An in-silico analysis reveals further evidence of an aggressive subset of lung carcinoids sharing molecular features of high-grade neuroendocrine neoplasms

Little is known as to whether there may be any pathogenetic link between pulmonary carcinoids and neuroendocrine carcinomas (NECs). A gene signature we previously found to cluster pulmonary carcinoids, large cell neuroendocrine carcinoma (LCNEC) and small cell lung carcinoma (SCLC), and which encompassed MEN1, MYC, MYCL1, RICTOR, RB1, SDHA, SRC and TP53 mutations or copy number variations (CNVs), was used to reclassify an independent cohort of 54 neuroendocrine neoplasms (NENs) [31 typical carcinoids (TC), 11 atypical carcinoids (AC) and 12 SCLC], by means of transcriptome and mutation data. Unsupervised clustering analysis identified two histology-independent clusters, namely CL1 and CL2, where 17/42 (40.5%) carcinoids and all the SCLC samples fell into the latter. CL2 carcinoids affected survival adversely, were enriched in T to G transversions or T > C/C > T transitions in the context of specific mutational signatures, presented with at least 1.5-fold change (FC) increase of gene mutations including TSC2, SMARCA2, SMARCA4, ERBB4 and PTPRZ1, differed for gene expression and showed epigenetic changes in charge of MYC and MTORC1 pathways, cellular senescence, inflammation, high-plasticity cell state and immune system exhaustion. Similar results were also found in two other independent validation sets comprising 101 lung NENs (24 carcinoids, 21 SCLC and 56 LCNEC) and 30 carcinoids, respectively. We herein confirmed an unexpected sharing of molecular traits along the spectrum of lung NENs, with a subset of genomically distinct aggressive carcinoids sharing molecular features of high-grade neuroendocrine neoplasms.

Thoracic ultrasound combined with low-dose computed tomography may represent useful screening strategy in highly exposed population in the industrial city of Taranto (Italy)

Objectives

We validated a screening protocol in which thoracic ultrasound (TUS) acts as a first-line complementary imaging technique in selecting patients which may deserve a second-line low-dose high resolution computed tomography (HRCT) scan among a population of asymptomatic high-risk subjects for interstitial lung abnormalities (ILA) and lung cancer. Due to heavy environmental pollution burden, the district Tamburi of Taranto has been chosen as "case study" for this purpose.

Methods

From July 2018 to October 2020, 677 patients aged between 45 and 65 year and who had been living in the Tamburi district of Taranto for at least 10 years were included in the study. After demographic, clinical and risk factor exposition data were collected, each participant underwent a complete TUS examination. These subjects were then asked to know if they agreed to perform a second-level examination by low-dose HRCT scan.

Results

On a total of 167 subjects (24.7%) who agreed to undergo a second-level HRCT, 85 patients (50.9%) actually showed pleuro-pulmonary abnormalities. Interstitial abnormalities were detected in a total of 36 patients on HRCT scan. In particular, 34 participants presented subpleural ILAs, that were classified in the fibrotic subtype in 7 cases. The remaining 2 patients showed non-subpleural interstitial abnormalities. Subpleural nodules were observed in 46 patients. TUS showed an overall diagnostic accuracy of 88.6% in detecting pleuro-pulmonary abnormalities in comparison with HRCT scan, with a sensitivity of 95.3%, a specificity of 81.7%, a positive predictive value of 84.4% and a negative predictive value of 94.4%. The matched evaluation of specific pulmonary abnormalities on HRTC scan (i.e., interstitial abnormalities or pulmonary nodules) with determinate sonographic findings revealed a reduction in both TUS sensibility and specificity. Focusing TUS evaluation on the assessment of interstitial abnormalities, a thickened pleural line showed a sensitivity of 63.9% and a specificity of 69.5%, hypoechoic striae showed a sensitivity of 38.9% and a specificity of 90.1% and subpleural nodules showed a sensitivity of 58.3% and a specificity of 77.1%. Regarding to the assessment of subpleural nodules, TUS showed a sensitivity of 60.9% and a specificity of 81.0%. However, the combined employment of TUS examination and HRCT scans allowed to identify 34 patients with early subpleural ILA and to detect three suspicious pulmonary nodules (of which two were intraparenchymal and one was a large subpleural mass), which revealed to be lung cancers on further investigations.

Conclusion

A first-line TUS examination might aid the identification of subjects highly exposed to environmental pollution, who could benefit of a second-line low-dose HRCT scan to find early interstitial lung diseases as well as lung cancer.

Protocol registration code

PLEURO-SCREENING-V1.0_15 Feb, 17.

miRNome profiling of lung cancer metastases revealed a key role for miRNA-PD-L1 axis in the modulation of chemotherapy response

Locally advanced non-small cell lung cancer (NSCLC) is frequent at diagnosis and requires multimodal treatment approaches. Neoadjuvant chemotherapy (NACT) followed by surgery is the treatment of choice for operable locally advanced NSCLC (Stage IIIA). However, the majority of patients are NACT-resistant and show persistent lymph nodal metastases (LNmets) and an adverse outcome. Therefore, the identification of mechanisms and biomarkers of NACT resistance is paramount for ameliorating the prognosis of patients with Stage IIIA NSCLC. Here, we investigated the miRNome and transcriptome of chemo-naïve LNmets collected from patients with Stage IIIA NSCLC (N = 64). We found that a microRNA signature accurately predicts NACT response. Mechanistically, we discovered a miR-455-5p/PD-L1 regulatory axis which drives chemotherapy resistance, hallmarks metastases with active IFN-γ response pathway (an inducer of PD-L1 expression), and impacts T cells viability and relative abundances in tumor microenvironment (TME). Our data provide new biomarkers to predict NACT response and add molecular insights relevant for improving the management of patients with locally advanced NSCLC.

Integrated molecular profiling of patient-derived ovarian cancer models identifies clinically relevant signatures and tumor vulnerabilities

High‐grade serous ovarian carcinoma (HGSOC) is a highly aggressive and intractable neoplasm, mainly because of its rapid dissemination into the abdominal cavity, a process that is favored by tumor‐associated peritoneal ascites. The precise molecular alterations involved in HGSOC onset and progression remain largely unknown due to the high biological and genetic heterogeneity of this tumor. We established a set of different tumor samples (termed the As11‐set) derived from a single HGSOC patient, consisting of peritoneal ascites, primary tumor cells, ovarian cancer stem cells (OCSC) and serially propagated tumor xenografts. The As11‐set was subjected to an integrated RNA‐seq and DNA‐seq analysis which unveiled molecular alterations that marked the different types of samples. Our profiling strategy yielded a panel of signatures relevant in HGSOC and in OCSC biology. When such signatures were used to interrogate the TCGA dataset from HGSOC patients, they exhibited prognostic and predictive power. The molecular alterations also identified potential vulnerabilities associated with OCSC, which were then tested functionally in stemness‐related assays. As a proof of concept, we defined PI3K signaling as a novel druggable target in OCSC.

Loss of circadian gene Timeless induces EMT and tumor progression in colorectal cancer via Zeb1-dependent mechanism

The circadian gene Timeless (TIM) provides a molecular bridge between circadian and cell cycle/DNA replication regulatory systems and has been recently involved in human cancer development and progression. However, its functional role in colorectal cancer (CRC), the third leading cause of cancer-related deaths worldwide, has not been fully clarified yet. Here, the analysis of two independent CRC patient cohorts (total 1159 samples) reveals that loss of TIM expression is an unfavorable prognostic factor significantly correlated with advanced tumor stage, metastatic spreading, and microsatellite stability status. Genome-wide expression profiling, in vitro and in vivo experiments, revealed that TIM knockdown induces the activation of the epithelial-to-mesenchymal transition (EMT) program. Accordingly, the analysis of a large set of human samples showed that TIM expression inversely correlated with a previously established gene signature of canonical EMT markers (EMT score), and its ectopic silencing promotes migration, invasion, and acquisition of stem-like phenotype in CRC cells. Mechanistically, we found that loss of TIM expression unleashes ZEB1 expression that in turn drives the EMT program and enhances the aggressive behavior of CRC cells. Besides, the deranged TIM-ZEB1 axis sets off the accumulation of DNA damage and delays DNA damage recovery. Furthermore, we show that the aggressive and genetically unstable 'CMS4 colorectal cancer molecular subtype' is characterized by a lower expression of TIM and that patients with the combination of low-TIM/high-ZEB1 expression have a poorer outcome. In conclusion, our results as a whole suggest the engagement of an unedited TIM-ZEB1 axis in key pathological processes driving malignant phenotype acquisition in colorectal carcinogenesis. Thus, TIM-ZEB1 expression profiling could provide a robust prognostic biomarker in CRC patients, supporting targeted therapeutic strategies with better treatment selection and patients' outcomes.

A Subset of Large Cell Neuroendocrine Carcinomas in the Gastroenteropancreatic Tract May Evolve from Pre-existing Well-Differentiated Neuroendocrine Tumors

In the gastro-entero-pancreatic (GEP) tract, neuroendocrine neoplasms (NENs) include well differentiated neuroendocrine tumors (NETs) and high-grade NE carcinomas (NECs), which are thought to make up separate and mutually exclusive tumor entities. Little is known, however, as to whether there may be any pathogenetic link between them. Clustering analysis of a 10-gene panel generated from a previously reported next-generation sequencing analysis on 48 GEP-NENs with clinical annotations was used in the study. Unsupervised cluster analysis showed three histology-independent clusters, namely, C1, C2, and C3, which accounted for 44% of patients but the entire array of mutations. All but two NECs fell into the clusters, yet with different prevalence rates (p < 0.0001). A model was devised according to which NETs were likely to evolve into NECs upon progression of C3 into C1 and C2, despite different morphology. The median Ki-67 labeling index was 5% in C3 showing better prognosis and 50% in C1 and C2 experiencing worse prognosis, with an impressive intra-tumor heterogeneity of diversely proliferating tumor areas. This study suggests that a subset of large cell NECs in the gastroenteropancreatic tract may evolve from pre-existing well-differentiated NETs.

Biomarkers and Lung Cancer Early Detection: State of the Art

Simple Summary

Lung cancer is the leading cause of cancer death worldwide. Detecting lung malignancies promptly is essential for any anticancer treatment to reduce mortality and morbidity, especially in high-risk individuals. The use of liquid biopsy to detect circulating biomarkers such as RNA, microRNA, DNA, proteins, autoantibodies in the blood, as well as circulating tumor cells (CTCs), can substantially change the way we manage lung cancer patients by improving disease stratification using intrinsic molecular characteristics, identification of therapeutic targets and monitoring molecular residual disease. Here, we made an update on recent developments in liquid biopsy-based biomarkers for lung cancer early diagnosis, and we propose guidelines for an accurate study design, execution, and data interpretation for biomarker development.

Abstract

Lung cancer burden is increasing, with 2 million deaths/year worldwide. Current limitations in early detection impede lung cancer diagnosis when the disease is still localized and thus more curable by surgery or multimodality treatment. Liquid biopsy is emerging as an important tool for lung cancer early detection and for monitoring therapy response. Here, we reviewed recent advances in liquid biopsy for early diagnosis of lung cancer. We summarized DNA- or RNA-based biomarkers, proteins, autoantibodies circulating in the blood, as well as circulating tumor cells (CTCs), and compared the most promising studies in terms of biomarkers prediction performance. While we observed an overall good performance for the proposed biomarkers, we noticed some critical aspects which may complicate the successful translation of these biomarkers into the clinical setting. We, therefore, proposed a roadmap for successful development of lung cancer biomarkers during the discovery, prioritization, and clinical validation phase. The integration of innovative minimally invasive biomarkers in screening programs is highly demanded to augment lung cancer early detection.

Aggressive early-stage lung adenocarcinoma is characterized by epithelial cell plasticity with acquirement of stem-like traits and immune evasion phenotype

Lung adenocarcinoma (LUAD) is the main non-small-cell lung cancer diagnosed in ~40-50% of all lung cancer cases. Despite the improvements in early detection and personalized medicine, even a sizable fraction of patients with early-stage LUAD would experience disease relapses and adverse prognosis. Previous reports indicated the existence of LUAD molecular subtypes characterized by specific gene expression and mutational profiles, and correlating with prognosis. However, the biological and molecular features of such subtypes have not been further explored. Consequently, the mechanisms driving the emergence of aggressive LUAD remained unclear. Here, we adopted a multi-tiered approach ranging from molecular to functional characterization of LUAD and used it on multiple cohorts of patients (for a total of 1227 patients) and LUAD cell lines. We investigated the tumor transcriptome and the mutational and immune gene expression profiles, and we used LUAD cell lines for cancer cell phenotypic screening. We found that loss of lung cell lineage and gain of stem cell-like characteristics, along with mutator and immune evasion phenotypes, explain the aggressive behavior of a specific subset of lung adenocarcinoma that we called C1-LUAD, including early-stage disease. This subset can be identified using a 10-gene prognostic signature. Poor prognosis patients appear to have this specific molecular lung adenocarcinoma subtype which is characterized by peculiar molecular and biological features. Our data support the hypothesis that transformed lung stem/progenitor cells and/or reprogrammed epithelial cells with CSC characteristics are hallmarks of this aggressive disease. Such discoveries suggest alternative, more aggressive, therapeutic strategies for early-stage C1-LUAD.

COVID-19 epidemic strongly affected cancer research in Italy: a survey of the Italian Cancer Society (SIC)

Background

Italy was among the first countries hit by the pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. The application of strict lockdown measures disproportionately affected both cancer patient care as well as basic and translational cancer research.

Materials and methods

The Italian Cancer Society (SIC) conducted a survey on the effect of lockdown on laboratories involved in cancer research in Italy. The survey was completed by 570 researchers at different stages of their career, working in cancer centers, research institutes and universities from 19 Italian regions.

Results

During the lockdown period, the impact of the COVID-19 pandemic emergency on face-to-face research activities was high, with a complete (47.7%) or partial (36.1%) shutdown of the laboratories. In the post-lockdown period, research activities were resumed in most of the respondents’ institutions (80.4%), though with some restrictions (77.2%). COVID-19 testing was offered to research personnel only in ~50% of research institutions. Overall, the response to the pandemic was fragmented as in many cases institutions adopted different strategies often aimed at limiting possible infections without a clearly defined contingency plan. Nevertheless, research was able to provide the first answers and possible ways out of the pandemic, also with the contribution of many cancer researchers that sacrificed their research programs to help overcome the pandemic by offering their knowledge and technologies.

Conclusions

Given the current persistence of an emergency situation in many European countries, a more adequate organization of research centers will be urgent and necessary to ensure the continuity of laboratory activities in a safe environment.

•

The SIC conducted a survey on the effect of COVID-19 lockdown on cancer research laboratories in Italy.

•

The impact of the lockdown on research activities was high, with complete or partial shutdown of >80% of the laboratories.

•

Response to the pandemic was fragmented with different strategies adopted without a clearly defined contingency plan.

•

An adequate organization of research centers is urgently needed to ensure laboratory activities in a safe environment.

Combined analysis of miR-200 family and its significance for breast cancer

While the molecular functions of miR-200 family have been deeply investigated, a role for these miRNAs as breast cancer biomarkers remains largely unexplored. In the attempt to clarify this, we profiled the miR-200 family members expression in a large cohort of breast cancer cases with a long follow-up (H-CSS cohort) and in TCGA-BRCA cohort. Overall, miR-200 family was found upregulated in breast tumors with respect to normal breast tissues while downregulated in more aggressive breast cancer molecular subtypes (i.e. Luminal B, HER2 and triple negative), consistently with their function as repressors of the epithelial-to-mesenchymal transition (EMT). In particular miR-141-3p was found differentially expressed in breast cancer molecular subtypes in both H-CSS and TCGA-BRCA cohorts, and the combined analysis of all miR-200 family members demonstrated a slight predictive accuracy on H-CSS cancer specific survival at 12 years (survival c-statistic: 0.646; 95%CI 0.538–0.754).

Abstract 2582: Investigating the origin and function of circulating miRNA in lung cancer

MicroRNAs (miRNAs) are small, highly conserved noncoding RNA molecules involved in the regulation of gene expression. MicroRNAs are resistant to harsh conditions and stably exist in body fluids (e.g. saliva, urine, breast milk, blood). Circulating cell-free miRNAs (cf-miRNA) were shown to be effective biomarkers for the early diagnosis of cancer. Furthermore, cf-miRNA were also found in exosomes that are nano-sized extracellular vesicles which exchange molecular information among cells. However, the understanding of origin of cf-miRNAs and of biological function still remains elusive. We recently identified a signature of cf-miRNAs diagnostic for lung cancer which we now hypothesize being released by lung cancer cells (EP-cf-miRNA) and by tumor microenvironment (TME-cf-miRNA). In particular, two cf-miRNAs, miR-29a and 223-3p, were selected as prototypes of EP- and TME-cf-miRNAs for further investigations.We found that the expression of miR-223-3p was higher in TME than in cancer cells of a cohort of 19 lung adenocarcinoma. In contrast, miR-29a-3p was frequently overexpressed (≥2 fold) in cancer cells. Interestingly, the serum concentration of cf-miR-29a was lower than miR-223-3p and this also in exosomes.We next investigated the expression profile of miR-29a/223-3p in a panel of lung normal and adenocarcinoma cell lines (N=14). miR-29a/223-3p were both expressed intracellularly and in exosomes. Of note, the miR-29a expression level resembles that observed in lung cancer cells from FFPE samples. Conversely, miR-223-3p expression was lower in the adenocarcinoma cell lines which further confirm a more TME origin. We are now expanding our analysis by screening the whole set of cf-miRNAs by high-throughput qPCR profile (OpenArray technology) and by applying laser capture microdissection to investigate single cancer epithelial cells and TME. Our work provides proof of principle demonstration of an effective approach to investigate cf-miRNA origin to unravel the role of cf-miRNA in lung adenocarcinoma.

Citation Format: Tommaso Colangelo, Francesco Mazzarelli, Roberto Cuttano, Elisa Dama, Valentina Melocchi, Paolo Graziano, Fabiola Fiordelisi, Fabrizio Bianchi. Investigating the origin and function of circulating miRNA in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2582.

Abstract 1792: Exploring new therapeutic options for chemoresistant locally advanced lung cancer

Background: Non-small-cell lung cancer (NSCLC) is the leading cause of cancer-related mortality worldwide. About one third of NSCLC patients present at diagnosis with locally advanced disease (stage IIIA) which are characterized by lymph node metastases. For this group of patients, neoadjuvant chemotherapy (NACT) followed by surgery is the best therapeutic option. However, clinical response to NACT is heterogeneous including patients with a complete eradication of lymph node metastases (pN0), and patients with persistent disease (pN2). Of note, 'pN0' patients showed a favourable prognosis (~50-60% survival, at 5-year) when compared to 'pN2' patients (~20-30% survival, at 5-year).

Methods: To identify new molecular determinants involved in NACT response, we recently performed whole-microRNA expression profiling of metastatic lung tumor cells, which were collected from mediastinal lymph nodes before NACT either by endobronchial ultrasound transbronchial aspiration (EBUS-TBNA) (n=11) or mediastinoscopy (n=41). In addition, we performed a meta-analysis of a cohort (n=84) of NSCLC (i.e. The Cancer Genome Atlas LUAD and LUSC dataset) with complete follow-up.

Results: We found a set of 20 miRNAs significantly differentially expressed in pN2 vs. pN0 tumors. Hierarchical clustering analysis using this 20-miRNA set revealed a clear separation of pN0 patients from pN2 patients. However, when the 20-miRNA set was used in the primary NSCLCs from TCGA dataset, the chemoresponsive and chemoresistant tumors could not be stratified. This possibly suggests unique properties of this 20-miRNA set and their modulated target genes in metastatic cells, and in the acquisition of a chemoresistant phenotype. Furthermore, by coupling miRNA and mRNA expression profile in metastatic samples, we rewired i) cancer intrinsic gene networks with a role in chemotherapy resistance, and ii) an augmented infiltration of tumor promoting immune cell populations (TILs).

Conclusions: Lung cancer metastases are intrinsically distinct and there exist molecular subtypes with different NACT response, identifiable by miRNA expression profile. Future efforts will be directed to identify the landscape of molecular mechanisms mediated by miRNAs, including the modulation of TILs possibly involved in the acquired chemoresistance.

Citation Format: Roberto Cuttano, Elisa Dama, Valentina Melocchi, Tommaso Colangelo, Cristiano Carbonelli, Giorgia Maroni, Elena Levantini, Fabrizio Bianchi. Exploring new therapeutic options for chemoresistant locally advanced lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1792.

Abstract 3097: Investigating an aggressive molecular subtype of stage I lung adenocarcinoma: Evidences for the acquirement of stem-like and immune evasion phenotype

Lung cancer early diagnosis is effective in reducing the risk of metastatic disease and improve overall survival. However, a significant fraction of patients (~20%) with early stage disease (Stage I) experience tumor recurrence and metastatic disease. Recent advances in high-throughput genomic screening allowed an in-depth molecular profile analyses of lung cancer, with particular emphasis for the identification of prognostic gene expression signatures. Indeed, we recently described the existence of an aggressive lung adenocarcinoma (LUAD) molecular subtype (Stage I), namely C1-LUAD, with a peculiar expression and mutational profile more resembling advanced metastatic cancer. Using an integrative approach relying on computational biology and lung cancer experimental models, we now discovered that this C1-subtype is characterized by stem-like and immune evading phenotype. In particular, gene-set enrichment analysis (GSEA) revealed that ‘C1-LUAD’ tumors are enriched in stem cell (SC) expression signatures (q-value&lt;0.05). Notably, the gene network characterizing the C1-LUAD subtype was downstream to known transcriptional modulators involved in SC biology. In line with this, we found several iPS/Stem and EMT biomarkers overexpressed in C1-LUAD and in a panel of C1-LUAD-like lung cancer cells. Furthermore, forced overexpression of HOXB7 gene, a biomarker of C1-LUAD and a member of the Antp homeobox family, promotes the expansion of lung sphere-forming cells and reprogramming into iPS cells. Lastly, we performed an analysis of the Immune Subtypes and ImmunoPhenoScore in C1-LUAD tumors coupled with tumor mutational burden (TMB) and intra-tumor genetic heterogeneity (ITH) profile, which revealed: i) a predominance of the tumor permissive ‘C1 wound healing' subtype (i.e. high Th2/TAMs, low CD8+Tc); ii) a reduction of the ‘C3 inflammatory' subtype; iii) an increased ITH; and iv) a reduction of neoantigen burden. These are hallmarks of cancer immunoediting process which ultimately favor tumor cell escape. In conclusion, we identified an aggressive subtype of LUAD characterized by a stem-like and immune evasion phenotype. C1-LUAD can be identified by qPCR analysis using a panel of 10 genes, previously validated in a large cohort of FFPE samples. Our findings can contribute to improve survival of lung cancer patients by anticipating diagnosis of aggressive Stage I tumors and may pave the way for developing more effective therapeutic strategies.

Citation Format: Valentina Melocchi, Elisa Dama, Roberto Cuttano, Tommaso Colangelo, Paolo Graziano, Fabrizio Bianchi. Investigating an aggressive molecular subtype of stage I lung adenocarcinoma: Evidences for the acquirement of stem-like and immune evasion phenotype [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3097.

Deciphering the Molecular Profile of Lung Cancer: New Strategies for the Early Detection and Prognostic Stratification

Recent advances in radiological imaging and genomic analysis are profoundly changing the way to manage lung cancer patients. Screening programs which couple lung cancer risk prediction models and low-dose computed tomography (LDCT) recently showed their effectiveness in the early diagnosis of lung tumors. In addition, the emerging field of radiomics is revolutionizing the approach to handle medical images, i.e., from a “simple” visual inspection to a high-throughput analysis of hundreds of quantitative features of images which can predict prognosis and therapy response. Yet, with the advent of next-generation sequencing (NGS) and the establishment of large genomic consortia, the whole mutational and transcriptomic profile of lung cancer has been unveiled and made publicly available via web services interfaces. This has tremendously accelerated the discovery of actionable mutations, as well as the identification of cancer biomarkers, which are pivotal for development of personalized targeted therapies. In this review, we will describe recent advances in cancer biomarkers discovery for early diagnosis, prognosis, and prediction of chemotherapy response.

Sensitive and affordable diagnostic assay for the quantitative detection of anaplastic lymphoma kinase (ALK) alterations in patients with non-small cell lung cancer

Accurate detection of altered anaplastic lymphoma kinase (ALK) expression is critical for the selection of lung cancer patients eligible for ALK-targeted therapies. To overcome intrinsic limitations and discrepancies of currently available companion diagnostics for ALK, we developed a simple, affordable and objective PCR-based predictive model for the quantitative measurement of any ALK fusion as well as wild-type ALK upregulation. This method, optimized for low-quantity/-quality RNA from FFPE samples, combines cDNA pre-amplification with ad hoc generated calibration curves. All the models we derived yielded concordant predictions when applied to a cohort of 51 lung tumors, and correctly identified all 17 ALK FISH-positive and 33 of the 34 ALK FISH-negative samples. The one discrepant case was confirmed as positive by IHC, thus raising the accuracy of our test to 100%. Importantly, our method was accurate when using low amounts of input RNA (10 ng), also in FFPE samples with limited tumor cellularity (5-10%) and in FFPE cytology specimens. Thus, our test is an easily implementable diagnostic tool for the rapid, efficacious and cost-effective screening of ALK status in patients with lung cancer.

Optimization and Standardization of Circulating MicroRNA Detection for Clinical Application: The miR-Test Case

BACKGROUND

The identification of circulating microRNAs (miRNAs) in the blood has been recently exploited for the development of minimally invasive tests for the early detection of cancer. Nevertheless, the clinical transferability of such tests is uncertain due to still-insufficient standardization and optimization of methods to detect circulating miRNAs in the clinical setting.

METHODS

We performed a series of tests to optimize the quantification of serum miRNAs that compose the miR-Test, a signature for lung cancer early detection, and systematically analyzed variables that could affect the performance of the test. We took advantage of a large-scale (&gt;1000 samples) validation study of the miR-Test that we recently published, to evaluate, in clinical samples, the effects of analytical and preanalytical variables on the quantification of circulating miRNAs and the clinical output of the signature (risk score).

RESULTS

We developed a streamlined and standardized pipeline for the processing of clinical serum samples that allows the isolation and analysis of circulating miRNAs by quantitative reverse-transcription PCR, with a throughput compatible with screening trials. The major source of analytical variation came from RNA isolation from serum, which could be corrected by use of external (spike-in) or endogenous miRNAs as a reference for normalization. We also introduced standard operating procedures and QC steps to check for unspecific fluctuations that arise from the lack of standardized criteria in the collection or handling of the samples (preanalytical factors).

CONCLUSIONS

We propose our methodology as a reference for the development of clinical-grade blood tests on the basis of miRNA detection.

Abstract 1575: Serum circulating miR–Test application: Standardized protocol for miR–Test clinical application

Lung cancer is leading cause of cancer death worldwide. Being lung cancer asymptomatic in its early stages, the majority of patients are diagnosed with advanced disease. Therefore, it is vital that screening programs and novel diagnostic tools are developed to increase lung cancer early detection. The development of a minimally invasive blood-based diagnostic tool would be ideal as a first-line screening procedure. An increasing number of studies are demonstrating that fluctuations of circulating miRNAs are associated to lung cancer. Recently, we described a serum circulating miRNA signature (miR-Test) diagnostic for asymptomatic, early stage, lung cancer, that was validated in a large cohort of individuals (N = 1115) enrolled in the lung cancer screening program COSMOS (Continuous Observation of SMOking Subjects). However, the transfer to the clinic of a blood test based on circ-miRNAs requires the establishment of standardized operating procedures (SOPs), working instructions and guidelines for all pre-analytical and analytical procedures.

We identified possible sources of variability affecting circulating miRNAs, analyzed their impact on the miR-Test performance, and defined a standardized protocol to optimize miR-Test application. Analysis of all possible technical and biological variation affecting circ-miRNAs level, revealed two main sources of variability: one related to analytical procedures for miRNAs extraction and quantification, and the other due to pre-analytical conditions, on how samples are prepared. The extraction causes the main source of analytical imprecision.

In conclusion, we identified an optimal protocol for the application of miR-Test for lung cancer early diagnosis.

Citation Format: Francesca Montani, Matteo Marzi, Fabio Dezi, Elisa Dama, Rose Mary Carletti, Giulia Veronesi, Francesco Nicassio, Pier Paolo Di Fiore, Fabrizio Bianchi. Serum circulating miR–Test application: Standardized protocol for miR–Test clinical application. [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 1575. doi:10.1158/1538-7445.AM2015-1575

Abstract 1573: miR-Test: a blood test for lung cancer early detection

Background:

Lung cancer is the leading cause of cancer death worldwide. As lung cancer is asymptomatic in its early stages, the majority of patients are diagnosed with advanced disease, when the tumor is unresectable. Consequently, the survival rate is very low: 15% at 5 years. It is vital, therefore, that screening programs and novel diagnostic tools are developed, which will increase the detection of lung cancer in its early stages (stage I-II), when the tumor is still curable, to reduce lung cancer mortality. Recently, we described a serum microRNA signature diagnostic for asymptomatic, early stage, lung cancer. The availability of reliable biomarkers to identify high-risk individuals might help to reduce the size of the target population for LDCT-based programs, thereby reducing costs and probably increasing compliance

Methods:

We performed a large-scale validation study of a miRNA blood test based on our signature (the miR-Test) in a population of high-risk individuals (N = 1115) enrolled in the lung cancer screening program COSMOS (Continuous Observation of SMOking Subjects), and other 74 lung cancer patients diagnosed outside of screening.

Results:

The miR-Test showed overall accuracy, specificity and sensitivity of 75%, 78%, and 75%, respectively, with an AUC of 0.85. The test appears to have a dual origin: the first from epithelial cells (the epithelial-like component); the second from cells of hematopoietic origin (the inflammatory-like component). Of note, we found that both components are needed to maintain a good performance of the miR-Test.

Conclusions:

The relatively high sensitivity of the miR-Test in detecting asymptomatic lung cancer and its high negative predictive value (NPV &gt; 99%), confirm the effectiveness of the test, both interms of its ability to identify asymptomatic lung cancer patients and to reduce significantly unnecessary CTs on healthy individuals.

Citation Format: Francesca Montani, Matteo Jacopo Marzi, Fabio Dezi, Elisa Dama, Rose Mary Carletti, Giuseppina Bonizzi, Raffaella Bertolotti, Massimo Bellomi, Cristiano Rampinelli, Patrick Maisonneuve, Lorenzo Spaggiari, Giulia Veronesi, Francesco Nicassio, Pier Paolo Di Fiore, Fabrizio Bianchi. miR-Test: a blood test for lung cancer early detection. [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 1573. doi:10.1158/1538-7445.AM2015-1573

miR-Test: a blood test for lung cancer early detection

Lung cancer is the leading cause of cancer death worldwide. Low-dose computed tomography screening (LDCT) was recently shown to anticipate the time of diagnosis, thus reducing lung cancer mortality. However, concerns persist about the feasibility and costs of large-scale LDCT programs. Such concerns may be addressed by clearly defining the target "high-risk" population that needs to be screened by LDCT. We recently identified a serum microRNA signature (the miR-Test) that could identify the optimal target population. Here, we performed a large-scale validation study of the miR-Test in high-risk individuals (n = 1115) enrolled in the Continuous Observation of Smoking Subjects (COSMOS) lung cancer screening program. The overall accuracy, sensitivity, and specificity of the miR-Test are 74.9% (95% confidence interval [CI] = 72.2% to 77.6%), 77.8% (95% CI = 64.2% to 91.4%), and 74.8% (95% CI = 72.1% to 77.5%), respectively; the area under the curve is 0.85 (95% CI = 0.78 to 0.92). These results argue that the miR-Test might represent a useful tool for lung cancer screening in high-risk individuals.

Marriage and parenthood among childhood cancer survivors: a report from the Italian AIEOP Off-Therapy Registry

BACKGROUND

The aim of this study was to describe the patterns of marriage and parenthood in a cohort of childhood cancer survivors included in the Off-Therapy Registry maintained by the Italian Association of Pediatric Hematology and Oncology.

DESIGN AND METHODS

We analyzed a cohort of 6,044 patients diagnosed with cancer between 1960 and 1998, while aged 0 to 14 years and who were 18 years old or older by December 2003. They were followed up through the regional vital statistics registers until death or the end of follow up (October 30, 2006), whichever occurred first, and their marital status and date of birth of their children were recorded. The cumulative probabilities of being married and having a first child were computed by gender and compared by tumor type within the cohort. Marriage and fertility rates (the latter defined as the number of live births per woman-year) were compared with those of the Italian population of the same age, gender, area of residence and calendar period by means of the observed to expected (O/E) ratios.

RESULTS

During the follow-up period, 4,633 (77%) subjects had not married. The marriage O/E ratios were 0.56 (95% CI: 0.51-0.61) and 0.70 (95% CI: 0.65-0.76) among men and women, respectively. Overall, 263 men had 367 liveborn children, and 473 women had 697 liveborn children. The female fertility O/E ratio was 0.57 (95% CI: 0.53-0.62) overall, and 1.08 (95% CI: 0.99-1.17) when analyses were restricted to married/cohabiting women

CONCLUSIONS

Childhood cancer survivors are less likely to marry and to have children than the general population, confirming the life-long impact of their previous disease on their social behavior and choices. The inclusion of counseling in the strategies of management and long-term surveillance of childhood cancer patients could be beneficial to survivors as they approach adulthood.

Evaluating access to pediatric cancer care centers of children and adolescents with rare tumors in Italy: the TREP project

BACKGROUND

A national project focusing on rare malignant pediatric tumors (the TREP project) was launched in Italy in 2000. The present study compared the number of these tumors expected to be diagnosed in Italy with the number of cases actually enrolled in the TREP database in 2000-2006.

METHODS

The predicted number of cases was calculated from incidence data from the Italian network of cancer registries (AIRTum).

RESULTS

The TREP database included 336 patients under 18 years, that is, 261 children and 75 adolescents, as compared to 305 and 400 expected cases, respectively. For the 0-14 years old age-group, the ratio of observed to expected cases was 1:1 for nasopharyngeal carcinoma, adrenocortical tumors, renal cell carcinoma, and gonadal non-germ-cell tumors, while for the 15-17-year old individuals there was a statistically significant under-reporting for all tumor types.

CONCLUSIONS

Our study showed that the TREP project succeeded in registering and treating the vast majority of the patients under 15 years of age with rare pediatric tumors, demonstrating the feasibility of cooperative protocols even for rare diseases. Conversely, there was a large gap between those registered compared to those expected for adolescents.

Health-related quality of life of long-term childhood cancer survivors: a population-based study from the Childhood Cancer Registry of Piedmont, Italy

AIM OF THE STUDY

To determine the Health Related Quality of Life (HRQL) in a population-based cohort of long-term survivors of childhood cancer in Piedmont, northwestern Italy.

PATIENTS AND METHODS

During 2003, a 15-item Health Utilities Index questionnaire was mailed to 1005 5-year survivors, identified from the population-based Childhood Cancer Registry of Piedmont, to derive scores for overall HRQL and for eight single attributes of health. Score differences were estimated as adjusted prevalence odds ratios.

RESULTS

A large majority of long-term survivors had moderately high scores for overall HRQL and for each of the single attributes. Males reported better overall HRQL and less morbidity with respect to dexterity, emotion and pain than females. Survivors diagnosed when they were 10-14 years of age had better overall HRQL and less morbidity with respect to emotion, cognition and pain than younger persons. Long-term survivors of central nervous system (CNS) tumours, retinoblastoma and bone tumours had greater impairment of overall HRQL, vision, ambulation, dexterity, cognition and pain than survivors of other forms of cancer.

CONCLUSION

Many survivors of childhood cancer in Piedmont had fairly good overall HRQL. Greater probability of impaired HRQL was seen for females, survivors of CNS tumours, retinoblastoma and bone tumours, and persons diagnosed before 10 years of age.

Expected number of childhood cancers in Italy from 2001 to 2015

The total number of children with incident cancer in Italy has never been specifically estimated. Specialized population-based Childhood Cancer Registries have only been operating in Piedmont (CCRP) and in the Marche region, while general population cancer registries cover about 20% of the Italian population. The number of expected cases of childhood cancer (0-14 years) in Italy in the period 2001-2015 has been estimated using CCRP incidence rates and annual percentage changes. The expected number of cases of all cancer types were 8,132, 8,672 and 8,944 in the periods 2001-2005, 2006-2010 and 2011-2015 respectively. These figures help evaluate the allocation of resources for the care of child cancer patients in Italy, and to estimate the number of cases expected to enter clinical trials.

Late deaths among five-year survivors of childhood cancer. A population-based study in Piedmont Region, Italy

BACKGROUND AND OBJECTIVES

The aim of this study was to analyze late mortality among 5-year survivors of childhood cancer, in Piedmont (Italy), in terms of risk factors and causes of death.

DESIGN AND METHODS

From 1967 to 1999, the Childhood Cancer Registry of Piedmont recorded 3164 incident cases. Patients identified only by a death certificate (n = 59), lost to follow-up (n = 32), alive with a period of observation shorter than 5 years at the end of follow-up (n = 65) and records corresponding to a second malignant tumor during childhood (n = 9) were excluded from the analyses.

RESULTS

Within 5 years after diagnosis, 1301 children died, and among the 1698 5- year survivors, 144 children subsequently died. Among 5-year survivors, cumulative mortality percentages increased from 5.1% (95% CI 4.0-6.2) at 10 years after diagnosis to 16.0% (12.2-19.8) at 35 years. Period of diagnosis (p = 0.006), age at diagnosis (p = 0.002), and tumor type (p = 0.003) were associated with late mortality. Most deaths were related to cancer recurrence (62.2%) and treatment-related sequelae (22.4%), including second malignant neoplasms, cardiac diseases and other late effects. Compared to the general population, children included in this study had a 9-fold increased risk of overall mortality, and experienced an absolute excess of 4.4 deaths per 1000 person-years.

INTERPRETATION AND CONCLUSIONS

Among 5-year survivors, patients treated more recently (after 1979) had a statistically significant lower risk of late death than those treated earlier. However, long-term survivors still experienced higher mortality rates than those in the general population, and recurrence or progression of the primary tumor was the first cause of death.

Updating long-term childhood cancer survival trend with period and mixed analysis: Good news from population-based estimates in Italy

An empirical evaluation of long-term period survival analysis was performed using data from the Childhood Cancer Registry of Piedmont, Italy. The aim was to update survival time trends and provide 25-year projections for children currently diagnosed with cancer. The observed survival experiences up to 15 years after diagnosis of five quinquennial cohorts (cohort analysis) were compared to the corresponding estimates obtained by period analysis. The two methods generally produced very similar findings, although period analysis estimates were slightly lower than those obtained from cohort analysis. We then used mixed analysis to assess time trends in long-term survival. This showed that the probability of surviving 25 years after a cancer in childhood has more than doubled compared to cohort analysis estimates from patients diagnosed more than 25 years ago (73% vs. 32%), providing further evidence of an ongoing improvement in prognosis.

Time trends and prognostic factors for survival from childhood cancer: a report from the Childhood Cancer Registry of Piedmont (Italy)

Survival after childhood cancer has been improving since the late 1970s in most developed countries. The Childhood Cancer Registry of Piedmont has been recording malignant tumors in children (0-14 years) throughout Piedmont since 1967. The present paper is based on the records of the 2,970 children diagnosed during the period 1970-2001; survival rates are estimated up to June 30, 2004. Based on records from the Registrar Offices of the relevant towns of residence, 1,698 children were reported to be alive, 1,252 deceased, and 20 were of unknown vital status. Over the period 1970-2001, 5-year survival rates for all tumor types combined showed a statistically significant increasing trend (p<0.0001). For acute lymphocytic leukemia, the survival rate increased steadily from 24.7% (95% CI 15.0-34.3) in 1970-1974 to 87.8% (82.1-93.6) in 1995-1999. Five-year survival rates for central nervous system tumors increased from 32.8% (21.0-44.6) in 1970-1974 to 80.3% (72.6-88.0) in 1990-1994 and decreased thereafter. Age of less than 1 year at time of diagnosis was a favorable prognostic factor for neuroblastoma and ganglioneuroblastoma. The extent of disease at diagnosis was related to prognosis for neuroblastoma and ganglioneuroblastoma and other selected solid tumors. A white blood cell count greater than 50,000 x 10(6) cells/l was associated with decreased survival in children with acute lymphocytic leukemia and acute non-lymphocytic leukemia. We have found positive trends in survival for all tumor types in Piedmont, similar to those reported by other population-based cancer registries. Age, extent of disease, and white blood cell count at diagnosis are prognostic factors for selected cancer sites.

Epidemiological aspects of craniopharyngioma

Craniopharyngioma is a benign intracranial tumor that can be clinically aggressive. The descriptive epidemiology of this tumor is not fully known, in part because of its borderline nature between a benign and malignant tumor, and in part because of its rarity. It has a bimodal age distribution with a peak between 5 and 14 years of age, and a second one in adults older than 65 years. The Childhood Cancer Registry of Piedmont, Italy, estimates an incidence of 1.4 cases per million children per year. Similar data are provided by other registries in Western countries, while higher rates have been observed in Asia and Africa. There are no known specific environmental risk factors for craniopharyngioma, and genetic predisposition is not demonstrated. Survival has dramatically improved in the last years.

Life expectancy as an indicator of outcome in follow-up of population-based cancer registries: the example of childhood leukemia

BACKGROUND

Survival analysis is a standard methodology to assess progress in oncology disease treatment. However, survival analysis commonly only measures survival during the treatment period (and the period immediately afterwards), and does not provide an estimate of life expectancy, which is often of more interest to patients and to health policy makers. In this paper we propose a method to estimate childhood acute lymphoblastic leukemia (ALL) life expectancy through the integration of traditional survival analysis and life expectancy tables.

PATIENTS AND METHODS

The study included 305 incident cases registered by the Childhood Cancer Registry of Piedmont in 1979-1991. Vital status on 30 June 2004 was known for 304 cases. Survival analyses were carried out using the Kaplan-Meier method and the Gompertz model, according to the time period of diagnosis and gender.

RESULTS

Cumulative survival at 5 years increased from 58.6% (95% CI 48.9-68.3) for cases diagnosed in March 1979-July 1982 to 79.1% (95% CI 70.8-87.5) in March 1987-February 1991 (P = 0.002). Average life expectancy increased from 46.1 years for boys and 42.6 years for girls diagnosed in March 1979-July 1982 to 58.3 and 69.1, respectively, in March 1987-February 1991.

CONCLUSIONS

These analyses show an improvement over the time period of diagnosis of life expectancy for children with ALL.

[Life expectancy as an indicator of outcome]

Usually survival studies evaluate the percentage of subjects alive or disease-free at a given point in time (cumulative survival percentage). These studies require a lengthy period both for follow up and for the collection of an exhaustive number of cases. In addition, for cancer types with a sharp gradient of cumulative mortality, the estimate may be unstable. On the database of children with Acute Lymphoblastic Leukaemia (ALL) collected by the Childhood Cancer Registry of Piedmont (CCRP) in 1979-1991, we have estimated an alternative time-dimensional index to estimate both patients' life expectancy of patient and number of years gained to death. These estimates have been compared in subsets of the database corresponding to different periods of diagnosis and efficacy of treatment. Life expectancy has been evaluated as the area under the survival curve, on the assumption that after a number of years since diagnosis, survivors have the same mortality rates of the general population. Clinicians are invited to take into consideration the approach described in the present note.