The Impact of COVID-19 on Treatment Practices for Patients With Early Breast Cancer: A Cross-Sectional Study From a Large Cancer Center in Italy

INTRODUCTION

The Coronavirus Disease 2019 (COVID-19) has disrupted health services worldwide. The evidence on the impact of the pandemic on cancer care provision, however, is conflicting. We aimed to audit the management of patients diagnosed with early breast cancer (EBC) during the pandemic in a large, tertiary-level cancer center in Italy.

METHODS

We conducted a cross-sectional study to track the route to first treatment for patients diagnosed with EBC during 2019, 2020, and 2021. We abstracted data for all consecutive patients referred to the Veneto Institute of Oncology (Padua, Italy). We defined as point of contact (POC) the date of the first consultation with a breast cancer specialist of the breast unit. First treatment was defined as either upfront surgery or neoadjuvant chemotherapy (NACT).

RESULTS

We reviewed medical records for 878 patients for whom an MDT report during 2019-2021 (April through June) was available. Of these, 431 (49%) were eligible. The proportion of screen-detected tumors was larger in 2019 and 2021 than in 2020 (59%). Conversely, the proportion of screen-detected tumors was offset by the proportion of palpable tumors in 2020 (P = .004). Distribution of tumor and nodal stage was unchanged over time, but in situ tumors were slightly fewer in 2020 than in 2019 or 2021. The adjusted odds ratio for treatment delay (45 days or more) was 0.87 for 2020 versus 2019 (95% CI, 0.5-1.53) and 0.9 for 2021 versus 2019 (95% CI, 0.52-1.55).

CONCLUSIONS

There was no evidence for major changes in the management of patients with EBC during 2019-2021 and no treatment delays were observed. Our findings suggest that more women presented with palpable nodules at diagnosis, but the stage distribution did not change over time. Validation on a larger cohort of patients is warranted to robustly assess the impact of the COVID-19 pandemic on treatment practices for patients with EBC.

Characterization of Gut Microbiome Composition in Patients with Triple-Negative Breast Cancer Treated with Neoadjuvant Chemotherapy

INTRODUCTION

Patients with triple-negative breast cancer (TNBC) achieving a pathological complete response (pCR) after neoadjuvant chemotherapy have a better event-free survival. The role of gut microbiome in early TNBC is underexplored.

METHODS

Microbiome was analyzed by 16SrRNA sequencing.

RESULTS

Twenty-five patients with TNBC treated with neoadjuvant anthracycline/taxane-based chemotherapy were included. Fifty-six percent achieved a pCR. Fecal samples were collected before (t0), at 1 (t1), and 8 weeks (t2) from chemotherapy. Overall, 68/75 samples (90.7%) were suitable for microbiome analysis. At t0, pCR group showed a significantly higher α-diversity as compared with no-pCR, (P = .049). The PERMANOVA test on β-diversity highlighted a significant difference in terms of BMI (P = 0.039). Among patients with available matched samples at t0 and t1, no significant variation in microbiome composition was reported over time.

CONCLUSIONS

Fecal microbiome analysis in early TNBC is feasible and deserves further investigation in order to unravel its complex correlation with immunity and cancer.

Diketo acid inhibitors of nsp13 of SARS-CoV-2 block viral replication

For RNA viruses, RNA helicases have long been recognized to play critical roles during virus replication cycles, facilitating proper folding and replication of viral RNAs, therefore representing an ideal target for drug discovery. SARS-CoV-2 helicase, the non-structural protein 13 (nsp13) is a highly conserved protein among all known coronaviruses, and, at the moment, is one of the most explored viral targets to identify new possible antiviral agents. In the present study, we present six diketo acids (DKAs) as nsp13 inhibitors able to block both SARS-CoV-2 nsp13 enzymatic functions. Among them four compounds were able to inhibit viral replication in the low micromolar range, being active also on other human coronaviruses such as HCoV229E and MERS CoV. The experimental investigation of the binding mode revealed ATP-non-competitive kinetics of inhibition, not affected by substrate-displacement effect, suggesting an allosteric binding mode that was further supported by molecular modelling calculations predicting the binding into an allosteric conserved site located in the RecA2 domain.

Pan-Yellow Fever Virus Detection and Lineage Assignment by Real-Time RT-PCR and Amplicon Sequencing

Yellow fever disease is a viral zoonosis that may result in a severe hemorrhagic disease. A safe and effective vaccine used in mass immunization campaigns has allowed control and mitigation against explosive outbreaks in endemic areas. Since the 1960's, re-emergent of the yellow fever virus has been observed. The timely implementation of control measures, to avoid or contain an ongoing outbreak requires rapid specific viral detection methods. Here a novel molecular assay, expected to detect all known yellow fever virus strains, is described. The method has demonstrated high sensitivity and specificity in real-time RT-PCR as well as in an endpoint RT-PCR set-up. Sequence alignment and phylogenetic analysis reveal that the amplicon resulting from the novel method covers a genomic region whose mutational profile is completely associated to the yellow fever viral lineages. Therefore, sequencing analysis of this amplicon allows for assignment of the viral lineage.

Abstract P3-03-01: The impact of the COVID19 pandemic on treatment practices for patients diagnosed with early breast cancer: a cross-sectional study from a large comprehensive cancer centre in Italy

The impact of the COVID19 pandemic on treatment practices for patients diagnosed with early breast cancer: a cross-sectional study from a large comprehensive cancer centre in Italy.

Introduction: The Coronavirus Disease 2019 (COVID19) has disrupted health services worldwide. The evidence on the impact of the pandemic on cancer care provision, however, is conflicting. Some reports found that management for patients diagnosed with early breast cancer (EBC) during the pandemic did not differ from pre-pandemic practices; other reports suggested that delays in breast cancer surgery may have occurred. We aimed to audit the management of patients diagnosed with EBC during the pandemic in a large, tertiary-level cancer centre in Italy.

Methods: We conducted a cross-sectional study to track the route to first treatment for patients diagnosed with EBC during 2019, 2020, and 2021. We abstracted data for all consecutive patients referred to the Veneto Institute of Oncology (Padua, Italy). We defined as point of contact (POC) the date of the first consultation with a breast cancer specialist of the breast unit. We considered patients with a first POC in the 6 months preceding the multidisciplinary (MDT) meeting and initiating a treatment within 6 months from the POC. We chose the 3-month period April-June because in 2020 it was when health services were first acutely disrupted. We analysed the same period for 2019 and 2021. First treatment was defined as either upfront surgery or neoadjuvant chemotherapy (NACT). The time to first treatment was defined as the interval between the first POC and the first treatment. We used the median time to first treatment in 2019 to define the threshold for treatment delay.

Results: We reviewed medical records for 878 patients for whom an MDT report during 2019-2021 (April through June) was available. Of these, 431 (49%) were eligible: 144 in 2019, 127 in 2020 and 150 in 2021. Median age at first POC was 61 years. The proportion of screen-detected tumours was larger in 2019 and 2021 than in 2020 (59%). Conversely, the proportion of screen-detected tumours was offset by the proportion of palpable tumours in 2020 (44% versus 56%). These differences were statistically significant (chi-square test 11.12, p=0.004). Distribution of tumour and nodal stage was unchanged over time, but in-situ tumours were slightly fewer in 2020 than in 2019 or 2021. The odds ratio for treatment delay (45 days or more) was 0.87 for 2020 versus 2019 (95% CI, 0.5-1.53) and 0.9 for 2021 versus 2019 (95% CI, 0.52-1.55), after adjusting for type of POC, presentation with symptoms, treatment type, tumour stage, nodal stage, and EBC subtype (i.e., luminal, HER2-positive, triple-negative).

Conclusions: There was no evidence for major changes in the management of EBC patients during 2019-2021 and no treatment delays were observed. However, our results show a slight decrease in the absolute number of patients being treated in 2020, offset by an increase in 2021 to levels comparable to 2019. Our findings suggest that disruption of breast cancer screening programmes may have impacted on the characteristics of the patient population, with a larger proportion of women presenting with palpable nodules. Validation on a larger, population-based cohort of patients is warranted to robustly assess the impact of the COVID19 pandemic on treatment practices and outcome for EBC patients.

Characteristics of the population

Citation Format: Fabio Girardi, Sabrina Marini, Francesca Porra, Ilaria Mietto, Sonia Carpentieri, Alberto Marchet, Tania Saibene, Marcello Lo Mele, Tommaso Giarratano, Carlo Alberto Giorgi, Eleonora Mioranza, Cristina Falci, Giovanni Faggioni, Francesca Caumo, Gaia Griguolo, Maria Vittoria Dieci, Valentina Guarneri. The impact of the COVID19 pandemic on treatment practices for patients diagnosed with early breast cancer: a cross-sectional study from a large comprehensive cancer centre in Italy. [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P3-03-01.

Durability of neutralizing antibodies against yellow fever virus after vaccination in healthy adults

In accordance with the World Health Organization, one dose of yellow fever vaccine may guarantee protection lifelong in healthy adults. However, relatively little information is still available from ad hoc studies. We evaluated the persistence of neutralizing antibodies, which are considered to be an immune correlate of protection, in a large number of military personnel vaccinated up to 47 years before. Overall, 322 individuals were studied. The median time from vaccination to blood collection for neutralizing antibody evaluation was 9 years, ranging from <1 to 47 years. Of the 322 participants, 319 had neutralizing antibodies (99.1 %). The highest median PRNT₅₀ value was observed in those vaccinated ≤1 year before (median PRNT₅₀ = 320). In conclusion, our study confirms on a larger scale that, in healthy adults, neutralizing antibodies may persist as long as 47 years after a single yellow fever vaccines dose.

Real-World Clinical Outcomes of Ribociclib in Combination with a Non-Steroidal Aromatase Inhibitor and a Luteinizing Hormone-Releasing Hormone Agonist in Premenopausal HR+/HER2− Advanced Breast Cancer Patients: An Italian Managed Access Program

Ribociclib plus an aromatase inhibitor and ovarian function suppression is the preferred first-line option for pre-/perimenopausal women with hormone receptor-positive/human epidermal growth factor receptor-2-negative advanced or metastatic breast cancer. We opened an italian managed access program (MAP) that permitted access to ribociclib to selected patients and allowed to collect informative results on the clinical impact of the therapy. The MAP (April 2018–May 2020) included 64 premenopausal patients, with characteristics similar to those of the MONALEESA-7 trial. Of 57 patients with a known response, 48 (84.2%) achieved a clinical benefit (i.e., complete response, N = 7 (12.3%); partial response, N = 17 (29.8%); stable disease, N = 24 (42.1%)), while 9 (15.8%) experienced tumor progression. Some patients (N = 15–23.4%) needed ribociclib dose reduction because of adverse events. Thereafter, the treatment was well tolerated, and no new safety signals emerged. Our study is the first reported Italian real-world evidence of ribociclib effectiveness in premenopausal HR+/HER2− advanced breast cancer patients. Response and clinical benefit rates were particularly encouraging compared with those of the ribociclib group of MONALEESA-7. Our work confirms that ribociclib in combination with endocrine therapy is highly effective in the treatment of premenopausal HR+/HER2− advanced breast cancer patients with an expected safety profile.

Rapid inactivation of SARS-CoV-2 with LED irradiation of visible spectrum wavelengths

Difficulty in controlling SARS-CoV-2 transmission made the ability to inactivate viruses in aerosols and fomites to be an important and attractive risk reduction measure. Evidence that light frequencies have the ability to inhibit microorganisms has already been reported by many studies which, however, focused on ultraviolet (UV) wavelengths, which are known to induce potential injury in humans. In the present study, the effect on suspensions of SARS-CoV-2 of a Light Emitting Diode (LED) device capable of radiating frequencies in the non-hazardous visible light spectrum (VIS) was investigated. In order to evaluate the efficiency of viral inactivation, plaque assay and western blot of viral proteins were performed. The observed results showed a significant reduction in infectious particles that had been exposed to the LED irradiation of visible light. Furthermore, the analysis of the intracellular expression of viral proteins confirmed the inactivating effect of this irradiation technology. This in vitro study revealed for the first time the inactivation of SARS-CoV-2 through LED irradiation with multiple wavelengths of the visible spectrum. However additional and more in-depth studies can aim to demonstrate the data obtained during these experiments in different matrices, in mutable environmental conditions and on other respiratory viruses such as the influenza virus. The type of LED technology can decisively contribute on reducing virus transmission through the continuous sanitation of common environments without risks for humans and animals.

Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus

A high-quality dataset of 3289 complete SARS-CoV-2 genomes collected in Europe and European Economic Area (EAA) in the early phase of the first wave of the pandemic was analyzed. Among all single nucleotide mutations, 41 had a frequency ≥ 1%, and the phylogenetic analysis showed at least 6 clusters with a specific mutational profile. These clusters were differentially distributed in the EU/EEA, showing a statistically significant association with the geographic origin. The analysis highlighted that the mutations C¹⁴⁴⁰⁸T and C¹⁴⁸⁰⁵T played an important role in clusters selection and further virus spread. Moreover, the molecular analysis suggests that the SARS-CoV-2 strain responsible for the first Italian confirmed COVID-19 case was already circulating outside the country.

Prognostic factors in phyllodes tumours of the breast: retrospective study on 166 consecutive cases

BACKGROUND

Phyllodes tumours (PTs) are rare fibroepithelial tumours accounting for <1% of all breast tumours. We assessed clinicopathological features and their prognostic effect in a single-institution patients' cohort.

METHODS

Patients diagnosed with PT between 2001 and 2018 at our institution were identified. Clinical, surgical and pathological features were collected. Phyllodes-related relapse was defined as locoregional or distant recurrence (contralateral excluded), whichever first.

RESULTS

A total of 166 patients were included: 115 with benign, 30 with borderline and 21 with malignant PTs. Features associated with malignant PT were younger age, larger T size, higher mitotic count, marked cytological atypia, stromal overgrowth, stromal hypercellularity, necrosis and heterologous differentiation (all p<0.01). The majority of patients with malignant PT underwent mastectomy (63.2% vs 3% of benign/borderline, p<0.001) and had negative surgical margins (83.3%). 4-year cumulative phyllodes-related relapse incidence was 7% for benign/borderline PT and 21.3% for malignant PT (p=0.107). In the entire cohort, marked cellular atypia and heterologous differentiation were associated with worse phyllodes-related relapse-free survival (HR 14.10, p=0.036 for marked vs mild atypia; HR 4.21, p=0.031 for heterologous differentiation present vs absent). For patients with benign PT, larger tumour size was associated with worse phyllodes-related relapse-free survival (HR 9.67, p=0.013 for T>5 cm vs T≤2 cm). Higher tumour-infiltrating lymphocytes (TILs) were associated with borderline and malignant PT (p=0.023); TILs were not associated with phyllodes-related relapse-free survival (HR 0.58, p=0.361 for TILs>2% vs≤2%). Overall, four patients died because of PT: three patients with malignant and one with borderline PT.

CONCLUSIONS

Patients with malignant PT had increased rates of phyllodes-related relapse and phyllodes-related death. Cellular atypia and heterologous differentiation were poor prognostic factors in the entire cohort; large tumour size was associated with an increased risk of phyllodes-related relapse in benign PT.

ESR1 Gene Mutation in Hormone Receptor-Positive HER2-Negative Metastatic Breast Cancer Patients: Concordance Between Tumor Tissue and Circulating Tumor DNA Analysis

Endocrine therapy represents the cornerstone of treatment in hormone receptor-positive (HR+), HER2-negative metastatic breast cancer (mBC). The natural course of this disease is marked by endocrine resistance, mainly due to Estrogen Receptor 1 (ESR1) acquired mutations. The aim of this study is to evaluate the concordance between ESR1 status in metastatic tumor specimens and matched circulating tumor DNA (ctDNA). Forty-three patients with HR+, HER2-negative mBC underwent both a metastatic tumor biopsy and a liquid biopsy at the time of disease progression. DNA extracted from formalin fixed paraffin embedded (FFPE) tumor specimens and ctDNA from matched plasma were analyzed by droplet digital (dd)PCR for the main ESR1 mutations (Y537S, Y537C, Y537N, D538G, E380Q). We observed a total mutation rate of 21%. We found six mutations on tissue biopsy: Y537S (1), D538G (2), Y537N (1), E380Q (2). Three patients with no mutations in tumor tissue had mutations detected in ctDNA. The total concordance rate between ESR1 status on tumor tissue and plasma was 91%. Our results confirm the potential role of liquid biopsy as a non-invasive alternative to tissue biopsy for ESR1 mutation assessment in mBC patients.

Abstract OT-32-01: A phase 2, open-label study of bintrafusp alfa monotherapy in patients with HMGA2-expressing triple-negative breast cancer

Background: Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer with few targeted treatment options and a poor prognosis. Despite approvals of the anti-PD-L1 monoclonal antibody (mAb) atezolizumab in combination with nab-paclitaxel for unresectable, locally advanced/metastatic TNBC that expresses PD-L1 (tumor-infiltrating immune cells ≥1% of tumor area), many recent studies of other anti-PD-(L)1 therapies in advanced TNBC have shown limited efficacy, likely due to intrinsic therapeutic resistance. Transforming growth factor β (TGF-β), which promotes cancer progression by inducing angiogenesis, fibrosis, and epithelial-mesenchymal transition (EMT), may attenuate the efficacy of or promote resistance to anti-PD-(L)1 therapies. Bintrafusp alfa is a first-in-class bifunctional fusion protein composed of the extracellular domain of the TGF-βRII receptor (a TGF-β “trap”) fused to a human IgG1 mAb blocking PD-L1. In a cohort of 33 patients with heavily pretreated, advanced TNBC that progressed during/after first-line therapy, bintrafusp alfa was safe and resulted in antitumor activity (NCT02517398). Exploratory biomarker analysis showed that high mobility group AT-hook 2 (HMGA2) expression was 32-fold higher in tumor samples from patients who experienced disease control than from patients who had progressive disease in that cohort. Elevated expression of HMGA2, a protein associated with TGF-β signaling and a known regulator of EMT, is associated with metastasis and poor survival in breast cancer. We present the study design of a phase 2 trial to evaluate the efficacy and safety of bintrafusp alfa in patients with pretreated metastatic TNBC that expresses high levels of HMGA2. Trial Design: This phase 2, multicenter, open-label study will evaluate bintrafusp alfa monotherapy in patients with HMGA2-expressing TNBC that progressed on ≥1 line of systemic therapy for their metastatic disease. Patients will receive bintrafusp alfa 1200 mg every 2 weeks until confirmed progression, unacceptable toxicity, or trial withdrawal. Eligibility Criteria: Patients must have histologically confirmed TNBC defined by ASCO-CAP guidelines (estrogen receptor: immunohistochemistry [IHC] &lt;1%; progesterone receptor: IHC &lt;1%; human epidermal growth factor receptor 2: in situ hybridization nonamplified or IHC 0/1), high tumor HMGA2 expression, ECOG performance status ≤1, and measurable disease by RECIST 1.1. Patients must have experienced disease progression while receiving the most recent therapy prior to enrollment. HMGA2 expression will be centrally determined on archival or fresh tumor tissue by RT-PCR. Prescreening for HMGA2 expression while receiving preceding treatment is allowed; a fresh tumor biopsy prior to study entry may be requested for exploratory biomarker analysis. Patients with prior exposure to immunotherapy are not eligible. Specific Aims: The primary endpoint is independent review committee-assessed objective response rate per RECIST 1.1. Key secondary endpoints include safety, duration of response, durable response rate, progression-free survival, and overall survival. Additional exploratory biomarker characteristics will also be investigated. Statistical Methods: Descriptive statistics, including mean, median, standard deviation, and range, will be used to characterize continuous variables. Frequency counts and percentages will be used to characterize categorical variables. Accrual: Planned enrollment is 29 patients. Contact Information: Leisha A. Emens, MD, PhD Email: emensla@upmc.edu

Citation Format: Leisha A Emens, Margaret E. Gatti-Mays, Joyce O’Shaughnessy, Luc Dirix, Giovanni Faggioni, Andrea Fontana, Jerome Martin-Babau, Christoph Helwig, Alice Huang, Riham Iadevaia, Laureen S Ojalvo. A phase 2, open-label study of bintrafusp alfa monotherapy in patients with HMGA2-expressing triple-negative breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr OT-32-01.

Magnetic beads combined with carbon black-based screen-printed electrodes for COVID-19: A reliable and miniaturized electrochemical immunosensor for SARS-CoV-2 detection in saliva

The diffusion of novel SARS-CoV-2 coronavirus over the world generated COVID-19 pandemic event as reported by World Health Organization on March 2020. The huge issue is the high infectivity and the absence of vaccine and customised drugs allowing for hard management of this outbreak, thus a rapid and on site analysis is a need to contain the spread of COVID-19. Herein, we developed an electrochemical immunoassay for rapid and smart detection of SARS-CoV-2 coronavirus in saliva. The electrochemical assay was conceived for Spike (S) protein or Nucleocapsid (N) protein detection using magnetic beads as support of immunological chain and secondary antibody with alkaline phosphatase as immunological label. The enzymatic by-product 1-naphtol was detected using screen-printed electrodes modified with carbon black nanomaterial. The analytical features of the electrochemical immunoassay were evaluated using the standard solution of S and N protein in buffer solution and untreated saliva with a detection limit equal to 19 ng/mL and 8 ng/mL in untreated saliva, respectively for S and N protein. Its effectiveness was assessed using cultured virus in biosafety level 3 and in saliva clinical samples comparing the data using the nasopharyngeal swab specimens tested with Real-Time PCR. The agreement of the data, the low detection limit achieved, the rapid analysis (30 min), the miniaturization, and portability of the instrument combined with the easiness to use and no-invasive sampling, confer to this analytical tool high potentiality for market entry as the first highly sensitive electrochemical immunoassay for SARS-CoV-2 detection in untreated saliva.

Synchronous and Metachronous Breast and Ovarian Cancer: Experience From Two Large Cancer Center

Purpose

We aimed to evaluate the clinico-pathological characteristics and survival outcomes of patients with synchronous or metachronous breast cancer (BC) and ovarian cancer (OC).

Materials and Methods

Patients with synchronous or metachronous BC and OC were retrospectively identified at two large cancer centers. Clinico-pathological characteristics, BRCA1/2 status and follow-up data were gathered. Patients were classified according to the first cancer diagnosis in the following groups: Breast Cancer first, Ovarian Cancer first, Synchronous Breast and Ovarian Cancer. Overall survival (OS) was calculated as the time interval between each cancer diagnosis to death or last follow-up.

Results

Overall, 270 patients were included: n = 194 (72%) in BC first group, n = 51 (19%) in OC first, and n = 25 (9%) in synchronous. BRCA status was available for 182 (67.4%) patients and 112 (62%) harbored pathogenetic mutations. BC first group included more frequently patients with BRCA mutation, triple negative BC phenotype and more aggressive OC features. Median time between the two diagnosis was longer in BC first group vs OC first group (95 vs 68 months, p = 0.021). A total of 105 OS events occurred, mostly related to OC (70.5%). We observed no differences in terms of OS according to the first cancer diagnosis. Age >50 years and advanced OC stage were negative independent prognostic factors for OS from the first diagnosis.

Conclusions

In this cohort of patients with BC and OC, survival was dominated by OC related mortality. These data may be useful to plan and carry out adequate and timely surveillance programs and preventive measures.

Validation of Residual Proliferative Cancer Burden as a Predictor of Long-Term Outcome Following Neoadjuvant Chemotherapy in Patients with Hormone Receptor-Positive/Human Epidermal Growth Receptor 2-Negative Breast Cancer

Background

The integration of residual cancer burden (RCB) and post‐treatment Ki67 as residual proliferative cancer burden (RPCB) has been proposed as a stronger predictor of long‐term outcome in unselected patients with breast cancer (BC) undergoing neoadjuvant chemotherapy (NACT), as compared with RCB. However, no specific analysis in hormone‐receptor‐positive (HR+) human epidermal growth receptor 2‐negative (HER2−) BC is available so far.

Materials and Methods

A cohort of 130 patients with HR+/HER2− BC who underwent NACT between 2000 and 2014 was included. Archival surgical specimens were evaluated for RCB. RPCB was calculated by combining RCB and Ki67 as previously described. Patients were categorized in four RCB and RPCB categories (pathological complete response and tertiles). Disease‐free survival (DFS) and overall survival (OS) estimates were determined by Kaplan‐Meier analysis and compared using the log‐rank test. Overall change of χ² and c‐indexes were used to compare the performance of the prognostic models.

Results

RPCB was calculated for 85 patients. After a median follow up of 8.5 years, RCB was associated with OS (p = .048) but not with DFS (p = .152); RPCB was instead significantly associated with both DFS and OS (p = .034 and p < .001, respectively). In terms of OS, RPCB provided a significant amount of prognostic information beyond RCB (∆χ² 5.73, p < .001). In addition, c‐index for OS prediction was significantly higher for RPCB as compared with RCB (0.79 vs. 0.61, p = .03).

Conclusion

This is the first study evaluating RPCB in patients with HR+/HER2− BC treated with NACT. In this independent cohort, RPCB was a strong predictor of DFS and OS. The better performance of RPCB versus RCB was in part due to the ability of RPCB to discriminate a subgroup of patients with a particularly worse prognosis after NACT, who may be candidates for clinical trials evaluating novel adjuvant strategies.

Implications for Practice

The present work validated residual proliferative cancer burden (RPCB) as a strong predictor of long‐term outcome in patients with hormone receptor‐positive human epidermal growth receptor 2‐negative (HR+/HER2−) breast cancer (BC) treated with neoadjuvant chemotherapy. In addition, results from the present study suggest RPCB as a promising tool to identify patients with HR+/HER2− BC who might potentially benefit from the inclusion in clinical trials evaluating novel or escalated postneoadjuvant treatment strategies because it allowed to discriminate a subgroup of patients with particularly poor prognosis despite having received subsequent endocrine therapy in the adjuvant setting.

This article reports on the prognostic value of the Residual Proliferative Cancer Burden index in a cohort of patients with HR‐positive HER2‐negative breast cancer undergoing neoadjuvant chemotherapy.

Whole genome and phylogenetic analysis of two SARS-CoV-2 strains isolated in Italy in January and February 2020: additional clues on multiple introductions and further circulation in Europe

Whole genome sequences of SARS-CoV-2 obtained from two patients, a Chinese tourist visiting Rome and an Italian, were compared with sequences from Europe and elsewhere. In a phylogenetic tree, the Italian patient’s sequence clustered with sequences from Germany while the tourist’s sequence clustered with other European sequences. Some additional European sequences in the tree segregated outside the two clusters containing the patients’ sequences. This suggests multiple SARS-CoV-2 introductions in Europe or virus evolution during circulation.

Coronavirus disease (COVID-19) in a paucisymptomatic patient: epidemiological and clinical challenge in settings with limited community transmission, Italy, February 2020

Data concerning the transmission of the novel severe acute respiratory syndrome coronavirus (SARS-CoV-2) in paucisymptomatic patients are lacking. We report an Italian paucisymptomatic case of coronavirus disease 2019 with multiple biological samples positive for SARS-CoV-2. This case was detected using the World Health Organization protocol on cases and contact investigation. Current discharge criteria and the impact of extra-pulmonary SARS-CoV-2 samples are discussed.

Use of scalp cooling device to prevent alopecia for early breast cancer patients receiving chemotherapy: A prospective study

Chemotherapy-induced alopecia (CIA) affects the majority of patients receiving chemotherapy (CT) for early breast cancer. It is a highly distressing side effect of CT, with psychological and social impact. Primary aim of the present analysis was to assess the efficacy of scalp cooling with DigniCap® in preventing CIA. Success rate was defined as patients' self-reported hair loss <50% according to Dean scale. In this analysis, we reported success rate at 3 weeks after the first CT course and at 3 weeks after the last CT course. Secondary endpoints included self-reported tolerability and patients' judgment on scalp cooling performance. Consecutive early breast cancer patients admitted to Istituto Oncologico Veneto who were recommended to receive neoadjuvant or adjuvant CT, were eligible to undergo scalp cooling during the CT administration within this study. 135 patients were included: 74% received adjuvant CT and 26% neoadjuvant CT (P < .001). The type of CT was: docetaxel-cyclophosphamide (26%), paclitaxel (23%), epirubicin-cyclophosphamide followed by paclitaxel (32%), and paclitaxel followed by epirubicincyclophosphamide (19%). The rate of success in preventing alopecia was 77% (104/135) at 3 weeks from the start of CT and 60% (81/135) at 3 weeks from the end of treatment. Higher success rates were reported in non-anthracycline (71%) compared to anthracycline-containing CT regimens (54%; P < 0.001). Premature discontinuation of scalp cooling was reported in 29/135 patients (21.5%), including withdrawal for alopecia (16/29), for low scalp cooling tolerability (8/29) or both (5/29). Scalp cooling was generally well tolerated. These results overall suggest that the use of scalp cooling is effective in preventing alopecia in the majority of early breast cancer patients receiving neoadjuvant or adjuvant CT, especially for patients undergoing a taxane-based non-anthracycline regimen.

Androgen Receptor Expression and Association With Distant Disease-Free Survival in Triple Negative Breast Cancer: Analysis of 263 Patients Treated With Standard Therapy for Stage I-III Disease

Background: We evaluated immunohistochemical AR expression and correlation with prognosis in a large series of homogeneously treated patients with primary TNBC.

Material and Methods: Patients diagnosed with stage I-III TNBC between 2000 and 2015 at Istituto Oncologico Veneto who received treatment with surgery and neoadjuvant and/or adjuvant chemotherapy were included. Whole tissue slides were stained for AR. AR-positive expression was defined as >1% of positively stained tumor cells. Distant-disease-free survival (DDFS) was calculated from diagnosis to distant relapse or death. Late-DDFS was calculated from the landmark of 3 years after diagnosis until distant relapse or death.

Results: We included 263 primary TNBC patients. Mean AR expression was 14% (range 0–100%), and 29.7% (n = 78) of patients were AR+. AR+ vs. AR- cases presented more frequently older age (p < 0.001), non-ductal histology (p < 0.001), G1-G2 (p = 0.003), lower Ki67 (p < 0.001) and lower TILs (p = 0.008). At a median follow up of 81 months, 23.6% of patients experienced a DDFS event: 33.3% of AR+ and 19.5% of AR- patients (p = 0.015). 5 years DDFS rates were 67.2% and 80.6% for AR+ and AR- patients (HR = 1.82 95%CI 1.10–3.02, p = 0.020). AR maintained an independent prognostic role beyond stage, but when TILs were added to the model only stage and TILs were independent prognostic factors. AR was the only factor significantly associated with late-DDFS: 16.4% of AR+ and 3.4% of AR- patients experienced a DDFS after the landmark of 3 years after diagnosis (p = 0.001). Late-DDFS rates at 5 years from the 3-year landmark were 75.8% for AR+ and 95.2% for AR- patients (log-rank p < 0.001; HR = 5.67, 95%CI 1.90–16.94, p = 0.002).

Conclusions: AR expression is associated with worse outcome for patients with TNBC. In particular, AR+ TNBC patients are at increased risk of late DDFS events. These results reinforce the rationale of AR targeting in AR+ TNBC.

Abstract P6-18-24: Lapatinib-based therapies after pertuzumab and/or T-DM1 for HER2+ metastatic breast cancer patients

Background:

Trastuzumab + pertuzumab + taxane and ado-trastuzumab emtansine (T-DM1) are standard first and second-line therapies for HER2+ metastatic breast cancer. Lapatinib is approved in combination with capecitabine in trastuzumab-resistant patients and in combination with letrozole in hormone receptor positive HER2+ pts for whom endocrine treatment is indicated. In Italy, L is also approved in combination with trastuzumab for hormone receptor-negative HER2+ pts. There are only few data on the activity of lapatinib in pts who received prior pertuzumab and /or T-DM1.

Methods: We retrospectively analysed HER2+ metastatic breast cancer pts who received lapatinib after prior pertuzumab and/or T-DM1 from July 2013 to June 2018. Objective response rate (ORR) was assessed according to RECIST 1.1. Progression-free survival (PFS) was calculated from lapatinib-based therapy starting to disease progression (PD) or last follow-up. Overall Survival (OS) was calculated from lapatinib-based therapy starting to death or last follow up.

Results: Data from 32 HER2+ mBC treated with lapatinib-based therapy were recorded: 30 pts (94%) received lapatinib combined with capecitabine, 1 pt received lapatinib combined with letrozole and 1 pt received lapatinib combined with trastuzumab. All patients had been treated with prior T-DM1 and 9 (28%) with prior pertuzumab for metastatic breast cancer. Setting of treatment with lapatinib-based therapy was: 2° line (n=2, 6%), 3° line (n=17, 53%) and &gt;4° line (n=13, 41%).

Patients characteristics were as follows: median age 55 years (range 35-71), hormone receptor positive 66% (n=21), stage IV at diagnosis 34% (n=11), visceral involvement at lapatinib-based therapy starting 91% (n=29).

As of June 2018, lapatinib-based therapy was ongoing for 4 pts and 28 pts discontinued treatment due to disease progression (median number of courses for these pts was 8.5, range 2-27).

ORR in evaluable pts was: complete response (n=1, 3%), partial response (n=13, 41%), stable disease (n=9, 28%), disease progression (n=9, 28%). Median PFS was 6.4 months (95% CI 3.0-9.8). As of June 2018, 14 pts (44%) were alive, median OS was 11.8 months (95% CI 9.9-13.6).

Conclusion: These results confirm that lapatinib-based therapy retains clinical efficacy in HER2+ metastatic breast cancer pts treated with prior pertuzumab and/or T-DM1 and represents a valid therapeutic option in this setting.

Citation Format: Frezzini S, Giarratano T, Dieci MV, Giorgi CA, Griguolo G, Vernaci G, Menichetti A, Mantiero M, Tasca G, Faggioni G, Falci C, Miglietta F, Mioranza E, Angelini S, Ghiotto C, Conte P, Guarneri V. Lapatinib-based therapies after pertuzumab and/or T-DM1 for HER2+ metastatic breast cancer patients [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P6-18-24.

The Italian 2017 Outbreak Chikungunya Virus Belongs to an Emerging Aedes albopictus-Adapted Virus Cluster Introduced From the Indian Subcontinent

Background

Chikungunya virus is an emerging mosquito-borne pathogen with a wide global distribution. With the severe morbidity that it causes, chikungunya virus is a major public health problem in the affected areas and poses a considerable risk for unaffected areas hosting competent vector populations. In the summer of 2017, Italy experienced a chikungunya virus outbreak that spread in the Lazio region and caused a secondary outbreak in the Calabrian village of Guardavalle, with a final case number of 436. The causative strain was recognized as an Indian Ocean lineage (IOL) virus.

Methods

To understand the underlying genetic and molecular features of the outbreak virus, viruses from mosquito pools and clinical samples were isolated in cell culture and subjected to whole-genome sequencing and genetic analyses.

Results

All 8 characterized genomes shared a high sequence identity. A distinct substitution pattern in the Italian 2017 viruses (including mutations in E1, E2, and nsP4) was partly shared with the Pakistani 2016 outbreak viruses. Evolutionary analyses indicate that these 2 recent outbreaks and several geographically widely distributed, travel-associated viruses form a cluster of rapidly emerging Indian-origin IOL viruses.

Conclusions

Our analyses show that the 2017 Italian outbreak virus belongs to a cluster of novel IOL chikungunya viruses originating in India. Their emergence calls for enhanced monitoring and strengthened preparedness measures, including vector control programs and raised awareness among general practitioners in countries potentially at risk.

Patterns of Fertility Preservation and Pregnancy Outcome After Breast Cancer at a Large Comprehensive Cancer Center

Background: In the last decades, long-term outcomes of breast cancer (BC) patients have improved, raising new survivorship issues, including fertility preservation and safety of pregnancy after BC. This study assesses evolution in patterns of fertility discussion/preservation over time and reports pregnancy outcomes in a cohort of young BC patients.

Methods: A retrospective cohort of 590 BC patients aged ≤40 diagnosed between 2000 and 2016 at a large cancer center was identified. Fertility counseling and preservation patterns for patients receiving chemotherapy were analyzed and compared for two cohorts: 2004–2006 and 2014–2016 (total n = 161). Outcomes were reported for patients with documented pregnancy after BC.

Results: Significantly, more patients diagnosed in 2014–2016 had evidence of discussion on fertility issues and/or application of fertility preservation techniques versus patients diagnosed in 2004–2006 (82.9% vs. 66.0%, p = 0.017). In particular, there was a significant difference in rate of documented fertility issues discussion (67.6% vs. 34.0%, p < 0.001). Age >35 and parity were associated with lower rates of fertility discussion/preservation. However, rates significantly improved over time (77.6% in 2014–2016 vs. 58.1% in 2004–2006 for patients aged >35, p = 0.046; 80.7% in 2014–2016 vs. 57.6% in 2004–2006 for patients with children at diagnosis, p = 0.018). Twenty-six patients with pregnancy after BC were identified; eight delivered at the age of >40. No complications for women or newborns were reported. Only two patients experienced BC relapse.

Conclusions: In this small retrospective cohort, no safety concerns were identified for pregnancy after BC. The importance attributed by clinicians to address fertility issues has increased over time.

Prevalence of Usutu and West Nile virus antibodies in human sera, Modena, Italy, 2012

A collection of 3069 human sera collected in the area of the municipality of Modena, Emilia Romagna, Italy, was retrospectively investigated for specific antibodies against Usutu (USUV) and West Nile viruses (WNV). All the samples resulting positive using a preliminary screening test were analyzed with the plaque reduction neutralization test. Overall, 24 sera were confirmed as positive for USUV (0.78%) and 13 for WNV (0.42%). The results suggest that in 2012, USUV was circulating more than WNV in North-eastern Italy.

Molecular evidence of Plasmodium vivax infection in Duffy negative symptomatic individuals from Dschang, West Cameroon

Background

Plasmodium vivax infection is known to be rare in West/Central Africa, the most accepted explanation being the lack of expression of erythroid Duffy antigen in the local human populations. Duffy negativity prevents the parasite to exploit the entry mechanism on the red blood cell surface. However, there are a growing number of reported vivax infections in Duffy-negative individuals. Data on P. vivax circulation in Cameroon are limited. The aim of the study was to evaluate the P. vivax presence, and its association with the Duffy genotype in West Cameroon.

Results

Overall, 484 blood samples were collected consecutively from febrile outpatients attending the Dschang’s Hospital (West Cameroon) during a 3-months period. Plasmodium vivax infection was detected by PCR in 5.6% (n = 27/484) of the cases, representing 38.6% (n = 27/70) of all Plasmodium infections detected. All P. vivax infected individuals showed a Duffy-negative genotype, and the frequency of Duffy-positive individuals in the whole tested population was 1.7%.

Conclusions

The results of this study confirm the circulation of P. vivax in Cameroon, as well as that the lack of expression of Duffy-antigen does not confer full protection against vivax malaria acquisition.

Co-circulation of Dengue and Chikungunya Viruses, Al Hudaydah, Yemen, 2012

We investigated 400 cases of dengue-like illness in persons hospitalized during an outbreak in Al Hudaydah, Yemen, in 2012. Overall, 116 dengue and 49 chikungunya cases were diagnosed. Dengue virus type 2 was the predominant serotype. The co-circulation of these viruses indicates that mosquitoborne infections represent a public health threat in Yemen.

Natural humoral immune response to ribosomal P0 protein in colorectal cancer patients

Background

Tumor associated antigens are useful in colorectal cancer (CRC) management. The ribosomal P proteins (P0, P1, P2) play an important role in protein synthesis and tumor formation. The immunogenicity of the ribosomal P0 protein in head and neck, in breast and prostate cancer patients and the overexpression of the carboxyl-terminal P0 epitope (C-22 P0) in some tumors were reported.

Methods

Sera from 72 colorectal tumor patients (67 malignant and 5 benign tumors) were compared with 73 healthy donor sera for the presence of antibodies to CEA, EGFR, ErbB2 and ribosomal P proteins by western blotting or ELISA. Expression of the C-22 P0 epitope on tissues and colon cancer cells was determined by immunoperoxidase staining and indirect immunofluorescence/western blotting, respectively, employing MAb 2B2. Biological effects of MAb 2B2 on colon cancer cells were assessed by the Sulforhodamine B cell proliferation assay, trypan blue exclusion test and cleaved caspase-3 detection. Fisher’s exact test was used to compare the number of auto-antibodies positive patients with healthy donors. Variation in the C-22 P0 expression, and in the number of apoptotic cells was evaluated by Student’s t-test. Variation in cell survival and cell death was evaluated by Newman-Keuls test.

Results

No significant humoral response was observed to CEA, EGFR and ErbB2 in CRC patients. Conversely, 7 out of 67 CRC patient sera reacted to ribosomal P proteins. The prevalence of P proteins auto-antibodies in CRC patients was significant. Five patients showed restricted P0 immunoreactivity, while two patients reacted simultaneously to all P proteins. The C-22 P0 epitope was homogenously expressed both in malignant tumors and the adjacent mucosa, but the intensity of expression was higher in the tumor. Starved colon cancer cells showed a higher C-22 P0 epitope plasma membrane expression compared to control cells. MAb 2B2 inhibited colon cancer cell growth and induced cell death in a dose dependent manner.

Conclusions

Our study shows a spontaneous humoral immune response to ribosomal P0 protein in CRC patients and the inhibition of in vitro cancer cell growth after C-22 P0 epitope targeting. The ribosomal P0 protein might be a useful immunological target in CRC patients.

Phylogeny of Dengue and Chikungunya viruses in Al Hudayda governorate, Yemen

Yemen, which is located in the southwestern end of the Arabian Peninsula, is one of countries most affected by recurrent epidemics caused by emerging vector-borne viruses. Dengue virus (DENV) outbreaks have been reported with increasing frequency in several governorates since the year 2000, and the Chikungunya virus (CHIKV) has been also responsible of large outbreaks and it is now a major public health problem in Yemen. We report the results of the phylogenetic analysis of DENV-2 and CHIKV isolates (NS1 and E1 genes, respectively) detected in an outbreak occurred in Al-Hudayda in 2012. Estimates of the introduction date of CHIKV and DENV-2, and the phylogeographic analysis of DENV-2 are also presented. Phylogenetic analysis showed that the Yemen isolates of DENV belonged to the lineage 2 Cosmopolitan subtype, whereas CHIKV isolates from Yemen belonged to the ECSA genotype. All the CHIKV isolates from Yemen were statistically supported and dated back to the year 2010 (95% HPD: 2009-2011); these sequences showed an alanine in the aminoacid position 226 of the E1 protein. Phylogeographic analysis of DENV-2 virus showed that cluster 1, which included Yemen isolates, dated back to 2003 Burkina Faso strains (95% HPD 1999-2007). The Yemen, cluster dated back to 2011 (95% HPD 2009-2012). Our study sheds light on the global spatiotemporal dynamics of DENV-2 and CHIKV in Yemen. This study reinforces both the need to monitor the spread of CHIKV and DENV, and to apply significant measures for vector control.

Virus investigation in ticks from migratory birds in Italy

The role of migratory birds in circulation tick-borne viruses needs to be better defined. In order to assess the potential role of migratory birds in exotic virus spread, we conducted a study to identify ticks collected from migratory birds in the Central Region of Italy, and performed molecular investigation for Crimea-Congo Hemorrhagic Fever (CCHFV), West Nile fever (WNFV) and Usutu (USUV) in the vectors. A total of 137 competent ticks were collected with predominance of Hyalomma species. Although, negative results were obtained for all viruses considered, the high proportion of Hyalomma ticks highlights the potential risk for the dissemination of tick-borne viruses through infested migratory birds.

Laboratory intercomparison of gene expression assays

The possibility of a large-scale acute radiation exposure necessitates the development of new methods that could provide rapid individual dose estimates with high sample throughput. The focus of the study was an intercomparison of laboratories' dose-assessment performances using gene expression assays. Lithium-heparinized whole blood from one healthy donor was irradiated (240 kVp, 1 Gy/min) immediately after venipuncture at approximately 37°C using single X-ray doses. Blood samples to establish calibration curves (0.25-4 Gy) as well as 10 blinded test samples (0.1-6.4 Gy) were incubated for 24 h at 37°C supplemented with an equal volume of medium and 10% fetal calf serum. For quantitative reverse transcription polymerase chain reaction (qRT-PCR), samples were lysed, stored at -20°C and shipped on ice. For the Chemical Ligation Dependent Probe Amplification methodology (CLPA), aliquots were incubated in 2 ml CLPA reaction buffer (DxTerity), mixed and shipped at room temperature. Assays were run in each laboratory according to locally established protocols. The mean absolute difference (MAD) of estimated doses relative to the true doses (in Gy) was calculated. We also merged doses into binary categories reflecting aspects of clinical/diagnostic relevance and examined accuracy, sensitivity and specificity. The earliest reported time on dose estimates was <8 h. The standard deviation of technical replicate measurements in 75% of all measurements was below 11%. MAD values of 0.3-0.5 Gy and 0.8-1.3 Gy divided the laboratories contributions into two groups. These fourfold differences in accuracy could be primarily explained by unexpected variances of the housekeeping gene (P = 0.0008) and performance differences in processing of calibration and blinded test samples by half of the contributing laboratories. Reported gene expression dose estimates aggregated into binary categories in general showed an accuracies and sensitivities of 93-100% and 76-100% for the groups, with low MAD and high MAD, respectively. In conclusion, gene expression-based dose estimates were reported quickly, and for laboratories with MAD between 0.3-0.5 Gy binary dose categories of clinical significance could be discriminated with an accuracy and sensitivity comparable to established cytogenetic assays.

West Nile alternative open reading frame (N-NS4B/WARF4) is produced in infected West Nile Virus (WNV) cells and induces humoral response in WNV infected individuals

Background

West Nile Virus (WNV) is a flavivirus that requires an efficient humoral and cellular host response for the control of neuroinvasive infection. We previously reported the existence of six alternative open reading frame proteins in WNV genome, one of which entitled WARF4 is exclusively restricted to the lineage I of the virus. WARF4 is able to elicit antibodies in WNV infected horses; however, there was no direct experimental proof of the existence of this novel protein. The purpose of this study was to demonstrate the in vitro production of WARF4 protein following WNV infection of cultured VERO cells and its immunity in WNV infected individuals.

Results

We produced a monoclonal antibody against WARF4 protein (MAb 3A12) which detected the novel protein in WNV lineage I-infected, cultured VERO cells while it did not react with WNV lineage II infected cells. MAb 3A12 specificity to WARF4 protein was confirmed by its reactivity to only one peptide among four analyzed that cover the full WARF4 amino acids sequence. In addition, WARF4 protein was expressed in the late phase of WNV lineage I infection. Western blotting and bioinformatics analyses strongly suggest that the protein could be translated by programmed −1 ribosomal frameshifting process. Since WARF4 is embedded in the NS4B gene, we rename this novel protein N-NS4B/WARF4. Furthermore, serological analysis shows that N-NS4B/WARF4 is able to elicit antibodies in WNV infected individuals.

Conclusions

N-NS4B/WARF4 is the second Alternative Reading Frame (ARF) protein that has been demonstrated to be produced following WNV infection and might represent a novel tool for a better characterization of immune response in WNV infected individuals. Further serological as well as functional studies are required to characterize the function of the N-NS4B/WARF4 protein. Since the virus might actually make an extensive use of ARFs, it appears important to investigate the novel six ARF putative proteins of WNV.

High throughput MLVA-16 typing for Brucella based on the microfluidics technology

Background

Brucellosis, a zoonosis caused by the genus Brucella, has been eradicated in Northern Europe, Australia, the USA and Canada, but remains endemic in most areas of the world. The strain and biovar typing of Brucella field samples isolated in outbreaks is useful for tracing back source of infection and may be crucial for discriminating naturally occurring outbreaks versus bioterrorist events, being Brucella a potential biological warfare agent. In the last years MLVA-16 has been described for Brucella spp. genotyping. The MLVA band profiles may be resolved by different techniques i.e. the manual agarose gels, the capillary electrophoresis sequencing systems or the microfluidic Lab-on-Chip electrophoresis. In this paper we described a high throughput system of MLVA-16 typing for Brucella spp. by using of the microfluidics technology.

Results

The Caliper LabChip 90 equipment was evaluated for MLVA-16 typing of sixty-three Brucella samples. Furthermore, in order to validate the system, DNA samples previously resolved by sequencing system and Agilent technology, were de novo genotyped. The comparison of the MLVA typing data obtained by the Caliper equipment and those previously obtained by the other analysis methods showed a good correlation. However the outputs were not accurate as the Caliper DNA fragment sizes showed discrepancies compared with real data and a conversion table from observed to expected data was created.

Conclusion

In this paper we described the MLVA-16 using a rapid, sophisticated microfluidics technology for detection of amplification product sizes. The comparison of the MLVA typing data produced by Caliper LabChip 90 system with the data obtained by different techniques showed a general concordance of the results. Furthermore this platform represents a significant improvement in terms of handling, data acquiring, computational efficiency and rapidity, allowing to perform the strain genotyping in a time equal to one sixth respect to other microfluidics systems as e.g. the Agilent 2100 bioanalyzer.

Finally, this platform can be considered a valid alternative to standard genotyping techniques, particularly useful dealing with a large number of samples in short time. These data confirmed that this technology represents a significative advancement in high-throughput accurate Brucella genotyping.

A FRET based melting curve analysis to detect nucleotide variations in HA receptor-binding site of H5N1 virus

Outbreaks of highly pathogenic H5N1 influenza A virus represent a major public health problem because of the possibility of direct transmission of these viruses from avian species to humans. For influenza H5N1 hemagglutinin, a switch from SA-a-2, 3-Gal to SA-a-2, 6-Gal receptor specificity is a critical step that could lead to inter-human transmission. The monitoring of the receptor-binding preference of H5N1 viruses represents an instrument to detect a potential pandemic virus. The aim of this study was to develop a method based on the fluorescence resonance energy transfer (FRET) technology and melting peaks analysis for rapid screening of pandemic H5N1 influenza A virus. Three selected probes corresponding to a 23bp nucleotide sequence of the avian receptor-binding site were used in a real-time RT-PCR to detect nucleotide variations. Five strains of avian influenza A viruses isolated from avian species and two synthesized HA gene were tested. The results showed that the melting peaks analysis is a reliable screening method for detecting the variability of the H5N1 receptor-binding site.

Evidence of a humoral response to a novel protein WARF4 embedded in the West Nile virus NS4B gene encoded by an alternative open reading frame

West Nile virus (WNV) is a flavivirus that is maintained in a bird-mosquito transmission cycle. Humans, horses and other non-avian vertebrates are usually incidental hosts. However, WNV is a neurotropic virus, which requires an efficient humoral response for the control of a neuroinvasive infection. The WNV genome encodes three structural (capsid, premembrane/membrane and envelope) and seven non-structural proteins. Bioinformatic analysis performed on the WNV genomes detected a conserved alternative open reading frame restricted to the lineage I virus. To quickly verify the existence of this putative protein, entitled West Nile Alternative Reading Frame 4 (WARF4), we produced a prokaryotic recombinant source of WARF4 and verified its immunogenicity in vivo by analyzing 43 horse serum samples, of which 15 were positive for antibodies to WNV premembrane and envelope (prM-E) proteins. Specific antibodies to WARF4 were significantly detected in 5 out of the 15 serum samples testing positive for antibodies to prM-E WNV proteins. Our findings provide evidence of a significant antibody response to the WARF4 protein in the serum of the horse testing positive for antibodies to prM-E proteins, thus indicating that this antigen might be a potential tool for further characterization of the immune response of WNV infections in humans as well.

Lab on a chip genotyping for Brucella spp. based on 15-loci multi locus VNTR analysis

BACKGROUND

Brucellosis is an important zoonosis caused by the genus Brucella. In addition Brucella represents potential biological warfare agents due to the high contagious rates for humans and animals. Therefore, the strain typing epidemiological tool may be crucial for tracing back source of infection in outbreaks and discriminating naturally occurring outbreaks versus bioterroristic event. A Multiple Locus Variable-number tandem repeats (VNTR) Analysis (MLVA) assay based on 15 polymorphic markers was previously described. The obtained MLVA band profiles may be resolved by techniques ranging from low cost manual agarose gels to the more expensive capillary electrophoresis sequencing. In this paper a rapid, accurate and reproducible system, based on the Lab on a chip technology was set up for Brucella spp. genotyping.

RESULTS

Seventeen DNA samples of Brucella strains isolated in Sicily, previously genotyped, and twelve DNA samples, provided by MLVA Brucella VNTR ring trial, were analyzed by MLVA-15 on Agilent 2100. The DNA fragment sizes produced by Agilent, compared with those expected, showed discrepancies; therefore, in order to assign the correct alleles to the Agilent DNA fragment sizes, a conversion table was produced. In order to validate the system twelve unknown DNA samples were analyzed by this method obtaining a full concordance with the VNTR ring trial results.

CONCLUSION

In this paper we described a rapid and specific detection method for the characterization of Brucella isolates. The comparison of the MLVA typing data produced by Agilent system with the data obtained by standard sequencing or ethidium bromide slab gel electrophoresis showed a general concordance of the results. Therefore this platform represents a fair compromise among costs, speed and specificity compared to any conventional molecular typing technique.

Fieldable genotyping of Bacillus anthracis and Yersinia pestis based on 25-loci Multi Locus VNTR Analysis

BACKGROUND

Anthrax and plague are diseases caused by Bacillus anthracis and Yersinia pestis respectively. These bacteria are etiological agents for worldwide zoonotic diseases and are considered among the most feared potential bioterror agents. Strain differentiation is difficult for these microorganisms because of their high intraspecies genome homogeneity. Moreover, fast strain identification and comparison with known genotypes may be crucial for naturally occurring outbreaks versus bioterrorist events discrimination.

RESULTS

Thirty-nine B. anthracis and ten Y. pestis strains, representative of the species genetic diversity, were genotyped by Agilent 2100 Bioanalyzer using previously described Multiple Locus VNTR Analysis assays (MLVA). Results were compared to previous data obtained by standard genotyping system (capillary electrophoresis on automatic sequencer) and, when necessary, direct amplicon sequencing. A reference comparison table containing actual fragment sizes, sequencer sizes and Agilent sizes was produced.

CONCLUSION

In this report an automated DNA electrophoresis apparatus which provides a cheaper alternative compared to capillary electrophoresis approaches was applied for genotyping of B. anthracis and Y. pestis. This equipment, uses pre-cast gels and provides easy transportation, low maintenance and overall general logistic requirements and costs, is easy to set up and provides rapid analysis. This platform is a candidate for on-site MLVA genotyping of biothreat agents as well as other bacterial pathogens. It is an alternative to the more expensive and demanding capillary electrophoresis methods, and to the less expensive but more time-consuming classical gel electrophoresis approach.

The ribosomal P0 protein induces a spontaneous immune response in patients with head and neck advanced stage carcinoma that is not dependent on its overexpression in carcinomas

A typical feature in systemic lupus erythemathosus patients is the presence of autoantibodies to the carboxyl-terminal homologous P proteins (P0, P1, P2) domain (C-22 P0 epitope). In this report we provide evidence for the in vivo immunogenicity of the P0 protein in head and neck cancer patients as well as overexpression by immunohistochemistry of the C-22 P0 epitope in invasive carcinomas (55/57). Overexpression of this epitope was also significantly associated with a number of pathological lesions arising in the head and neck stratified epithelium including acanthosis (8/8), benign tumors (11/11), dysplasia (23/25) and in situ carcinomas (9/9). Intermediate cell layer restricted epitope overexpression was observed in well differentiated carcinomas, while undifferentiated tumors showed overexpression throughout the cell layers. Employing recombinant P proteins, sera from 40 of the 57 carcinoma patients and 39 normal donors, were subjected to immunoblot analysis. Immunity to P0 protein (7/40) was associated with malignancy and with advanced disease stage, but it was not dependent on the C-22 P0 epitope overexpression, although it was the preferential autoantibody target in 4 patients. Increased expression of the C-22 P0 epitope on the surface of pharynx cancer cells following cellular stress in vitro, may imply P0 protein presentation as an in vivo autoantibody target in cancer patients. Evidence for immunity to the P0 protein, as well as overexpression in patients with head and neck carcinoma may be relevant for monitoring cancer progression, in planning immunotherapeutic strategies, and contribute to the understanding of immuno-biological behaviour of head and neck carcinomas.

Genotyping of Bacillus anthracis strains based on automated capillary 25-loci multiple locus variable-number tandem repeats analysis

BACKGROUND

The genome of Bacillus anthracis, the etiological agent of anthrax, is highly monomorphic which makes differentiation between strains difficult. A Multiple Locus Variable-number tandem repeats (VNTR) Analysis (MLVA) assay based on 20 markers was previously described. It has considerable discrimination power, reproducibility, and low cost, especially since the markers proposed can be typed by agarose-gel electrophoresis. However in an emergency situation, faster genotyping and access to representative databases is necessary.

RESULTS

Genotyping of B. anthracis reference strains and isolates from France and Italy was done using a 25 loci MLVA assay combining 21 previously described loci and 4 new ones. DNA was amplified in 4 multiplex PCR reactions and the length of the resulting 25 amplicons was estimated by automated capillary electrophoresis. The results were reproducible and the data were consistent with other gel based methods once differences in mobility patterns were taken into account. Some alleles previously unresolved by agarose gel electrophoresis could be resolved by capillary electrophoresis, thus further increasing the assay resolution. One particular locus, Bams30, is the result of a recombination between a 27 bp tandem repeat and a 9 bp tandem repeat. The analysis of the array illustrates the evolution process of tandem repeats.

CONCLUSION

In a crisis situation of suspected bioterrorism, standardization, speed and accuracy, together with the availability of reference typing data are important issues, as illustrated by the 2001 anthrax letters event. In this report we describe an upgrade of the previously published MLVA method for genotyping of B. anthracis and apply the method to the typing of French and Italian B. anthracis strain collections. The increased number of markers studied compared to reports using only 8 loci greatly improves the discrimination power of the technique. An Italian strain belonging to the B branch was described, and two new branches, D and E, are proposed. Owing to the upgrading achieved here, precise genotyping can now be produced either by automated capillary electrophoresis, or by the more accessible but slower and for some markers slightly less accurate agarose gel methodology.

Rapid single tube genotyping of ACP1 by FRET based amplification and dual color melting curve analysis

Erythrocyte acid phosphatase (ACP1), also named low molecular weight phosphotyrosine phosphatase (LMW-PTP) is an enzyme involved in signal transduction pathways of tyrosine kinase receptor. The precise physiological role of ACP1 remains to be elucidated, however recent advancements suggest that it may play an important role in the control of cell proliferation. ACP1 is a highly polymorphic enzyme that has been investigated by case-control studies for decades. Initially based on protein electrophoresis, the phenotype of ACP1 is now detected by DNA-based techniques. Here, we report a new rapid single tube genotyping method for ACP1 by FRET based amplification and dual color melting curve analysis. This method does not require a post-procedure amplification process and allows unambiguous genotyping of 30 samples in less than 1 h.

Identification of two SNPs in the 5' flanking region of the ACP1 gene and evaluation of disequilibrium among polymorphic sites

We have studied the 5' flanking region of the ACP1 gene looking for new polymorphisms. Two SNPs, DdeI and FokI restricted, have been found in this region. We determined the genotype of DdeI and FokI SNPs, as well as of three other known SNPs, codon 43 (CfoI restricted), codon 41 and codon 105 (TaqI restricted), located respectively in exons 3, 4 and 6 in 62 unrelated subjects from the Italian population. Haplotype distribution for the ten possible pairs of loci were determined by a maximum likelihood procedure. Overall, statistically significant deviations from expected frequencies assuming equilibrium have been observed for the following pairs: FokI/codon 41, FokI/TaqI, codon 41/TaqI (complete association), DdeI/FokI, DdeI/codon 41 and DdeI/TaqI. The data suggest that the FokI area could include sequences operating in strict functional association with sequences included in the codon 41/TaqI area, possibly in order to regulate the F/S isoforms ratio of the A* and *B alleles. Since the ratio between the concentration of the two F and S isoforms is different for the three ACP1 alleles, we suggest that the ACP1 locus has been subjected to strong selective pressure to obtain an optimal alternative splicing mechanism of the *A and *B alleles. The *C variant, on the other hand, seems completely independent from sequences in the FokI/codon 41/TaqI areas, resulting in an inverted F/S ratio compared to that found for *A and *B alleles.

The genetics of signal transduction and the outcome of diagnostic tests in growth retardation

The effects of 'normal' genetic variability of signal transduction on endocrine function may be more evident during stimulation tests than is observed in basal states, thereby contributing to a greater understanding of the possible role of signal transduction genetics in the pathogenesis of endocrine disorders. In the present study, we have studied the outcome of growth hormone (GH) stimulation testing by insulin in growth-retarded children in relation to the genotype of ACP1 (acid phosphatase locus 1; also referred to as cLMWPTP, cytosolic low molecular weight phosphotyrosine phosphatase). ACP1 is an enzyme, expressed as two distinct isoforms designated F and S, that down-regulates insulin receptor signal transduction and which shows a genetic polymorphism with strong quantitative enzymatic differences among genotypes. In this study, we examined 116 growth-retarded children of which 101 were genotyped for ACP1. We found that the basal level of GH is higher in ACP1 genotypes with low concentrations of the S isoform than in genotypes with high S isoform concentrations (P<0.02). Additionally, during GH stimulation with insulin, the genotypes with low S isoform concentrations were found to perform better (P<0.005) and to react more promptly than the genotypes with high S isoform concentrations (P<0.05). These findings suggest that high S isoform ACP1 activity slows down the effect of insulin, resulting in a retardation of its metabolic effect.

Phosphotyrosine-protein-phosphatase and diabetic disorders. Further studies on the relationship between low molecular weight acid phosphatase genotype and degree of glycemic control

We have studied a new sample of 276 NIDDM patients from the population of Penne (Italy). Comparison of the new data with those of 214 diabetic pregnant women from the population of Rome reported in a previous paper has shown that the pattern of association between low molecular weight acid phosphatase genotype and degree of glycemic control is similar in the two classes of diabetic patients. Among nonobese subjects the proportion of ACP1*A (the allele showing the lowest enzymatic activity) is lower in diabetic patients with high glycemic levels (mean value greater than 8.9 mmol/l) than in diabetic patients with a low glycemic level (mean value less than 8.9 mmol/l). Among obese subjects no significant association is observed between glycemic levels and ACP1. Among nonobese subjects the concentration of f isoform of ACP1 is higher in patients showing a high glycemic level than in patients showing a low glycemic level. No significant difference is observed for s isoform.