Significant Improvement in Detecting BRAF, KRAS, and EGFR Mutations Using Next-Generation Sequencing as Compared with FDA-Cleared Kits.

INTRODUCTION: We compared mutations detected in EGFR, KRAS, and BRAF genes using next-generation sequencing (NGS) and confirmed by Sanger sequencing with mutations that could be detected by FDA-cleared testing kits. METHODS: Paraffin-embedded tissue from 822 patients was tested for mutations in EGFR, KRAS, and BRAF by NGS. Sanger sequencing of hot spots was used with locked nucleic acid to increase sensitivity for specific hot-spot mutations. This included 442 (54%) lung cancers, 168 (20%) colorectal cancers, 29 (4%) brain tumors, 33 (4%) melanomas, 14 (2%) thyroid cancers, and 16% others (pancreas, head and neck, and cancer of unknown origin). Results were compared with the approved list of detectable mutations in FDA kits for EGFR, KRAS, and BRAF. RESULTS: Of the 101 patients with EGFR abnormalities as detected by NGS, only 58 (57%) were detectable by cobas v2 and only 35 (35%) by therascreen. Therefore, 42 and 65%, respectively, more mutations were detected by NGS, including two patients with EGFR amplification. Of the 117 patients with BRAF mutation detected by NGS, 62 (53%) mutations were within codon 600, detectable by commercial kits, but 55 (47%) of the mutations were outside codon V600, detected by NGS only. Of the 321 patients with mutations in KRAS detected by NGS, 284 (88.5%) had mutations detectable by therascreen and 300 (93.5%) had mutations detectable by cobas. Therefore, 11.5 and 6.5% additional KRAS mutations were detected by NGS, respectively. CONCLUSION: NGS provides significantly more comprehensive testing for mutations as compared with FDA-cleared kits currently available commercially.

Tourniquet use in combat trauma: U.K. military experience.

AIM: To determine the prevalence of tourniquet use in combat trauma, the contribution to lives saved and the complications of their use in this environment. POPULATION: All casualties treated at U.K. field hospital facilities in Iraq and Afghanistan and meeting criteria for entry into U.K. Joint Theatre Trauma Registry (JTTR) from 04 Feb 03 to 30 Sep 07. METHODS: Cases were identified from U.K. JTTR. Casualties from Permanent Joint Overseas Bases (PJOBs) were excluded. ISS, NISS, TRISS and ASCOT were calculated automatically within JTTR from AIS 2005 (Military) codes. RESULTS: 1375 patients met U.K. JTTR entry criteria for the period specified (excluding PJOBs). 70/1375 patients (5.1%) were treated with one or more tourniquets (total 107 tourniquet applications). 61/70 (87%) survived their injuries. 17/70 (24%) patients had 2 or more tourniquets applied. 64/70 patients received a tourniquet after April 2006, when tourniquets were introduced as an individual first aid item. 43/70 (61%) patients were U.K. military. CONCLUSIONS: ISS and TRISS are poorly representative of injury severity and outcome for combat trauma involving isolated multiple limb injuries and cannot be used to discriminate whether a tourniquet is life-saving. The presence of severe isolated limb injuries, profound hypovolaemic shock and the requirement for massive transfusion reasonably identifies a cohort where the use of one or more tourniquets pre-hospital to control external bleeding can be said to be life-saving.

Tourniquet use in combat trauma: UK military experience.

AIM: To determine the prevalence of tourniquet use in combat trauma, the contribution to lives saved and the complications of their use in this environment. POPULATION: All casualties treated at UK field hospital facilities in Iraq and Afghanistan and meeting criteria for entry into UK Joint Theatre Trauma Registry (JTTR) from 04 Feb 03 to 30 Sep 07. METHODS: Cases were identified from UK JTTR. Casualties from Permanent Joint Overseas Bases (PJOBs) were excluded. ISS, NISS, TRISS and ASCOT were calculated automatically within JTTR from AIS 2005 (Military) codes. RESULTS: 1375 patients met UK JTTR entry criteria for the period specified (excluding PJOBs). 70/1375 patients (5.1%) were treated with one or more tourniquets (total 107 tourniquet applications). 61/70 (87%) survived their injuries. 17/70 (24%) patients had 2 or more tourniquets applied. 64/70 patients received a tourniquet after April 2006, when tourniquets were introduced as an individual first aid item. 43/70 (61%) patients were UK military. CONCLUSIONS: ISS and TRISS are poorly representative of injury severity and outcome for combat trauma involving isolated multiple limb injuries and cannot be used to discriminate whether a tourniquet is life-saving. The presence of severe isolated limb injuries, profound hypovolaemic shock and the requirement for massive transfusion reasonably identifies a cohort where the use of one or more tourniquets pre-hospital to control external bleeding can be said to be life-saving.

Apolipoprotein epsilon4 allele and problems with orientation are associated with a persistent decline in cognition in community-dwelling elderly persons.

BACKGROUND: A decline in cognitive test scores in elderly persons can signal the beginning of a descent into dementia or may indicate only a short-term cognitive disturbance. It would be clinically useful to distinguish between the two outcomes and to identify characteristics of each. METHODS: Four hundred thirty-seven community-dwelling elderly persons were given the Mini-Mental State Examination (MMSE) annually for an average of 7 years. A low score between baseline and final MMSE was identified. A low score 3 or more points lower than baseline score indicated cognitive decline. This decline was called persistent if the final MMSE score was also at least 3 points lower than baseline MMSE score; otherwise, the decline was considered transient. RESULTS: Twenty participants (4.6%) experienced a persistent cognitive decline, 67 participants (15.3%) experienced a transient cognitive decline. Presence of the apolipoprotein epsilon4 allele was significantly associated with persistent cognitive decline (age-adjusted odd ratio [OR] = 11.46, p < .0001) but not with transient cognitive decline (age-adjusted OR = 1.53, p = .219). Incorrect answers on the orientation part of the MMSE at the time of cognitive decline was associated with persistent decline compared to transient decline (age-adjusted OR = 3.58, p = .058). CONCLUSIONS: Persistent cognitive decline is an infrequent occurrence in community-dwelling elderly persons. Presence of the epsilon4 allele and errors made by the subject on questions of orientation may be useful in determining whether a cognitive decline is likely to be persistent.

The effect of human tissue factor pathway inhibitor-2 on the growth and metastasis of fibrosarcoma tumors in athymic mice.

Human tissue factor pathway inhibitor-2 (TFPI-2) is a matrix-associated Kunitz inhibitor that inhibits the plasmin- and trypsin-mediated activation of zymogen matrix metalloproteinases involved in tumor progression, invasion, and metastasis. To directly assess its role in tumor growth and metastasis in vivo, we stably transfected HT-1080 fibrosarcoma cells expressing either fully active wild-type human TFPI-2 (WT) or inactive R24Q TFPI-2 (QT) and examined their ability to form tumors and metastasize in athymic mice in comparison to mock-transfected cells (MT). MT and QT fibrosarcoma tumors grew 2 to 3 times larger than WT tumors. Tumor metastasis was confined to the lung and was observed in 75% of mice treated with either MT or QT cells, whereas only 42% of mice treated with WT cells developed lung metastases. Real-time quantitative reverse transcriptase-polymerase chain reaction (RT-PCR) analyses of each tumor group revealed 3- to 6-fold lower levels of murine vascular endothelial growth factor gene expression in WT tumors in relation to either MT or QT tumors. Comparative tumor gene expression analysis revealed that several human genes implicated in oncogenesis, invasion, metastasis, apoptosis, and angiogenesis had significantly altered levels of expression in WT tumors. Our collective data demonstrate that secretion of inhibitory TFPI-2 by a highly metastatic tumor cell markedly inhibits its growth and metastasis in vivo by regulating pericellular extracellular matrix (ECM) remodeling and angiogenesis.

Squamous cell carcinoma and mammary abscess formation through squamous metaplasia in Smad4/Dpc4 conditional knockout mice.

Smad4 is a central mediator for TGFbeta signals, which play important functions in many biological processes. To study the role of Smad4 in mammary gland development and neoplasia, we disrupted this gene in mammary epithelium using a Cre-loxP approach. Smad4 is expressed in the mammary gland throughout development; however, its inactivation did not cause abnormal development of the gland during the first three pregnancies. Instead, lack of Smad4 gradually induced cell proliferation, alveolar hyperplasia and transdifferentiation of mammary epithelial cells into squamous epithelial cells. Consequently, all mutant mice developed squamous cell carcinoma and/or mammary abscesses between 5 and 16 months of age. We demonstrated that absence of Smad4 resulted in beta-catenin accumulation at onset and throughout the process of transdifferentiation, implicating beta-catenin, a key component of the Wnt signaling pathway, in the development of squamous metaplasia in Smad4-null mammary glands. We further demonstrated that TGFbeta1 treatment degraded beta-catenin and induced epithelial-mesenchymal transformation in cultured mammary epithelial cells. However, such actions were blocked in the absence of Smad4. These findings indicate that TGFbeta/Smad4 signals play a role in cell fate maintenance during mammary gland development and neoplasia.

Mouse models orthologous to FGFR3-related skeletal dysplasias.

Fibroblast growth factor receptor 3 (FGFR3) is one of the membrane bound tyrosine kinases that mediate the actions of fibroblast growth factor (FGF) family members. Missense mutations in the coding regions of FGFR3 have been identified in allelic forms of short-limbed dwarfism. Using gene targeting, we demonstrated that Fgfr3 plays an essential role in endochondral ossification and that a loss-of-function mutation causes accelerated and prolonged long bone growth. Using a number of molecular genetic approaches, we also have introduced into the mouse genome a series of mutations that correspond to the missense mutations identified in individuals with achondroplasia and thanatophoric dysplasia. These mouse models mimic the human condition and can be used for further studies to identify and characterize in vivo changes associated with various Fgfr3 mutations. In addition, these models may be beneficial in future studies to attempt novel treatment strategies for short-limbed dwarfism.

Senescence, aging, and malignant transformation mediated by p53 in mice lacking the Brca1 full-length isoform.

Senescence may function as a two-edged sword that brings unexpected consequences to organisms. Here we provide evidence to support this theory by showing that the absence of the Brca1 full-length isoform causes senescence in mutant embryos and cultured cells as well as aging and tumorigenesis in adult mice. Haploid loss of p53 overcame embryonic senescence but failed to prevent the adult mutant mice from prematurely aging, which included decreased life span, reduced body fat deposition, osteoporosis, skin atrophy, and decreased wound healing. We further demonstrate that mutant cells that escaped senescence had undergone clonal selection for faster proliferation and extensive genetic/molecular alterations, including overexpression of cyclin D1 and cyclin A and loss of p53. These observations provide the first in vivo evidence that links cell senescence to aging due to impaired function of Brca1 at the expense of tumorigenesis.

BRCA1 supports XIST RNA concentration on the inactive X chromosome.

BRCA1, a breast and ovarian tumor suppressor, colocalizes with markers of the inactive X chromosome (Xi) on Xi in female somatic cells and associates with XIST RNA, as detected by chromatin immunoprecipitation. Breast and ovarian carcinoma cells lacking BRCA1 show evidence of defects in Xi chromatin structure. Reconstitution of BRCA1-deficient cells with wt BRCA1 led to the appearance of focal XIST RNA staining without altering XIST abundance. Inhibiting BRCA1 synthesis in a suitable reporter line led to increased expression of an otherwise silenced Xi-located GFP transgene. These observations suggest that loss of BRCA1 in female cells may lead to Xi perturbation and destabilization of its silenced state.

Mammary tumors in mice conditionally mutant for Brca1 exhibit gross genomic instability and centrosome amplification yet display a recurring distribution of genomic imbalances that is similar to human breast cancer.

BRCA1 mutation carriers have an increased susceptibility to breast and ovarian cancer. Excision of exon 11 of Brca1 in the mouse, using a conditional knockout (Cre-loxP) approach, results in mammary tumor formation after long latency. To characterize the genomic instability observed in these tumors, to establish a comparative map of chromosomal imbalances and to contribute to the validation of this mouse model of breast cancer, we have characterized chromosomal imbalances and aberrations using comparative genomic hybridization (CGH), and spectral karyotyping (SKY). We found that all tumors exhibit chromosome instability as evidenced by structural chromosomal aberrations and aneuploidy, yet they display a pattern of chromosomal gain and loss that is similar to the pattern in human breast carcinomas. Of note, nine of 15 tumors exhibited a gain of distal chromosome 11, a region that is orthologous to human chromosome 17q11-qter, the mapping position of Erbb2. However, our analysis suggests that genes distal to Erbb2 are the main targets of amplification. Four of the tumors also exhibited a copy number loss of proximal chromosome 11 (11A-B), a region orthologous to human 17p. In eight of the tumors we observed whole or partial gain of chromosome 15 centering on 15D2-D3 (orthologous to human chromosome 8q24), the map location of the c-Myc gene, and six of the tumors exhibited copy number loss of whole or partial chromosome 14, including 14D3, the map location of Rb1. We conclude that despite the tremendous shuffling of chromosomes during the course of mammalian evolution, the pattern of genomic imbalances is conserved between BRCA1-associated mammary gland tumors in mice and humans. Western blot analysis showed that while p53 is absent or mutated in some tumors, at least two tumors revealed wild-type protein, suggesting that other genetic events may lead to tumorigenesis. Similar to BRCA1-deficient mouse embryonic fibroblasts, the tumor cells contained supernumerary functional centrosomes with intact centrioles whose presence results in multipolar mitoses and aneuploidy.

Smad3 in the mammary epithelium has a nonredundant role in the induction of apoptosis, but not in the regulation of proliferation or differentiation by transforming growth factor-beta.

Transforming growth factor-beta (TGF-beta) regulates proliferation, morphogenesis, and functional differentiation in the mammary gland and plays complex roles in mammary tumorigenesis. Here we show that the signaling mediators Smad1-Smad5 are expressed at all stages of mammary gland development. To begin to investigate which Smads mediate which TGF-beta responses, we have analyzed mammary gland development in Smad3 null mice. Smad3 null virgin females showed delayed mammary gland development. However, this phenotype was secondary to ovarian insufficiency because Smad3 null mammary epithelium developed normally in hormonally supplemented Smad3 null mice or when transplanted into wild-type hosts. Absence of Smad3 had no effect on the ability of TGF-beta to inhibit the growth of mammary epithelial cells in culture, and no compensatory changes in expression or activation of Smad2 were seen in the Smad3 null epithelium. A small but significant decrease in apoptotic cells was seen in involuting glands from Smad3 null transplants. The results suggest that epithelial Smad3 is dispensable for TGF-beta effects on proliferation and differentiation in the mammary gland, but that it contributes in a nonredundant manner to the induction of apoptosis.