Microsatellite instability (MSI) is an important indicator of larger genome instability and has been linked to many genetic diseases, including Lynch syndrome. MSI status is also an independent ...prognostic factor for favorable survival in multiple cancer types, such as colorectal and endometrial. It also informs the choice of chemotherapeutic agents. However, the current PCR-electrophoresis-based detection procedure is laborious and time-consuming, often requiring visual inspection to categorize samples. We developed MSIsensor, a C++ program for automatically detecting somatic microsatellite changes. It computes length distributions of microsatellites per site in paired tumor and normal sequence data, subsequently using these to statistically compare observed distributions in both samples. Comprehensive testing indicates MSIsensor is an efficient and effective tool for deriving MSI status from standard tumor-normal paired sequence data.
https://github.com/ding-lab/msisensor
Individuals with upper limb loss lack sensation of the missing hand, which can negatively impact their daily function. Several groups have attempted to restore this sensation through electrical ...stimulation of residual nerves. The purpose of this study was to explore the utility of regenerative peripheral nerve interfaces (RPNIs) in eliciting referred sensation. In four participants with upper limb loss, we characterized the quality and location of sensation elicited through electrical stimulation of RPNIs over time. We also measured functional stimulation ranges (sensory perception and discomfort thresholds), sensitivity to changes in stimulation amplitude, and ability to differentiate objects of different stiffness and sizes. Over a period of up to 54 months, stimulation of RPNIs elicited sensations that were consistent in quality (e.g. tingling, kinesthesia) and were perceived in the missing hand and forearm. The location of elicited sensation was partially-stable to stable in 13 of 14 RPNIs. For 5 of 7 RPNIs tested, participants demonstrated a sensitivity to changes in stimulation amplitude, with an average just noticeable difference of 45 nC. In a case study, one participant was provided RPNI stimulation proportional to prosthetic grip force. She identified four objects of different sizes and stiffness with 56% accuracy with stimulation alone and 100% accuracy when stimulation was combined with visual feedback of hand position. Collectively, these experiments suggest that RPNIs have the potential to be used in future bi-directional prosthetic systems.
Although most activating mutations of epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancers (NSCLCs) are sensitive to available EGFR tyrosine kinase inhibitors (TKIs), a subset ...with alterations in exon 20 of EGFR and HER2 are intrinsically resistant and lack an effective therapy. We used in silico, in vitro, and in vivo testing to model structural alterations induced by exon 20 mutations and to identify effective inhibitors. 3D modeling indicated alterations restricted the size of the drug-binding pocket, limiting the binding of large, rigid inhibitors. We found that poziotinib, owing to its small size and flexibility, can circumvent these steric changes and is a potent inhibitor of the most common EGFR and HER2 exon 20 mutants. Poziotinib demonstrated greater activity than approved EGFR TKIs in vitro and in patient-derived xenograft models of EGFR or HER2 exon 20 mutant NSCLC and in genetically engineered mouse models of NSCLC. In a phase 2 trial, the first 11 patients with NSCLC with EGFR exon 20 mutations receiving poziotinib had a confirmed objective response rate of 64%. These data identify poziotinib as a potent, clinically active inhibitor of EGFR and HER2 exon 20 mutations and illuminate the molecular features of TKIs that may circumvent steric changes induced by these mutations.
The Cancer Genome Atlas (TCGA) has used the latest sequencing and analysis methods to identify somatic variants across thousands of tumours. Here we present data and analytical results for point ...mutations and small insertions/deletions from 3,281 tumours across 12 tumour types as part of the TCGA Pan-Cancer effort. We illustrate the distributions of mutation frequencies, types and contexts across tumour types, and establish their links to tissues of origin, environmental/carcinogen influences, and DNA repair defects. Using the integrated data sets, we identified 127 significantly mutated genes from well-known (for example, mitogen-activated protein kinase, phosphatidylinositol-3-OH kinase, Wnt/β-catenin and receptor tyrosine kinase signalling pathways, and cell cycle control) and emerging (for example, histone, histone modification, splicing, metabolism and proteolysis) cellular processes in cancer. The average number of mutations in these significantly mutated genes varies across tumour types; most tumours have two to six, indicating that the number of driver mutations required during oncogenesis is relatively small. Mutations in transcriptional factors/regulators show tissue specificity, whereas histone modifiers are often mutated across several cancer types. Clinical association analysis identifies genes having a significant effect on survival, and investigations of mutations with respect to clonal/subclonal architecture delineate their temporal orders during tumorigenesis. Taken together, these results lay the groundwork for developing new diagnostics and individualizing cancer treatment.
Rosai-Dorfman Disease (RDD), an entity first described in 1969 is a rare disorder characterized by proliferation of histiocytes that primarily occurs in lymph nodes. In the breast, RDD is extremely ...rare. Although the disease typically has a slow progressive nature, it is important to recognize it as it can mimic malignancy.
We present a case of a 17-year-old male with no significant past medical history who presented to the pediatric surgery office for evaluation of a left-sided breast mass that was suspicious for malignancy. The ultrasound findings were non-diagnostic at the time. Although further workup of this mass may have been achieved by CT scan, MRI or core biopsy, the decision was made to proceed with upfront surgical resection for both diagnostic and therapeutic purposes. Final immunohistochemistry of the mass revealed atypical large histiocytes positive for CD68 with co-expression of S100 consistent with RDD. At the time of publication, the patient is alive and well. He has not received any further therapy for RDD and there were no signs of recurrence.
The diagnosis of Rosai-Dorfman disease can be quite challenging. Given the variable presentation and nonspecific imaging findings, definitive diagnosis relies on histopathologic findings. Pediatric patients with unifocal RDD involving the breast can be effectively treated with surgical resection safely as both a diagnostic and therapeutic option.
Pediatric osteosarcoma is characterized by multiple somatic chromosomal lesions, including structural variations (SVs) and copy number alterations (CNAs). To define the landscape of somatic mutations ...in pediatric osteosarcoma, we performed whole-genome sequencing of DNA from 20 osteosarcoma tumor samples and matched normal tissue in a discovery cohort, as well as 14 samples in a validation cohort. Single-nucleotide variations (SNVs) exhibited a pattern of localized hypermutation called kataegis in 50% of the tumors. We identified p53 pathway lesions in all tumors in the discovery cohort, nine of which were translocations in the first intron of the TP53 gene. Beyond TP53, the RB1, ATRX, and DLG2 genes showed recurrent somatic alterations in 29%-53% of the tumors. These data highlight the power of whole-genome sequencing for identifying recurrent somatic alterations in cancer genomes that may be missed using other methods.
In 2007, we published our initial experience in treating inoperable non-small-cell lung cancer (NSCLC) with intensity-modulated radiation therapy (IMRT). The current report is an update of that ...experience with long-term follow-up.
Patients in this retrospective review were 165 patients who began definitive radiotherapy, with or without chemotherapy, for newly diagnosed, pathologically confirmed NSCLC to a dose of ≥60 Gy from 2005 to 2006. Early and late toxicities assessed included treatment-related pneumonitis (TRP), pulmonary fibrosis, esophagitis, and esophageal stricture, scored mainly according to the Common Terminology Criteria for Adverse Events 3.0. Other variables monitored were radiation-associated dermatitis and changes in body weight and Karnofsky performance status. The Kaplan-Meier method was used to compute survival and freedom from radiation-related acute and late toxicities as a function of time.
Most patients (89%) had Stage III to IV disease. The median radiation dose was 66 Gy given in 33 fractions (range, 60-76 Gy, 1.8-2.3 Gy per fraction). Median overall survival time was 1.8 years; the 2-year and 3-year overall survival rates were 46% and 30%. Rates of Grade ≥3 maximum TRP (TRP(max)) were 11% at 6 months and 14% at 12 months. At 18 months, 86% of patients had developed Grade ≥1 maximum pulmonary fibrosis (pulmonary fibrosis(max)) and 7% Grade ≥2 pulmonary fibrosis(max). The median times to maximum esophagitis (esophagitis(max)) were 3 weeks (range, 1-13 weeks) for Grade 2 and 6 weeks (range, 3-13 weeks) for Grade 3. A higher percentage of patients who experienced Grade 3 esophagitis(max) later developed Grade 2 to 3 esophageal stricture.
In our experience, using IMRT to treat NSCLC leads to low rates of pulmonary and esophageal toxicity, and favorable clinical outcomes in terms of survival.
Genome-wide gene-expression studies have shown that hundreds of yeast genes are induced or repressed transiently by changes in temperature; many are annotated to stress response on this basis. To ...obtain a genome-scale assessment of which genes are functionally important for innate and/or acquired thermotolerance, we combined the use of a barcoded pool of ∼4,800 nonessential, prototrophic Saccharomyces cerevisiae deletion strains with Illumina-based deep-sequencing technology. As reported in other recent studies that have used deletion mutants to study stress responses, we observed that gene deletions resulting in the highest thermosensitivity generally are not the same as those transcriptionally induced in response to heat stress. Functional analysis of identified genes revealed that metabolism, cellular signaling, and chromatin regulation play roles in regulating thermotolerance and in acquired thermotolerance. However, for most of the genes identified, the molecular mechanism behind this action remains unclear. In fact, a large fraction of identified genes are annotated as having unknown functions, further underscoring our incomplete understanding of the response to heat shock. We suggest that survival after heat shock depends on a small number of genes that function in assessing the metabolic health of the cell and/or regulate its growth in a changing environment.
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