Intratumor heterogeneity and branched evolution revealed by multiregion sequencing.

BACKGROUND: Intratumor heterogeneity may foster tumor evolution and adaptation and hinder personalized-medicine strategies that depend on results from single tumor-biopsy samples. METHODS: To examine intratumor heterogeneity, we performed exome sequencing, chromosome aberration analysis, and ploidy profiling on multiple spatially separated samples obtained from primary renal carcinomas and associated metastatic sites. We characterized the consequences of intratumor heterogeneity using immunohistochemical analysis, mutation functional analysis, and profiling of messenger RNA expression. RESULTS: Phylogenetic reconstruction revealed branched evolutionary tumor growth, with 63 to 69% of all somatic mutations not detectable across every tumor region. Intratumor heterogeneity was observed for a mutation within an autoinhibitory domain of the mammalian target of rapamycin (mTOR) kinase, correlating with S6 and 4EBP phosphorylation in vivo and constitutive activation of mTOR kinase activity in vitro. Mutational intratumor heterogeneity was seen for multiple tumor-suppressor genes converging on loss of function; SETD2, PTEN, and KDM5C underwent multiple distinct and spatially separated inactivating mutations within a single tumor, suggesting convergent phenotypic evolution. Gene-expression signatures of good and poor prognosis were detected in different regions of the same tumor. Allelic composition and ploidy profiling analysis revealed extensive intratumor heterogeneity, with 26 of 30 tumor samples from four tumors harboring divergent allelic-imbalance profiles and with ploidy heterogeneity in two of four tumors. CONCLUSIONS: Intratumor heterogeneity can lead to underestimation of the tumor genomics landscape portrayed from single tumor-biopsy samples and may present major challenges to personalized-medicine and biomarker development. Intratumor heterogeneity, associated with heterogeneous protein function, may foster tumor adaptation and therapeutic failure through Darwinian selection. (Funded by the Medical Research Council and others.).

Rapid frozen section immunostaining of melanocytes by microphthalmia-associated transcription factor.

Mohs micrographic surgery (MMS) has increasingly become an accepted therapy for melanoma in situ on chronically sun damaged skin (CSDS). However, melanocytes are difficult to locate in frozen material on hematoxylin and eosin. In addition, determining the cut-off between the melanoma and the "atypical melanocytic hyperplasia" in CSDS can be challenging in frozen or formalin-fixed paraffin-embedded sections, with or without immunohistochemistry (IHC). In this article, we report the use of a rapid, 35-minute protocol using microphthalmia-associated transcription factor (MITF) IHC for identifying melanocytes in frozen tissue for its potential use in MMS. In contrast to melanoma antigen recognized by T cells (MART-1), MITF is a nuclear stain, which simplifies identification of melanocytes and quantification of melanocytic parameters. In this study, MITF IHC in frozen sections yielded equivalent melanocyte nuclear diameter and density measurements compared with formalin-fixed paraffin-embedded sections. Nuclear diameter measurements obtained with MITF were similar to that previously reported with MART-1, but the melanocyte density figures were lower. Reliable labeling of melanocytes in frozen sections required the use of diaminobenzidine (DAB) chromogen with Giemsa counterstaining and a buffer devoid of surfactant. Our experience with MITF IHC indicates that it is a dependable immunostain in frozen sections, and may prove to be useful in MMS as an adjunct to hematoxylin and eosin and MART-1 IHC for interpretation of margins for melanoma in situ on CSDS.

Surgical management of melanoma-in-situ using a staged marginal and central excision technique.

Melanoma-in-situ (MIS) represents 45% of all melanomas. The margins of MIS are often poorly defined with extensive subclinical disease. Standard fusiform excision with 5-mm margins results in positive margins in up to a third of cases. To decrease the incidence of involved margins, we use a staged excision approach for MIS. First, patients undergo excision under local anesthesia of a 2- to 3-mm "contoured" rim of tissue optimally 5 mm beyond the visible extent of the lesion. Formalin-fixed paraffin-embedded en face sections from this excision are then evaluated, if necessary with the aid of immunohistochemical stains. Any positive margins are further excised. When all margins are negative, the central area is then excised and reconstructed. A total of 61 patients with MIS or lentigo maligna melanoma underwent staged contoured excisions from 2004 to 2007 at Moffitt Cancer Center. We analyzed data only from patients with MIS of the head and neck. Patients with known invasive melanoma or non-head and neck primary disease were excluded. Demographics, tumor characteristics, margin status, number of stages, and type of reconstruction and recurrences were evaluated. Forty-nine patients with MIS of the head and neck, 28 (57%) male and 21 (43%) female, 42 to 88-years-old (median 72; mean 70), underwent staged contoured margin excision before definitive central tumor excision and reconstruction. The final surgical defect size ranged from 2 to 130 cm(2) (median 16 cm(2)). Twelve patients (24%) required reexcision of at least one margin; the median number of reexcisions was 1 (range 1-2). There seemed to be a positive association between lesion size and margin status (as well as number of excisions needed to clear the margin). Unsuspected invasive melanoma was found in the central specimen in six patients (12%). Even small tumors could have unsuspected invasive melanoma: invasive cancer was seen in 4 (21%) of 19 tumors < or =2 cm in greatest dimension and 2 (7%) of 30 > 2 cm, respectively. Surgical defects were reconstructed with flaps in 18 (37%), full-thickness grafts in 20 (41%), and split-thickness grafts in 10 patients (20%). Median time from first margin excision to completion/final reconstruction was 7 days (range 7-63 days). No local recurrences have been reported at a median follow-up of 14 months (range 1-36 months). This technique allows for careful margin analysis and subsequent central tumor excision with simultaneous reconstruction. This approach minimizes the need for a second major operation, which would have been necessary in 24% of our patients if treated by a one-stage excisional approach. It is noteworthy that 12% of MIS patients had invasive melanoma in the final excision specimen. This reinforces the importance of adequate full-thickness biopsies of suspicious pigmented lesions before any type of surgical management. With short follow-up, local control has been achieved by this technique in 100% of cases.

Surgical management of melanoma in situ on chronically sun-damaged skin.

BACKGROUND: Lentigo maligna (LM) commonly presents as a slow-growing pigmented macular lesion in chronically sun-damaged skin and may progress to invasive melanoma. Many regard it as a subtype of melanoma in situ (MIS), and surgical excision remains the preferred treatment, but standard 5-mm surgical margins recommended for typical MIS are often insufficient for LM due to its indistinct borders both clinically and histologically. METHODS: A search of the literature was conducted to review specialized surgical techniques for the treatment of LM, focusing on methods that employ total peripheral margin assessment prior to definitive closure, using either frozen or permanent histologic sections. RESULTS: Many investigators have reported surgical modalities utilizing permanent sections for margin control, including variations of the "square" procedure and "perimeter" technique. Recurrence rates are low with these methods, but only short-term data have been reported. Similarly, several studies have demonstrated the efficacy of Mohs micrographic surgery (MMS) for treatment of MIS, with recurrence rates generally less than 1% over 3 to 5 years of follow-up. Many investigators have had success with immunohistochemical stains to identify melanocytes on frozen sections, aiding margin assessment in MMS. CONCLUSIONS: Compared to standard excision, methods that employ surgical margin control offer superior cure rates for LM and should be utilized when available. Total peripheral margin assessment using staged excisions and permanent sections is a simple and effective alternative to MMS for institutions that lack the resources for intraoperative frozen section analysis.

Gold nanoparticles decorated with oligo(ethylene glycol) thiols: kinetics of colloid aggregation driven by depletion forces.

We have studied the kinetics of the phase-separation process of mixtures of colloid and protein in solutions by real-time UV-vis spectroscopy. Complementary small-angle X-ray scattering (SAXS) was employed to determine the structures involved. The colloids used are gold nanoparticles functionalized with protein resistant oligo(ethylene glycol) (OEG) thiol, HS(CH2)11(OCH2CH2)6OMe (EG6OMe). After mixing with protein solution above a critical concentration, c*, SAXS measurements show that a scattering maximum appears after a short induction time at q = 0.0322 A-1, which increases its intensity with time but the peak position does not change with time, protein concentration and salt addition. The peak corresponds to the distance of the nearest neighbor in the aggregates. The upturn of scattering intensities in the low q-range developed with time indicating the formation of aggregates. No Bragg peaks corresponding to the formation of colloidal crystallites could be observed before the clusters dropped out from the solution. The growth kinetics of aggregates is followed in detail by real-time UV-vis spectroscopy, using the flocculation parameter defined as the integral of the absorption in the range of 600-800 nm wavelengths. At low salt addition (<0.5 M), a kinetic crossover from reaction-limited cluster aggregation (RLCA) to diffusion-limited cluster aggregation (DLCA) growth model is observed, and interpreted as being due to the effective repulsive interaction barrier between colloids within the depletion potential. Above 0.5 M NaCl, the surface charge of proteins is screened significantly, and the repulsive potential barrier disappeared, thus the growth kinetics can be described by a DLCA model only.

Gold nanoparticles decorated with oligo(ethylene glycol) thiols: protein resistance and colloidal stability.

The interactions between proteins and gold colloids functionalized with protein-resistant oligo(ethylene glycol) (OEG) thiol, HS(CH2)11(OCH2CH2)6OMe (EG6OMe), in aqueous solution have been studied by small-angle X-ray scattering (SAXS) and UV-vis spectroscopy. The mean size, 2R, and the size distribution of the decorated gold colloids have been characterized by SAXS. The monolayer-protected gold colloids have no correlations due to the low volume fraction in solution and are stable in a wide range of temperatures (5-70 degrees C), pH (1.3-12.4), and ionic strength (0-1.0 M). In contrast, protein (bovine serum albumin) solutions with concentrations in the range of 60-200 mg/mL (4.6-14.5 vol %) show a pronounced correlation peak in SAXS, which results from the repulsive electrostatic interaction between charged proteins. These protein interactions show significant dependence on ionic strength, as would be expected for an electrostatic interaction (Zhang et al. J. Phys. Chem. B 2007, 111, 251). For a mixture of proteins and gold colloids, the protein-protein interaction changes little upon mixing with OEG-decorated gold colloids. In contrast, the colloid-colloid interaction is found to be strongly dependent on the protein concentration and the size of the colloid itself. Adding protein to a colloidal solution results in an attractive depletion interaction between functionalized gold colloids, and above a critical protein concentration, c*, the colloids form aggregates and flocculate. Adding salt to such mixtures enhances the depletion effect and decreases the critical protein concentration. The aggregation is a reversible process (i.e., diluting the solution leads to dissolution of aggregates). The results also indicate that the charge of the OEG self-assembled monolayer at a curved interface has a rather limited effect on the colloidal stabilization and the repulsive interaction with proteins.