Comprehensive genome profiling by next generation sequencing of circulating tumor DNA in solid tumors: a single academic institution experience

Background:

Recently, new evidence of the next-generation sequencing (NGS) liquid biopsy utility in clinical practice has been developed. This assay is emerging as a new promising tool to use as a noninvasive biomarker for cancer mutation profiling. Additional data supporting the clinical validity of cell free DNA (cfDNA) based testing is necessary to inform optimal use of these assays in the clinic.

Materials and methods:

A total of 398 cancer patients were analyzed by FoundationOne Liquid Analysis (F1LA), a genomic profiling assay and by standard NGS diagnostic ThermoFisher platform. The association between diagnostic technique was evaluated using a Poisson regression model. FoundationOne Liquid (F1L) and FoundationOne Liquid CDx (F1LCDx) detect 70 and 324 cancer-related genes alterations, respectively, including genomic signatures tumor fraction, blood tumor mutational burden (only for the 324 genes version), and microsatellite instability high status. Both assays used a single DNA extraction method to obtain cfDNA. The real-life clinical impact and feasibility of F1L and F1LCDx were evaluated across different solid tumors in our department.

Results:

Between 1 January 2019 and 28 February 2021, 398 samples of different tumor types from 398 patients were analyzed (overall success rate: 92%, in FoundationOne Liquid CDx Analysis success rate: 97%). Most frequent molecular alterations were TP53 (74), APC (40), DNMT3A (39), KRAS (23). The comprehensive clinical impact of F1LA compared with standard diagnostic was 64.7% versus 22.1% [risk ratio (RR) = 2.94; p < 0.001] and the potential clinical impact was 58.6% versus 11.0% (RR = 5.32; p < 0.001), respectively. Furthermore, some clinical cases were selected, in which F1LA detected actionable alterations offering an unexpected therapeutic choice.

Conclusions:

Although additional studies are needed to better select patients and setting, NGS F1LA is a useful, noninvasive, and repeatable assay to guide therapeutic choice in oncology. It provides a snapshot of cancer heterogeneity profile that could be incorporated in routinely clinical practice.

Immune-Based Therapy in Triple-Negative Breast Cancer: From Molecular Biology to Clinical Practice

Triple-negative breast cancer (TNBC) has been considered for many years an orphan disease in terms of therapeutic options, with conventional chemotherapy (CT) still representing the mainstay of treatment in the majority of patients. Although breast cancer (BC) has been historically considered a "cold tumor", exciting progress in the genomic field leading to the characterization of the molecular portrait and the immune profile of TNBC has opened the door to novel therapeutic strategies, including Immune Checkpoint Inhibitors (ICIs), Poly ADP-Ribose Polymerase (PARP) inhibitors and Antibody Drug Conjugates (ADCs). In particular, compared to standard CT, the immune-based approach has been demonstrated to improve progression-free survival (PFS) and overall survival (OS) in metastatic PD-L1-positive TNBC and the pathological complete response rate in the early setting, regardless of PD-L1 expression. To date, PD-L1 has been widely used as a predictor of the response to ICIs; however, many patients do not benefit from the addition of immunotherapy. Therefore, PD-L1 is not a reliable predictive biomarker of the response, and its accuracy remains controversial due to the lack of a consensus about the assay, the antibody, and the scoring system to adopt, as well as the spatial and temporal heterogeneity of the PD-L1 status. In the precision medicine era, there is an urgent need to identify more sensitive biomarkers in the BC immune oncology field other than just PD-L1 expression. Through the characterization of the tumor microenvironment (TME), the analysis of peripheral blood and the evaluation of immune gene signatures, novel potential biomarkers have been explored, such as the Tumor Mutational Burden (TMB), Microsatellite Instability/Mismatch Repair Deficiency (MSI/dMMR) status, genomic and epigenomic alterations and tumor-infiltrating lymphocytes (TILs). This review aims to summarize the recent knowledge on BC immunograms and on the biomarkers proposed to support ICI-based therapy in TNBC, as well as to provide an overview of the potential strategies to enhance the immune response in order to overcome the mechanisms of resistance.

OUP accepted manuscript

CoronaVirus disease-2019 has changed the delivery of health care worldwide and the pandemic has challenged oncologists to reorganize cancer care. Recently, progress has been made in the field of precision medicine to provide to patients with cancer the best therapeutic choice for their individual needs. In this context, the Foundation Medicine (FMI)-Liquid@Home project has emerged as a key weapon to deal with the new pandemic situation. FoundationOne Liquid Assay (F1L) is a next-generation sequences-based liquid biopsy service, able to detect 324 molecular alterations and genomic signatures, from May 2020 available at patients’ home (FMI-Liquid@Home). We analyzed time and costs saving for patients with cancer, their caregivers and National Healthcare System (NHS) with FMI-Liquid@Home versus F1L performed at our Department. Different variables have been evaluated. Between May 2020 and August 2021, 218 FMI-Liquid@Home were performed for patients with cancer in Italy. Among these, our Department performed 153 FMI-Liquid@Home with the success rate of 98% (vs. 95% for F1L in the hospital). Time saving for patients and their caregivers was 494.86 and 427.36 hours, respectively, and costs saving was 13 548.70€. Moreover, for working people these savings were 1084.71 hours and 31 239.65€, respectively. In addition, the total gain for the hospital was 163.5 hours and 6785€, whereas for NHS was 1084.71 hours and 51 573.60€, respectively. FMI-Liquid@Home service appears to be useful and convenient allowing time and costs saving for patients, caregivers, and NHS. Born during the COVID-19 pandemic, it could be integrated in oncological daily routine in the future. Therefore, additional studies are needed to better understand the overall gain and how to integrate this service in different countries.

Lobular Breast Cancer Conspicuity on Digital Breast Tomosynthesis Compared to Synthesized 2D Mammography: A Multireader Study

Objectives: To compare the conspicuity of lobular breast cancers at digital breast tomosynthesis (DBT) versus synthesized 2D mammography (synt2D). Materials and methods: Seventy-six women (mean age 61.2 years, range 50–74 years) submitted to biopsy in our institution, from 2019 to 2021, with proven invasive lobular breast cancer (ILC) were enrolled in this retrospective study. The participants underwent DBT and synt2D. Five breast radiologists, with different years of experience in breast imaging, independently assigned a conspicuity score (ordinal 6-point scale) to DBT and synt2D. Lesion conspicuity was compared, for each reader, between the synt2D overall conspicuity interpretation and DBT overall conspicuity interpretation using a Wilcoxon matched pairs test. Results: A total of 50/78 (64%) cancers were detected on both synt2D and DBT by all the readers, while 28/78 (26%) cancers where not recognized by at least one reader on synt2D. For each reader, in comparison with synt2D, DBT increased significantly the conspicuity of ILC (p < 0.0001). The raw proportion of high versus low conspicuity by modality confirmed that cancers were more likely to have high conspicuity at DBT than synt2D. Conclusions: ILCs were more likely to have high conspicuity at DBT than at synt2D, increasing the chances of the detection of ILC breast cancer.

Feasibility of next-generation sequencing in clinical practice: results of a pilot study in the Department of Precision Medicine at the University of Campania 'Luigi Vanvitelli'

Background

The emerging role of next-generation sequencing (NGS) targeted panels is revolutionising our approach to cancer patients, providing information on gene alterations helpful for diagnosis and clinical decision, in a short time and with acceptable costs.

Materials and methods

In this work, we evaluated the clinical application of FoundationOne CDx test, a hybrid capture-based NGS. This test identifies alterations in 324 genes, tumour mutational burden and genomic signatures as microsatellite instability. The decision to obtain the NGS assay for a particular patient was done according to investigator’s choice.

Results

Overall, 122 tumour specimens were analysed, of which 84 (68.85%) succeeded. The success rate was influenced by type of specimen formalin-fixed paraffin embedded (FFPE block vs FFPE slides), by origin of the sample (surgery vs biopsy) and by time of fixation (<5 years vs ≥5 years). The most frequent subgroups of effective reports derived from colorectal cancer (25 samples), non-small-cell lung cancer (16 samples), ovarian cancer (10 samples), biliary tract cancer (9 samples), breast cancer (7 samples), gastric cancer (7 samples). The most frequent alterations found in whole population referred to TP53 (45.9%), KRAS (19.6%) and APC (13.9%). Furthermore, we performed an analysis of patients in whom this comprehensive genomic profiling (CGP) had a relevance for the patient’s disease.

Conclusions

On our opinion, CGP could be proposed in clinical practice in order to select patients that could most benefit from the analysis proposed, like patients with good performance status without any available treatments or with unexpected resistance to a therapy.

Pancreatic Cancer Molecular Classifications: From Bulk Genomics to Single Cell Analysis

Pancreatic cancer represents one of the most lethal disease worldwide but still orphan of a molecularly driven therapeutic approach, although many genomic and transcriptomic classifications have been proposed over the years. Clinical heterogeneity is a hallmark of this disease, as different patients show different responses to the same therapeutic regimens. However, genomic analyses revealed quite a homogeneous disease picture, with very common mutations in four genes only (KRAS, TP53, CDKN2A, and SMAD4) and a long tail of other mutated genes, with doubtful pathogenic meaning. Even bulk transcriptomic classifications could not resolve this great heterogeneity, as many informations related to small cell populations within cancer tissue could be lost. At the same time, single cell analysis has emerged as a powerful tool to dissect intratumoral heterogeneity like never before, with possibility of generating a new disease taxonomy at unprecedented molecular resolution. In this review, we summarize the most relevant genomic, bulk and single-cell transcriptomic classifications of pancreatic cancer, and try to understand how novel technologies, like single cell analysis, could lead to novel therapeutic strategies for this highly lethal disease.

Nivolumab in Heavily Pretreated Metastatic Gastric Cancer Patients: Real-Life Data from a Western Population

PURPOSE

ATTRACTION-2 trial assessed the role of Nivolumab as a new standard treatment for Asian patients with pretreated metastatic gastric cancer (mGC). The aim of this analysis was to evaluate the safety and efficacy of Nivolumab in a real-life Western population, considering the lack of evidence to date.

PATIENTS AND METHODS

Patients progressed after ≥2 chemotherapy regimens and able to receive Nivolumab (3 mg/kg q14) were eligible for the analysis.

RESULTS

16 patients received Nivolumab as third (81.3%) or fourth line (18.7%) from September 2017 to July 2019. The safety was in line with the literature and only one patient discontinued treatment due to persistent hematological toxicity. Overall response rate and disease control rate were 18.7% and 31.2%, respectively. Median duration of response was 5 months. With a median follow-up of 21 months, median OS was 6 months (7, 21 and 22 months in the responders) and median PFS 3 months. PD-L1 and microsatellite status were retrospectively collected in 12 patients. All the major responders were MSI, although no statistically significant difference in OS or PFS was observed according to molecular analysis.

CONCLUSION

Nivolumab is feasible and effective in Western patients with mGC. Further investigation is urgently needed also in non-Asians.

Nab-paclitaxel plus gemcitabine as first line therapy in metastatic pancreatic cancer patients relapsed after gemcitabine adjuvant treatment

Nab-paclitaxel plus gemcitabine (Nab-Gem) represents one of the standard regimen for first-line treatment of metastatic pancreatic adenocarcinoma (mPDAC). However, few data are available in mPDAC relapsed after gemcitabine as adjuvant treatment. Our study aims to evaluate the efficacy and feasibility of Nab-Gem as first-line treatment for mPDAC patients previously treated with adjuvant treatment. We retrospectively analyzed the safety and efficacy data of 36 patients, who received first-line Nab-Gem after gemcitabine as adjuvant treatment. All patients received gemcitabine after radical surgery. Median disease-free survival was 12 months (95% CI 9.7-14.3); at relapse, all patients received Nab-Gem. We observed an objective response rate and disease control rate of 11.1% and 63.9%, respectively. With a median follow-up of 47 months, median progression-free survival was 5 months (95% CI 1.0-9.0), whereas median overall survival (OS) was 13 months (95% CI 5.5-20.5). Median OS was higher in patients with a relapse ≥ 7 months after the end of adjuvant treatment than in patients relapsed < 7 months (14 vs. 8 months, respectively, p: 0.52). Our results show that first-line Nab-Gem is feasible and effective in patients previously treated with gemcitabine as adjuvant treatment.

Agreement between digital breast tomosynthesis and pathologic tumour size for staging breast cancer, and comparison with standard mammography

PURPOSE

Tomosynthesis is proposed to improve breast cancer assessment and staging. We compared tomosynthesis and mammography in estimating the size of newly-diagnosed breast cancers.

METHODS

All pathologically-confirmed cancers detected in the STORM-2 trial (90 cancers, 85 women) were retrospectively measured on tomosynthesis by two independent readers. One reader also measured cancers on mammography. Relative mean differences (MDs) and 95% limits of agreement (LOA) with pathology were estimated for tomosynthesis and mammography within a single reader (Analysis 1) and between two readers (Analysis 2).

RESULTS

Where cancers were detected and hence measured by both tests, tomosynthesis overestimated pathologic size relative to mammography (Analysis 1: MD 5% versus 1%, Analysis 2: 7% versus 3%; P = 0.10 both analyses). There was similar, large measurement variability for both tests (LOA range: -60% to +166%). Overestimation by tomosynthesis was attributable to the subgroup with dense breasts (MDs = 12-13% versus 4% for mammography). There was low average bias for both tests in the low-density subgroup (MDs = 0-4%). LOA were larger in dense breasts for both tomosynthesis and mammography (P ≤ 0.02 all comparisons). Cancers detected only by tomosynthesis were more frequently in dense breasts (60-68%): for those tumours size was estimated with increased measurement variability (LOA ranging from -75% to +293%).

CONCLUSIONS

On average, tomosynthesis overestimates pathologic tumour size in women with dense breasts; that difference is more likely to impact management in women with larger tumours. The main advantage of tomosynthesis appears to be detecting mammographically-occult cancers; however tomosynthesis less accurately measured those cancers in dense breasts (large measurement variability).

Pancreatic duct abnormalities in focal autoimmune pancreatitis: MR/MRCP imaging findings

AIM

To evaluate the magnetic resonance (MR) imaging-MR cholangiopancreatographic (MRCP) findings of focal forms of autoimmune pancreatitis (AIP) to describe ductal involvement at diagnosis.

METHODS

MR examinations of 123 patients affected by AIP were analysed. We included 26 patients who satisfied International Consensus Diagnostic Criteria and were suffering from focal AIP. Image analysis included: site of parenchymal enlargement, main pancreatic duct (MPD) diameter, MPD stenosis, stricture length, presence of upstream dilation within the stricture, signal intensity, and pancreatic enhancement.

RESULTS

Signal intensity abnormalities were localized in the head in 10/26 (38.5%) and in the body-tail in 16/26 (61.5%) patients. MRCP showed a single MPD stenosis in 12/26 (46.1%) and multiple MPD stenosis in 14/26 (53.8%) patients, without a dilation of the upstream MPD (mean: 3.83 mm). Lesions showed hypointensity on T1-weighted images in all patients, and hyperintensity on T2-weighted images in 22/26 (84.6%) patients. The affected parenchyma was hypovascular during the arterial phase in 25/26 (96.2%) patients with contrast retention.

CONCLUSIONS

MR-MRCP are effective techniques for the diagnosis of AIP showing the loss of the physiological lobulation and the typical contrastographic appearance. The presence of multiple, long stenoses without an upstream MPD dilation at MRCP suggests the diagnosis of AIP, and can be useful in differential diagnosis of pancreatic adenocarcinoma.

KEY POINTS

• MRI represents the gold standard in the diagnosis of AIP. • MRCP is an increasingly useful technique in the diagnosis of focal AIP. • MRCP could be a problem-solving tool in the differential diagnosis of AIP.

Evolution of ventriculomegaly: comparison between foetal MR imaging and postnatal diagnostic imaging

PURPOSE

We evaluated the evolution of ventriculomegaly (VM) by comparing foetal magnetic resonance imaging (MRI) with postnatal transcranial ultrasonography (US) and/or encephalic MRI.

MATERIALS AND METHODS

Between January 2006 and April 2011, 70 foetuses with a mean gestational age of 28 weeks and 4 days (range, 18-36) weeks with VM on foetal MRI were assessed in this prospective study. Half-Fourier rapid acquisition with relaxation enhancement (RARE) T2-weighted, T1-weighted and diffusion-weighted (DWI) images along the three orthogonal planes according to the longitudinal axis of the mother, and subsequently of the foetal brain, were acquired. Quantitative image analysis included the transverse diameter of lateral ventricles in axial and coronal planes. Qualitative image analysis included searching for associated structural anomalies.

RESULTS

Thirty-four of 70 patients with a diagnosis of VM on foetal MRI underwent postnatal imaging. Twenty-five of those 34 (73%) had mild, four (12%) had moderate and five (15%) had severe VM on MRI. Normalisation of the diameter of lateral ventricles was observed in 16 of the 34 (47%) newborns. Among these 16, 13 (81%) had mild and three (19%) had moderate VM (two isolated and one associated VM). VM stabilisation was observed in 16 of the 34 (47%) babies. Among them, 11 (69%) had mild (eight isolated and three associated), one (6%) had moderate associated and four (25%) had severe associated VM. Progression from mild to severe (associated) VM was observed in two of the 34 (6%) babies.

CONCLUSIONS

The absence of associated anomalies and a mild VM are favourable prognostic factors in the evolution of VM.

Multifocal branch-duct intraductal papillary mucinous neoplasms (IPMNs) of the pancreas: magnetic resonance (MR) imaging pattern and evolution over time

PURPOSE

The aim of our study was to follow the evolution over time of multifocal intraductal papillary mucinous neoplasms (IPMN) of the pancreatic duct side branches by means of magnetic resonance imaging (MRI).

MATERIALS AND METHODS

A total of 155 patients with multifocal IPMN of the side branches were examined with MRI and MR cholangiopancreatography (MRI/MRCP). Inclusion criteria were patients with ≥2 dilated side branches involving any site of the parenchyma; presence of communication with the main pancreatic duct and previous investigations by MRI/MRCP within at least six months. Median follow-up was 25.8 months (range, 12-217). Patients with a follow-up period shorter than 12 months (n=33) and those with a diagnosis of multifocal IPMN of the side branches without any follow-up (n=14) were excluded from the study. The final study population thus comprised 108 patients. A double, quantitative and qualitative, analysis was carried out. The quantitative image analysis included: number of dilated side branches in the head-uncinate process and body-tail; maximum diameter of lesions in the head-uncinate process; maximum diameter in the body-tail; maximum diameter of the main pancreatic duct in the head and body-tail. The qualitative image analysis included: presence of malformations or anatomical variants of the pancreatic ductal system; site of the lesions (head-uncinate process, body-tail, ubiquitous, bridge morphology); presence of gravity-dependent intraluminal filling defects; presence of enhancing mural nodules.

RESULTS

At diagnosis, the mean number of cystic lesions of the side branches was 7.09. The mean diameter of the cystic lesions was 13.7 mm. The mean diameter of the main pancreatic duct was 3.6 mm. At follow-up, the mean number of cystic lesions was 7.76. The mean diameter of the cystic lesions was 13.9 mm. The mean diameter of the main pancreatic duct was 3.7 mm. Intraluminal filling defects in the side branches were seen in 18/108 patients (16.6%); enhancing mural nodules were seen in 3/108 patients (2.7%).

CONCLUSIONS

Multifocal IPMN of the branch ducts shows a very slow growth and evolution over time. In our study, only 3/108 patients showed mural nodules which, however, did not require any surgical procedure, indicating that careful nonoperative management may be safe and effective in asymptomatic patients.

Perfusion CT can predict tumoral grading of pancreatic adenocarcinoma

OBJECTIVES

To describe perfusion CT features of locally advanced pancreatic ductal adenocarcinoma and to evaluate correlation with tumor grading.

METHODS

Thirty-two patients with locally advanced pancreatic adenocarcinoma were included in this study. Lesions were evaluated by P-CT and biopsy after patient's informed consent. P-CT parameters have been assessed on a large single and on 6 small intratumoral ROIs. Values obtained have been compared and related to the tumor grading using Mann-Whitney U test. Sensibility, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy in predicting tumor grading have been calculated for cut-off values chosen by using ROC curves.

RESULTS

Out of 32 lesions, 12 were classified as low grade and 20 as high grade. A statistically significant difference between high and low grade neoplasms were demonstrated for PEI and BV parameters. PEI and BV cut-off values were respectively 17.8 HU and 14.8 ml/100g. PEI identified high grade neoplasms with a 65% sensitivity, 92% specificity, 93% PPV, 61% NPV and 75% accuracy. BV identified high grade neoplasms with a 80% sensitivity, 75% specificity, 84% PPV, 69% NPV, 78% accuracy. Considering both PEI and BV, P-CT identified high grade lesions with a 60% sensitivity, 100% specificity, 100% PPV, 60% NPV and 75% accuracy.

CONCLUSIONS

PEI and BV perfusion CT parameters proved their efficiency in identifying high grade pancreatic adenocarcinoma.

[Various features of neonatal outcome in assisted fertilization pregnancies]

Assisted pregnancies have been often considered as high risk pregnancies because of several factors as increased maternal age, primary sterility, pharmacological treatments, embryos and gametes manipulation in the first weeks of life. Many studies showed high rates of perinatal morbidity (especially low birth weight and prematurity), and an increase of maternal morbidity and mortality. The present study was designed to analyse correlation between morbidity and twinning rate, and to show the distribution of birth weight in a population of neonates after assisted reproductive techniques (ART). We studied 352 newborns (168 singletons, 126 twins, 42 triplets, 16 quadruplets) from assisted pregnancies; morbidity was 7.1% in singletons, 11.9% in twins, 21.4% in triplets, raising to 56.3% in quadruplets. Our experience suggests that multiple gestations after ART seem to have an increased incidence of neonatal complications.

[Congenital malformations and asymmetric crying facies]

Asymmetric crying face (ACF) means a congenital anomaly caused by either agenesis or hypoplasia of the depressor anguli oris muscle. This defect is on only one corner of the mouth since the birth, affects lower lip, and is particularly evident when the newborn is crying. Lesions at different levels of seventh nerve can cause similar and confounding weakness of the facial expressions. But, in case of ACF, forehead wrinkling, eye closure, nasolabial fold depth, and tearing are normal and symmetric functions. ACF can be either as single plain aesthetic defect or as early only index of several congenital malformations, especially of heart and genitourinary tract. Our study recognized 80 ACF cases in 11,643 newborn's population during a 34 consecutive month period: 34 on right side and 46 on left side of the mouth. ACF population presented a higher malformative risk than general population (on average 4.73% versus 3.3% of our base-line). Congenital anomalies were found more frequently associated with left ACF (3 versus 1, for a general rate of 6.52% versus 2.94%), on the same body side when anomaly was affecting pair organs. Those 3 congenital malformations were on genitourinary tract, 2 of which detected by ultrasonography. We did not find any congenital cardiac defects. According to opinion of numerous other researchers, we think ACF is not to be considered a simple aesthetic anomaly: therefore, in front of all ACF cases, a thorough search for associated anomalies should be performed.