Comparison of endoscopic ultrasound tissue acquisition methods for genomic analysis of pancreatic cancer

BACKGROUND AND AIM

Tumor genotyping may allow for improved prognostication and targeted therapy for pancreatic ductal adenocarcinoma (PDAC). We aimed to compare endoscopic ultrasonography (EUS) with fine needle aspiration (FNA) to fine needle biopsy (FNB) for obtaining sufficient tissue for genomic analysis and theranostic potential.

METHODS

A retrospective cohort study of patients that underwent EUS-FNA or EUS-FNB with either positive or suspicious cytology for PDAC between March 2016 and December 2017. Demographic, procedural, and cytology data were recorded. Genetic alterations were recorded, and Kaplan-Meier survival curves were calculated.

RESULTS

The study included 167 patients: 145 patients had FNA and 22 patients underwent FNB. Overall, 117 samples (70.1%) were sufficient for targeted next-generation sequencing. FNB resulted in a higher proportion of patients with sufficient samples compared with FNA (90.9% vs 66.9%; P = 0.02). In multivariable modeling, only FNB (odds ratio 4.95, 95% confidence interval 1.11-22.05, P = 0.04) was associated with sufficient sampling for genomic testing. FNB was more likely to obtain sufficient tissue from tumors ≤ 3 cm (100% vs 68.4%, P = 0.017) and tumors located in the head/neck of the pancreas (100% vs 63.1%, P = 0.03) compared with FNA. The most commonly identified alterations were in KRAS (88%), TP53 (68%), and SMAD4 (16%).

CONCLUSIONS

Endoscopic ultrasonography can reliably obtain sufficient tissue from PDAC for targeted genomic sequencing for prognostication and theranostics. FNB should be considered when tumor genotyping is requested, especially for tumors ≤ 3 cm or tumors located in the head/neck of the pancreas.

Identification of sex chromosome molecular markers using RAPDs and fluorescent in situ hybridization in rainbow trout

The goal of this work is to identify molecular markers associated with the sex chromosomes in rainbow trout to study the mode of sex determination mechanisms in this species. Using the RAPD assay and bulked segregant analysis, two markers were identified that generated polymorphic bands amplifying preferentially in males of the Mount Lassen and Scottish strains of rainbow trout. Chromosomal localization using fluorescent in situ hybridization of a 900 bp probe developed from one of these markers revealed a brightly defined signal on a chromosome that could morphologically be classified as the Y chromosome.

Association of Aeromonas hydrophila and Vibrio alginolyticus with Larval Mortalities of Scallop (Argopecten purpuratus)

A bacteriological study was carried out in a hatchery of Argopecten purpuratus located in northern Chile which had been affected by severe larval mortalities. The phenotypic characterization of the bacterial strains revealed that Vibrio alginolyticus was the predominant species isolated in the majority of samples taken from the different units of the hatchery (microalgae, swimming larvae, seawater of larval culture tanks, and a reservoir tank of 50-μm filtered seawater). However, the bacterial population of dying larvae was composed of only Aeromonas hydrophila strains which proved to be resistant to most of the chemotherapeutic agents tested. The bioassays conducted to evaluate the effect of these bacteria on larval survival showed that all of the isolated Vibrio and Aeromonas strains possessed a high degree of pathogenicity, since they produced dying larvae on concentrations ranging from 5.5 x 10(4) to 5.5 x 10(2) cells/ml. The possible virulence mechanism of these bacteria is discussed, as well as the potential use of drugs to prevent larval mortalities.

Informed consent for blood transfusion: what do medicine residents tell? What do patients understand?

Blood transfusion is a common intervention in the hospital setting, and its benefits may not be clear but it has associated risks. Despite this, transfusion consent may not be obtained satisfactorily. We assessed transfusion consent effectiveness by comparing information given by residents with information understood by patients who receive transfusions. Medicine department residents who obtained consent were surveyed via telephone in conjunction with bedside surveys of adult inpatients who received transfusions. A total of 43 patient and 34 resident surveys were completed. Deficiencies in the transfusion consent process were noted. Discussed transfusion benefits (such as wound healing) were not always true benefits whereas some important risks (such as transfusion-related acute lung injury) were infrequently conferred. Risks were more often reported as "not discussed" than benefits. Only a few participants were aware of the hospital's Transfusion Health Guide, which provides information on transfusion benefits, risks, and alternatives.

Characterization of sex chromosomes in rainbow trout and coho salmon using fluorescence in situ hybridization (FISH)

With the aim of characterizing the sex chromosomes of rainbow trout (Oncorhynchus mykiss) and to identify the sex chromosomes of coho salmon (O. kisutch), we used molecular markers OmyP9, 5S rDNA, and a growth hormone gene fragment (GH2), as FISH probes. Metaphase chromosomes were obtained from lymphocyte cultures from farm specimens of rainbow trout and coho salmon. Rainbow trout sex marker OmyP9 hybridizes on the sex chromosomes of rainbow trout, while in coho salmon, fluorescent signals were localized in the medial region of the long arm of one subtelocentric chromosome pair. This hybridization pattern together with the hybridization of a GH2 intron probe on a chromosome pair having the same morphology, suggests that a subtelocentric pair could be the sex chromosomes in this species. We confirm that in rainbow trout, one of the two loci for 5S rDNA genes is on the X chromosome. In males of this species that lack a heteromorphic sex pair (XX males), the 5S rDNA probe hybridized to both subtelocentrics. This finding is discussed in relation to the hypothesis of intraspecific polymorphism of sex chromosomes in rainbow trout.

Development and characterization of DNA sequence OmyP9 associated with the sex chromosomes in rainbow trout

This work describes the construction and characterization of a sequence characterized amplified DNA region (SCAR DNA), designated OmyP9, that was derived from a RAPD marker associated with the sex chromosomes in rainbow trout. A RsaI restriction fragment length polymorphism in OmyP9 identifies variants A, B and C. We found six OmyP9 variant phenotypes - A, B, C, AB, BC and ABC, in 186 individuals of seven different rainbow trout strains. The patterns of inheritance of OmyP9 in 139 fingerlings from 10 crosses of three strains of rainbow trout were studied. The males had a greater representation of the A variant (93.3%) suggesting an association with the Y chromosome. All male fingerlings analysed inherited the A variant from their male parents. These results support the hypothesis that OmyP9 is located on the sex chromosomes of rainbow trout, and that for the males studied the A variant is located on the Y chromosome in a region close to sex determinants and/or in a sector where the genetic recombination between X and Y is restricted. The present evidence also supports our previous hypothesis that OmyP9 is organized as a tandem repeated sequence in the sex chromosomes of rainbow trout. We feel that the OmyP9 RsaI marker can be used for sex identification in crosses where it is possible to determine the phenotype of the parents.

Heavy metals in human bones in different historical epochs

The concentration of the metals lead, copper, zinc, cadmium and iron was determined in bone remains belonging to 30 individuals buried in the Region of Cartagena dating from different historical periods and in eight persons who had died in recent times. The metals content with respect to lead, cadmium and copper was determined either by anodic stripping voltammetry or by atomic absorption spectroscopy on the basis of the concentrations present in the bone remains. In all cases, zinc and iron were quantified by means of atomic absorption spectroscopy. The lead concentrations found in the bone remains in our city are greater than those reported in the literature for other locations. This led to the consideration of the sources of these metals in our area, both the contribution from atmospheric aerosols as well as that from the soil in the area. Correlation analysis leads us to consider the presence of the studied metals in the analysed bone samples to be the consequence of analogous inputs, namely the inhalation of atmospheric aerosols and diverse contributions in the diet. The lowest values found in the studied bone remains correspond to the Neolithic period, with similar contents to present-day samples with respect to lead, copper, cadmium and iron. As regards the evolution over time of the concentrations of the metals under study, a clear increase in these is observed between the Neolithic period and the grouping made up of the Bronze Age, Roman domination and the Byzantine period. The trend lines used to classify the samples into 7 periods show that the maximum values of lead correspond to the Roman and Byzantine periods. For copper, this peak is found in the Byzantine Period and for iron, in the Islamic Period. Zinc shows an increasing tendency over the periods under study and cadmium is the only metal whose trend lines shows a decreasing slope.

Tracheal Glomus Tumor: A Case Report and Review of the Literature

Glomus tumors are rare neoplasms that typically occur within the dermis or subcutis of the subungual space. Primary glomus tumors of the thorax are exceedingly uncommon, thus standard-of-care management is lacking. In this report we describe the management of a patient presenting with a symptomatic glomus tumor of the posterior trachea, and provide a comprehensive review including all documented tracheal glomus tumor reports.

A phase I dose escalation trial of nab-paclitaxel and fixed dose radiation in patients with unresectable or borderline resectable pancreatic cancer

PURPOSE

Patients with locally advanced pancreatic cancer typically have poor outcomes, with a median survival of approximately 16 months. Novel methods to improve outcomes are needed. Nab-paclitaxel (Abraxane) has shown efficacy in pancreatic cancer and is FDA-approved for metastatic disease in combination with gemcitabine. Nab-paclitaxel is also a promising radiosensitizer based on laboratory studies, but it has never been clinically tested with definitive radiotherapy for locally advanced pancreatic carcinoma.

METHODS

We performed a phase 1 study using a 3 + 3 dose escalation strategy to determine the safety and tolerability of dose-escalated nab-paclitaxel with fractionated radiotherapy for patients with unresectable or borderline resectable pancreatic cancer. Following induction chemotherapy with two cycles of nab-paclitaxel and gemcitabine, patients were treated with weekly nab-paclitaxel and daily radiotherapy to a dose of 52.5 Gy in 25 fractions. Final dose-limiting toxicity (DLT) determination was performed at day 65 after the start of radiotherapy.

RESULTS

Nine patients received nab-paclitaxel at a dose level of either 100 mg/m² (n = 3) or 125 mg/m² (n = 6). There were no observed grade 3 gastrointestinal toxicities. One DLT (grade 3 neuropathy) was observed in a patient who received 125 mg/m² of nab-paclitaxel. Other grade 3 toxicities included fatigue (11%), anemia (11%) and neutropenia (11%). No grade 4 toxicities were observed. Following chemoradiotherapy, four patients (borderline resectable, n = 2 and unresectable, n = 2) underwent surgical resection, all with negative margins and with significant treatment effect with limited tumor viability.

CONCLUSIONS

The combination of fractionated radiation and weekly full dose nab-paclitaxel was safe and well-tolerated.

Pleural mass forming extramedullary hematopoiesis masquerading as a malignant neoplasm

Extramedullary hematopoiesis (EMH) represents the presence of immature hematopoietic elements and their differentiation into mature blood components outside of the medullary bone and may be seen in a variety of circumstances in the postnatal period, but is most strongly associated with disorders of the hematopoietic system. Postnatally, EMH is typically identified at sites of fetal hematopoiesis, the spleen, and liver, but occasional reports have identified it in nearly every tissue of the body. We report a case of EMH presenting as pleural mass, initially suspected to represent a neoplastic process in a patient with multiple comorbidities, including history of carcinoma, but without co-existing hematologic disorder. On-site evaluation of the fine-needle aspiration specimen was initially suspicious for a malignant neoplasm, but further evaluation revealed the lesion to be a mass forming focus of non-hepatosplenic EMH. In the era of increasing utilization of imaging, mass forming EMH is increasingly detected. When unsuspected, EMH may present a diagnostic challenge for the pathologist and may be confused for a neoplastic process.

Villous Adenoma Arising in the Native Bladder Mucosa and the Upper Urinary Tract With Coexisting Neuroendocrine Carcinoma Following Augmentation Cystoplasty

Villous adenomas arising in the bladder following augmentation cystoplasty procedures are exceedingly rare. Even rarer is their occurrence in the native bladder mucosa and the upper urinary tract. In this article, we present a unique case of multifocal recurrent villous adenoma involving native bladder mucosa of an augmented bladder, bilateral ureters, and renal pelvis, with coexistent foci of adenocarcinoma and neuroendocrine carcinoma, in a patient with history of augmentation colocystoplasty. We additionally discuss the pathogenesis of development of carcinoma in the setting of augmentation cystoplasty.

Metastatic solid tumors to the testis: a clinicopathologic evaluation of 157 cases from an international collaboration

To elucidate the spectrum of metastatic solid tumors to the testis and their clinicopathologic features. The databases and files of 26 pathology departments from 9 countries on 3 continents were surveyed to identify metastatic solid tumors to the testis and to characterize their clinicopathologic features in detail. We compiled a series of 157 cases of metastatic solid tumors that secondarily involved the testis. The mean patient age at diagnosis was 64 years (range, 12-93 years). Most patients (127/144; 88%) had clinical manifestation of the disease, with testicular mass/nodule (89/127; 70%) being the most common finding. The main mechanism of testicular involvement was metastasis in 154/157 (98%) cases. Bilateral testicular involvement was present in 12/157 (8%) patients. Concurrent or prior extratesticular metastases were present in 78/101 (77%) patients. The diagnosis was made mainly in orchiectomy specimens (150/157; 95%). Different types of carcinomas (138/157; 87%), most commonly adenocarcinoma (72/157; 46%), were the most common malignancies. The most common primary carcinomas included prostatic (51/149; 34%), renal (29/149; 20%), and colorectal (13/149; 9%). Intratubular growth was identified in 13/124 (11%) cases and paratesticular involvement was found in 73/152 (48%) cases. In patients with available follow-up (110/157; 70%), more than half (58/110; 53%) died of disease. In this largest series compiled to date, we found that most secondary tumors of the testis represent metastases from the genitourinary and gastrointestinal tract carcinomas and typically occur in the setting of disseminated disease.

Bayesian approach to interpreting somatic cancer sequencing data: a case in point

Cancer lineage/tissue-of-origin assignment in cancers of unknown primary remains a challenge even when aided by massively parallel sequencing. The stakes are high for patients as many contemporary therapeutic strategies are disease-specific, and the biological differences can influence the patients' responses. Herein, we provide an example of how Bayesian analysis can be used to merge data from clinical history, histology, immunohistochemistry (IHC) and cancer DNA sequencing to assist in tissue-of-origin assignment. Iterative Bayesian analysis is performed through a set of simple calculations to calculate the OR between the differential diagnoses. We illustrate a clinical case, where the distinction between a primary lung versus metastatic bladder cancer was aided meaningfully by iterative Bayesian analyses, incorporating IHC and sequencing data.

Multilocus DNA-fingerprinting using oligonucleotide probes (GATA)4 and (GGAT)4 in rainbow trout (Oncorhynchus mykiss)

Oligonucleotide probes (GATA)4 and (GGAT)4 for minisatellite loci produced DNA fingerprinting patterns which are unique in individual rainbow trout. These patterns can be used to monitor the efficiency of manipulation of production characters in gynogenetic individuals. The (GATA)4 probe produced highly individual patterns that differentiated individuals among gynogenetic offspring, and could be easily scored.