Frequency of SARS-CoV-2 variants identified by real-time PCR in the AUNA healthcare network, Peru

Introduction

In Peru, on 11 February 2023, the Ministry of Health registered 4 million patients infected with COVID-19 and around 219,260 deaths. In 2020, the SARS-CoV-2 virus was acquiring mutations that impacted the properties of transmissibility, infectivity, and immune evasion, leading to new lineages. In the present study, the frequency of COVID-19 variants was determined during 2021 and 2022 in patients treated in the AUNA healthcare network.

Methods

The methodology used to detect mutations and identify variants was the Allplex™ SARS-CoV-2 Variants Assay I, II, and VII kit RT-PCR. The frequency of variants was presented by epidemiological weeks.

Results

In total, 544 positive samples were evaluated, where the Delta, Omicron, and Gamma variants were identified. The Delta variant was found in 242 (44.5%) patients between epidemiological weeks 39 and 52 in 2021. In the case of Gamma, it was observed in 8 (1.5%) patients at weeks 39, 41, 43, 45, and 46 of 2021. The Omicron variant was the most frequent with 289 (53.1%) patients during weeks 49 to 52 of 2021 and 1 to 22 of 2022. During weeks 1 through 22 of 2022, it was possible to discriminate between BA. 1 (n = 32) and BA.2 (n = 82).

Conclusion

The rapid identification of COVID-19 variants through the RT-PCR methodology contributes to timely epidemiological surveillance, as well as appropriate patient management.

Host-Pathogen Interaction: Biology and Public Health

Interactions between host and pathogenic microorganisms are common in nature and have a significant impact on host health, often leading to several types of infections. These interactions have evolved as a result of the ongoing battle between the host's defense mechanisms and the pathogens' invasion strategies. In this chapter, we will explore the evolution of host-pathogen interactions, explore their molecular mechanisms, examine the different stages of interaction, and discuss the development of pharmacological treatments. Understanding these interactions is crucial for improving public health, as it enables us to develop effective strategies to prevent and control infectious diseases. By gaining insights into the intricate dynamics between pathogens and their hosts, we can work towards reducing the burden of such diseases on society.

Genomic profiling of tissue and blood predicts survival outcomes in patients with resected pleural mesothelioma

PURPOSE

Pleural mesothelioma (PM) is an aggressive tumor still considered incurable, in part due to the lack of predictive biomarkers. Little is known about the clinical implications of molecular alterations in resectable PM tissues and blood. Here, we characterized genetic alterations to identify prognostic and predictive biomarkers in patients with resected PM.

EXPERIMENTAL DESIGN

Targeted next-generation sequencing was performed in retrospective pleural tumor tissue and paired plasma samples from stage IB-IIIB resected PM. Association between prognosis and presence of specific mutations was validated in silico.

RESULTS

Thirty PM tissues and paired blood samples from 12 patients were analyzed. High tissue tumor mutational burden (TMB) (>10 mutations/Mb), tissue median minor allele frequency (MAF) (>9 mutations/Mb), and blood TMB (>6 mutations/Mb), tissue KMT2C, PBRM1, PKHD1,EPHB1 and blood LIFR mutations correlated with longer disease-free survival and/or overall survival. High concordance (>80%) between tissue and blood was found for some mutations.

CONCLUSIONS

Tissue TMB and MAF, blood TMB, and specific mutations correlated with outcomes in patients with resected PM and should be further studied to validate their role as prognostic biomarkers and potentially predictive factors for combinations with immune-checkpoint inhibitors. This suggest that molecular profiling could identify longer survivors in patients with resected PM.

Subpopulation treatment effect pattern plot analysis: a prognostic model for distant recurrence-free survival to estimate delayed adjuvant chemotherapy initiation effect in triple-negative breast cancer

Introduction

Triple-negative breast cancer (TNBC) is a heterogeneous disease associated with a poor prognosis. Delaying in time to start adjuvant chemotherapy (TTC) has been related to an increased risk of distant recurrence-free survival (DRFS). We aimed to develop a prognostic model to estimate the effects of delayed TTC among TNBC risk subgroups.

Materials and methods

We analyzed 687 TNBC patients who received adjuvant chemotherapy at the Instituto Nacional de Enfermedades Neoplasicas (Lima, Peru). Database was randomly divided to create a discovery set (n=344) and a validation set (n=343). Univariate and multivariate Cox regression models were performed to identify prognostic factors for DRFS. Risk stratification was implemented through two models developed based on proportional hazard ratios from significant clinicopathological characteristics. Subpopulation treatment effect pattern plot (STEPP) analysis was performed to determine the best prognostic cut-off points for stratifying TNBC subgroups according to risk scores and estimate Kaplan-Meier differences in 10-year DRFS comparing TTC (≤30 vs.>30 days).

Results

In univariate analysis, patients aged ≥70 years (HR=4.65; 95% CI: 2.32-9.34; p=<0.001), those at stages pT3-T4 (HR=3.28; 95% CI: 1.57-6.83; p=0.002), and pN2-N3 (HR=3.00; 95% CI: 1.90-4.76; p=<0.001) were notably associated with higher risk. STEPP analysis defined three risk subgroups for each model. Model N°01 categorized patients into low (score: 0-31), intermediate (score:32-64), and high-risk (score: 65-100) cohorts; meanwhile, Model N°02: low (score: 0-26), intermediate (score: 27-55), and high (score: 56-100). Kaplan-Meier plots showed that in the discovery set, patients with TTC>30 days experienced a 17.5% decrease in 10-year DRFS rate (95%CI=6.7-28.3), and the impact was more remarkable in patients who belong to the high-risk subgroup (53.3% decrease in 10 years-DRFS rate). Similar results were found in the validation set.

Conclusions

We developed two prognostic models based on age, pT, and pN to select the best one to classify TNBC. For Model N°02, delayed adjuvant chemotherapy conferred a higher risk of relapse in patients ≥70 years and who were characterized by pT3/T4 and pN2/N3. Thus, more efforts should be considered to avoid delayed TTC in TNBC patients, especially those in high-risk subgroups.

Landscape of germline BRCA1/BRCA2 variants in breast and ovarian cancer in Peru

Background

There is an increasing amount of data from Latin America on the characterization of BRCA variants; however, there is limited information from Peru. We conducted a retrospective study to describe germline pathogenic/likely pathogenic(P/LP) variants and variants of uncertain/unknown significance (VUS) in the BRCA1 and BRCA2 genes in Peru, in patients with breast and ovarian cancer, candidates for treatment with poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitors.

Methods

The patients were evaluated during the period 2019-2021. Genomic DNA was isolated from peripheral blood samples and targeted sequencing was performed using the Ampliseq BRCA panel. Genetic variant interpretation was carried out in accordance with the recommendations of the American College of Medical Genetics and ClinVar. During this period, 525 patients (143 with breast cancer and 382 with ovarian cancer) were studied.

Results

We found that 14.7% (21/143) of breast cancer patients and 20.7% (79/382) of ovarian cancer patients were carriers of P/LP variants in BRCA1/2. The most frequent pathogenic variants detected in BRCA1 were c.2105dupT (BIC: 2224insT, n=12, 18.75%), c.68_69delAG (BIC: 185delAG, n=6, 9.38%), c.140G>T and c.815_824dupAGCCATGTGG (n=5, 7.81%), while in BRCA2 were c.8023A>G (n=6, 16.67%), c.6024dupG (BIC: 6252insG, n=4, 11.11%), and c.9235delG (BIC: 9463delG, n=3, 8.33%). Regarding VUS, we found that 6.99% (10/143) of breast cancer patients and 7.33% (28/382) of ovarian cancer patients were carriers of a VUS in BRCA1/2. For BRCA1, the most frequent VUS was c.93C>G (n=2), and for BRCA2, c.5465A>T (n=4), c.3101T>C (n=3), c.205C>A and c.437T>C (n=2).

Conclusion

We found a frequency of 14.7% germline mutations in breast cancer patients and 20.7% in ovarian cancer patients. The most recurrent mutations were BRCA1 c.2105dupT and BRCA2 c.8023A>G. We found that BRCA2 c.8023A>G, c.6024dupG, and c.9235delG were not previously reported in Peruvian patients. BRCA1 c.2344dupA is a novel mutation that has not been previously reported in any database. The frequency of VUS in our cohort was 7.2%.

Super-infection by multiple microorganisms in COVID-19 patients

Introduction: This study aimed to describe the clinical characteristics of patients with COVID-19 co-infected with multiple multidrug-resistant bacteria.

Methods: Patients hospitalized in the AUNA network between January and May 2021, diagnosed with COVID-19 and at least two other infecting microorganisms, were retrospectively included in the analysis. Clinical and epidemiological data were extracted from clinical records. The susceptibility levels of the microorganisms were determined using automated methods. Antibiotic resistance was established among infecting bacteria accounting for ≥5 isolates.

Results: A total of 27 patients (21 male and 6 female patients) met the inclusion criteria, with a maximum of eight co-infecting bacteria or fungi during admission time. Seven patients (25.9%) died, with a higher but not significant lethality among women (50% vs. 19.0%). A total of 15 patients presented at least one established comorbidity, with hypertension being the most frequent. The time elapsed between COVID-19 diagnosis and hospital attendance was 7.0 days, with that of patients with a fatal outcome being longer than that of living patients (10.6 vs. 5.4). Up to 20 different microorganisms were isolated, with Pseudomonas aeruginosa being the most common (34 isolates). In general, antibiotic resistance levels were high, especially in Acinetobacter baumannii isolates, with resistance levels of 88.9% to all antimicrobial agents tested, except colistin (0%).

Conclusion: In conclusion, the present results show the presence of multiple microorganisms that co-infect COVID-19 patients. When fatal outcome rates are in the range of other reports, the presence of a series of multidrug-resistant microorganisms is of concern, showing the need to reinforce control measures to limit the expansion of almost untreatable microorganisms.

Framework for Adoption of Next-Generation Sequencing (NGS) Globally in the Oncology Area

Radical new possibilities of improved treatment of cancer are on offer from an advanced medical technology already demonstrating its significance: next-generation sequencing (NGS). This refined testing provides unprecedentedly precise diagnoses and permits the use of focused and highly personalized treatments. However, across regions globally, many cancer patients will continue to be denied the benefits of NGS as long as some of the yawning gaps in its implementation remain unattended. The challenges at the regional and national levels are linked because putting the solutions into effect is highly dependent on cooperation between regional- and national-level cooperation, which could be hindered by shortfalls in interpretation or understanding. The aim of the paper was to define and explore the necessary conditions for NGS and make recommendations for effective implementation based on extensive exchanges with policy makers and stakeholders. As a result, the European Alliance for Personalised Medicine (EAPM) developed a maturity framework structured around demand-side and supply-side issues to enable interested stakeholders in different countries to self-evaluate according to a common matrix. A questionnaire was designed to identify the current status of NGS implementation, and it was submitted to different experts in different institutions globally. This revealed significant variability in the different aspects of NGS uptake. Within different regions globally, to ensure those conditions are right, this can be improved by linking efforts made at the national level, where patients have needs and where care is delivered, and at the global level, where major policy initiatives in the health field are underway or in preparation, many of which offer direct or indirect pathways for building those conditions. In addition, in a period when consensus is still incomplete and catching up is needed at a political level to ensure rational allocation of resources-even within individual countries-to enable the best ways to make the necessary provisions for NGS, a key recommendation is to examine where closer links between national and regional actions could complement, support, and mutually reinforce efforts to improve the situation for patients.

A nationwide pilot study on breast cancer screening in Peru

Introduction

A high prevalence of advanced breast cancer (BC) is a common scenario in Latin America. In Peru, the frequency of BC at Stages III/IV is ≈50% despite implementation of a programme for breast cancer screening (BCS) along the country. We carried out a study to assess the feasibility and develop an instrument to evaluate the knowledge, barriers and perception about BCS in a nationwide pilot study in Peru among candidates for BCS.

Methods

We conducted a systematic review of 2,558 reports indexed in PubMed, Scopus, Web of Science, Medline-Ovid and EMBASE, regarding to our study theme. In total, 111 were selected and a 51-items survey was developed (eight items about sociodemographic characteristics). Patients were recruited in public hospitals or private clinics, in rural and urban areas of nine departments of Peru.

Results

We surveyed 488 women from: Lima (150), Cajamarca (93), Ica (59), Arequipa (56), Loreto (48), Ancash (38), Junín (15), Puerto Maldonado (15) and Huancavelica (14); 27.9% of them were from rural areas. The mean of age was 53.3 years (standard deviation ± 9.1). Regarding education level, 29.8% had primary, 33.2% secondary and 37.0% higher education. In total, 28.7% of women did not know the term 'mammogram' and 47.1% reported never receiving a BCS (36.9% from urban and 73.5% from rural population). In women that underwent BCS, only 67% knew it is for healthy women. In total, 54.1% of patients had low levels of knowledge about risk factors for BC (i.e. 87.5% of women respond that injuries in the breast produce cancer). Cultural, economic and geographic barriers were significantly associated with having a mammogram where 56.9% of participants considered a cost ≤ 7 USD as appropriate. Mammogram was perceived as too painful for 54.9% of women. In addition, women with a self-perception of low-risk for BC and a fatalistic perception of cancer were less likely to have a BCS.

Conclusion

We found that it is feasible to conduct a large-scale study in Peru. The results of this pilot study highlight an urgent need of extensive education and awareness about BCS in Peru.

First report of CrpP prevalence in a South American country

The presence of crpP was established in 201 Pseudomonas aeruginosa isolates from 9 Peruvian hospitals. The 76.6% (154/201) of the isolates presented the crpP gene. Overall, 123/201 (61.2%) isolates were non-susceptible to ciprofloxacin. The prevalence of crpP-possessing P. aeruginosa in Peru is higher than in other geographical areas.

Characteristics of gastric cancer around the world

Gastric cancer is one of the most important malignancies in the world due to the high burden of disease and lethality. In this work, we compared the main characteristics of gastric cancer between different regions of the world. We reviewed public repositories to retrieve epidemiological, molecular, clinicopathological, and risk factor data. Eastern Asia presents the highest incidence of gastric cancer, followed by eastern and central Europe. Intestinal histology was more frequent in Caucasians, while gastric tumors located in the cardias were less frequent in Africa and Latin America. TP53, LRP1B, and ARID1A are consistently the most frequently altered genes in all population groups. Gastric cancer is most frequent in men. African patients tend to be younger and have a higher proportion of women patients. Different patterns can be observed in the presentation of gastric cancer between different regions of the world. More research is needed in Latin America and Africa since these populations are underrepresented.

Empowering quality data - the gordian knot of bringing real innovation into healthcare system

OBJECTIVES

The introduction of Personalised Medicine (PM) into healthcare systems could benefit from a clearer understanding of the distinct national and regional frameworks around the world. Recent engagement by international regulators on maximising the use of real-world evidence (RWE) has highlighted the scope for improving the exploitation of the treasure-trove of health data that is currently largely neglected in many countries. The European Alliance for Personalised Medicine (EAPM) led an international study aimed at identifying the current status of conditions.

METHODS

A literature review examined how far such frameworks exist, with a view to identifying conducive factors - and crucial gaps. This extensive review of key factors across 22 countries and 5 regions revealed a wide variety of attitudes, approaches, provisions and conditions, and permitted the construction of a comprehensive overview of the current status of PM. Based on seven key pillars identified from the literature review and expert panels, the data was quantified, and on the basis of further analysis, an index was developed to allow comparison country by country and region by region.

RESULTS

The results show that United States of America is leading according to overall outcome whereas Kenya scored the least in the overall outcome.

CONCLUSIONS

Still, common approaches exist that could help accelerate take-up of opportunities even in the less prosperous parts of the world.

Fighting Cancer around the World: A Framework for Action

Tackling cancer is a major challenge right on the global level. Europe is only the tip of an iceberg of cancer around the world. Prosperous developed countries share the same problems besetting Europe-and the countries and regions with fewer resources and less propitious conditions are in many cases struggling often heroically against a growing tide of disease. This paper offers a view on these geographically wider, but essentially similar, challenges, and on the prospects for and barriers to better results in this ceaseless battle. A series of panels have been organized by the European Alliance for Personalised Medicine (EAPM) to identify different aspects of cancer care around the globe. There is significant diversity in key issues such as NGS, RWE, molecular diagnostics, and reimbursement in different regions. In all, it leads to disparities in access and diagnostics, patients' engagement, and efforts for a better understanding of cancer.

Genomic landscape of the lung cancer in the young

Background

Lung cancer in the young is a rare entity of great interest due to the high frequency of targetable mutations. In this study, we explored the genomic landscape of non-small cell lung cancer (NSCLC) in young patients and compared it with genetic alterations in older patients.

Methods

Comparative study of the genomic profile of NSCLC young (≤40 years old) vs older patients (>40 years old) from Instituto Nacional de Enfermedades Neoplásicas (INEN) in Lima, Peru. Archival paraffin-embedded tumor samples were profiled with FoundationOne CDx assay to identify short variants alterations (insertions and deletions), copy number variations (CNV), tumor mutational burden and microsatellite instability in 324 driver genes and rearrangements in 28 commonly rearranged genes. A targetable alteration was defined as any alteration in a driver oncogene for which an FDA approved therapy existed at the time of study enrollment.

Results

Overall, 62 tumors were profiled, 32 from young and 30 from older patients. All clinicopathological features (smoking status, clinical stage, and histology) were similar between groups, except for gender (65.6% of females in the younger group vs 40% in the older group, P=0.043). At least one actionable mutation was present in 84.4% and 83.3% in younger and older patients, respectively. Alteration rates in the main genes were: BRAF, 3.1%(n=1) vs 0%; EGFR, 46.9% (n=15) vs 43.3% (n=13); ERBB2, 12.5% (n=4) vs 16.7% (n=5); KRAS, 15.6% (n=5) vs 16.7% (n=5); ALK, 6.3% (n=2) vs 3.3% (n=1); RET, 0.0% vs 3.3% (n=1); ROS1, 3.1% (n=1) vs 3.3% (n=1); NTRK1, 0.0% vs 3.3% (n=1) and MET, 3.1% (n=1) vs 13.3% (n=4). Mean TMB was 4.04 Mut/Mb (SD ± 3.98) for young vs 8.06 Mut/Mb (SD ± 9.84) for older patients (P=0.016). There were not significant differences in CNV, frequency of gene rearrangements, or microsatellites instability.

Conclusion

NSCLC in the young in our cohort was characterized by a high frequency of actionable genetic aberrations and a low TMB, which was also true for our older patients. The enrichment of actionable mutations in young patients described in other reports might be attributed to differences in the etiology and clinicopathological characteristics between younger and older patients and therefore not be applicable to all populations.

Prognostic Capability of TNBC 3-Gene Score among Triple-Negative Breast Cancer Subtypes

Background: Triple-negative breast cancer (TNBC) is a complex and molecularly heterogeneous entity, with the poorest outcome compared with other breast cancer subtypes. Previously, we developed a TNBC 3-gene score with a significant prognostic capability. This study aims to test the 3-gene score in the different TNBC subtypes. Methods: Data from 204 TNBC patients treated with neoadjuvant chemotherapy were retrieved from public datasets and pooled (GSE25066, GSE58812, and GSE16446). After removing batch effects, cases were classified into Lehman’s TNBC subtypes and then the TNBC 3-gene score was used to evaluate the risk of distant recurrence in each subgroup. In addition, the association with tumor-infiltrating lymphocyte (TILs) levels was evaluated in a retrospective group of 72 TNBC cases. Results: The TNBC 3-gene score was able to discriminate patients with different risks within the pooled cohort (HR = 2.41 for high vs. low risk; 95%CI: 1.50−3.86). The score showed predictive capability in the immunomodulatory subtype (HR = 4.16; 95%CI: 1.63−10.60) and in the mesenchymal stem-like subtype (HR = 18.76; 95%CI: 1.68−208.97). In the basal-like 1, basal-like-2, and mesenchymal subtypes, the observed differential risk patterns showed no statistical significance. The score had poor predictive capability in the luminal androgen receptor subtype (p = 0.765). In addition, a low TNBC 3-gene score was related to a high level of TIL infiltration (p < 0.001). Conclusions: The TNBC 3-gene score is able to predict the risk of distant recurrence in TNBC patients, specifically in the immunomodulatory and mesenchymal stem-like subtype. Despite a small sample size in each subgroup, an improved prognostic capability was seen in TNBC subtypes with tumor-infiltrating components.

Abstract 3673: Socioeconomic disparities and the genomic landscape of gastric cancer

Background: Gastric cancer is a malignancy of diverse etiology and exposition to risk factors may vary in distinct socioeconomic (SE) groups. Our aim was to compare the landscape of genomic alterations in malignant gastric tumors between different socioeconomic groups in Peru.

Methods: We conducted a preliminary prospective study in one private clinic and two public hospitals in Lima and Ica (Peru). We evaluated 20 patients with gastric carcinomas, 10 of which were classified as low SE status (LSE) and 10 as medium/high SE status (MHSE), according to the Peruvian Association of Market Intelligence Companies (APEIM) classification system. We conducted a comprehensive genomic profiling of gastric tumors with the FoundationOne CDx platform. We compared rates of alterations in single nucleotide variants, copy number variations, tumor mutation burden, microsatellite instability, and pathways altered.

Results: In our cohort, the mean age at diagnosis was 67.5 yo vs 61 yo, while 40% vs 55.6% were male patients, for LSE vs MHSE, respectively. We found alterations in driver genes in 19 patients (10 LSE and 9 MHSE). Histological analysis of the tumor samples revealed a higher proportion of intestinal histology in the LSE group (80%) compared to MHSE (55.6%). On the other hand, the diffuse subtype pattern was more prevalent in the MHSE group (33%) compared to LSE (20%). One case of mixed histology was observed in the high SE group. Both LSE and HMSE showed a similar distribution of Bormann Classification/type, where most of the samples were of class III/IV (75%) followed by class I/II (25%). Furthermore, genomic profiling analysis showed 45 driver alterations in LSE, while only 25 alterations were detected in MHSE. the most frequently altered genes were TP53 and KRAS in both SE groups, but with a higher incidence in LSE (60% and 20%, respectively). Components of the MAPK pathway were altered in 50% vs 33.3%, while the DNA repair pathway was altered in 20% vs 11%, in LSE vs MHSE, respectively. The PI3K/Akt pathway was altered in only one case of LSE. Median of tumor mutation burden was 6.1Mut/Mb in LSE vs 5.3Mut/Mb MHSE. Only one case with microsatellite instability was found in LSE.

Conclusions: Despite the limitations of this preliminary study, we observed some differences in the genomic background between patients from different socioeconomic groups. Therefore, the need of a thorough diagnosis approach that leads to the use of a comprehensive treatment that includes targeted therapy and immunotherapy could be different based on the SE status of the patient. Further research on this topic will be necessary.

Citation Format: Daniel Zanabria, Marco Galvez-Nino, Cristina Eunbee Cho, Williams Fajardo, Luis Saravia, Jhajaira Araujo, Alejandro Alfaro, Lidia Quispe, Melanie Cornejo, Paula Medina, Junior Carbajal, Paola Montenegro, Alejandra Zevallos, Alfredo Aguilar, Joseph A. Pinto. Socioeconomic disparities and the genomic landscape of gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3673.

Life expectancy and cancer survival in Oncosalud: outcomes over a 15-year period in a Peruvian private institution

Background

There is a large gap in the data on cancer outcomes in Latin America, making it difficult to establish adequate cancer control policies in the region. The aim of our study was to describe the survival, life expectancy estimates and life expectancy changes over time for a large cohort of Peruvian patients insured with Oncosalud, a private healthcare system.

Patients and methods

We evaluated a retrospective cohort of patients diagnosed between 2000 and 2015 in Oncosalud (Lima-Peru). Cases included colon, rectum, stomach, bladder, breast, prostate and non-melanoma skin cancers. Survival was evaluated with the Kaplan–Meier methodology. The standard period life table was used to estimate the excess mortality risks of patients in our cohort compared to the population covered by the Peruvian Superintendence of Banks, Insurance Companies and Pension Funds (SBS). The years of life lost was estimated based on SBS population, matching patients by age and sex.

Results

A large cohort of 7,687 Peruvian cancer patients managed in a 15-year period was eligible. If patients survive 5 years after a cancer diagnosis, life expectancy tends to be close to that of a population without cancer. The number of years of life lost at diagnosis was higher at the youngest ages, steadily decreasing thereafter. During the first years after cancer diagnosis, young patients face a much higher loss in life expectancy than older ones. Patients suffering from colon, rectum, stomach and bladder cancer are the most affected by the years of life lost.

Conclusion

In cancer patients surviving ≥ 5 years, life expectancy becomes similar to that observed in a population with similar socioeconomic characteristics. The estimated survival rate in our cohort is higher than that reported by public cancer registries in Peru. This could be explained by the different socio-economic background and access to specialised cancer care.

Abstract P3-12-24: Landscape of germline BRCA1 and BRCA2 mutations in breast cancer in Peru

BACKGROUND: Breast cancer (BC) is the most common cancer and the second leading cause of cancer-related deaths worldwide. Mutations in tumor suppressor genes BRCA1 and BRCA2 are the most common cause of hereditary breast and ovarian cancer. Additionally, carriers of germline BRCA1/2 mutations also have an elevated risk of other malignancies. Identification of mutations within these genes is essential for determining early cancer detection and risk-reducing strategies in carriers and establishing a therapeutic approach in breast cancer patients. The aims of this study were to evaluate the prevalence and spectrumof germline BRCA1 and BRCA2 variants in peruvian breast cancer patients. METHODS: Patients with HER2Neu negative BC referred to ONCOGENOMICS laboratory from 2019 to2021 to assessed poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitor treatment were included in the study. Blood samples were collected to assess the status of germline BRCA1 and BRCA2. Next Generation Sequencing (NGS) was performed using the Ampliseq for Illumina BRCA panel and run on the Illumina MiSeq. The Human Genome Variation Society (HGVS) nomenclature guidelines (http://varnomen.hgvs.org/) were used to annotate identified variants and the ClinVar database (www.ncbi.nlm.nih.gov/clinvar/) was used to determine the clinical significance of all reported variants. Current American College of Medical Genetics (ACMG) guidelines were also used for further classification. RESULTS: A total of 155 HER2Neu negative BC cases were evaluated. Median age at BRCA1/2 evaluation was 51 (23-82) years, 78.1% (121) were negative HR status (triple-negative BC, TNBC); 21.9% (34) were positive HR status; 33.5% (52) were clinical stage III and 66.5% (103) were clinical stage IV. Most patients were from Lima-Callao (65.8%) followed by patients from the coast (23.9%), highlands (9%) and rainforest(1.3%). Only 18.7% of patients were from public health centers. The prevalence of pathogenic (P) and likely pathogenic (LP) variants in BRCA1/2 was 13.5% (21) (13 in BRCA1 and 8 in BRCA2). The pathogenic variant in BRCA1 c.2105dupT (p.Leu702Phefs*10) was found in 3 cases (2 Lima-Callao and 1 coast). All variants identified in BRCA1 were in TNBC. In BRCA2, half of pathogenic variants were found in TNBC. The prevalence of variants of uncertain significance (VUS) was 6.4% (10). In BRCA2, we identified 7 VUS and the variant c.5465A&gt;T (p.Asn1822Ile) was found in 3 cases with positive HR status. Only one VUS was found in BRCA1. CONCLUSION: BRCA1 and BRCA2 germline mutations were identified in 13.5% of peruvian HER2Neu negative BC patients. A higher rate of P/LP variants was found in BRCA1. TNBC patients demostrated a higher prevalence in BRCA1 variants.

Citation Format: Joseph A Pinto, Yomali Ferreyra, Alicia M Cock-Rada, Franco Doimi, Jhoysi Casas, Jhajaira Araujo, Gina Rosas, Leny Bravo, Carolina Belmar-López. Landscape of germline BRCA1 and BRCA2 mutations in breast cancer in Peru [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-12-24.

Sex, immunity, and cancer

The composition of the tumor microenvironment is the complex result of the interaction between tumoral and host factors. Since there are several differences in the regulation of gene circuits between sexes, mainly influenced by sex hormones, the tumor-host interaction presents some differences, leading tumors to evolve under different conditions. Nowadays, it is well known the existence of sexual dimorphism in the regulation of the immune system, where women present an improved immunity to various infectious agents and, on the other hand, a higher incidence of autoimmune diseases than men. In oncology, differences in cancer susceptibility, response to treatment, and clinical outcomes between men and women patients are well known. Recently, sex-specific differences have also been reported in mutations in driver genes and the prognostic value of several biomarkers. Sex has been a widely forgotten biomarker in cancer therapy, but it has recently acquired great relevance due to the different results seen in immunotherapy treatment.

Influence of Sex in the Molecular Characteristics and Outcomes of Malignant Tumors

Background

Sex is frequently underestimated as a prognostic biomarker in cancer. In this study, we evaluated a large cohort of patients and public datasets to determine the influence of sex on clinical outcomes, mutational status, and activation of immune pathways in different types of cancer.

Methods

A cohort of 13,619 Oncosalud-affiliated patients bearing sex-unrelated cancers was followed over a 20-year period. Hazard ratios (HRs) for death were estimated for female vs. male patients for each cancer type and then pooled in a meta-analysis to obtain an overall HR. In addition, the mutational status of the main actionable genes in melanoma (MEL), colorectal cancer (CRC), and lung cancer was compared between sexes. Finally, a gene set enrichment analysis (GSEA) of publicly available data was conducted, to assess differences in immune processes between sexes in MEL, gastric adenocarcinoma (GC), head and neck cancer (HNC), colon cancer (CC), liver cancer (LC), pancreatic cancer (PC), thyroid cancer (TC), and clear renal cell carcinoma (CCRCC).

Results

Overall, women had a decreased risk of death (HR = 0.73, CI95: 8%-42%), with improved overall survival (OS) in HNC, leukemia, lung cancer, lymphoma, MEL, multiple myeloma (MM), and non-melanoma skin cancer. Regarding the analysis of actionable mutations, only differences in EGFR alterations were observed (27.7% for men vs. 34.4% for women, p = 0.035). The number of differentially activated immune processes was higher in women with HNC, LC, CC, GC, MEL, PC, and TC and included cellular processes, responses to different stimuli, immune system development, immune response activation, multiorganism processes, and localization of immune cells. Only in CCRCC was a higher activation of immune pathways observed in men.

Conclusions

The study shows an improved survival rate, increased activation of immune system pathways, and an enrichment of EGFR alterations in female patients of our cohort. Enhancement of the immune response in female cancer patients is a phenomenon that should be further explored to improve the efficacy of immunotherapy.

Thrombosis in abdominal vessels associated with COVID-19 Infection: A report of three cases

Hypercoagulability related to SARS-CoV-2 infection is one of the main extrapulmonary complications of COVID-19. We present three cases of intrabdominal thrombotic complications related to the state of hypercoagulability of COVID-19 and its tomographic features. Hypercoagulability state should be taking into account in the interpretation of radiological images in all infected patients with COVID-19.

Characteristics of COVID-19 in cancer patients: a cross-sectional study in Peru

BACKGROUND

Cancer patients are at higher risk of infection and severity of Coronavirus Disease-19 (COVID-19). Management of patients infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is challenging due to the scarce scientific information and treatment guidelines. In this work, we present our Institutional experience with our first 100 patients with oncological malignancies and COVID-19.

PATIENTS AND METHODS

We conducted a cross-sectional study of the first 100 patients hospitalised at the Instituto Nacional de Enfermedades Neoplasicas (Lima, Peru) who were positive for SARS-CoV-2 by reverse transcriptase (RT)-PCR during the period 30 March to 20 June. Clinicopathological variables of the oncological disease as well as risk factors, management and outcomes to COVID-19 were evaluated.

RESULTS

The mean age was 43.5 years old (standard deviations: ±24.8) where 57% were male patients. In total, 44%, 37% and 19% were adult patients bearing solid tumours, adults with haematologic malignancies and paediatric patients, respectively. Hypertension was the most frequent comorbidity (23%) followed by chronic lung disease (10%). COVID-19-associated symptoms included cough (65%), fever (57%) and dyspnoea (56%). Twelve percent of patients were asymptomatic. Nosocomial infections were more frequent in paediatric patients (84.2%) than in adult patients (16.0%). Patients with uncontrolled oncological disease were most frequent (72%). Anaemia was present in 67% of patients, 68% had lymphopenia, 62% had ferritin value > 500 mcg/L, 85% had elevated lactate dehydrogenase (LDH), 83% D-dimer > 500 ng/mL and 80% C-Reactive Protein > 8 mg/L. The most common complication was acute respiratory failure (42%). Overall fatality rate was 39% where the main cause of mortality was acute respiratory distress syndrome (64.1%).

CONCLUSION

Paediatric patients had better outcomes than adult populations, and a high number of asymptomatic carriers and nosocomial infection, early diagnosis are recommended. Considering oncological treatments 30 days before COVID-19 diagnosis, our data did not reveal an increased mortality.

PUM1 and RNase P genes as potential cell-free DNA markers in breast cancer

BACKGROUND

Cell-free DNA (cfDNA) is used in clinical research to identify biomarkers for diagnosis of and follow-up on cancer. Here, we propose a fast and innovative approach using traditional housekeeping genes as cfDNA targets in a copy number analysis. We focus on the application of highly sensitive technology such as digital PCR (dPCR) to differentiate breast cancer (BC) patients and controls by quantifying regions of PUM1 and RPPH1 (RNase P) in plasma samples.

METHODS

We conducted a case-control study with 82 BC patients and 82 healthy women. cfDNA was isolated from plasma using magnetic beads and quantified by spectrophotometry to estimate total cfDNA. Then, both PUM1 and RPPH1 genes were specifically quantified by dPCR. Data analysis was calibrated using a reference genomic DNA in different concentrations.

RESULTS

We found RNase P and PUM1 values were correlated in the patient group (intraclass correlation coefficient [ICC] = 0.842), but they did not have any correlation in healthy women (ICC = 0.519). In dPCR quantification, PUM1 showed the capacity to distinguish early-stage patients and controls with good specificity (98.67%) and sensitivity (100%). Conversely, RNase P had lower cfDNA levels in triple-negative BC patients than luminal subtypes (p < 0.025 for both), confirming their utility for patient classification.

CONCLUSION

We propose the PUM1 gene as a cfDNA marker for early diagnosis of BC and RNase P as a cfDNA marker related to hormonal status and subtype classification in BC. Further studies with larger sample sizes are warranted.

Telemedicine and the current opportunities for the management of oncological patients in Peru in the context of COVID-19 pandemic

COVID-19 pandemic is the more challenging public health emergency of the century, producing the collapse of health systems and unprecedented levels of morbidity and mortality around the world, especially in low resource settings. Patients with chronic diseases are the most affected, not only due to the high susceptibility to SARS-CoV-2 infection but also due to the decrease in opportunities for timely care. In this dark landscape, telemedicine, before limited to very specific scenarios, has become one of our main tools to manage cancer patients, particularly in Latin America where COVID-19 has had a strong impact on the public health. Telemedicine can provide rapid access to specialized cancer care in a scenario complicated, reducing the exposure of patients and healthcare personnel to the SARS-CoV-2. In this review, we would like to share our experience and our workflow using telemedicine at Oncosalud-AUNA, a private clinic in Peru.

Breast cancer mortality trends in Peruvian women

BACKGROUND

Breast cancer (BC) is the most common malignancy in Latin American women, but with a wide variability with respect to their mortality. This study aims to estimate the mortality rates from BC in Peruvian women and to assess mortality trends over 15 years.

METHODS

We calculated BC age-standardized mortality rate (ASMR) per 100,000 women-years using the world standard SEGI population. We estimated joinpoint regression models for BC in Peru and its geographical areas. The spatial analysis was performed using the Moran's I statistic.

RESULTS

In a 15-year period, Peru had a mortality rate of 9.97 per 100,000 women-years. The coastal region had the highest mortality rate (12.15 per 100,000 women-years), followed by the highlands region (4.71 per 100,000 women-years). In 2003, the highest ASMR for BC were in the provinces of Lima, Arequipa, and La Libertad (above 8.0 per 100,000 women-years), whereas in 2017, the highest ASMR were in Tumbes, Callao, and Moquegua (above 13.0 per women-years). The mortality trend for BC has been declining in the coastal region since 2005 (APC = - 1.35, p < 0.05), whereas the highlands region experienced an upward trend throughout the study period (APC = 4.26, p < 0.05). The rainforest region had a stable trend. Spatial analysis showed a Local Indicator of Spatial Association of 0.26 (p < 0.05).

CONCLUSION

We found regional differences in the mortality trends over 15 years. Although the coastal region experienced a downward trend, the highlands had an upward mortality trend in the entire study period. It is necessary to implement tailored public health interventions to reduce BC mortality in Peru.

Profile of entrectinib in the treatment of ROS1-positive non-small cell lung cancer: Evidence to date

ROS proto-oncogene 1 (ROS1) encodes a type I integral membrane protein with tyrosine kinase activity and whose activating alterations are involved in the aggressiveness of several tumor types. Fusions involving ROS1 gene are present in 1-2% of lung adenocarcinomas and other solid tumors. Entrectinib, also known as RXDX-101, is a potent second-generation, multitarget oral inhibitor against NTRK1, NTRK2, NTRK3, ALK, and ROS1 with the ability to cross the blood-brain barrier. Results of Phase I and II trials have led the Food and Drug Administration to grant approval to entrectinib for the treatment of patients with metastatic, ROS1-positive non-small cell lung cancer (NSCLC). In this review, we will describe the biology of ROS1, as well as results of the efficacy and safety of different clinical trials evaluating entrectinib in ROS1-positive NSCLC.

Impact of the Delayed Initiation of Adjuvant Chemotherapy in the Outcome of Triple Negative Breast Cancer

BACKGROUND

Adjuvant chemotherapy decreases the recurrence risk and improves survival rates; however, it is unclear whether a delayed initiation is associated with adverse outcomes, especially in triple negative breast cancer (TNBC). In this study, we evaluated the influence of the time to start adjuvant chemotherapy (TTC) in the outcomes of TNBC.

PATIENTS AND METHODS

We retrospectively analyzed 15 years of data from patients with TNBC who received adjuvant chemotherapy at the Instituto Nacional de Enfermedades Neoplasicas (Lima, Peru). TTC was categorized into 4 groups: ≤ 30, 31 to 60, 61 to 90, and ≥ 91 days. We evaluated overall survival (OS) and distant recurrence-free survival (DRFS). Cox proportional hazard models were used to identify prognostic factors.

RESULTS

In total, 687 patients were included. The mean age at diagnosis was 49.1 years (SD, 11.8 years), and most (62.6%) patients had pathologic stage T2. The median TTC was 48.1 days (SD, 27.4 days); 189 (27.5%) received chemotherapy ≤ 30 days; 329 (47.9%), between 31 and 60 days; 115 (16.7%), between 61 and 90 days; and 54 (7.9%) in ≥ 90 days. In the multivariate analysis, a TTC between 31 and 60 days (hazard ratio [HR], 1.78; 95% confidence interval [CI], 1.17-2.72), 61 and 90 days (HR, 2.38; 95%CI, 1.43-3.97), and ≥ 91 days (HR, 2.45; 95% CI, 1.32-4.55) was associated with an increased mortality in contrast with a TTC < 30 days. Although a TTC between 31 and 60 days, 61 and 90 days, and ≥ 91 days was associated with an increased risk of DRFS (HR, 1.86; 95% CI, 1.24-2.79; HR, 2.34, 95% CI, 1.42-3.867; and HR, 3.16; 95% CI, 1.78-5.61, respectively).

CONCLUSION

A delaying in TTC ≥ 30 days was associated with poorer outcomes. Our data suggest that several efforts should be conducted to avoid a delayed TTC in patients with TNBC.

The hispanic landscape of triple negative breast cancer

Triple-negative breast cancer (TNBC) is a heterogeneous and complex disease characterized by the absence of immunohistochemical expression of estrogen receptor, progesterone receptor and HER2. These breast tumors present an aggressive biology and offer few opportunities to be treated with targeted therapy resulting in bad disease outcomes. The epidemiology of TNBC is intriguing where the understanding of its biology has progressed quickly. One of the peculiarities of this type of cancer is a high prevalence in Afrodescendants and Hispanic patients compared to Caucasian women. In this review we describe some features of TNBC, focusing in the Hispanic population, such as epidemiological, clinicopathological features and molecular features and the correlation between TNBC prevalence and the human development index.

Clinical consequences of resistance to ALK inhibitors in non-small cell lung cancer

Introduction: ALK rearrangements are present in 2-7% of non-small cell lung cancer (NSCLC) cases, where the EML4-ALK fusion is the most frequent. Rearrangement of ALK with other fusion partners occurs only in ≈5% of NSCLC ALK-positive. These patients have benefited from ALK inhibitors, and currently, there are three generations of drugs as the standard of care. The first-generation ALK inhibitor crizotinib is approved in the front-line setting for the treatment of advanced NSCLC; unfortunately, these tumors may eventually develop resistance to this molecule. The Second-generation ALK inhibitors, ceritinib, alectinib, and brigatinib, are approved for patients recently diagnosed or in relapse. The third-generation inhibitor lorlatininb is approved for patients who have developed resistance to any ALK inhibitor.Areas covered: In this review, an unstructured search in Pubmed and SCOPUS was conducted. We summarized the mechanisms of resistance to ALK inhibitors and its consequences in the treatment-decision making in advanced or metastatic NSCLC after failure to a first-line ALK inhibitor.Expert opinion: Currently, there are a growing number of options of therapeutic agents against ALK+ NSCLC (approved and in development); however, adequate selection and sequencing of agents are crucial to deal with the tumor evolution.

Breast-conserving surgery vs. total mastectomy in patients with triple negative breast cancer in early stages: A propensity score analysis

BACKGROUND

Breast-conserving surgery (BCS) as an alternative to total mastectomy (TM) in patients with early-stage triple-negative breast cancer (TNBC) is not widely spread.

OBJECTIVE

We aimed to compare the overall survival (OS) and disease-free survival (DFS) between both surgical approaches in early-stage TNBC patients at 10 years.

METHODS

We conducted a retrospective cohort study in TNBC female patients with stage I-IIa, treated at a single-center during the period of 2000-2014. We estimated and compared the survival rates with the Kaplan Meier and Long-rank test. Propensity scores were calculated with the generalized boosted regression model and were used in the multivariate Cox regression analysis with the covariate adjustment method.

RESULTS

We included 288 patients, 111 in the BCS vs. 177 in the TM group. The median follow-up was 102 months. Moreover, the patients in the BCS group had superior OS (85% vs. 81%, p = 0.56) and DFS (83% vs. 80%, p = 0.42) at 10 years. In the multivariate Cox analysis, BCS decreased the mortality risk (HR: 0.79, 95% CI: 0.37-1.67, p = 0.538), and the locoregional or distant recurrence risk (HR: 0.67, 95% CI: 0.32-1.41, p = 0.294), albeit with no statistical significance.

CONCLUSION

BCS is a safe alternative to TM in Latin-American patients with early-stage TNBC.

Patterns of Mutation Enrichment in Metastatic Triple-Negative Breast Cancer

Background:

Triple-negative breast cancer (TNBC) is a heterogeneous disease with aggressive biology and complex tumor evolution. Our purpose was to identify enrichment patterns of genomic alterations in metastatic triple-negative breast cancer (mTNBC).

Methods:

Genomic data were retrieved (mutations and copy number variations) from 550 primary TNBC tumors from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) and The Cancer Genome Atlas (TCGA) data sets and 58 mTNBC tumors from “Mutational Profile of Metastatic Breast Cancers” and “The Metastatic Breast Cancer Project.” Statistical analysis of microarray data between primary and metastatic tumors was performed using a chi-square test, and the percentage of mutation enrichment in mTNBC cases was estimated. P-values were adjusted for multiple testing with Benjamini-Hochberg method with a false-discovery rate (FDR) <.05. In addition, we identified dominant hallmarks of cancer in mTNBC.

Results:

Seven genes with mutations were enriched in mTNBC after correcting for multiple testing. These included TTN, HMCN1, RELN, PKHD1L1, DMD, FRAS1, and RYR3. Only RPS6KB2 amplification was statistically significant in mTNBC; on the contrary, deletion of the genes TET1, RHOA, EPHA5, SET, KCNJ5, ABCG4, NKX3-1, SDHB, IGF2, and BRCA1 were the most frequent. The molecular alterations related to the hallmark of “genetic instability and mutation” were predominant in mTNBC. Interestingly, the hallmark of “activating immune destruction” was the least represented in mTNBC.

Conclusion:

Despite the study limitations, we identified recurrent patterns of genomic alterations with potential contribution to tumor evolution. Deletions were the aberrations more commonly found in mTNBC. Several molecular alterations are potentially targetable.

Abstract 1518: Gene expression profile and gender differences related with immune processes in solid tumors

Background: We have described before differences in gene expression profile (GEP) of immune gene-sets between genders in non-small cell lung cancers (NSCLC). On the other hand, there are reports mentioning the benefit of immune checkpoint inhibitors (ICI) could be influenced by gender, suggesting differences in immune processes (IP). We decided to evaluate if there are gender-specific differences in solid tumors including melanoma, gastric adenocarcinomas (GAC), head and neck cancer (HNC) and clear renal cell carcinoma (CCRCC).

Methods: GEO (https://www.ncbi.nlm.nih.gov/geo/) datasets were retrieved and analyzed for melanoma, GAC, HNC and CCRCC that contained GEP across Affymetrix and Illumina Microarrays of primary tumors. Datasets were manually verified and cases without gender information or non-tumoral tissue were excluded. Cell lines were not considered in our analysis. Data was pre-processed and gene-set enrichment analysis (GSEA) was conducted individually in the datasets GSE6791, GSE30784, GSE78060, GSE34105, GSE65858 (HNC); GSE73731, GSE36895, GSE11904, GSE40435 (CCRCC); GSE26899, GSE26901 (GAC) and GSE15605 (melanoma). Immune process (IP) grouped by gene ontology and identified with a p-value&lt;0.05 and a FDR&lt;25% were considered enriched.

Results: The number of IP enriched in women was higher than men in HNC (306 IP), GAC (297 IP) followed by melanoma (128 IP) and CCRCC (30 IP). Pathways significantly enriched in women in the four evaluated malignancies were: activation of immune response, activation of innate immune response, antigen receptor mediated signaling pathway, immune response regulating cell surface receptor signaling pathway, positive regulation of innate immune response, regulation of innate immune response and T cell receptor signaling pathway. In contrast to other cancers, only CCRCC showed enrichment of immune gene sets in males.

Conclusions: We find strong patterns of GEP of immune genes in tumors from female patients, suggesting gender-specific patterns of response to ICI. This pool of immune genes differentially expressed could be used as candidate biomarkers for prediction of response to immunotherapy.

Citation Format: Jhajaira M. Araujo, Luis E. Raez, Christian D. Rolfo, Luis J. Schwarz, Ulises Infante-Huaytalla, Kevin J. Paez, Luis R. García, Hober Alvarado, Fany P. Ramos, Sheyla S. Delgado-Espinoza, Jhon B. Cardenas-Farfan, Joshuan J. Barboza-Meca, Jose Caballero-Alvarado, Joseph A. Pinto. Gene expression profile and gender differences related with immune processes in solid tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1518.

Patterns of mutation enrichment in metastatic triple-negative breast cancer

e12596

Background: Triple-Negative breast cancer (TNBC) is a group of heterogeneous tumors with aggressive biology. The purpose of this research was to evaluate enrichment patterns of genomic alterations in metastatic TNBC (mTNBC). Methods: We retrieved genomic data (mutations and copy number variation) from 550 primaries TNBC (pTNBC) from the projects METABRIC and TCGA and 58 mTNBC from the projects “Mutational Profile of Metastatic Breast Cancers” and “The metastatic Breast Cancer Project”. Differences in the proportions of mutations between primary vs. metastatic tumors were evaluated by the Chisquare test and the percentage of enrichment in mTNBC was estimated. Pvalues were adjusted for multiple testing with the Benjamini-Hochberg method with and a FDR < 0.05. In addition we conducted an analysis of the hallmarks of cancers enriched in mTNBC. Results: In total, mutations in eight genes were significantly enriched in mTNBC after correcting for multiple testing. These genes included TTN, HMCN1, RELN, PKHD1L1, DMD, FRAS1 and RYR3. In the other hand, only amplification of RPS6KB2 was enriched in mTNBC. Deletions were enriched more frequently in the genes TET1, RHOA, EPHA5, SET, KCNJ5, ABCG4, NKX3-1, SDHB, IGF2, BRCA1, among others. The hallmark of “genetic instability and mutation” was over represented while the hallmark “activating immune destruction” was the least represented between the enriched genetic alterations in mTNBC. Conclusions: Despite the study limitations, we identified that deletions are the aberrations more commonly enriched in mTNBC while some biological processes could be targetable in order to improve the therapeutic opportunities in TNBC.

ALK rearrangements: Biology, detection and opportunities of therapy in non-small cell lung cancer

The ALK receptor tyrosine kinase (ALK) gene encodes a transmembrane protein rearranged in 2-7% of non-small cell lung cancer (NSCLC) cases. This gene has become the second most studied therapeutic target after EGFR due to the implied therapeutic opportunities. While the diagnostic of ALK rearrangements is well established, small molecules targeting ALK are in constant evolution because tumor cells eventually will develop mechanisms of resistance. In this review we describe the biology of the ALK gene, alterations, epidemiology, diagnostic tests as well as strategies of treatment.

Abstract P4-01-09: Combined analysis of tissue and blood biopsies by NGS in patients with advanced breast cancer identifies targetable molecular alterations

Background: Targeted-next generation sequencing (t-NGS) analysis in tissue and peripheral blood is increasingly performed in patients with advanced cancer. Liquid biopsy is a non-invasive method that allows to understand the molecular changes occurring in the tumor in real-time, derived from intratumor heterogeneity and/or therapeutic pressure. In the present work we sought to elucidate the ability of liquid biopsy to detect mutations related with acquired resistance.

Methods: 190 formalin-fixed paraffin-embedded (FFPE) samples from primary and metastatic tumors of patients with advanced breast cancer (ABC) were analyzed by OncoDEEP® (1000X depth of coverage of 75 gene alterations including point mutations, insertions/deletions, gene fusions and copy number variations), and comparison between targeted-NGS results from matched primary/metastatic tumors (FFPE) and cell-free DNA (cfDNA) recovery from plasma analyzed by OncoSTRAT&GO® in 34 patients with ABC (193 genes with 1000x and 40 genes with 10000x depth coverage for FFPE and plasma, respectively).

Results: Of the 190 FFPEs analyzed by OncoDEEP®, 41% were triple negative breast cancer (TNBC), 49% hormone receptor positive (HR+) and 11% were HER2+. Mutations in TP53 (44.2%), PIK3CA (41.1%) and ERBB2 (9.47%) were the most frequent. As expected, PIK3CA and TP53 mutations were significantly higher in HR+ and TNBC tumors, respectively (PIK3CA: 53.8% for HR+ vs 28.6% and 30% for TNBC and HER2+, respectively; TP53 68.8% for TNBC vs 26.9 and 30% in HR+ and HER2+, respectively; in both cases p&lt;0.001). Interestingly, the alteration c.1459-7C&gt;T in JAK1 (unknown significance) was detected in 8% of patients (9.7% and 6.5% in HR+ and TNBC, respectively). Also, in contrast to other reports, high frequencies of APC alterations were found exclusively in HR+ tumors (previously reported as germline mutations). From the OncoSTRAT&GO® analysis (tumor tissue and cfDNA), ESR1 and FGFR mutations in HR+ ABC were significantly more present in cfDNA (9/20 mutations found [45%]] compared to tumor tissue analysis (18/93 mutations found [19.3%]) (p=0.02), and in three patients, mutations in ESR1 and FGRF were only detected in cfDNA. Finally, 11/34 cases (32.3%) showed gene mutations only in cfDNA with predominant alterations in MAPK signaling pathway (54.5%), TP53 (36.4%) and ESR1 (18.2%), the latest as previously described.

Conclusions: JAK1 and APC mutations need further evaluation to establish their clinical significance in ABC. The combination of tumor tissue and cfDNA t-NGS analyses into clinical routine enables detailed and comprehensive evaluation of tumor heterogeneity under therapeutic pressure; in our cohort, known mutations for acquired resistance to endocrine therapy (ESR1 and FGFR2) were better detected by cfDNA compared to tumor tissue (45% vs 19.3%) in HR+ ABC patients, increasing the probability to identify early drug resistance to prioritize patients' selection into clinical trials with targeted agents.

Citation Format: Salvador JF, Pinto JA, Araujo JM, Tirado-Hurtado I, Flores CJ, Chirinos LA, Requena MC, Carpio S, Finzel Pérez A, Aguilar A, Demol F, Schwarz LJ. Combined analysis of tissue and blood biopsies by NGS in patients with advanced breast cancer identifies targetable molecular alterations [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 P4-01-09.

Precision medicine for locally advanced breast cancer: frontiers and challenges in Latin America

Advances in high-throughput technologies and their involvement in the 'omics' of cancer have made possible the identification of hundreds of biomarkers and the development of predictive and prognostic platforms that model the management of cancer from evidence-based medicine to precision medicine. Latin America (LATAM) is a region characterised by fragmented healthcare, high rates of poverty and disparities to access to a basic standard of care not only for cancer but also for other complex diseases. Patients from the public setting cannot afford targeted therapy, the facilities offering genomic platforms are scarce and the use of high-precision radiotherapy is limited to few facilities. Despite the fact that LATAM oncologists are well-trained in the use of genomic platforms and constantly participate in genomic projects, a medical practice based in precision oncology is a great challenge and frequently limited to private practice. In breast cancer, we are waiting for the results of large basket trials to incorporate the detection of actionable mutations to select targeted treatments, in a similar way to the management of lung cancer. On the other hand and paradoxically, in the 'one fit is not for all' era, clinical and genomic studies continue grouping our patients under the single label 'Latin American' or 'Hispanic' despite the different ancestries and genomic backgrounds seen in the region. More regional cancer genomic initiatives and public availability of this data are needed in order to develop more precise oncology in locally advanced breast cancer.

Barriers in Latin America for the management of locally advanced breast cancer

Breast cancer (BC) is a highly prevalent malignancy in Latin American women, most cases being diagnosed at locally advanced or metastatic stages when options for cancer care are limited. Despite its label as a public health problem in the region, Latin American BC patients face several barriers in accessing standard of care treatment when compared with patients from developed countries. In this review, we analyse the landscape of the four main identified barriers in the region: i) high burden of locally advanced/advanced BC; ii) inadequate access to medical resources; iii) deficient access to specialised cancer care and iv) insufficient BC research in Latin America. Unfortunately, these barriers represent the main factors associated with the BC poor outcomes seen in the region. Targeted actions should be conducted independently by each country and as a region to overcome these limitations and create an enhanced model of BC care.

Abstract 1585: Evaluation of circulating free DNA in non-metastatic breast cancer

Background Circulating free DNA (cfDNA) is becoming an important tool in diagnosis and prognosis in several types of cancer. In this study we evaluated the association between cfDNA concentrations in peripheral blood with tumoral features of non-metastatic breast cancer patients.

Methods cfDNA was extracted from plasma of peripheral blood of patients with non-metastatic breast cancer and healthy controls. In patients, blood samples were collected before and after surgery, while in controls samples were collected after their results of breast cancer screening. Detection of copy number of PUM1 and RNaseP genes were performed in a QuantStudio® 3D Digital PCR System and quantification was obtained with QuantStudio® 3D AnalysisSuite™ Cloud Software. Raw values were compared among the different clinicopathologic features.

Results In total 26 patients and 25 controls were included. There were significant differences between controls and patients for levels counts of PUM1 and RNaseP genes (p&lt;0.0001 in both cases). In patients, median concentrations before and after surgery for PUM1 were 10.6 copies/uL (range: 2.2-16.3) vs. 7.6 copies/uL (range: 1.3-12.8), respectively (P=0.04) and for RNaseP were 6.6 copies/uL (range: 0.9-20.0) vs. 5.3 copies/uL (range: 0.5-16.0), respectively (P=0.103). Hormonal tumors produced more cfDNA in terms of RNaseP at diagnosis (7.9 vs. 5.6, P=0.049). When we compared patients according to their hormonal status with controls, RNaseP was able to identified positive hormonal receptors patients (P&lt;0.0001). There were no significant differences between other clinicopathologic features. There was a significant decrease after surgery of RNaseP levels in node negative tumors (P=0.049) and PUM1 levels in &gt;10mm tumors (P=0.041).

Conclusions Our results suggest that PUM1 is a better diagnostic biomarker for non-metastatic breast cancer because RNaseP loss sensitivity in negative hormone receptor cases. Hormonal tumors produced more circulating free DNA. RNaseP could be used to monitor node negative patients and PUM1 to patients with &gt;10mm tumors.

Citation Format: Jhajaira M. Araujo, Jaime Ponce, Alexis Murillo, Pamela Rebaza, Pierina Danos, Alfredo Aguilar, Ricardo Fujita, Henry L. Gomez, Joseph A. Pinto, Jose Buleje. Evaluation of circulating free DNA in non-metastatic breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1585.

Gender and outcomes in non-small cell lung cancer: an old prognostic variable comes back for targeted therapy and immunotherapy?

Background

There are well-known differences in gender outcome in non-small cell lung cancer (NSCLC) and other cancers. In this work, we evaluated several randomised clinical trials to explore the gender influence in the outcome of patients with NSCLC treated with targeted therapy and immunotherapy.

Methods

We performed a series of meta-analysis to compare the gender outcome in the routine setting for overall survival and progression-free survival (PFS) in phase III randomised clinical trials comparing EGFR inhibitors versus chemotherapy (OPTIMAL, LUX-lung 3, LUX-lung 6, EURTAC, ENSURE and WTJOG); ALK inhibitors versus chemotherapy (ASCEND 4, ASCEND 5, PROFILE 1014 and NCT009323893) and anti-PD1 checkpoint inhibitors versus chemotherapy (CheckMate 017, CheckMate 026, CheckMate 057, KEYNOTE 010 and KEYNOTE 024).

Results

Female patients with NSCLC have a reduced risk of death compared with men (HR=0.73; 95% CI 0.67 to 0.79; p<0.00001). Women had a better benefit from EGFR inhibitors than men (HR=0.34; 95% CI 0.28 to 0.40; p<0.00001 vs HR=0.44; 95% CI 0.34 to 0.56; p<0.00001, respectively). The benefit from ALK inhibitors was similar for both genders (HR=0.51; 95% CI 0.42 to 0.61; p<0.00001 vs HR=0.48; 95% CI 0.39 to 0.59; p<0.00001, for women and men, respectively). Anti-PD1 inhibitors significantly improved the PFS in male patients when compared with chemotherapy (HR=0.76; 95% CI 0.68 to 0.86; p<0.00001); in contrast, women showed no benefit in 5/5 randomised trials (HR=1.03; 95% CI 0.89 to 1.20; p=0.69).

Conclusions

In this exploratory study, some targeted treatments were influenced by gender. Despite differences in outcomes that could be attributed to different histology, EGFR and smoking status, gender should be evaluated more deeply as prognostic variable in patients with NSCLC.

DNA Damage Inducible Transcript 4 Gene: The Switch of the Metabolism as Potential Target in Cancer

DNA damage inducible transcript 4 (DDIT4) gene is expressed under stress situations turning off the metabolic activity triggered by the mammalian target of rapamycin (mTOR). Several in vitro and in vivo works have demonstrated the ability of DDIT4 to generate resistance to cancer therapy. The link between the metabolism suppression and aggressiveness features of cancer cells remains poorly understood since anti-mTOR agents who are part of the repertoire of drugs used for systemic treatment of cancer achieving variable results. Interestingly, the high DDIT4 expression is associated with worse outcomes compared to tumors with low DDIT4 expression, seen in a wide variety of solid and hematological tumors, which suggests the driver role of this gene and provide the basis to target it as part of a new therapeutic strategy. In this review, we highlight our current knowledge about the biology of DDIT4 and its role as a prognostic biomarker, encompassing the motives for the development of target drugs against DDIT4 as a better target than mTOR inhibitors.

Primary and metastatic brain cancer genomics and emerging biomarkers for immunomodulatory cancer treatment

Recent studies with immunomodulatory agents targeting both cytotoxic T-lymphocyte protein 4 (CTLA4) and programmed cell death 1 (PD1)/programmed cell death ligand 1 (PDL1) have shown to be very effective in several cancers revealing an unexpected great activity in patients with both primary and metastatic brain tumors. Combining anti-CTLA4 and anti-PD1 agents as upfront systemic therapy has revealed to further increase the clinical benefit observed with single agent, even at cost of higher toxicity. Since the brain is an immunological specialized area it's crucial to establish the specific composition of the brain tumors' microenvironment in order to predict the potential activity of immunomodulatory agents. This review briefly summarizes the basis of the brain immunogenicity, providing the most updated clinical evidences in terms of immune-checkpoint inhibitors efficacy and toxicity in both primary and metastatic brain tumors with the final aim of defining potential biomarkers for immunomodulatory cancer treatment.

Repeated observation of immune gene sets enrichment in women with non-small cell lung cancer

There are different biological and clinical patterns of lung cancer between genders indicating intrinsic differences leading to increased sensitivity to cigarette smoke-induced DNA damage, mutational patterns of KRAS and better clinical outcomes in women while differences between genders at gene-expression levels was not previously reported. Here we show an enrichment of immune genes in NSCLC in women compared to men. We found in a GSEA analysis (by biological processes annotated from Gene Ontology) of six public datasets a repeated observation of immune gene sets enrichment in women. "Immune system process", "immune response", "defense response", "cellular defense response" and "regulation of immune system process" were the gene sets most over-represented while APOBEC3G, APOBEC3F, LAT, CD1D and CCL5 represented the top-five core genes. Characterization of immune cell composition with the platform CIBERSORT showed no differences between genders; however, there were differences when tumor tissues were compared to normal tissues. Our results suggest different immune responses in NSCLC between genders that could be related with the different clinical outcome.

History of the development of radiotherapy in Latin America

Radiotherapy was the first nonsurgical treatment for malignant tumours and represents one of the oldest disciplines of oncology. In Latin America, as in many parts of the world, the history of modern oncology begins with the implementation of radiation therapy facilities. The development of radiotherapy in Latin America was possible thanks to the seminal work of radiation oncologists in different countries. As a large territory, there is a need to implement modern facilities and equipment, but unfortunately there are disparities in the access and quality of radiotherapy services across Latin America and even within individual countries. In this review, we describe the history, challenges and success in the implementation of radiotherapy and the frustration caused by the lack of facilities in several Latin American countries.