Vladimir Iakovlev

Multilevel Whole-Genome Analysis Reveals Candidate Biomarkers in Clear Cell Renal Cell Carcinoma

Renal cell carcinoma (RCC) is the most common neoplasm of the kidney. We conducted an integrated analysis of copy number, gene expression (mRNA and miRNA), protein expression, and methylation changes in clear cell renal cell carcinoma (ccRCC). We used a stepwise approach to identify the most significant copy number aberrations (CNA) and identified regions of peak and broad copy number gain and loss, including peak gains (3q21, 5q32, 5q34-q35, 7p11, 7q21, 8q24, 11q13, and 12q14) and deletions (1p36, 2q34-q37, 3p25, 4q33-q35, 6q23-q27, and 9p21). These regions harbor novel tumor-related genes and miRNAs not previously reported in renal carcinoma. Integration of genome-wide expression data and gene set enrichment analysis revealed 75 gene sets significantly altered in tumors with CNAs compared with tumors without aberration. We also identified genes located in peak CNAs with concordant methylation changes (hypomethylated in copy number gains such as STC2 and CCND1 and hypermethylated in deletions such as CLCNKB, VHL, and CDKN2A/2B). For other genes, such as CA9, expression represents the net outcome of opposing forces (deletion and hypomethylation) that also significantly influences patient survival. We also validated the prognostic value of miRNA let-7i in RCCs. miR-138, located in chromosome 3p deletion, was also found to have suppressive effects on tumor proliferation and migration abilities. Our findings provide a significant advance in the delineation of the ccRCC genome by better defining the impact of CNAs in conjunction with methylation changes on the expression of cancer-related genes, miRNAs, and proteins and their influence on patient survival.

Microvascular density as an independent predictor of clinical outcome in renal cell carcinoma: an automated image analysis study

Tumor microvascular density (MVD) has been shown to correlate with the aggressiveness of several cancers. With the introduction of targeted anti-angiogenic therapy, assessment of MVD has the potential not only as a prognostic but also as a therapeutic marker. The significance of tumor vascularity in clear cell renal cell carcinoma (ccRCC) has been debated, with studies showing contradictory results. Previous studies were limited by manual quantification of MVD within a small area of tumor. Since then, the validity of this method has been questioned. To avoid the inaccuracies of manual quantification, we employed a computerized image analysis, which allowed assessment of large areas of tumor and adjacent normal tissue. The latter was used as an internal reference for normalization. MVD and vascular endothelial growth factor (VEGF) were assessed in 57 cases of ccRCC. Sections were immunostained for CD34 and VEGF. Areas of ccRCC and normal kidney medulla were analyzed within scanned images using software that counted CD34-positive vessels and measured the intensity of VEGF staining. We obtained unadjusted values from tumoral areas and calculated adjusted values as tumor/normal ratios. Unadjusted MVD had no association with clinical outcome. However, similarly to tumor stage, higher adjusted MVD was associated with shorter disease-free survival (log-rank P=0.037, Cox P=0.02). This was significant in univariate and multivariate analyses. MVD did not correlate with tumor stage, pointing to its independent prognostic value. As expected due to the known molecular abnormalities in ccRCC, most tumors showed higher VEGF expression than normal tissue. Higher adjusted VEGF was associated with high tumor grade (P=0.049). The finding of increased MVD as an independent marker of tumor aggressiveness may prove useful in the development of new tests for prognostic and therapeutic guidance. Digital techniques can provide more accurate assessment of immunomarkers and may reveal less obvious associations.

Safety considerations for synthetic sling surgery

Implantation of a synthetic midurethral sling (SMUS) is the most commonly performed anti-incontinence operation in women worldwide. The effectiveness of the SMUS is comparable to that of the historical gold standards—autologous fascial slings and the Burch colposuspension. Much controversy, however, has evolved regarding the safety of this type of sling. Overall, the quality of the studies with respect to assessing risks of SMUS-associated complications is currently poor. The most common risks in patients with SMUS include urethral obstruction requiring surgery (2.3% of patients with SMUS), vaginal, bladder and/or urethral erosion requiring surgery (1.8%) and refractory chronic pain (4.1%); these data likely represent the minimum risks. In addition, the failure rate of SMUS implantation surgery is probably at least 5% in patients with stress urinary incontinence (SUI). Furthermore, at least one-third of patients undergoing sling excision surgery develop recurrent SUI. Considering the additional risks of refractory overactive bladder, fistulas and bowel perforations, among others, the overall risk of a negative outcome after SMUS implantation surgery is ≥15%.

Degradation of polypropylene in vivo: A microscopic analysis of meshes explanted from patients

Polypropylene meshes, originally introduced for hernia repair, are presently utilized in several anatomical sites. Several million are implanted annually worldwide. Depending on the device, up to 10% will be excised to treat complications. The excised meshes can provide material to study the complications, however, they have remained underutilized over the last decades and the mechanisms of complications continue to be incompletely understood. The fundamental question as to whether polypropylene degrades in vivo is still debated. We have examined 164 excised meshes using conventional microscopy to search for features of polypropylene degradation. Four specimens were also examined by transmission electron microscopy. The degraded material, detected by its ability to absorb dyes in the degradation nanopores, formed a continuous layer at the surface of the mesh fibers. It retained birefringence, inclusions of non-degraded polypropylene, and showed ability to meld with the non-degraded fiber core when heated by the surgical cautery. Several features indicated that the degradation layer formed in vivo: inflammatory cells trapped within fissures, melting caused by cautery of excision surgery, and gradual but progressive growth of the degradation layer while in the body. Cracking of the degraded material indicated a contribution to clinically important mesh stiffening and deformation. Chemical products of degradation need to be analyzed and studied for their role in the mesh-body interactions. The described methods can also be used to study degradation of other materials.

Emphysematous oesophagitis associated with Sarcina organisms in a patient receiving anti‐inflammatory therapy

DNA sequencing (Figure 2H). According to these findings, EPH could be reconsidered as a forerunner towards AAH in the multistep progression which leads, first, to in-situ adenocarcinoma (bronchioloalveolar carcinoma) and then to minimally invasive adenocarcinoma and invasive adenocarcinoma. In fact, EPH and AAH share not only an early-onset age, but also the peripheral occurrence, which can result in pneumothorax. Moreover, previous ultrastructural studies have detected in AAH cells the presence of cytoplasmic lamellar bodies and nuclear branching microtubules, suggesting a histogenesis from type II pneumocytes. AAH is more frequent in women while, until now, no EPH has been described in female patients. This datum underlines its male predilection, due probably to hormonal influences or different lifestyles (occupational exposure, smoking habits). The presence of mitotic figures appears to be the morphological watershed between these two on continuous entities and in-situ adenocarcinoma. For the future, a detailed molecular characterization of EPH on a large series, involving various protoncogenes (EGFR, V-erb-b2 avian erythroblastic leukaemia viral oncogene homologue 2 (ERBB2) and Kirsten rat sarcoma (KRAS)], is advocated, in order to resolve this question.

Oxidation and degradation of polypropylene transvaginal mesh

Abstract Polypropylene (PP) transvaginal mesh (TVM) repair for stress urinary incontinence (SUI) has shown promising short-term objective cure rates. However, life-altering complications have been associated with the placement of PP mesh for SUI repair. PP degradation as a result of the foreign body reaction (FBR) has been proposed as a contributing factor to mesh complications. We hypothesized that PP oxidizes under in vitro conditions simulating the FBR, resulting in degradation of the PP. Three PP mid-urethral slings from two commercial manufacturers were evaluated. Test specimens (n = 6) were incubated in oxidative medium for up to 5 weeks. Oxidation was assessed by Fourier Transform Infrared Spectroscopy (FTIR), and degradation was evaluated by scanning electron microscopy (SEM). FTIR spectra of the slings revealed evidence of carbonyl and hydroxyl peaks after 5 weeks of incubation time, providing evidence of oxidation of PP. SEM images at 5 weeks showed evidence of surface degradation, including pitting and flaking. Thus, oxidation and degradation of PP pelvic mesh were evidenced by chemical and physical changes under simulated in vivo conditions. To assess changes in PP surface chemistry in vivo, fibers were recovered from PP mesh explanted from a single patient without formalin fixation, untreated (n = 5) or scraped (n = 5) to remove tissue, and analyzed by X-ray photoelectron spectroscopy. Mechanical scraping removed adherent tissue, revealing an underlying layer of oxidized PP. These findings underscore the need for further research into the relative contribution of oxidative degradation to complications associated with PP-based TVM devices in larger cohorts of patients.

In vivo polypropylene mesh degradation is hardly a myth.

Dear Editor, We read with interest the article by Thames et al. entitled, “The myth: in vivo degradation of polypropylene-based meshes” [1]. The authors dispute the occurrence of degradation (the process of breaking down or deteriorating) of polypropylene (PP) mesh in vivo, reporting a novel cleaning method using multiple cycles of prolonged ultrasonication, shaking, and bleach (NaOCl) treatments of explanted mesh samples. Assessing the exposed surface and not analyzing the material removed, they conclude that the cracked layer—the typical feature of degraded polymer—seen on explanted meshes is an adsorbed protein-formaldehyde complex, rather than degraded PP as reported in numerous other publications. Of note, the authors are affiliated with Exponent, a business consulting firm retained by defendants in the mesh litigation. Furthermore, according to their disclosure, their findings were based on work paid for by Ethicon, Inc. [1]. In drawing their conclusions, the authors ignore the vast body of peer-reviewed literature describing PP degradation and fail to address the histological findings reported by other researchers [2–5]. Furthermore, their investigations utilize an unproven and unvalidated methodology, apparently designed specifically to remove all detachable material nonselectively (including protein and degraded PP) from the surface of the mesh fibers. Polypropylene is a thermoplastic polymer, well known in the ex vivo setting to undergo oxidative degradation. All forms of polypropylene are susceptible to oxidative attack at the tertiary hydrogen–carbon bond, resulting in the breaking of the PP molecular chain. This process continues until no more PP can be oxidized. Degradation appears on the external surface as cracks and fissures and results in hardening and shrinkage of the material. Anti-oxidants are normally added to PP to prevent polymer degradation, as is the case with all PP mesh used in surgical applications. There is a large body of published literature, estimated to be well over 100 peer-reviewed articles, accepting or describing the degradation of PP in variable conditions and the degradation of other implantable polymers in the body.We are not aware of any other peer-reviewed journal article supporting the notion that PP does not degrade in the body, as posited by Thames et al. [1]. There is a substantial volume of literature describing PP degradation based on analysis of the surface of PP implants exposed after appropriate gentle cleaning of the tissue. Liebert et al. [2] in 1976 reported the oxidation of unstabilized PP filaments in vivo in a subcutaneous implantation model in hamsters, using Fourier transform infrared spectroscopy (FTIR) measurements. An induction time of 108 days was faster than originally estimated by Liebert for oxidation by molecular oxygen (O2). This finding suggested that enzymes or other chemicals secreted by cells accelerated the oxidation reaction in their experiment. In a 1998 in vivo study, Prolene® sutures implanted for 1–2 years in a canine thoraco-abdominal An author’s reply to this comment is available at doi:10.1007/s00192016-3237-8.

Clinical study of ex vivo photoacoustic imaging in endoscopic mucosal resection tissues

Accurate endoscopic detection and dysplasia in patients with Barrett’s esophagus (BE) remains a major unmet clinical need. Current diagnosis use multiple biopsies under endoscopic image guidance, where up to 99% of the tissue remains unsampled, leading to significant risk of missing dysplasia. We conducted an ex vivo clinical trial using photoacoustic imaging (PAI) in patients undergoing endoscopic mucosal resection (EMR) with known high-grade dysplasia for the purpose of characterizing the esophageal microvascular pattern, with the long-term goal of performing in vivo endoscopic PAI for dysplasia detection and therapeutic guidance. EMR tissues were mounted immediately on an agar layer and covered with ultrasound gel. Digital photography guided the placement of the PAI transducer (40 MHz center frequency). The luminal side of the specimen was scanned over a field of view of 14 mm (width) by 15 mm (depth) at 680, 750, 824, 850 and 970 nm. Acoustic images were simultaneously acquired. Tissues were then sliced and fixed in formalin for histopathology with H and E staining. Analysis consisted of co-registration and correlation between the intrinsic PAI features and the histological images. The initial PAI + ultrasound images from 8 BE patients have demonstrated the technical feasibility of this approach and point to the potential of PAI to reveal the microvascular pattern within EMR specimens. There are several technical factors to be considered in rigorous interpretation of the PAI characteristics, including the loss of blood from the ex vivo specimens and the limited depth penetration of the photoacoustic signal.

A feasibility study of photoacoustic imaging of ex vivo endoscopic mucosal resection tissues from Barrett’s esophagus patients

Background and study aims  Accurate endoscopic detection of dysplasia in patients with Barrett’s esophagus (BE) remains a major clinical challenge. The current standard is to take multiple biopsies under endoscopic image guidance, but this leaves the majority of the tissue unsampled, leading to significant risk of missing dysplasia. Furthermore, determining whether there is submucosal invasion is essential for proper staging. Hence, there is a clinical need for a rapid in vivo wide-field imaging method to identify dysplasia in BE, with the capability of imaging beyond the mucosal layer. We conducted an ex vivo feasibility study using photoacoustic imaging (PAI) in patients undergoing endoscopic mucosal resection (EMR) for known dysplasia. The objective was to characterize the esophageal microvascular pattern, with the long-term goal of performing in vivo endoscopic PAI for dysplasia detection and therapeutic guidance. Materials and methods  EMR tissues were mounted luminal side up. The tissues were scanned over a field of view of 14 mm (width) by 15 mm (depth) at 680, 750, and 850 nm (40 MHz acoustic central frequency). Ultrasound and photoacoustic images were simultaneously acquired. Tissues were then sliced and fixed in formalin for histopathology with hematoxylin and eosin staining. A total of 13 EMR specimens from eight patients were included in the analysis, which consisted of co-registration of the photoacoustic images with corresponding pathologist-classified histological images. We conducted mean difference test of the total hemoglobin distribution between tissue classes. Results  Dysplastic and nondysplastic BE can be distinguished from squamous tissue in 84 % of region-of-interest comparisons (42/50). However, the ability of intrinsic PAI to distinguish dysplasia from NDBE, which is the clinically important challenge, was only about 33 % (10/30). Conclusion  We demonstrated the technical feasibility of this approach. Based on our ex vivo data, changes in total hemoglobin content from intrinsic PAI (i. e. without exogenous contrast) can differentiate BE from squamous esophageal mucosa. However, most likely intrinsic PAI is unable to differentiate dysplastic from nondysplastic BE with adequate sensitivity for clinical translation.

Abstract 4747: Genomic alterations in ductal carcinoma in situ compared with Invasive breast cancer: a quantitative real-time PCR study

Introduction: Several molecular markers have been investigated as possible prognostic factors for ductal carcinoma in situ (DCIS) progression to invasive ductal cancer (IDC). DCIS is regarded as a non-obligate precursor of IDC as it is frequently found adjacent to or surrounded by invasive breast cancer. Previously, we carried out genomic analyses that demonstrated that DCIS has specific genetic alterations that were conserved in invasive disease. Nevertheless, it is still unknown whether DCIS is merely a marker of increased risk, or actually a driver of the progression to IDC.Thus, it is crucial to better understand the genetic aberrations that underlie DCIS progression to IDC. Methodology: We conducted array chromosomal genomic hybridization on pure DCIS, IDC and DCIS paired with IDC, with 30 cases each (all were microdissected). Three chromosomal regions were selected based on the rate of their detection, which was significantly different (p Results: 61 samples were analyzed by comparing DCIS and IDC copy numbers of genes within the selected chromosomal regions. The median relative gene quantities were 1.66(4p15.33), 1.34(5q11.2) and 1.25(5q31.3). In all regions, IDC showed higher levels of amplification than DCIS with varying degrees of significance. Not all differences between DCIS and IDC in individual genes were significant. This observation may be attributed to focal variations in gene copy numbers and noise from Q-RT-PCR methods. 4p15.33 and 5q31.3 regions demonstrated significant gain in IDC compared to DCIS (p = 0.021). Genes within these regions include miRNA 572 (MIR572) and integrin alpha 2 (ITGA2). MIR572 is known to be involved in post-transcriptional regulation of gene expression, whereas ITGA2 encodes the alpha subunit of a transmembrane receptor for collagens. In the Chromosome 5q31.3 region, paired samples of DCIS and IDC also showed a trend in gene copy numbers, with IDC having a higher value than DCIS. Conclusions: Our findings demonstrate that there are specific genetic alterations associated with DCIS progression to IDC. In particular, MIR572 within Chromosome 4p15.33 and ITGA2 within Chromosome 5q31.3 may serve as candidate regions to predict the progression of DCIS to IDC. Note: This abstract was not presented at the meeting. Citation Format: Trillium E. Chang, Keisha Warren, Ranju Nair, Tian Y. Lu, Adewunmi Adeoye, Vladimir Iakovlev, Susan J. Done. Genomic alterations in ductal carcinoma in situ compared with Invasive breast cancer: a quantitative real-time PCR study. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4747. doi:10.1158/1538-7445.AM2015-4747