Combining germline, tissue and liquid biopsy analysis by comprehensive genomic profiling to improve the yield of actionable variants in a real-world cancer cohort.

BACKGROUND: Comprehensive next-generation sequencing is widely used for precision oncology and precision prevention approaches. We aimed to determine the yield of actionable gene variants, the capacity to uncover hereditary predisposition and liquid biopsy appropriateness instead of, or in addition to, tumor tissue analysis, in a real-world cohort of cancer patients, who may benefit the most from comprehensive genomic profiling. METHODS: Seventy-eight matched germline/tumor tissue/liquid biopsy DNA and RNA samples were profiled using the Hereditary Cancer Panel (germline) and the TruSight Oncology 500 panel (tumor tissue/cfDNA) from 23 patients consecutively enrolled at our center according to at least one of the following criteria: no available therapeutic options; long responding patients potentially fit for other therapies; rare tumor; suspected hereditary cancer; primary cancer with high metastatic potential; tumor of unknown primary origin. Variants were annotated for OncoKB and AMP/ASCO/CAP classification. RESULTS: The overall yield of actionable somatic and germline variants was 57% (13/23 patients), and 43.5%, excluding variants previously identified by somatic or germline routine testing. The accuracy of tumor/cfDNA germline-focused analysis was demonstrated by overlapping results of germline testing. Five germline variants in BRCA1, VHL, CHEK1, ATM genes would have been missed without extended genomic profiling. A previously undetected BRAF p.V600E mutation was emblematic of the clinical utility of this approach in a patient with a liver undifferentiated embryonal sarcoma responsive to BRAF/MEK inhibition. CONCLUSIONS: Our study confirms the clinical relevance of performing extended parallel tumor DNA and cfDNA testing to broaden therapeutic options, to longitudinally monitor cfDNA during patient treatment, and to uncover possible hereditary predisposition following tumor sequencing in patient care.

Evaluating mismatch repair deficiency in colorectal cancer biopsy specimens.

Mismatch repair (MMR) testing on all new cases of colorectal cancer (CRC) has customarily been preferably performed on surgical specimens, as more tissue is available; however, new clinical trials for the use of immune checkpoint inhibitors in the neoadjuvant setting require MMR testing on biopsy samples. This study aims at identifying advantages, disadvantages and any potential pitfalls in MMR evaluation on biopsy tissue and how to cope with them. The study is prospective-retrospective, recruiting 141 biopsies (86 proficient (p)MMR and 55 deficient (d)MMR) and 97 paired surgical specimens (48 pMMR; 49 dMMR). In biopsy specimens, a high number of indeterminate stains was observed, in particular for MLH1 (31 cases, 56.4%). The main reasons were a punctate nuclear expression of MLH1, relatively weak MLH1 nuclear expression compared to internal controls, or both (making MLH1 loss difficult to interpret), which was solved by reducing primary incubation times for MLH1. A mean of  ≥ 5 biopsies had adequate immunostains, compared to ≤ 3 biopsies in inadequate cases. Conversely, surgical specimens rarely suffered from indeterminate reactions, while weaker staining intensity (p < 0.007) for MLH1 and PMS2 and increased patchiness grade (p < 0.0001) were seen. Central artefacts were almost exclusive to surgical specimens. MMR status classification was possible in 92/97 matched biopsy/resection specimen cases, and all of these were concordant (47 pMMR and 45 dMMR). Evaluation of MMR status on CRC biopsy samples is feasible, if pitfalls in interpretation are known, making laboratory-specific appropriate staining protocols fundamental for high-quality diagnoses.

Obstetrics and Gynecology Emergency Department Activity during Lockdown in a Teaching Hospital, Hub Center, for COVID-19.

Background: The lockdown related to the SARS-CoV-2 pandemic has imposed profound changes in the interaction of the population with hospitals and emergency departments. The main aim of this research was to evaluate the impact of lockdown on the activity of obstetrics and gynecology emergency department (OGED) in a teaching hospital, hub center, for COVID-19. Methods: The study considers all visits to the OGED with their different triage color codes that represent the clinical severity of each case (from the most severe to the least one: red, yellow, green, white). Data were selected through the "PSNet" triage program and collected anonymously. We analyzed frequency distributions of the variables separately for each woman and calculated mean and standard deviations for continuous variables. We then analyzed the association between factors and outcomes for categorical variables (expressed as a number and percentage of the total) using the chi-square test (χ2). The level of significance was established with p < 0.05. Statistical analysis was performed using SPSS Statistics V20.0. Given the fact that the study has a retrospective observational nature and it is based on an anonymous routine database, approval by the Local Ethics Committee was not necessary. Results: The relative decrease of patients presenting to OGED in 2020 was -50.96%. The percentage of nonpregnant women was significantly lower in 2020 compared to 2019 (p ≤ 0.0001; Δ = -79.46%). Regarding the obstetric group, we saw an important decrease of visits in 2020 compared to 2019 (p < 0.0001; Δ = -40%). The prevalence of yellow codes was significantly higher in 2020 (Δ = +29.72%), while that of white (Δ = -61.58%) and green (Δ = -52.22%) codes was significantly lower (p ≤ 0.0001). Comparing the diagnoses at discharge, we could highlight significant reductions in 2020 for more than one diagnosis: bleeding (p ≤ 0.0001; Δ = -70.42%), pain (p ≤ 0.0001; Δ = -81.22%), urinary diseases (p = 0.004; Δ = -75.64%), and gastrointestinal diseases (p ≤ 0.0001; Δ = -87.50%). Conclusions: An evident change emerged in relation to the dynamics between the local obstetrical and gynecological population, and OGED resources. The COVID-19 lockdown greatly reduced the rate of admission to OGED without time-related obstetric and gynecological complications. The reduction of admissions suggests a more appropriate use of the ED by patients that may inspire future policies for the implementation of emergency services.

Integrative molecular analysis of combined small-cell lung carcinomas identifies major subtypes with different therapeutic opportunities.

BACKGROUND: Combined small-cell lung cancer (C-SCLC) is composed of SCLC admixed with a non-small-cell cancer component. They currently receive the same treatment as SCLC. The recent evidence that SCLC may belong to either of two lineages, neuroendocrine (NE) or non-NE, with different vulnerability to specific cell death pathways such as ferroptosis, opens new therapeutic opportunities also for C-SCLC. MATERIALS AND METHODS: Thirteen C-SCLCs, including five with adenocarcinoma (CoADC), five with large-cell neuroendocrine carcinoma (CoLCNEC) and three with squamous cell carcinoma (CoSQC) components, were assessed for alterations in 409 genes and transcriptomic profiling of 20 815 genes. RESULTS: All 13 cases harbored TP53 (12 cases) and/or RB1 (7 cases) inactivation, which was accompanied by mutated KRAS in 4 and PTEN in 3 cases. Potentially targetable alterations included two KRAS G12C, two PIK3CA and one EGFR mutations. Comparison of C-SCLC transcriptomes with those of 57 pure histology lung cancers (17 ADCs, 20 SQCs, 11 LCNECs, 9 SCLCs) showed that CoLCNEC and CoADC constituted a standalone group of NE tumors, while CoSQC transcriptional setup was overlapping that of pure SQC. Using transcriptional signatures of NE versus non-NE SCLC as classifier, CoLCNEC was clearly NE while CoSQC was strongly non-NE and CoADC exhibited a heterogeneous phenotype. Similarly, using ferroptosis sensitivity/resistance markers, CoSQC was classified as sensitive (as expected for non-NE), CoLCNEC as resistant (as expected for NE) and CoADC showed a heterogeneous pattern. CONCLUSIONS: These data support routine molecular profiling of C-SCLC to search for targetable driver alterations and to precisely classify them according to therapeutically relevant subgroups (e.g. NE versus non-NE).

Functional and radiological outcomes after bridging therapy versus direct thrombectomy in stroke patients with unknown onset: Bridging therapy versus direct thrombectomy in unknown onset stroke patients with 10-point ASPECTS.

BACKGROUND AND PURPOSE: The aim was to assess functional and radiological outcomes after bridging therapy (intravenous thrombolysis plus mechanical thrombectomy) versus direct mechanical thrombectomy (MT) in unknown onset stroke patients. METHODS: A cohort study was conducted on prospectively collected data from unknown onset stroke patients who received endovascular procedures at ≤6 h from symptom recognition or awakening time. RESULTS: Of the 349 patients with a 10-point Alberta Stroke Program Early Computed Tomography Score (ASPECTS), 248 received bridging and 101 received direct MT. Of the 134 patients with 6-9-point ASPECTS, 123 received bridging and 111 received direct MT. Each patient treated with bridging was propensity score matched with a patient treated with direct MT for age, sex, study period, pre-stroke disability, stroke severity, type of stroke onset, symptom recognition to groin time (or awakening to groin time), ASPECTS and procedure time. In the two matched groups with 10-point ASPECTS (n = 73 vs. n = 73), bridging was associated with higher rates of excellent outcome (46.6% vs. 28.8%; odds ratio 2.302, 95% confidence interval 1.010-5.244) and successful recanalization (83.6% vs. 63%; odds ratio 3.028, 95% confidence interval 1.369-6.693) compared with direct MT; no significant association was found between bridging and direct MT with regard to rate of symptomatic intracerebral hemorrhage (0% vs. 1.4%). In the two matched groups with 6-9-point ASPECTS (n = 45 vs. n = 45), no significant associations were found between bridging and direct MT with regard to rates of excellent functional outcome (44.4% vs. 31.1%), successful recanalization (73.3% vs. 76.5%) and symptomatic intracerebral hemorrhage (0% vs. 0%). CONCLUSIONS: Bridging at ≤ 6 h of symptom recognition or awakening time was associated with better functional and radiological outcomes in unknown onset stroke patients with 10-point ASPECTS.

Optical fiber sensors for monitoring in critical care.

Monitoring of key physiological and pharmacological parameters is an important part of a closed loop control system in critical care. Optical fiber sensors provide a versatile platform technology that can be easily incorporated into existing in-dwelling catheters or face masks. With appropriate functional coatings they can be used to monitor a range of relevant parameters and two different examples are presented: (i) respiration monitoring; (ii) drug level monitoring. Respiration monitoring involves monitoring of temperature and humidity in inhaled and exhaled breath. The optical fiber sensor consists of a fiber Bragg grating to measure temperature and a tip coating whose refractive index changes with humidity. The sensor is demonstrated to be able to track breath to breath changes when incorporated into a mask. Drug level monitoring is demonstrated in vitro using a long period grating coated with molecularly imprinted polymer nanoparticles that are sensitive to fentanyl. The sensor has a limit of detection of 50ng/ml.

Quality control in diagnostic immunohistochemistry: integrated on-slide positive controls.

Standardization in immunohistochemistry is a priority in modern pathology and requires strict quality control. Cost containment has also become fundamental and auditing of all procedures must take into account both these principles. Positive controls must be routinely performed so that their positivity guarantees the appropriateness of the immunohistochemical procedure. The aim of this study is to develop a low cost (utilizing a punch biopsy-PB-tool) procedure to construct positive controls which can be integrated in the patient's tissue slide. Sixteen frequently used control blocks were selected and multiple cylindrical samples were obtained using a 5-mm diameter punch biopsy tool, separately re-embedding them in single blocks. For each diagnostic immunoreaction requiring a positive control, an integrated PB-control section (cut from the appropriate PB-control block) was added to the top right corner of the diagnostic slide before immunostaining. This integrated control technique permitted a saving of 4.75% in total direct lab costs and proved to be technically feasible and reliable. Our proposal is easy to perform and within the reach of all pathology labs, requires easily available tools, its application costs is less than using external paired controls and ensures that a specific control for each slide is always available.

Anti-tumoral effects of somatostatin analogs: a lesson from the CLARINET study.

Octreotide and lanreotide, the first-generation somatostatin analogs, successfully control hormone hyperproduction, and related syndromes, in patients with acromegaly and neuroendocrine tumors. However, their anti-tumor effect, rather evident in large number of pituitary adenomas in acromegalic patients, has been hypothesized for a long time in patients with neuroendocrine tumors as well, although a significant tumor shrinkage has rarely been observed. However, the recent publication of the CLARINET study has strengthened the evidence, already emerged with the PROMID trial, that the long-term treatment with the first-generation long-acting somatostatin analogs may exert an anti-tumor activity on G1 and G2 enteropancreatic neuroendocrine tumors, as well. After the publication, majority of international guidelines have updated their algorithms in line with these results and this class of drugs obtained the indication as anti-tumor agents in the majority of patients with neuroendocrine tumors.

Mixed malignant mullerian tumor with neuroendocrine features in an irradiated uterus for cervical carcinoma. A unique association? A morphological, immunohistochemisty and ultrastructural study.

Chemo-radiation represents an effective therapy for carcinoma of the uterine cervix. The endometrium may however receive a consistent dose of mutagenic radiations and patients may have an increased risk of secondary malignancies. Endometrial mixed malignant mullerian tumor (MMMT) is a rare, highly aggressive disease, and neuroendocrine features are even rarer. A 68 years old woman underwent radio-chemotherapy for a squamous cell carcinoma of the cervix. Follow up was uneventful until, eight years after radio-chemotherapy, imaging exams detected a diffuse enlargement of the uterine body. Radical hysterectomy revealed a multiphasic lesion with both sarcomatous and mixed carcinomatous components. The carcinomatous, component presented neuroendocrine histologic and ultrastuctural features and an intense expression of neuroendocrine immunohistochemistry markers. No residual cervical carcinoma was documented (pR0). The patient died of disease after 9 months. Reported cases further demonstrate how the irradiation of the uterus for cervical cancer carries a not negligible risk of developing a second endometrial cancer. The second cancer may develop years after initial therapy and may have aggressive histologic and clinical features. This case underlines the importance for a long follow-up in women having received radio-chemotherapy alone.

Atomic and molecular layer deposition: off the beaten track.

Atomic layer deposition (ALD) is a gas-phase deposition technique that, by relying on self-terminating surface chemistry, enables the control of the amount of deposited material down to the atomic level. While mostly used in semiconductor technology for the deposition of ceramic oxides and nitrides on wafers, ALD lends itself to the deposition of a wealth of materials on virtually every substrate. In particular, ALD and its organic counterpart molecular layer deposition (MLD), have opened up attractive avenues for the synthesis of novel nanostructured materials. However, as most ALD processes were developed and optimized for semiconductor technology, these might not be optimal for applications in fields such as catalysis, energy storage, and health. For this reason, novel applications for ALD often require new surface chemistries, process conditions, and reactor types. As a result, recent developments in ALD technology have marked a considerable departure from the standard set by well-established ALD processes. The aim of this review is twofold: firstly, to capture the recent departure of ALD from its original development; and secondly, to pinpoint the unexplored paths through which ALD can advance further in terms of synthesis of novel materials. To that end, we provide a review of the recent developments of ALD and MLD of materials that are gaining increasing attention on various substrates, with particular emphasis on high-surface-area substrates. Furthermore, we present a critical review of the effects of the process conditions, namely, temperature, pressure, and time on ALD growth. Finally, we also give a brief overview of the recent advances in ALD reactors and energy-enhanced ALD processes.

Two-dimensional self-assembly of benzotriazole on an inert substrate.

The ultra-high vacuum (UHV) room temperature adsorption of benzotriazole (BTAH), a well-known corrosion inhibitor for copper, has been investigated on the pristine Au(111) surface using a combination of surface sensitive techniques. The dimensionality of the molecule is reduced from the 3D crystal structure to a 2-dimensional surface confinement, which induces the formation of hydrogen bonded 1-dimensional molecular chains consisting of alternating pro-S and pro-R enantiomers mainly. The 0-dimensional system is characteristic of gas-phase BTAH, which undergoes a tautomeric equilibrium, with consequences for the resulting adsorbed species. The balance between hydrogen bonding, inter-chain van der Waals interactions and surface-molecule interactions, and the correlation with the dimensionality of the system, are discussed in light of the experimental results and a computational description of the observed features.

Segmental infarction of the testis: can frozen sections avoid orchidectomy?

Segmental infarction (SI) of the testis is a rare condition that can masquerade as a mass lesion, thus requiring exclusion of tumour. If clinical exams do not exclude a neoplastic lesion with certainty, orchidectomy is usually performed. A case of SI of the testis is presented; the use of frozen section of the enucleated mass demonstrated the ischaemic nature of the lesion, so avoiding orchidectomy. The 8 year follow-up was uneventful. The use of frozen section in SI could permit the selection of cases in which testicular-sparing surgery should be considered.

(S)-Lysine adsorption induces the formation of gold nanofingers on Au{111}.

STM imaging following the adsorption of (S)-lysine on Au{111} leads to the observation of Au nanofingers whose growth directions correlate with the unit cell vectors of ordered 2-D phases of lysine. The likely mechanism of surface restructuring is discussed.

Chemotherapy with 5-fluorouracil, cisplatin and streptozocin for neuroendocrine tumours.

BACKGROUND: The role of chemotherapy for neuroendocrine tumours remains controversial and there is no standard regimen. METHOD: We report the outcome for a consecutive series of chemonaive patients with metastatic or locally advanced neuroendocrine tumours treated with a combination of 5-fluorouracil (500 mg m(-2)), cisplatin (70 mg m(-2)) and streptozocin (1000 mg m(-2)) (FCiSt) administered three weekly for up to six cycles. Patients were assessed for radiological response, toxicity and survival. RESULTS: In the 79 patients assessable for response, treatment with FCiSt was associated with an overall response rate of 33% (38% for pancreatic primary sites and 25% for non-pancreatic primary sites). Stable disease occurred in a further 51%, with progression in 16%. The median time to progression was 9.1 months and median overall survival was 31.5 months. The most common grade 3-4 toxicity was neutropaenia (28% patients) but grade 3-4 infection was rare (7%). The most frequent non-haematological grade 3-4 toxicity was nausea and vomiting (17%). Prognostic factors included Ki-67, mitotic index, grade and chromogranin A, whereas response to chemotherapy was predicted by mitotic index, grade and alpha-fetoprotein. CONCLUSIONS: FCiSt is an effective regimen for neuroendocrine tumours with an acceptable toxicity profile. Grade and mitotic index are the best predictors of response.

A simple, noninvasive test for the diagnosis of liver fibrosis in patients with hepatitis C recurrence after liver transplantation.

Recurrent hepatitis C is a common cause of graft loss in patients undergoing liver transplantation, and serial protocol liver biopsies have been used to identify patients at risk of graft loss from rapid fibrosis progression. The aim of this study was to derive a simple noninvasive index to predict fibrosis in patients with recurrent hepatitis C post-transplant. A retrospective study was performed assessing serial liver biopsies for post-transplant chronic hepatitis C infection. One hundred eighty-five patients were included in the analysis; median age 53 years (interquartile range 48-59) and 140 (76%) were male. Liver histology showed 53 (29%) had Ishak fibrosis stages F0/F1, 31 (17%) had F2, 29 (16%) had F3, 19 (10%) had F4 and 53 (29%) had F5/F6. The London Transplant Centres' (LTC) score was derived combining aspartate aminotransferase (AST IU/L), time from liver transplant (TFLT months), international normalized ratio and platelets. Diagnostic accuracy of the LTC score was assessed using area under receiver-operating characteristic (ROC) curves. The area under the ROC curve for moderate fibrosis (F >or= 2) was 0.78 (95% CI, 0.70-0.86; P < 0.0001), for advanced fibrosis (F4-6) was 0.80 (95% CI, 0.72-0.87; P < 0.0001) and for cirrhosis was 0.80 (95% CI, 0.72-0.88; P < 0.0001). An optimal cut-off value of 6.3 distinguished patients with no or mild fibrosis (F

Prospective comparison of Fibroscan, King's score and liver biopsy for the assessment of cirrhosis in chronic hepatitis C infection.

Historically, liver biopsy (LB) was the sole method to evaluate the severity of hepatic fibrosis in patients with chronic hepatitis C infection. However, LB is expensive and associated with a risk of severe complications. Therefore, noninvasive tests have been developed to assess the severity of liver fibrosis. The accuracy of Fibroscan (FS) and King's score (KS) was evaluated individually and in combination using liver histology as the reference standard. One hundred and eighty-seven patients were identified who had undergone a biopsy with a diagnosis of chronic hepatitis C virus (HCV) mono-infection (HCV RNA-positive by RT-PCR), attending King's College Hospital (n = 88) or the Royal Free Hospital (n = 99) (London) between May 2006 and December 2007. Liver fibrosis was scored using the Ishak method; significant fibrosis was defined as Ishak fibrosis stage F3-F6, and cirrhosis defined as Ishak fibrosis F5-F6. The diagnostic accuracy of each test was assessed by area under receiver operator characteristic curves (AUROC). Median age was 49 years (43-54) and 115 (61%) were male. The AUROC for FS, KS and FS + KS for the diagnosis of Ishak F3-F6 were 0.83, 0.82 and 0.85, respectively and for the diagnosis of cirrhosis (>or=F5) were 0.96, 0.89 and 0.93, respectively. The negative predictive values for the diagnosis of cirrhosis using the optimal cut-off results for fibrsocan (10.05 kPa), KS (24.3) and the two combined (26.1) were 98%, 91% and 94%, respectively. The noninvasive markers and, particularly, FS were effective tests for the prediction of cirrhosis in chronic hepatitis C. Both KS and FS also had clinical utility for the prediction of Ishak fibrosis stages F3-F6.