Can Google Trends analysis confirm the public's need for information about the rare association of facial nerve paralysis with COVID-19 or the COVID-19 vaccination?

Facial nerve paralysis or Bell's palsy have been suggested as possible consequences of SARS-CoV-2 infections, as well as possible side effects of COVID-19 vaccinations. Google Trends data have been used to evaluate worldwide levels of public awareness for these topics for pre- and post-pandemic years. The results demonstrate a relatively low public interest in facial nerve paralysis in comparison to other more common COVID-19 related topics. Some peaks of interest in Bell's palsy can most likely be explained as triggered by the media. Therefore, Google Trends has shown public's relatively low awareness of this rare neurological phenomenon during the pandemic.

Individual and poly-substance use and condomless sex among HIV-uninfected adults reporting heterosexual sex in a multi-site cohort

BACKGROUND

We analyzed the association between substance use (SU) and condomless sex (CS) among HIV-negative adults reporting heterosexual sex in the Seek, Test, Treat, and Retain (STTR) consortium. We describe the impact of SU as well as person/partner and context-related factors on CS, identifying combinations of factors that indicate the highest likelihood of CS.

METHODS

We analyzed data from four US-based STTR studies to examine the effect of SU on CS using two SU exposures: 1) recent SU (within 3 months) and 2) SU before/during sex. Behavioral data were collected via 1:1 or self-administered computerized interviews. Adjusted individual-study, multivariable relative risk regression was used to examine the relationship between CS and SU. We also examined interactions with type of sex and partner HIV status. Pooled effect estimates were calculated using traditional fixed-effects meta-analysis. We analyzed data for recent SU (n = 6781; 82% men, median age = 33 years) and SU before/during sex (n = 2915; 69% men, median age = 40 years).

RESULTS

For both exposure classifications, any SU other than cannabis increased the likelihood of CS relative to non-SU (8-16%, p-values< 0.001). In the recent SU group, however, polysubstance use did not increase the likelihood of CS compared to single-substance use. Cannabis use did not increase the likelihood of CS, regardless of frequency of use. Type of sex was associated with CS; those reporting vaginal and anal sex had a higher likelihood of CS compared to vaginal sex only for both exposure classifications (18-21%, p < 0.001). Recent SU increased likelihood of CS among those reporting vaginal sex only (9-10%, p < 0.001); results were similar for those reporting vaginal and anal sex (5-8%, p < 0.01). SU before/during sex increased the likelihood of CS among those reporting vaginal sex only (20%; p < 0.001) and among those reporting vaginal and anal sex (7%; p = 0.002). Single- and poly-SU before/during sex increased the likelihood of CS for those with exclusively HIV-negative partners (7-8%, p ≤ 0.02), and for those reporting HIV-negative and HIV-status unknown partners (9-13%, p ≤ 0.03).

CONCLUSION

Except for cannabis, any SU increased the likelihood of CS. CS was associated with having perceived HIV-negative partners and with having had both anal/vaginal sex.

Global genome analysis reveals a vast and dynamic anellovirus landscape within the human virome

Anelloviruses are a ubiquitous component of healthy human viromes and remain highly prevalent after being acquired early in life. The full extent of "anellome" diversity and its evolutionary dynamics remain unexplored. We employed in-depth sequencing of blood-transfusion donor(s)-recipient pairs coupled with public genomic resources for a large-scale assembly of anellovirus genomes and used the data to characterize global and personal anellovirus diversity through time. The breadth of the anellome is much greater than previously appreciated, and individuals harbor unique anellomes and transmit lineages that can persist for several months within a diverse milieu of endemic host lineages. Anellovirus sequence diversity is shaped by extensive recombination at all levels of divergence, hindering traditional phylogenetic analyses. Our findings illuminate the transmission dynamics and vast diversity of anelloviruses and set the foundation for future studies to characterize their biology.

A multimodality test to guide the management of patients with a pancreatic cyst

Pancreatic cysts are common and often pose a management dilemma, because some cysts are precancerous, whereas others have little risk of developing into invasive cancers. We used supervised machine learning techniques to develop a comprehensive test, CompCyst, to guide the management of patients with pancreatic cysts. The test is based on selected clinical features, imaging characteristics, and cyst fluid genetic and biochemical markers. Using data from 436 patients with pancreatic cysts, we trained CompCyst to classify patients as those who required surgery, those who should be routinely monitored, and those who did not require further surveillance. We then tested CompCyst in an independent cohort of 426 patients, with histopathology used as the gold standard. We found that clinical management informed by the CompCyst test was more accurate than the management dictated by conventional clinical and imaging criteria alone. Application of the CompCyst test would have spared surgery in more than half of the patients who underwent unnecessary resection of their cysts. CompCyst therefore has the potential to reduce the patient morbidity and economic costs associated with current standard-of-care pancreatic cyst management practices.

Incidence and distribution of UroSEEK gene panel in a multi-institutional cohort of bladder urothelial carcinoma

Noninvasive approaches for early detection of bladder cancer are actively being investigated. We recently developed a urine- based molecular assay for the detection and surveillance of bladder neoplasms (UroSEEK). UroSEEK is designed to detect alterations in 11 genes that include most common genetic alterations in bladder cancer. In this study, we analyzed 527 cases, including 373 noninvasive and 154 invasive urothelial carcinomas of bladder from transurethral resections or cystectomies performed at four institutions (1991-2016). Two different mutational analysis assays of a representative tumor area were performed: first, a singleplex PCR assay for evaluation of the TERT promoter region (TERTSeqS) and second, a multiplex PCR assay using primers designed to amplify regions of interest of 10 (FGFR3, PIK3CA, TP53, HRAS, KRAS, ERBB2, CDKN2A, MET, MLL, and VHL) genes (UroSeqS). Overall, 92% of all bladder tumors were positive for at least one genetic alteration in the UroSEEK panel. We found TERT promoter mutations in 77% of low-grade noninvasive papillary carcinomas, with a relatively lower incidence of 65% in high-grade noninvasive papillary carcinomas and carcinomas in situ; p = 0.017. Seventy-two percent of pT1 and 63% of muscle-invasive bladder tumors harbored TERT promoter mutations with g.1295228C>T alteration being the most common in all groups. FGFR3 and PIK3CA mutations were more frequent in low-grade noninvasive papillary carcinomas compared with high-grade noninvasive papillary carcinomas and carcinomas in situ (p < 0.0001), while the opposite was true for TP53 (p < 0.0001). Significantly higher rates of TP53 and CDKN2A mutation rates (p = 0.005 and 0.035, respectively) were encountered in muscle-invasive bladder tumors compared with those of pT1 stage. The overwhelming majority of all investigated tumors showed at least one mutation among UroSEEK assay genes, confirming the comprehensive coverage of the panel and supporting its potential utility as a noninvasive urine-based assay.

Intraductal Papillary Mucinous Neoplasms Arise From Multiple Independent Clones, Each With Distinct Mutations

BACKGROUND & AIMS

Intraductal papillary mucinous neoplasms (IPMNs) are lesions that can progress to invasive pancreatic cancer and constitute an important system for studies of pancreatic tumorigenesis. We performed comprehensive genomic analyses of entire IPMNs to determine the diversity of somatic mutations in genes that promote tumorigenesis.

METHODS

We microdissected neoplastic tissues from 6-24 regions each of 20 resected IPMNs, resulting in 227 neoplastic samples that were analyzed by capture-based targeted sequencing. Somatic mutations in genes associated with pancreatic tumorigenesis were assessed across entire IPMN lesions, and the resulting data were supported by evolutionary modeling, whole-exome sequencing, and in situ detection of mutations.

RESULTS

We found a high prevalence of heterogeneity among mutations in IPMNs. Heterogeneity in mutations in KRAS and GNAS was significantly more prevalent in IPMNs with low-grade dysplasia than in IPMNs with high-grade dysplasia (P < .02). Whole-exome sequencing confirmed that IPMNs contained multiple independent clones, each with distinct mutations, as originally indicated by targeted sequencing and evolutionary modeling. We also found evidence for convergent evolution of mutations in RNF43 and TP53, which are acquired during later stages of tumorigenesis.

CONCLUSIONS

In an analysis of the heterogeneity of mutations throughout IPMNs, we found that early-stage IPMNs contain multiple independent clones, each with distinct mutations, indicating their polyclonal origin. These findings challenge the model in which pancreatic neoplasms arise from a single clone. Increasing our understanding of the mechanisms of IPMN polyclonality could lead to strategies to identify patients at increased risk for pancreatic cancer.

Evaluation of liquid from the Papanicolaou test and other liquid biopsies for the detection of endometrial and ovarian cancers

We report the detection of endometrial and ovarian cancers based on genetic analyses of DNA recovered from the fluids obtained during a routine Papanicolaou (Pap) test. The new test, called PapSEEK, incorporates assays for mutations in 18 genes as well as an assay for aneuploidy. In Pap brush samples from 382 endometrial cancer patients, 81% [95% confidence interval (CI), 77 to 85%] were positive, including 78% of patients with early-stage disease. The sensitivity in 245 ovarian cancer patients was 33% (95% CI, 27 to 39%), including 34% of patients with early-stage disease. In contrast, only 1.4% of 714 women without cancer had positive Pap brush samples (specificity, ~99%). Next, we showed that intrauterine sampling with a Tao brush increased the detection of malignancy over endocervical sampling with a Pap brush: 93% of 123 (95% CI, 87 to 97%) patients with endometrial cancer and 45% of 51 (95% CI, 31 to 60%) patients with ovarian cancer were positive, whereas none of the samples from 125 women without cancer were positive (specificity, 100%). Finally, in 83 ovarian cancer patients in whom plasma was available, circulating tumor DNA was found in 43% of patients (95% CI, 33 to 55%). When plasma and Pap brush samples were both tested, the sensitivity for ovarian cancer increased to 63% (95% CI, 51 to 73%). These results demonstrate the potential of mutation-based diagnostics to detect gynecologic cancers at a stage when they are more likely to be curable.

Alignment of diet prescription to genotype does not promote greater weight loss success in women with obesity participating in an exercise and weight loss program

OBJECTIVE

Genetics contribute to variability in individual response to weight-loss interventions. The objective of this study was to determine the efficacy of a commercially available exercise and weight-loss program and whether alignment of diet to genotype related to lipid metabolism promotes greater success.

DESIGN

Sedentary women with obesity (n = 63) had genotype (FABP2rs1799883, PPARG2rs1801282, ADRB3rs4994C3, ADRB2rs1042713, rs1042714) determined using a direct-to-consumer genetic screening kit purported to promote greater weight-loss success through dietary recommendations based on these genes. Participants were randomly assigned to follow a moderate carbohydrate (MC) or lower carbohydrate (LC) hypo-energetic diet that aligned (A) or did not align (NA) with genotype for 24 weeks while participating in a resistance training and walking program. Data were analysed by general linear model repeated measures adjusted for baseline variables and are presented as mean (95% confidence interval) changes from baseline.

RESULTS

Participants in the LC group experienced greater improvements (p = 0.051, ηp 2 = 0.025) in per cent changes in body composition (weight: MC -3.32 [-1.4, -5.2], LC -5.82 [-4.1, -7.6]; fat mass: MC -7.25 [-3.2, -11.2], LC -10.93 [-7.3, -14.5]; fat-free mass: MC -0.32 [1.4, -2.0], LC -1.48 [0.7, -3.0]; and body fat percentage: MC -4.19 [-1.6, -6.8], LC -5.60 [-3.3, -7.9] %). No significant differences were observed between genotype groups (weight: A -5.00 [-3.3, -6.7], NA -4.14 [-2.2, -6.1]; fat mass: A -10.15 [-7.0, -13.6], NA -8.02 [-4.0, -12.0]; fat-free mass: A -1.23 [0.3, -2.8], NA -0.56 [1.12, -2.3]; and body fat: A -5.28 [-3.0, -7.6], NA -4.51 [-1.9, -7.1] %).

CONCLUSIONS

Adherence to this exercise and weight-loss program promoted improvements in body composition and health outcomes. While individuals following the LC diet experienced greater benefits, alignment of these diets to this genetic profile did not promote greater health outcomes.

Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs)

Aneuploidy is a feature of most cancer cells, and a myriad of approaches have been developed to detect it in clinical samples. We previously described primers that could be used to amplify ∼38,000 unique long interspersed nucleotide elements (LINEs) from throughout the genome. Here we have developed an approach to evaluate the sequencing data obtained from these amplicons. This approach, called Within-Sample AneupLoidy DetectiOn (WALDO), employs supervised machine learning to detect the small changes in multiple chromosome arms that are often present in cancers. We used WALDO to search for chromosome arm gains and losses in 1,677 tumors and in 1,522 liquid biopsies of blood from cancer patients or normal individuals. Aneuploidy was detected in 95% of cancer biopsies and in 22% of liquid biopsies. Using single-nucleotide polymorphisms within the amplified LINEs, WALDO concomitantly assesses allelic imbalances, microsatellite instability, and sample identification. WALDO can be used on samples containing only a few nanograms of DNA and as little as 1% neoplastic content and has a variety of applications in cancer diagnostics and forensic science.

Vorkommen und Bekämpfung des Clostridium-perfringens-Typ-A-assoziierten Durchfalls der Saugferkel unter besonderer Berücksichtigung der Immunprophylaxe

Gegenstand und Ziel: Clostridium perfringens Typ A wird häufig in Verbindung mit Durchfällen von Saugferkeln isoliert. Die Bedeutung des Alpha-(α-) und Beta(β)2-Toxins für die Pathogenese der Erkrankung ist nicht abschließend geklärt. Zur Bekämpfung der Erkrankung wurden in der Vergangenheit insbesondere stallspezifische Impfstoffe eingesetzt. Ziel der Untersuchungen war die Typisierung und quantitative Bestimmung des α- und β2-Toxins von C.-perfringens-Stämmen, die im Rahmen der Herstellung bestandsspezifischer Impfstoffe isoliert wurden. Mithilfe eines Intoxikationsmodells wurde weiterhin die Wirksamkeit eines kommerziell erhältlichen Impfstoffs gegen den C.-perfringens-Typ-A-assoziierten Durchfall der Saugferkel geprüft. Material und Methoden: Im ersten Teil der Untersuchungen wurden 1434 C.-perfringens-Stämme, die von an Durchfall erkrankten Ferkeln stammten, mithilfe einer Multiplex-PCR typisiert. Gleichzeitig wurde das α- und β2-Toxin-Bildungsvermögen der Stämme mittels ELISA-Tests untersucht. Zur Prüfung der α- und β2-toxoidhaltigen C.-perfringens-Typ-A-Vakzine für Schweine (Clostriporc A, IDT Biologika GmbH) wurden im zweiten Teil der Untersuchungen 18 Jungsauen im letzten Drittel der Trächtigkeit zweimal im Abstand von 3 Wochen immunisiert. Ergebnisse: 87,9% der Stämme gehörten zur Toxovar A (cpa, cpb2), 6,3% zur Toxovar A (cpa) und 5,8% zur Toxovar C (cpa, cpb, cpb2). Bei der quantitativen Untersuchung des Toxinbildungsvermögens der C.-perfringens-Typ-A-Stämme (cpa, cpb2) zeichneten sich Stämme, die geringe oder mittlere Gehalte des α-Toxins bildeten, häufig durch eine starke Expression des β2-Toxins aus. Die geimpften Sauen bildeten Antikörper gegen das α- und β2-Toxin, die über das Kolostrum auf die Nachzucht übertragen wurden und neugeborene Ferkel signifikant (p < 0,05) vor einer Intoxikation mit einem α- und β2-toxinhaltigen Überstand eines heterologen C.-perfringens-Typ-A-Stammes schützten. Schlussfolgerung und klinische Relevanz: Die Ergebnisse unterstreichen die Bedeutung von α- und β2-toxinbildenden C.-perfringens-Typ-A-Stämmen im Durchfallgeschehen der Saugferkel. Im Intoxikationsmodell ließ sich eine deutliche Schutzwirkung der eingesetzten Vakzine vor dem α- und β2-Toxin nachweisen.

Circulating tumor DNA analysis detects minimal residual disease and predicts recurrence in patients with stage II colon cancer

Detection of circulating tumor DNA (ctDNA) after resection of stage II colon cancer may identify patients at the highest risk of recurrence and help inform adjuvant treatment decisions. We used massively parallel sequencing-based assays to evaluate the ability of ctDNA to detect minimal residual disease in 1046 plasma samples from a prospective cohort of 230 patients with resected stage II colon cancer. In patients not treated with adjuvant chemotherapy, ctDNA was detected postoperatively in 14 of 178 (7.9%) patients, 11 (79%) of whom had recurred at a median follow-up of 27 months; recurrence occurred in only 16 (9.8 %) of 164 patients with negative ctDNA [hazard ratio (HR), 18; 95% confidence interval (CI), 7.9 to 40; P < 0.001]. In patients treated with chemotherapy, the presence of ctDNA after completion of chemotherapy was also associated with an inferior recurrence-free survival (HR, 11; 95% CI, 1.8 to 68; P = 0.001). ctDNA detection after stage II colon cancer resection provides direct evidence of residual disease and identifies patients at very high risk of recurrence.

Spectrum of genetic mutations in de novo PUNLMP of the urinary bladder

Our group and others have previously demonstrated the presence of TERT promoter mutations (TERT-mut) in 60-80% of urothelial carcinomas and some of their histologic variants. Five other genes have been frequently implicated in bladder cancer: FGRF3, TP53, PIK3CA, HRAS, and CDKN2A. In the current study, we sought to determine the prevalence of mutations in TERT and these five other genes in de novo papillary urothelial neoplasms of low malignant potential (PUNLMP) of the urinary bladder. A retrospective search of our archives for PUNLMP was performed and 30 de novo cases were identified and included in the study. We found mutations in TERT (TERT-mut) and FGFR3 (FGFR3-mut) to be the most common alterations in the cohort (63 and 60%, respectively). The majority of the TERT-mut-positive tumors (84%) had a g.1295228C > T alteration with the remaining tumors demonstrating g.1295250C > T. Approximately one fourth of tumors had TP53 mutations. These findings support the potential utility of a uniform genetic mutation panel to detect bladder cancers of various subtypes.

A novel approach for selecting combination clinical markers of pathology applied to a large retrospective cohort of surgically resected pancreatic cysts

OBJECTIVE

Our objective was to develop an approach for selecting combinatorial markers of pathology from diverse clinical data types. We demonstrate this approach on the problem of pancreatic cyst classification.

MATERIALS AND METHODS

We analyzed 1026 patients with surgically resected pancreatic cysts, comprising 584 intraductal papillary mucinous neoplasms, 332 serous cystadenomas, 78 mucinous cystic neoplasms, and 42 solid-pseudopapillary neoplasms. To derive optimal markers for cyst classification from the preoperative clinical and radiological data, we developed a statistical approach for combining any number of categorical, dichotomous, or continuous-valued clinical parameters into individual predictors of pathology. The approach is unbiased and statistically rigorous. Millions of feature combinations were tested using 10-fold cross-validation, and the most informative features were validated in an independent cohort of 130 patients with surgically resected pancreatic cysts.

RESULTS

We identified combinatorial clinical markers that classified serous cystadenomas with 95% sensitivity and 83% specificity; solid-pseudopapillary neoplasms with 89% sensitivity and 86% specificity; mucinous cystic neoplasms with 91% sensitivity and 83% specificity; and intraductal papillary mucinous neoplasms with 94% sensitivity and 90% specificity. No individual features were as accurate as the combination markers. We further validated these combinatorial markers on an independent cohort of 130 pancreatic cysts, and achieved high and well-balanced accuracies. Overall sensitivity and specificity for identifying patients requiring surgical resection was 84% and 81%, respectively.

CONCLUSIONS

Our approach identified combinatorial markers for pancreatic cyst classification that had improved performance relative to the individual features they comprise. In principle, this approach can be applied to any clinical dataset comprising dichotomous, categorical, and continuous-valued parameters.

High prevalence of TERT promoter mutations in micropapillary urothelial carcinoma

Somatic activating mutations in the promoter of the telomerase reverse transcriptase (TERT) gene are the most common genetic alterations in urothelial carcinoma (UC) of the bladder and upper urinary tract. Little is known, however, about TERT-mutation status in the relatively uncommon but clinically aggressive micropapillary (MPC) variant. We evaluated the presence of TERT promoter mutations in MPC of the bladder and upper urinary tract. A retrospective search of our archives for MPC and UC with micropapillary features (2005-2014) was performed. All slides were reviewed to confirm the histologic diagnosis. Thirty-three specimens from 31 patients had FFPE blocks available for DNA analysis and were included in the study. Intratumoral areas of non-micropapillary histology were also evaluated when present. Samples were analyzed with Safe-SeqS, a sequencing error reduction technology, and sequenced using the Illumina MiSeq platform. TERT promoter mutations were detected in all specimens with pure MPC (18 of 18) and UC with focal micropapillary features (15 of 15). Similar to conventional UC, the predominant mutations identified occurred at positions -124 (C228T) (85 %) and -146 (C250T) (12 %) bp upstream of the TERT ATG start site. In heterogeneous tumors with focal variant histology, intratumoral concordant mutations were found in variant (MPC and non-MPC) and corresponding conventional UC. We found TERT promoter mutations, commonly found in conventional UC, to be frequently present in MPC. Our finding of concordant intratumoral mutational alterations in cases with focal variant histology lends support to the common oncogenesis origin of UC and its variant histology.

Diagnostic potential of tumor DNA from ovarian cyst fluid

We determined whether the mutations found in ovarian cancers could be identified in the patients' ovarian cyst fluids. Tumor-specific mutations were detectable in the cyst fluids of 19 of 23 (83%) borderline tumors, 10 of 13 (77%) type I cancers, and 18 of 18 (100%) type II cancers. In contrast, no mutations were found in the cyst fluids of 18 patients with benign tumors or non-neoplastic cysts. Though large, prospective studies are needed to demonstrate the safety and clinical utility of this approach, our results suggest that the genetic evaluation of cyst fluids might be able to inform the management of the large number of women with these lesions.

DOI:http://dx.doi.org/10.7554/eLife.15175.001

More than a third of women develop ovarian cysts during their lifetimes. The vast majority of these cysts are harmless, but a small number are caused by ovarian cancers. These cancers often produce no symptoms until the disease has spread throughout the abdomen or to other organs, so many women go undiagnosed until their chances of being successfully treated are low. Currently, there is no reliable way to determine whether an ovarian cyst is cancerous without performing surgery. As a result, many women undergo unnecessary, invasive surgeries for harmless ovarian cysts.

Tumors shed cells and cell fragments into any fluid that surrounds them. Fluids from cysts in the pancreas, kidney, and thyroid are routinely examined to identify whether they contain cancerous cells. Now, Wang, Sundfeldt et al. show that ovarian cancers also shed DNA into the surrounding cyst fluid. Furthermore, mutations found in this DNA can provide valuable information about whether the cysts are cancerous.

The study was performed by extracting DNA from the fluid in ovarian cysts that had been surgically removed from 77 women. Of these cysts, 10 were harmless cysts, 12 were benign tumors, 31 were invasive cancers, and 24 were so-called borderline tumors, which fall somewhere between the benign tumors and invasive cancers. Only cysts associated with the borderline tumors and invasive cancers need to be surgically removed. Here, Wang, Sundfeldt et al. report that DNA mutations that are characteristic of ovarian cancers were found in 87% of the cysts associated with borderline tumors and invasive cancers. In contrast, these mutations were not found in any of the cysts that do not require surgery.

Fluid can be extracted from an ovarian cyst with a needle during an outpatient visit. Therefore, the results presented by Wang, Sundfeldt et al. suggest a relatively straightforward way of testing the DNA from ovarian cysts before deciding whether surgery is really necessary. First, however, larger studies that follow women with cysts over time will be necessary to confirm that this type of testing is effective and safe.

DOI:http://dx.doi.org/10.7554/eLife.15175.002

Detection of somatic mutations and HPV in the saliva and plasma of patients with head and neck squamous cell carcinomas

To explore the potential of tumor-specific DNA as a biomarker for head and neck squamous cell carcinomas (HNSCC), we queried DNA from saliva or plasma of 93 HNSCC patients. We searched for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n = 10) and 95% (n = 37), respectively. When segregated by site, tumor DNA was detected in 100% (n = 15), 91% (n = 22), 100% (n = 7), and 100% (n = 3) of patients with tumors of the oral cavity, oropharynx, larynx, and hypopharynx, respectively. In saliva, tumor DNA was found in 100% of patients with oral cavity cancers and in 47 to 70% of patients with cancers of the other sites. In plasma, tumor DNA was found in 80% of patients with oral cavity cancers, and in 86 to 100% of patients with cancers of the other sites. Thus, saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in saliva was found postsurgically in three patients before clinical diagnosis of recurrence, but in none of the five patients without recurrence. Tumor DNA in the saliva and plasma appears to be a potentially valuable biomarker for detection of HNSCC.

Detection of TERT promoter mutations in primary adenocarcinoma of the urinary bladder

TERT promoter mutations (TERT-mut) have been detected in 60% to 80% of urothelial carcinomas. A molecular urine-based screening assay for the detection of TERT-mut is currently being pursued by our group and others. A small but significant number of bladder carcinomas are adenocarcinoma. The current study assesses the incidence of TERT-mut in primary adenocarcinomas of urinary bladder. A retrospective search of our institutional pathology records identified 23 cystectomy specimens with a diagnosis of adenocarcinoma (2000-2014). All slides were reviewed by a senior urologic pathologist to confirm tumor type and select a representative formalin-fixed, paraffin-embedded block for mutational analysis. Adequate material for DNA testing was available in 14 cases (7 enteric type and 7 not otherwise specified). TERT-mut sequencing analysis was performed using previously described SafeSeq technique. Overall, 28.5% of primary adenocarcinoma harbored TERT-mut. Interestingly, 57% of nonenteric adenocarcinomas were mutation positive, whereas none of the enteric-type tumors harbored mutations. Similar to urothelial carcinoma, we found a relatively higher rate of TERT-mut among nonenteric-type adenocarcinomas further supporting the potential utility of TERT-mut urine-based screening assay for bladder cancer.

A combination of molecular markers and clinical features improve the classification of pancreatic cysts

BACKGROUND & AIMS

The management of pancreatic cysts poses challenges to both patients and their physicians. We investigated whether a combination of molecular markers and clinical information could improve the classification of pancreatic cysts and management of patients.

METHODS

We performed a multi-center, retrospective study of 130 patients with resected pancreatic cystic neoplasms (12 serous cystadenomas, 10 solid pseudopapillary neoplasms, 12 mucinous cystic neoplasms, and 96 intraductal papillary mucinous neoplasms). Cyst fluid was analyzed to identify subtle mutations in genes known to be mutated in pancreatic cysts (BRAF, CDKN2A, CTNNB1, GNAS, KRAS, NRAS, PIK3CA, RNF43, SMAD4, TP53, and VHL); to identify loss of heterozygozity at CDKN2A, RNF43, SMAD4, TP53, and VHL tumor suppressor loci; and to identify aneuploidy. The analyses were performed using specialized technologies for implementing and interpreting massively parallel sequencing data acquisition. An algorithm was used to select markers that could classify cyst type and grade. The accuracy of the molecular markers was compared with that of clinical markers and a combination of molecular and clinical markers.

RESULTS

We identified molecular markers and clinical features that classified cyst type with 90%-100% sensitivity and 92%-98% specificity. The molecular marker panel correctly identified 67 of the 74 patients who did not require surgery and could, therefore, reduce the number of unnecessary operations by 91%.

CONCLUSIONS

We identified a panel of molecular markers and clinical features that show promise for the accurate classification of cystic neoplasms of the pancreas and identification of cysts that require surgery.

[Breastfeeding Rates and Duration in Germany - A Systematic Review]

Aim: 20 years after establishment of the National Breastfeeding Committee, the present work, based on published data on breastfeeding, is aimed at providing insight into the development of breastfeeding behaviour in Germany. Methods: To identify relevant publications, a comprehensive literature search was conducted in PubMed and Web of Science using the search terms "breast feeding" or "breastfeeding" in combination with "Germany". The publication period was limited to the period 1995-2014. Results: A total of 35 studies with data on breastfeeding for the birth cohorts of 1990-2012 were identified. Most of the data had been collected in regional or local surveys, often retrospectively. About 60% of the studies had been conducted with the primary aim of collecting data on breastfeeding or infant nutrition. Over the past 2 decades, breastfeeding rates were always relatively high at the beginning (72-97%). However, they declined significantly within the first 2 months, and by the age of 6 months, only about 50% of infants were still breastfed. Conclusion: Breastfeeding support and early assistance should be offered to a greater extent in order to achieve sustainable improvement of breastfeeding frequency and duration in Germany. Regarding the quality of data collected on breastfeeding, it seems crucial to implement standardised approaches to monitor breastfeeding in Germany.

Engineering targeted chromosomal amplifications in human breast epithelial cells

Chromosomal amplifications are among the most common genetic alterations found in human cancers. However, experimental systems to study the processes that lead to specific, recurrent amplification events in human cancers are lacking. Moreover, some common amplifications, such as that at 8p11-12 in breast cancer, harbor multiple driver oncogenes, which are poorly modeled by conventional overexpression approaches. We sought to develop an experimental system to model recurrent chromosomal amplification events in human cell lines. Our strategy is to use homologous-recombination-mediated gene targeting to deliver a dominantly selectable, amplifiable marker to a specified chromosomal location. We used adeno-associated virus vectors to target human MCF-7 breast cancer cells at the ZNF703 locus, in the recurrent 8p11-12 amplicon, using the E. coli inosine monophosphate dehydrogenase (IMPDH) enzyme as a marker. We applied selective pressure using IMPDH inhibitors. Surviving clones were found to have increased copy number of ZNF703 (average 2.5-fold increase) by droplet digital PCR and FISH. Genome-wide array comparative genomic hybridization confirmed that amplifications had occurred on the short arm of chromosome 8, without changes on 8q or other chromosomes. Patterns of amplification were variable and similar to those seen in primary human breast cancers, including “sawtooth” patterns, distal copy number loss, and large continuous regions of copy number gain. This system will allow study of the cis- and trans-acting factors that are permissive for chromosomal amplification and provide a model to analyze oncogene cooperativity in amplifications harboring multiple candidate driver genes.

[On the seasonality of dermatoses: a retrospective analysis of search engine query data depending on the season]

BACKGROUND

The volume of search engine queries about disease-relevant items reflects public interest and correlates with disease prevalence as proven by the example of flu (influenza). Other influences include media attention or holidays.

STUDY GOAL

The present work investigates if the seasonality of prevalence or symptom severity of dermatoses correlates with search engine query data.

METHODS

The relative weekly volume of dermatological relevant search terms was assessed by the online tool Google Trends for the years 2009-2013. For each item, the degree of seasonality was calculated via frequency analysis and a geometric approach.

RESULTS

Many dermatoses show a marked seasonality, reflected by search engine query volumes. Unexpected seasonal variations of these queries suggest a previously unknown variability of the respective disease prevalence. Furthermore, using the example of allergic rhinitis, a close correlation of search engine query data with actual pollen count can be demonstrated.

DISCUSSION

In many cases, search engine query data are appropriate to estimate seasonal variability in prevalence of common dermatoses. This finding may be useful for real-time analysis and formation of hypotheses concerning pathogenetic or symptom aggravating mechanisms and may thus contribute to improvement of diagnostics and prevention of skin diseases.

[Childhood craniopharyngioma with hypothalamic obesity - no long-term weight reduction due to rehabilitation programs]

BACKGROUND

Severe obesity due to hypothalamic involvement has major impact on prognosis in long-term survivors of childhood craniopharyngioma. The long-term effects of rehabilitation efforts on weight development and obesity in these patients are not analyzed up to now.

PATIENTS AND METHODS

108 patients with childhood craniopharyngioma recruited in HIT Endo before 2001 were included in the study. Long-term weight development (BMI SDS after >10 yrs follow-up) was analyzed in regard to rehabilitation, which was performed in 31 of 108 (29%) patients (one rehabilitation in 4 patients (13%), more than one in 21 patients (68%), 6 patients unknown) in 13 German rehabilitation -clinics.

RESULTS

84% of patients underwent rehabilitation in order to reduce hypothalamic obesity (BMI>+ 2 SD), whereas 12% of patients were normal weight. Childhood craniopharyngioma pa-tients with rehabilitation presented with higher BMI at diagnosis (median BMI: +1.32 SD; range: -1.08 to + 7.00 SD) and at last evaluation (median BMI: +4.93 SD; range: -0.20 to + 13.13 SD) when compared with patients without rehabilitation (median BMI at diagnosis: +0.24 SD; range: -2.67 to + 6.98 SD; BMI at evaluation: +2.09 SD; range: -1.48 to + 10.23 SD). A long-term weight reducing effect of rehabilitation was no detectable regardless of degree of obesity, frequency of rehabilitation, and hospital of rehabilitation.

CONCLUSION

Treatment options for hypothalamic obesity in terms of rehabilitation are limited. Accordingly, strategies for prevention of hypothalamic lesions and psychosocial effects of rehabilitation are currently in focus for improvement of prognosis in childhood craniopharyngioma patients.

Abstract 4004: Molecular characterization of circulating glioblastoma cells identifies a mesenchymal-like tumor cell subpopulation

Glioblastoma (GBM), the most common and aggressive form of glioma, is often heterogeneous, diffusely invasive and hypervascularized. Despite being aggressive, extracranial metastases are rare, suggesting constraints on hematologic dissemination or distant survival of primary GBM cells. We recently developed a novel microfluidic device, termed the CTC-iChip, for efficient, antigen agnostic capture of rare circulating tumor cells (CTCs). Using the CTC-iChip, we set out to determine whether GBM cells can be detected in the blood of mice using two orthotopic xenograft models representing diffuse (GBM8) and focal (GBM24) GBM. CTCs were identified in 5/11 and 2/5 mice bearing GBM8 and GBM24 xenografts, respectively. CTC numbers did not correlate with tumor size or latency. We then expanded our analysis to patients and identified CTCs in 12/38 GBM patients with a median 5.3 cells per ml (range: 0 to 48.2 cells per ml). To understand the molecular characteristics of GBM CTCs, we analyzed the expression of 49 GBM-specific and stem cell transcripts in single GBM CTCs from both mouse xenografts models as well as GBM patients. The expression of mesenchymal gene transcripts including VIM, TGFBR2, TGFB, and SERPINE1 was elevated in CTCs compared with cultured cells and matched primary tumor cells. Moreover, CTCs exhibited lower proliferative indices and decreased neural lineage transcripts. To determine the pathophysiologic significance of this expression profile and the prospective origin of GBM CTCs, RNA-ISH was performed on xenografts and patient tumor samples. In the highly migratory GBM8 xenograft model, broad tumor cell expression of CTC/mesenchymal transcripts was observed. However, in the GBM24 focal tumor growth model, CTC/mesenchymal gene transcripts were predominantly expressed in regions of tumor invasion, migration along fiber tracts, and around regions of necrosis. Similarly, RNA-ISH analysis of 6 GBM patient tumors revealed prominent expression of CTC/mesenchymal genes in peri-necrotic and migratory pseudopalisading cells. Finally, RNA-ISH analysis of a rare case of metastatic GBM revealed a significant enrichment of GBM/mesenchymal gene expressing tumor cells within lung and lymph node metastases. Taken together, these data provide the first evidence for the hematologic circulation of GBM cells and reveal the involvement of mesenchymal features in the pathophysiology of malignant brain tumors.

Citation Format: James P. Sullivan, Brian V. Nahed, Andrew S. Chi, Marissa N. Madden, Samantha M. Oliveira, Simeon Springer, Hiroaki Wakimoto, Deepak Bhere, Khalid Shah, Phil Spuhler, Ajay M. Shah, David N. Louis, Mehmet Toner, Shyamala Maheswaran, Daniel A. Haber. Molecular characterization of circulating glioblastoma cells identifies a mesenchymal-like tumor cell subpopulation. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 4004. doi:10.1158/1538-7445.AM2014-4004

Vehicle and positive control values from the in vivo rodent comet assay and biomonitoring studies using human lymphocytes: historical database and influence of technical aspects

There is increased interest in the in vivo comet assay in rodents as a follow-up approach for determining the biological relevance of chemicals that are genotoxic in in vitro assays. This is partly because, unlike other assays, DNA damage can be assessed in this assay in virtually any tissue. Since background levels of DNA damage can vary with the species, tissue, and cell processing method, a robust historical control database covering multiple tissues is essential. We describe extensive vehicle and positive control data for multiple tissues from rats and mice. In addition, we report historical data from control and genotoxin-treated human blood. Technical issues impacting comet results are described, including the method of cell preparation and freezing. Cell preparation by scraping (stomach and other GI tract organs) resulted in higher % tail DNA than mincing (liver, spleen, kidney etc) or direct collection (blood or bone marrow). Treatment with the positive control genotoxicant, ethyl methanesulfonate (EMS) in rats and methyl methanesulfonate in mice, resulted in statistically significant increases in % tail DNA. Background DNA damage was not markedly increased when cell suspensions were stored frozen prior to preparing slides, and the outcome of the assay was unchanged (EMS was always positive). In conclusion, historical data from our laboratory for the in vivo comet assay for multiple tissues from rats and mice, as well as human blood show very good reproducibility. These data and recommendations provided are aimed at contributing to the design and proper interpretation of results from comet assays.

Brain tumor cells in circulation are enriched for mesenchymal gene expression

Glioblastoma (GBM) is a highly aggressive brain cancer characterized by local invasion and angiogenic recruitment, yet metastatic dissemination is extremely rare. Here, we adapted a microfluidic device to deplete hematopoietic cells from blood specimens of patients with GBM, uncovering evidence of circulating brain tumor cells (CTC). Staining and scoring criteria for GBM CTCs were first established using orthotopic patient-derived xenografts (PDX), and then applied clinically: CTCs were identified in at least one blood specimen from 13 of 33 patients (39%; 26 of 87 samples). Single GBM CTCs isolated from both patients and mouse PDX models demonstrated enrichment for mesenchymal over neural differentiation markers compared with primary GBMs. Within primary GBMs, RNA in situ hybridization identified a subpopulation of highly migratory mesenchymal tumor cells, and in a rare patient with disseminated GBM, systemic lesions were exclusively mesenchymal. Thus, a mesenchymal subset of GBM cells invades the vasculature and may proliferate outside the brain.

SIGNIFICANCE

GBMs are locally invasive within the brain but rarely metastasize to distant organs, exemplifying the debate over "seed" versus "soil." We demonstrate that GBMs shed CTCs with invasive mesenchymal characteristics into the circulation. Rare metastatic GBM lesions are primarily mesenchymal and show additional mutations absent in the primary tumor.

Improved ankle and knee control with a dual-channel functional electrical stimulation system in chronic hemiplegia. A case report

The aim of tis report is to describe the effects of a dual-channel functional electrical stimulation (FES) system applied daily as an orthotic device to the dorsiflexors and hamstrings muscles in a subject with chronic hemiparesis. Prior to the application of FES, the patient's gait was characterized by a footdrop and knee hyperextension during stance. measurements of gait performance were collected before FES application, after a conditioning period of six weeks, and following ten months of daily use. Outcomes included lower limb kinematics and temporal gait measures. The kinematic assessments indicated significant benefits for gait with the dorsiflexors and hamstrings FES, as compared to no stimulation and peroneal FES alone. In addition ot improved ankle control, knee hyperextension was reduced during stance, and the self-selected comfortable gait velocity increased following ten months of daily use. The results of this report suggest that dual-channel FES for the dorsiflexors and hamstrings muscles may affect ankle and knee control beyond that witch can be attributed to peroneal stimulation alone. The positive effects observed in this case study point to the potential of dual-channel FES as a viable treatment options in the rehabilitation of patients with similar impairments.

TERT promoter mutations occur early in urothelial neoplasia and are biomarkers of early disease and disease recurrence in urine

Activating mutations occur in the promoter of the telomerase reverse transcriptase (TERT) gene in 66% of muscle-invasive urothelial carcinomas. To explore their role in bladder cancer development and to assess their utility as urine markers for early detection, we sequenced the TERT promoter in 76 well-characterized papillary and flat noninvasive urothelial carcinomas, including 28 pTa low-grade transitional cell carcinomas (TCC), 31 pTa high-grade TCCs, and 17 pTis carcinoma in situ lesions. We also evaluated the sequence of the TERT promoter in a separate series of 14 early bladder neoplasms and matched follow-up urine samples to determine whether urine TERT status was an indicator of disease recurrence. A high rate of TERT promoter mutation was observed in both papillary and flat lesions, as well as in low- and high-grade noninvasive urothelial neoplasms (mean: 74%). In addition, among patients whose tumors harbored TERT promoter mutations, the same mutations were present in follow-up urines in seven of eight patients that recurred but in none of the six patients that did not recur (P < 0.001). TERT promoter mutations occur in both papillary and flat lesions, are the most frequent genetic alterations identified to date in noninvasive precursor lesions of the bladder, are detectable in urine, and seem to be strongly associated with bladder cancer recurrence. These provocative results suggest that TERT promoter mutations may offer a useful urinary biomarker for both early detection and monitoring of bladder neoplasia.