-oncology physician office visits.

Neutrophilia and post-radiation thrombocytopenia predict for poor prognosis in radiation-treated glioma patients

Introduction

Poor outcomes in glioma patients indicate a need to determine prognostic indicators of survival to better guide patient specific treatment options. While preoperative neutrophil-to-lymphocyte ratio (NLR), platelet-to-lymphocyte ratio (PLR), and monocyte-to-lymphocyte ratio (MLR) have been suggested as prognostic systemic inflammation markers, the impact of post-radiation changes in these cell types is unclear. We sought to identify which hematologic cell measurements before, during, or after radiation predicted for patient survival.

Methods

A cohort of 182 patients with pathologically confirmed gliomas treated at our institution was retrospectively reviewed. Patient blood samples were collected within one month before, during, or within 3 months after radiation for quantification of hematologic cell counts, for which failure patterns were evaluated. Multivariable cox proportional hazards analysis for overall survival (OS) and progression-free survival (PFS) was performed to control for patient variables.

Results

Multivariable analysis identified pre-radiation NLR > 4.0 (Hazard ratio = 1.847, p = 0.0039) and neutrophilia prior to (Hazard ratio = 1.706, p = 0.0185), during (Hazard ratio = 1.641, p = 0.0277), or after (Hazard ratio = 1.517, p = 0.0879) radiation as significant predictors of worse OS, with similar results for PFS. Post-radiation PLR > 200 (Hazard ratio = 0.587, p = 0.0062) and a percent increase in platelets after radiation (Hazard ratio = 0.387, p = 0.0077) were also associated with improved OS. Patients receiving more than 15 fractions of radiation exhibited greater post-radiation decreases in neutrophil and platelet counts than those receiving fewer. Patients receiving dexamethasone during radiation exhibited greater increases in neutrophil counts than those not receiving steroids. Lymphopenia, changes in lymphocyte counts, monocytosis, MLR, and changes in monocyte counts did not impact patient survival.

Conclusion

Neutrophilia at any time interval surrounding radiotherapy, pre-radiation NLR, and post-radiation thrombocytopenia, but not lymphocytes or monocytes, are predictors of poor patient survival in glioma patients.

3D printed integrated bolus/headrest for radiation therapy for malignancies involving the posterior scalp and neck

Background

Malignancies of the head and neck region, encompassing cutaneous, mucosal, and sarcomatous histologies, are complex entities to manage, comprising of coordination between surgery, radiation therapy, and systemic therapy. Malignancies of the posterior scalp are particular challenging to treat with radiation therapy, given its irregular contours and anatomy as well as the superficial location of the target volume. Bolus material is commonly used in radiation therapy to ensure that the dose to the skin and subcutaneous tissue is appropriate and adequate, accounting for the buildup effect of megavoltage photon treatment. The use of commercially available bolus material on the posterior scalp potentially creates air gaps between the bolus and posterior scalp.

Case presentations

In this report, we created and utilized a custom 3D-printed integrated bolus and headrest for 5 patients to irradiate malignancies involving the posterior scalp, including those with cutaneous squamous cell carcinoma, melanoma, malignant peripheral nerve sheath tumor, and dermal sarcoma. Treatment setup was consistently reproducible, and patients tolerated treatment well without any unexpected adverse effects.

Conclusions

We found that the use of this custom 3D-printed integrated bolus/headrest allowed for comfortable, consistent, and reproducible treatment set up while minimizing the risk of creating significant air gaps and should be considered in the radiotherapeutic management of patients with posterior scalp malignancies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s41205-022-00152-w.

Registration-guided deep learning image segmentation for cone beam CT-based online adaptive radiotherapy

PURPOSE

Adaptive radiotherapy (ART), especially online ART, effectively accounts for positioning errors and anatomical changes. One key component of online ART process is accurately and efficiently delineating organs at risk (OARs) and targets on online images, such as Cone Beam Computed Tomography (CBCT). Direct application of deep learning (DL)-based segmentation to CBCT images suffered from issues such as low image quality and limited available contour labels for training. To overcome these obstacles to online CBCT segmentation, we propose a registration-guided DL (RgDL) segmentation framework that integrates image registration algorithms and DL segmentation models.

METHODS

The RgDL framework is composed of two components: image registration and registration-guided DL segmentation. The image registration algorithm transforms / deforms planning contours, which were subsequently used as guidance by the DL model to obtain accurate final segmentations. We had two implementations of the proposed framework-Rig-RgDL (Rig for rigid body) and Def-RgDL (Def for deformable)-with rigid body (RB) registration or deformable image registration (DIR) as the registration algorithm, respectively, and U-Net as the DL model architecture. The two implementations of RgDL framework were trained and evaluated on seven OARs in an institutional clinical Head and Neck (HN) dataset.

RESULTS

Compared to the baseline approaches using the registration or the DL alone, RgDLs achieved more accurate segmentation, as measured by higher mean Dice similarity coefficients (DSC) and other distance-based metrics. Rig-RgDL achieved a DSC of 84.5% on seven OARs on average, higher than RB or DL alone by 4.5% and 4.7%. The average DSC of Def-RgDL was 86.5%, higher than DIR or DL alone by 2.4% and 6.7%. The inference time required by the DL model component to generate final segmentations of seven OARs was less than one second in RgDL. By examining the contours from RgDLs and DL case by case, we found that RgDL was less susceptible to image artifacts. We also studied how the performances of RgDL and DL vary with the size of the training dataset. The DSC of DL dropped by 12.1% as the number of training data decreased from 22 to 5, while RgDL only dropped by 3.4%.

CONCLUSION

By incorporating the patient-specific registration guidance to a population-based DL segmentation model, RgDL framework overcame the obstacles associated with online CBCT segmentation, including low image quality and insufficient training data, and achieved better segmentation accuracy than baseline methods. The resulting segmentation accuracy and efficiency show promise for applying this RgDL framework for online ART. This article is protected by copyright. All rights reserved.

Facile and direct detection of human papillomavirus (HPV) DNA in cells using loop-mediated isothermal amplification (LAMP)

Human papillomavirus (HPV)-mediated cancers, particularly cervical and oropharyngeal cancer, lead to hundreds of thousands of deaths worldwide each year. Simple, straightforward, and cost-effective detection of HPV DNA from patients with these malignancies or at risk for developing cancer can improve outcomes for patients, serving as a tool for early detection, monitoring treatment response, and assessment of cancer recurrence. Loop-mediated isothermal amplification (LAMP) is a simple and robust method for the detection and amplification of DNA in a single tube, utilizing the Bst strand-displacing DNA polymerase. We developed a workflow utilizing LAMP for the visual detection of HPV DNA in oral rinses. We demonstrate that LAMP is able to easily discriminate between two of the high-risk HPV subtypes, HPV16 and HPV18. We then utilized LAMP to visually detect HPV DNA directly from cells in oral rinses, mimicking a clinical inspired scenario of detecting HPV DNA in clinical samples. Our results suggest that LAMP is a robust, colorimetric assay method for the detection of HPV DNA in complex cellular samples, and further development is warranted to bring LAMP into the clinic.

Quality of Anatomic Staging of Breast Carcinoma in Hospitals in the United States, With Focus on Measurement of Tumor Dimension

OBJECTIVES

We investigated the accuracy of clinical breast carcinoma anatomic staging and the greatest tumor dimension measurements.

METHODS

We compared clinical stage and greatest dimension values with the pathologic reference standard values using 57,747 cases from the 2016 US National Cancer Institute Surveillance, Epidemiology, and End Results program who were treated by surgical resection without prior neoadjuvant therapy.

RESULTS

Agreement for clinical vs pathologic anatomic TNM group stage, overall, is 74.3% ± 0.4%. Lymph node N staging overall agrees very well (85.1% ± 0.4%). Based on tumor dimension and location, T staging has an agreement of only 64.2% ± 0.4%, worsening to 55% without carcinoma in situ (Tis) cases. In approximately 25% of cases, pathologic T stage is higher than clinical T stage. The mean difference in the greatest dimension is 1.36 ± 9.59 mm with pathologic values being generally larger than clinical values; pathologic and clinical measurements correlate well. T-stage disagreement is associated with histology, tumor grade, tumor size, N stage, patient age, periodic biases in tumor size measurements, and overuse of family T-stage categories. Pathologic measurement biases include rounding and specimen-slicing intervals.

CONCLUSIONS

Clinical and pathologic T-staging values agree only moderately. Pathologists face challenges in increasing the precision of gross tumor measurements, with the goal of improving the accuracy of clinical T staging and measurement.

Clinical Non-Small Cell Lung Cancer Staging and Tumor Length Measurement Results From U.S. Cancer Hospitals

RATIONALE AND OBJECTIVES

Examine the accuracy of clinical non-small cell lung cancer staging and tumor length measurements, which are critical to prognosis and treatment planning.

MATERIALS AND METHODS

Compare clinical and pathological staging and lengths using 10,320 2016 National Cancer Institute Surveillance, Epidemiology, and End Results (SEER) and 559 2010-2018 non-SEER single-institute surgically-treated cases, and analyze modifiable causes of disagreement.

RESULTS

The SEER clinical and pathological group-stages agree only 62.3% ± 0.9% over all stage categories. The lymph node N-stage agrees much better at 83.0% ± 1.0%, but the tumor length-location T-stage agrees only 57.7% ± 0.8% with approximately 29% of the cases having a greater pathology than clinical T-stage. Individual T-stage category agreements with respect to the number of pathology cases are Tis, T1a, T1b, T2a, T2b, T3, T4: 89.9% ± 10.0%; 78.7% ± 1.7%; 51.8% ± 1.9%; 46.1% ± 1.3%; 40.5% ± 3.1%; 44.1% ± 2.2%; 56.4% ± 4.7%, respectively. Most of the single-institute results statistically agree with SEER's. Excluding Tis cases, the mean difference in SEER tumor length is ∼1.18 ± 9.26 mm (confidence interval: 0.97-1.39 mm) with pathological lengths being longer than clinical lengths except for small tumors; the two measurements correlate well (Pearson-r >0.87, confidence interval: 0.86-0.87). Reasons for disagreement include the use of family-category descriptors (e.g., T1) instead of their subcategories (e.g., T1a and T1b), which worsens the T-stage agreement by over 15%. Disagreement is also associated with higher tumor grade, larger resected specimens, higher N-stage, patient age, and periodic biases in clinical and pathological tumor size measurements.

CONCLUSIONS

By including preliminary non-small cell lung cancer clinical stage values in their evaluation, diagnostic radiologists can improve the accuracy of staging and standardize tumor-size measurements, which improves patient care.

Simplified, standardized methods to assess the accuracy of clinical cancer staging

BACKGROUND

Hospitals lack intuitive methods to monitor their accuracy of clinical cancer staging, which is critical to treatment planning, prognosis, refinements, and registering quality data.

METHODS

We introduce a tabulation framework to compare clinical staging with the reference-standard pathological staging, and quantify systematic errors. As an example, we analyzed 9,644 2016 U.S. National Cancer Institute SEER surgically-treated non-small cell lung cancer (NSCLC) cases, and computed concordance with different denominators to compare with incompatible past results.

RESULTS

The concordance for clinical versus pathological lymph node N-stage is very good, 83.4 ± 1.0%, but the tumor length-location T-stage is only 58.1 ± 0.9%. There are intuitive insights to the causes of discordance. Approximately 29% of the cases are pathological T-stage greater than clinical T-stage, and 12% lower than the clinical T-stage, which is due partly to the fact that surgically-treated NSCLC are typically lower-stage cancer cases, which results in a bounded higher probability for pathological upstaging. Individual T-stage categories Tis, T1a, T1b, T2a, T2b, T3, T4 invariant percent-concordances are 85.2 ± 9.7 + 10.3%; 72.7 ± 1.6 + 11.3%; 46.6 ± 1.8 + 10.9%; 54.6 ± 1.6 - 20.5%; 41.6 ± 3.3 - 0.1%; 54.7 ± 2.8 - 24.1%; 55.2 ± 4.7 + 2.6%, respectively. Each percent-concordance is referenced to an averaged number of pathological and clinical cases. The first error number quantifies statistical fluctuations; the second quantifies clinical and pathological staging biases. Lastly, comparison of over and under staging versus clinical characteristics provides further insights.

CONCLUSIONS

Clinical NSCLC staging accuracy and concordance with pathological values can improve. As a first step, the framework enables standardizing comparing staging results and detecting possible problem areas. Cancer hospitals and registries can implement the efficient framework to monitor staging accuracy.

Genomic analyses of early responses to radiation inglioblastoma reveal new alterations at transcription,splicing, and translation levels

High-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance is a common problem and a major contributor to tumor relapse. Understanding the molecular mechanisms driving response to radiation is critical for identifying regulatory routes that could be targeted to improve treatment response. We conducted an integrated analysis in the U251 and U343 glioblastoma cell lines to map early alterations in the expression of genes at three levels: transcription, splicing, and translation in response to ionizing radiation. Changes at the transcriptional level were the most prevalent response. Downregulated genes are strongly associated with cell cycle and DNA replication and linked to a coordinated module of expression. Alterations in this group are likely driven by decreased expression of the transcription factor FOXM1 and members of the E2F family. Genes involved in RNA regulatory mechanisms were affected at the mRNA, splicing, and translation levels, highlighting their importance in radiation-response. We identified a number of oncogenic factors, with an increased expression upon radiation exposure, including BCL6, RRM2B, IDO1, FTH1, APIP, and LRIG2 and lncRNAs NEAT1 and FTX. Several of these targets have been previously implicated in radio-resistance. Therefore, antagonizing their effects post-radiation could increase therapeutic efficacy. Our integrated analysis provides a comprehensive view of early response to radiation in glioblastoma. We identify new biological processes involved in altered expression of various oncogenic factors and suggest new target options to increase radiation sensitivity and prevent relapse.

miR-125a-5p Functions as Tumor Suppressor microRNA And Is a Marker of Locoregional Recurrence And Poor prognosis in Head And Neck Cancer

MicroRNAs (miRNAs) are short single-stranded RNAs, measuring 21 to 23 nucleotides in length and regulate gene expression at the post-transcriptional level through mRNA destabilization or repressing protein synthesis. Dysregulation of miRNAs can lead to tumorigenesis through changes in regulation of key cellular processes such as cell proliferation, cell survival, and apoptosis. miR-125a-5p has been implicated as a tumor suppressor miRNA in malignancies such as non-small cell lung cancer and colon cancer. However, the role of miR-125a-5p has not been fully investigated in head and neck squamous cell carcinoma (HNSCC). We performed microRNA microarray profiling of HNSCC tumor samples obtained from a prospective clinical trial evaluating the role of postoperative radiotherapy in head and neck cancer. We also mined through The Cancer Genome Atlas to evaluate expression and survival data. Biological experiments, including cell proliferation, flow cytometry, cell migration and invasion, clonogenic survival, and fluorescent microscopy, were conducted using HN5 and UM-SCC-22B cell lines. miR-125a-5p downregulation was associated with recurrent disease in a panel of high-risk HNSCC and then confirmed poor survival associated with low expression in HNSCC via the Cancer Genome Atlas, suggesting that miR-125a-5p acts as a tumor suppressor miRNA. We then demonstrated that miR-125a-5p regulates cell proliferation through cell cycle regulation at the G₁/S transition. We also show that miR-125a-5p can alter cell migration and modulate sensitivity to ionizing radiation. Finally, we identified putative mRNA targets of miR-125a-5p, including ERBB2, EIF4EBP1, and TXNRD1, which support the tumor suppressive mechanism of miR-125a-5p. Functional validation of ERBB2 suggests that miR-125a-5p affects cell proliferation and sensitivity to ionizing radiation, in part, through ERBB2. Our data suggests that miR-125a-5p acts as a tumor suppressor miRNA, has potential as a diagnostic tool and may be a potential therapeutic target for the management and treatment of squamous cell carcinoma of the head and neck.

Novel Use of an Image-Guided Stereotactic Approach in Trauma for Localization of Transcranial Bullet

Penetrating brain injuries from gunshot wounds can carry a poor prognosis and require an aggressive, multifaceted approach to obtain a good prognosis and outcome. An initial evaluation requires appropriate imaging studies followed by management and prophylaxis against increased intracranial pressure, infection, and seizures. Surgical management is then followed to ensure the watertight closure of any wounds, removal of any areas of hematoma, and removal of any potential areas of infection. In this paper, we report the case of a patient who presented with a self-inflicted gunshot wound to the head and then received aggressive medical and surgical management. This case presents that an image-guided stereotactic approach with suitable medical management should be used in patients with penetrating missile injuries to the head.

Deep inspiration breathhold for left-sided breast cancer patients with unfavorable cardiac anatomy requiring internal mammary nodal irradiation

PURPOSE

The purpose of this study was to evaluate the utility of moderate deep inspiration breathhold (mDIBH) in reducing heart exposure in left breast cancer patients who have unfavorable cardiac anatomy and need internal mammary lymph node (IMLN) radiation therapy (RT).

METHODS AND MATERIALS

We used maximum heart distance (MHD), defined as the maximum distance of the heart within the treatment field, >1 cm as a surrogate for unfavorable cardiac anatomy. Twenty-two left breast cancer patients with unfavorable cardiac anatomy requiring IMLN-RT underwent free-breathing (FB) and mDIBH computed tomography simulation and planning. Three-dimensional partially wide tangents (3D-PWTs) and intensity modulated RT plans were generated. Dose-volume histograms were used to compare heart and lung dosimetric parameters. Duration of treatment delivery was recorded for all fractions.

RESULTS

MHD decreased significantly in mDIBH scans. mDIBH significantly reduced mean heart dose (222.7 vs 578.4 cGy; P < .0001) and percentage of left lung receiving doses ≥20 Gy (V20; 31.93 vs 38.41%; P = .0006) in both 3D-PWT and intensity modulated RT plans. The change in MHD after breathhold reliably predicted mean heart dose reduction after mDIBH. Radiation was effectively delivered in 11.31 ± 3.40 minutes with an average of 10.06 ± 2.74 breathholds per fraction.

CONCLUSIONS

mDIBH is efficient and can effectively decrease mean heart dose in patients with unfavorable cardiac anatomy who need IMLN-RT, thus simplifying planning and delivery for them. The reduction in mean heart dose is proportional to the reduction in maximum heart distance.

Streptococcus pneumoniae meningitis complicated by an intramedullary abscess: a case report and review of the literature

BACKGROUND

Intramedullary abscess is a rare neurosurgical condition that usually arises in the setting of penetrating trauma to the spinal cord, infected congenital dural sinuses, or tuberculosis.

CASE PRESENTATION

We describe a case of a 35-year-old African American male who presented with sepsis and a clinical picture of meningitis. The patient continued to have declining neurological status with decreasing sensation and worsening motor strength in all four extremities. He was found to have an intramedullary abscess in the cervical spinal cord that was treated with a decompressive posterior cervical laminectomy and drainage. The patient began to have a partial recovery of neurological function postoperatively. We also review the literature on intramedullary abscess that suggests the clinical presentation of our patient was a rare complication of acute meningitis.

CONCLUSIONS

Intramedullary abscess formation is a rare entity, and a high index of suspicion for intramedullary abscess is the key for making the diagnosis and expediting treatment for these patients.

Musashi1 Impacts Radio-Resistance in Glioblastoma by Controlling DNA-Protein Kinase Catalytic Subunit

The conserved RNA-binding protein Musashi1 (MSI1) has been characterized as a stem cell marker, controlling the balance between self-renewal and differentiation and as a key oncogenic factor in numerous solid tumors, including glioblastoma. To explore the potential use of MSI1 targeting in therapy, we studied MSI1 in the context of radiation sensitivity. Knockdown of MSI1 led to a decrease in cell survival and an increase in DNA damage compared to control in cells treated with ionizing radiation. We subsequently examined mechanisms of double-strand break repair and found that loss of MSI1 reduces the frequency of nonhomologous end-joining. This phenomenon could be attributed to the decreased expression of DNA-protein kinase catalytic subunit, which we have previously identified as a target of MSI1. Collectively, our results suggest a role for MSI1 in double-strand break repair and that its inhibition may enhance the effect of radiotherapy.

Computational challenges, tools, and resources for analyzing co- and post-transcriptional events in high throughput

Co- and post-transcriptional regulation of gene expression is complex and multifaceted, spanning the complete RNA lifecycle from genesis to decay. High-throughput profiling of the constituent events and processes is achieved through a range of technologies that continue to expand and evolve. Fully leveraging the resulting data is nontrivial, and requires the use of computational methods and tools carefully crafted for specific data sources and often intended to probe particular biological processes. Drawing upon databases of information pre-compiled by other researchers can further elevate analyses. Within this review, we describe the major co- and post-transcriptional events in the RNA lifecycle that are amenable to high-throughput profiling. We place specific emphasis on the analysis of the resulting data, in particular the computational tools and resources available, as well as looking toward future challenges that remain to be addressed.

RNA binding protein HuR regulates the expression of ABCA1

ABCA1 is a major regulator of cellular cholesterol efflux and plasma HDL biogenesis. Even though the transcriptional activation of ABCA1 is well established, the posttranscriptional regulation of ABCA1 expression is poorly understood. Here, we investigate the potential contribution of the RNA binding protein (RBP) human antigen R (HuR) on the posttranscriptional regulation of ABCA1 expression. RNA immunoprecipitation assays demonstrate a direct interaction between HuR and ABCA1 mRNA. We found that HuR binds to the 3' untranslated region of ABCA1 and increases ABCA1 translation, while HuR silencing reduces ABCA1 expression and cholesterol efflux to ApoA1 in human hepatic (Huh-7) and monocytic (THP-1) cells. Interestingly, cellular cholesterol levels regulate the expression, intracellular localization, and interaction between HuR and ABCA1 mRNA. Finally, we found that HuR expression was significantly increased in macrophages from human atherosclerotic plaques, suggesting an important role for this RBP in controlling macrophage cholesterol metabolism in vivo. In summary, we have identified HuR as a novel posttranscriptional regulator of ABCA1 expression and cellular cholesterol homeostasis, thereby opening new avenues for increasing cholesterol efflux from atherosclerotic foam macrophages and raising circulat-ing HDL cholesterol levels.

Genomic analyses reveal broad impact of miR-137 on genes associated with malignant transformation and neuronal differentiation in glioblastoma cells

miR-137 plays critical roles in the nervous system and tumor development; an increase in its expression is required for neuronal differentiation while its reduction is implicated in gliomagenesis. To evaluate the potential of miR-137 in glioblastoma therapy, we conducted genome-wide target mapping in glioblastoma cells by measuring the level of association between PABP and mRNAs in cells transfected with miR-137 mimics vs. controls via RIPSeq. Impact on mRNA levels was also measured by RNASeq. By combining the results of both experimental approaches, 1468 genes were found to be negatively impacted by miR-137--among them, 595 (40%) contain miR-137 predicted sites. The most relevant targets include oncogenic proteins and key players in neurogenesis like c-KIT, YBX1, AKT2, CDC42, CDK6 and TGFβ2. Interestingly, we observed that several identified miR-137 targets are also predicted to be regulated by miR-124, miR-128 and miR-7, which are equally implicated in neuronal differentiation and gliomagenesis. We suggest that the concomitant increase of these four miRNAs in neuronal stem cells or their repression in tumor cells could produce a robust regulatory effect with major consequences to neuronal differentiation and tumorigenesis.

The RNA-binding protein Musashi1 affects medulloblastoma growth via a network of cancer-related genes and is an indicator of poor prognosis

Musashi1 (Msi1) is a highly conserved RNA-binding protein that is required during the development of the nervous system. Msi1 has been characterized as a stem cell marker, controlling the balance between self-renewal and differentiation, and has also been implicated in tumorigenesis, being highly expressed in multiple tumor types. We analyzed Msi1 expression in a large cohort of medulloblastoma samples and found that Msi1 is highly expressed in tumor tissue compared with normal cerebellum. Notably, high Msi1 expression levels proved to be a sign of poor prognosis. Msi1 expression was determined to be particularly high in molecular subgroups 3 and 4 of medulloblastoma. We determined that Msi1 is required for tumorigenesis because inhibition of Msi1 expression by small-interfering RNAs reduced the growth of Daoy medulloblastoma cells in xenografts. To characterize the participation of Msi1 in medulloblastoma, we conducted different high-throughput analyses. Ribonucleoprotein immunoprecipitation followed by microarray analysis (RIP-chip) was used to identify mRNA species preferentially associated with Msi1 protein in Daoy cells. We also used cluster analysis to identify genes with similar or opposite expression patterns to Msi1 in our medulloblastoma cohort. A network study identified RAC1, CTGF, SDCBP, SRC, PRL, and SHC1 as major nodes of an Msi1-associated network. Our results suggest that Msi1 functions as a regulator of multiple processes in medulloblastoma formation and could become an important therapeutic target.

The oncogenic RNA-binding protein Musashi1 is regulated by HuR via mRNA translation and stability in glioblastoma cells

Musashi1 (Msi1) is an evolutionarily conserved RNA-binding protein (RBP) that has profound implications in cellular processes such as stem cell maintenance, nervous system development, and tumorigenesis. Msi1 is highly expressed in many cancers, including glioblastoma, whereas in normal tissues, its expression is restricted to stem cells. Unfortunately, the factors that modulate Msi1 expression and trigger high levels in tumors are largely unknown. The Msi1 mRNA has a long 3' untranslated region (UTR) containing several AU- and U-rich sequences. This type of sequence motif is often targeted by HuR, another important RBP known to be highly expressed in tumor tissue such as glioblastoma and to regulate a variety of cancer-related genes. In this report, we show an interaction between HuR and the Msi1 3'-UTR, resulting in a positive regulation of Msi1 expression. We show that HuR increased MSI1 mRNA stability and promoted its translation. We also present evidence that expression of HuR and Msi1 correlate positively in clinical glioblastoma samples. Finally, we show that inhibition of cell proliferation, increased apoptosis, and changes in cell-cycle profile as a result of silencing HuR are partially rescued when Msi1 is ectopically expressed. In summary, our results suggest that HuR is an important regulator of Msi1 in glioblastoma and that this regulation has important biological consequences during gliomagenesis.

Musashi1: an RBP with versatile functions in normal and cancer stem cells

Musashi1 (Msi1) is a highly conserved RNA binding protein that was initially identified in Drosophila by its ability to regulate sensory organ development and asymmetric cell division. Studies in mammalian cells reveal multiple functions for Musashi1 in normal and abnormal processes by mediating different post-transcriptional processes. According to our recent studies, Musashi1 very likely controls hundreds of targets, forming networks that regulate apoptosis, differentiation, proliferation and cell cycle. Musashi1 is a characteristic stem cell marker that regulates the balance between self-renewal and differentiation. Over-expression of Musashi1 has been associated with numerous tumor types and its function is required for tumor growth in breast, colon, medulloblastoma and glioblastoma. Musashi1 has also been implicated in neurogenesis and neurodegenerative diseases, and is emerging as a potential therapeutic target in both regenerative medicine and cancer.

The oncogenic RNA-binding protein Musashi1 is regulated by tumor suppressor miRNAs

Musashi1 (Msi1) is an evolutionarily conserved RNA-binding protein that has been implicated in processes like stem cell fate, nervous system development, and tumorigenesis via its activities as a specific regulator of translation. While Msi1 is barely detected in normal adult tissue, it has been observed to be highly expressed in numerous tumor types (e.g. breast, colon, medulloblastoma, glioblastoma, and et cetera). Unfortunately, the molecular cues that are responsible for Msi1 upregulation in cancer cells are largely unknown. Tumor suppressor microRNAs (miRNAs) are known for targeting genes with oncogenic properties like Msi1 and for being either downregulated or deleted in tumor tissue. We observed that Msi1 long 3'UTR region is potentially targeted by several tumor suppressor miRNAs (miR-34a, -101, -128, -137, and -138). Western blotting of endogenous Msi1 protein as well as luciferase assays confirmed Msi1 regulation by these tumor suppressor miRNAs. Furthermore, we observed when examining different cellular states that these miRNAs and Msi1 have opposite expression profiles. Cell proliferation inhibition induced by the tumor suppressor miRNAs was partially rescued by Msi1 transgenic expression. We conclude that tumor suppressor miRNAs are direct and influential regulators of Msi1, affecting its expression pattern during tumorigenesis of malignant nervous system tumors.

Insect nicotinic acetylcholine receptor agonists as flea adulticides in small animals

Fleas are significant ectoparasites of small animals. They can be a severe irritant to animals and serve as a vector for a number of infectious diseases. In this article, we discuss the pharmacological characteristics of four insect nicotinic acetylcholine receptor (nAChR) agonists used as flea adulticides in dogs and cats, which include three neonicotinoids (imidacloprid, nitenpyram, and dinotefuran) and a macrocyclic lactone (spinosad). Insect nAChR agonists are one of the most important classes of insecticides, which are used to control sucking insects on both plants and animals. These novel compounds provide a new approach for practitioners to safely and effectively eliminate adult fleas.

Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes

Musashi1 (Msi1) is a highly conserved RNA-binding protein with pivotal functions in stem cell maintenance, nervous system development, and tumorigenesis. Despite its importance, only three direct mRNA targets have been characterized so far: m-numb, CDKN1A, and c-mos. Msi1 has been shown to affect their translation by binding to short elements located in the 3'-untranslated region. To better understand Msi1 functions, we initially performed an RIP-Chip analysis in HEK293T cells; this method consists of isolation of specific RNA-protein complexes followed by identification of the RNA component via microarrays. A group of 64 mRNAs was found to be enriched in the Msi1-associated population compared with controls. These genes belong to two main functional categories pertinent to tumorigenesis: 1) cell cycle, cell proliferation, cell differentiation, and apoptosis and 2) protein modification (including ubiquitination and ubiquitin cycle). To corroborate our findings, we examined the impact of Msi1 expression on both mRNA (transcriptomic) and protein (proteomic) expression levels. Genes whose mRNA levels were affected by Msi1 expression have a Gene Ontology distribution similar to RIP-Chip results, reinforcing Msi1 participation in cancer-related processes. The proteomics study revealed that Msi1 can have either positive or negative effects on gene expression of its direct targets. In summary, our results indicate that Msi1 affects a network of genes and could function as a master regulator during development and tumor formation.

Plasma vasopressin concentrations in healthy foals from birth to 3 months of age

BACKGROUND

Arginine vasopressin (AVP) has received increased attention in equine critical care but there is minimal information of AVP concentration in foals. The clinical usefulness of measuring AVP in ill foals depends on knowledge of age-related changes in AVP concentrations in healthy foals.

HYPOTHESIS

Plasma AVP concentrations will be significantly different when measured from birth to 3 months of age in healthy foals.

ANIMALS

Thirteen healthy university-owned foals.

METHODS

Prospective, observational study. Blood was collected from healthy foals at birth and 3, 5, 7, 10, 14, 21, 28, 42, 56, and 84 days of age. Plasma was harvested and plasma AVP concentrations were determined by radioimmunoassay.

RESULTS

No statistically significant differences were detected in plasma AVP concentrations over the study period. Plasma AVP concentrations over the entire study period was 6.2+/-2.5 pg/mL.

CONCLUSIONS AND CLINICAL IMPORTANCE

There was no age-related variation in plasma AVP concentrations detected in healthy foals from birth to 3 months of age suggesting that AVP concentrations are similar across foals of these ages.

Statistical evaluation of FRAM gamma-ray isotopic analysis data

High-purity germanium (HPGe) detector gamma-ray spectra were analyzed using the FRAM (fixed energy, response function analysis with multiple efficiencies) gamma-ray isotopic analysis software. The analyses are based on multiple measurements of samples having well-documented isotopic composition from mass spectrometry measurements. Statistical analyses of the FRAM results are reported, the errors in FRAM analyses arising from the choice of detector type and the energy region are discussed, and the errors that resulted from sample-dependent and analysis-dependent effects are quantified.

Aldosterone resistance in kidney transplantation is in part induced by a down-regulation of mineralocorticoid receptor expression1

BACKGROUND

After renal transplantation immunosuppressive drugs-like cyclosporin A (CsA) and FK506 induce either hypoaldosteronism or pseudo-hypoaldosteronism presenting with hyperkalemia and metabolic acidosis. We investigated the relationship between renal allograft function under CsA therapy and plasma aldosterone concentration, potassium- and water homeostasis and mineralocorticoid receptor (MR) expression level in peripheral leukocytes.

METHODS

We studied 21 renal transplant patients under CsA therapy and 12 healthy controls. Transplant recipients were studied before and under fludrocortisone treatment. Using quantitative reverse-phase polymerase chain reaction (RT-PCR) specific for the MR, we analyzed the level of expression of MR in peripheral leukocytes.

RESULTS

In acidotic transplant recipients (HCO(3) 18.5 +/- 1.2 mM) renal function was only slightly impaired with 2.0 +/- 0.2 mg creatinine/dL when compared with 1.8 +/- 0.3 mg/dL (ns) in non-acidotic patients (HCO(3) 23.0 +/- 2.8 mM). Mean plasma aldosterone levels in renal transplant recipients did not differ from control levels (150 +/- 33 pg/mL vs. 148 +/- 33 pg/mL, ns). In contrast, the expression level of MR in peripheral leukocytes of renal transplant recipients treated with CsA was significantly decreased when compared with healthy controls without renal disease (120 +/- 78 vs. 423 +/- 73 RNA molecules/0.5 microg total RNA, p < 0.01). The level of expression of MR in renal transplant recipients did not differ between acidotic patients and non-acidotic patients (ns). The application of fludrocortisone reversed hyperkalemia and metabolic acidosis without significant effect on MR expression.

CONCLUSIONS

The present data demonstrate that hyperkalemia and metabolic acidosis following CsA treatment in kidney transplantation might be associated with a down-regulation of MR expression on peripheral leukocytes. Electrolyte imbalance is reversible on application of fludrocortisone. This observation supports fludrocortisone treatment in transplant patients with severe electrolyte disturbances.

The nucleotide sequence of chromosome I from Saccharomyces cerevisiae

Chromosome I from the yeast Saccharomyces cerevisiae contains a DNA molecule of approximately 231 kbp and is the smallest naturally occurring functional eukaryotic nuclear chromosome so far characterized. The nucleotide sequence of this chromosome has been determined as part of an international collaboration to sequence the entire yeast genome. The chromosome contains 89 open reading frames and 4 tRNA genes. The central 165 kbp of the chromosome resembles other large sequenced regions of the yeast genome in both its high density and distribution of genes. In contrast, the remaining sequences flanking this DNA that comprise the two ends of the chromosome and make up more than 25% of the DNA molecule have a much lower gene density, are largely not transcribed, contain no genes essential for vegetative growth, and contain several apparent pseudogenes and a 15-kbp redundant sequence. These terminally repetitive regions consist of a telomeric repeat called W', flanked by DNA closely related to the yeast FLO1 gene. The low gene density, presence of pseudogenes, and lack of expression are consistent with the idea that these terminal regions represent the yeast equivalent of heterochromatin. The occurrence of such a high proportion of DNA with so little information suggests that its presence gives this chromosome the critical length required for proper function.