Lung Cancer Biopsies Research Articles

Liquid Biopsy for Small Cell Lung Cancer either De Novo or Transformed: Systematic Review of Different Applications and Meta-Analysis.

Simple SummarySmall cell lung cancer (SCLC) is an aggressive tumor, which can occur either de novo or from the histologic transformation of non-small cell lung cancer. Liquid biopsy has demonstrated its capability to detect, characterize and monitor different cancers. The aim of this systematic review was to assess the potential added value of liquid biopsy, in terms of circulating tumor DNA (ctDNA) and circulating tumor cells (CTCs), in the management of SCLC, either de novo or transformed. We found ctDNA analysis as the most valuable and feasible technology to be integrated into clinical for disease monitoring (response, relapse, transformation) or for genomic profiling of SCLC, with a potential use also for prognostic stratification. CTCs hold a strong prognostic significance, as confirmed by our meta-analysis (even if potentially biased), but the heterogeneity of available data, the lack of agreed cut-offs, and the less affordable technology make CTCs more difficult to be integrated into present clinical practice.Background: The potential added value of liquid biopsy (LB) is not well determined in the case of small cell lung cancer (SCLC), an aggressive tumor that can occur either de novo or from the histologic transformation of non-small cell lung cancer (NSCLC). Methods: A systematic review of studies adopting LB in patients with SCLC have been performed to assess the clinical utility of circulating tumor DNA (ctDNA) or circulating tumor cells (CTCs). Results: After a screening of 728 records, 62 studies (32 evaluating CTCs, 27 ctDNA, and 3 both) met predetermined eligibility criteria. Only four studies evaluated LB in the diagnostic setting for SCLC, while its prognostic significance was evaluated in 38 studies and prominently supported by both ctDNA and CTCs. A meta-analysis of 11 studies as for CTCs enumeration showed an HR for overall survival of 2.63 (1.71–4.05), with a potential publication bias. The feasibility of tumor genomic profiling and the predictive role of LB in terms of response/resistance to chemotherapy was assessed in 11 and 24 studies, respectively, with greater consistency for those regarding ctDNA. Intriguingly, several case reports suggest that LB can indirectly capture the transition to SCLC in NSCLC treated with EGFR tyrosine kinase inhibitors. Conclusions: While dedicated trials are needed, LB holds potential clinical roles in both de novo and transformed SCLC. CtDNA analysis appears the most valuable and practicable tool for both disease monitoring and genomic profiling.

Liquid biopsy in non-small cell lung cancer-current status and future outlook-a narrative review.

Lung cancer ranks first as the cause of cancer-associated deaths gobally. The American Cancer Society estimates for 228,820 new cases and 135,720 deaths from lung cancer in the United States for the year 2020. Targeted treatment options have rapidly emerged for non-small cell lung cancer (NSCLC) within the past decade. Screening for molecular aberrations is mainly done by tissue biopsy. However, in some cases a biopsy is not possible, or patients do not consent to it. Hence, liquid biopsy remains the only option. Relevant data about the topic of liquid biopsy, with a special focus on NSCLC, was obtained via a PubMed search. We included mainly literature published from 2010 onwards, omitting older studies whenever possible. With this review of the literature, we give an overview of different liquid biopsy approaches, as well as their respective advantages and disadvantages. We have reviewed the assessment of epidermal growth factor receptor (EGFR) mutation status in particular, and go into detail with current use of liquid biopsy in everyday clinical practice. Today, liquid biopsy is still infrequently used, depending on the treatment center, but popularity is steadily increasing. Various different approaches are already available, but costs and level of sensitivity significantly differ between techniques. By using liquid biopsy more widely in selected patients, complication rates can be reduced, and constant disease monitoring is made considerably easier.

Emerging Lab-on-a-Chip Approaches for Liquid Biopsy in Lung Cancer: Status in CTCs and ctDNA Research and Clinical Validation.

Simple SummaryLung cancer (LCa) remains the leading cause of cancer-related mortality worldwide, with late diagnosis and limited therapeutic approaches still constraining patient’s outcome. In recent years, liquid biopsies have significantly improved the disease characterization and brought new insights into LCa diagnosis and management. The integration of microfluidic devices in liquid biopsies have shown promising results regarding circulating biomarkers isolation and analysis and these tools are expected to establish automatized and standardized results for liquid biopsies in the near future. Herein, we review the status of lab-on-a-chip approaches for liquid biopsies in LCa and highlight their current applications for circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) research and clinical validation studies.Despite the intensive efforts dedicated to cancer diagnosis and treatment, lung cancer (LCa) remains the leading cause of cancer-related mortality, worldwide. The poor survival rate among lung cancer patients commonly results from diagnosis at late-stage, limitations in characterizing tumor heterogeneity and the lack of non-invasive tools for detection of residual disease and early recurrence. Henceforth, research on liquid biopsies has been increasingly devoted to overcoming these major limitations and improving management of LCa patients. Liquid biopsy is an emerging field that has evolved significantly in recent years due its minimally invasive nature and potential to assess various disease biomarkers. Several strategies for characterization of circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA) have been developed. With the aim of standardizing diagnostic and follow-up practices, microfluidic devices have been introduced to improve biomarkers isolation efficiency and specificity. Nonetheless, implementation of lab-on-a-chip platforms in clinical practice may face some challenges, considering its recent application to liquid biopsies. In this review, recent advances and strategies for the use of liquid biopsies in LCa management are discussed, focusing on high-throughput microfluidic devices applied for CTCs and ctDNA isolation and detection, current clinical validation studies and potential clinical utility.

CD5L as an Extracellular Vesicle-Derived Biomarker for Liquid Biopsy of Lung Cancer.

Cancer screening and diagnosis can be achieved by analyzing specific molecules within serum-derived extracellular vesicles (EVs). This study sought to profile EV-derived proteins to identify potential lung cancer biomarkers. EVs were isolated from 80 serum samples from healthy individuals and cancer patients via polyethylene glycol (PEG)-based precipitation and immunoaffinity separation using antibodies against CD9, CD63, CD81, and EpCAM. Proteomic analysis was performed using 2-D gel electrophoresis and matrix-assisted laser desorption ionization–time-of-flight mass spectrometry (MALDI–TOF MS). The expression of proteins that were differentially upregulated in the EVs or tissue of lung cancer samples was validated by Western blotting. The area under the curve (AUC) was calculated to assess the predictability of each differentially expressed protein (DEP) for lung cancer. A total of 55 upregulated protein spots were selected, seven of which (CD5L, CLEC3B, ITIH4, SERFINF1, SAA4, SERFINC1, and C20ORF3) were found to be expressed at high levels in patient-derived EVs by Western blotting. Meanwhile, only the expression of EV CD5L correlated with that in cancer tissues. CD5L also demonstrated the highest AUC value (0.943) and was found to be the core regulator in a pathway related to cell dysfunction. Cumulatively, these results show that EV-derived CD5L may represent a potential biomarker—detected via a liquid biopsy—for the noninvasive diagnosis of lung cancer.

Neuroendocrine Differentiation in Non-Small Cell Lung Cancer and its Relation to Different Pathologic Features: An Immunohistochemical Study

Objectives: To identify the relevance of neuroendocrine differentiation in non-small cell lung cancer and its correlation with different pathological features. Materials and Methods: A total number of 30 cases of per cutaneous CT guided biopsies of primary non-small lung cancer were collected in the pathology department of Misr University for Science and Technology Giza, Egypt and private practice in the time period from January 2018 till December 2020. Immunohistochemical study for neuroendocrine differentiation was performed using mono clonal antibodies against synaptophysin, chromogranin A and CD56. For all selected cases, clinical and pathological data such as age, gender, histologic types, grade and clinical stage were collected, tabulated and statistically analyzed with the results of neuroendocrine markers expression. Cases with incomplete pathological data and cases with histologic picture of neuroendocrine differentiation were excluded. Results: A total number of 30 cases of primary non-small lung cancer were enrolled in this study. The median age of patients was 61.5 years. There were 21 (70%) males and 9 (30%) females. Regarding neuroendocrine markers, positivity for either marker was identified in 23.3% of non-small cell lung cancer. Chromogranin A was positively expressed in 9 (30%) of cases, synaptophysin was positively expressed in 7 (23.3%) of cases and CD56 was positively expressed in 5 (16.7%) of cases. Only 2 cases (6.7%) showed co-expression of two markers. It was found that there was a high significant relation between chromogranin A expression and clinical stage. Chromogranin A expression was significantly higher in stage III than stage I and II (P<0.001). There was no statistical significant difference between synaptophysin, chromogranin A and CD56 expressions and the rest of the studied pathologic data. Conclusion: A considerable number of non-small cell lung cancer has neuroendocrine differentiation for at least one neuroendocrine marker despite absence of morphologic features. Much less number of cases showed expression of two markers. A reasonable panel of neuroendocrine markers is recommended to detect this differentiation which may have a clinical impact and optimize an alternative therapeutic option.

Abstract PO-006: Artificial intelligence aided interpretation of ALK fluorescent in situ hybridization for lung cancer: An algorithm development based on 10-year-annotated quality control files in central laboratory

Abstract Molecular testing became the most important part of lung cancer diagnostics. Among them, an interpretation of fluorescent in situ hybridization (FISH) is challenging for the routine clinical samples with various amounts and quality. In this study, we trained a variant of DenseNet, a convolutional neural network model with the highest performance in image classification and suitable for quality assessment. Train dataset is composed of the arbitrarily classified dataset made and assessed by a professional pathologist during routine molecular test using whole-slide tissue images and molecular profiles including DNA density and the signal intensity of FISH obtained from 15,000 tests from lung cancer biopsies and resections, which were sent to the central laboratory for molecular studies from 45 hospitals nationwide. The performance of our platform is tested and compared to the quality assessment dataset made from each a general pathologist and a technician. The performance of our method for classifying DNA concentration and the signal intensity of FISH is comparable to that of a general pathologist and technicians. we are under improving its average area under the curve (AUC) over 0.85. This result suggests that a deep learning model based on a convolutional neural network can assist pathologists and pathology technician in rigorous assessing the quality of tissue morphology and signal of FISH for tissue samples with various molecular quality before or during the molecular test and can be applied to quality control of lung cancer molecular testing in a central laboratory. Citation Format: Tae-Jung Kim, Ho Chul Kang, Yonggeun Lee, Seokman Seo, Donghwan Kim, Sungjin Cho. Artificial intelligence aided interpretation of ALK fluorescent in situ hybridization for lung cancer: An algorithm development based on 10-year-annotated quality control files in central laboratory [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr PO-006.

P89.03 Demonstrating VALUE of Liquid Biopsy for Lung Cancer in a Public Healthcare System

Liquid biopsy (LB) is an important alternative for advanced lung cancer patients in diagnosing resistance or where tissue genotyping has failed. The VALUE study examines clinical outcomes and utility of LB for molecular diagnosis in treatment naive stage IV lung adenocarcinoma patients. [Preliminary data previously presented at ASCO2020. Final study results will be available for WCLC2021] This study is being conducted at 6 Canadian centres (NCT03576937) using Guardant360TM (G360), a validated cell-free DNA next-generation sequencing assay that identifies variants in 74 cancer-associated genes, including fusions and copy number gain. Patients with treatment-naïve advanced non-squamous lung carcinoma, ≤10 pack-year smoking history, and measurable disease are eligible (N=150). Patients receive standard of care tumour tissue (TT) molecular profiling (EGFR, ALK +/- ROS1) and LB. The primary endpoint is response rate to first-line therapy (RECIST 1.1); secondary endpoints include incremental targetable alterations identified through G360 (EGFR, ALK, BRAF, ERBB2, KRAS (G12C), NTRK, MET (amplification, exon 14 skipping), RET, ROS1), turnaround time (TAT) and successful molecular profiling rates. To date, 150 eligible patients have been enrolled. Demographic data are available for the first 100 patients, treatment data for 89 and 60 have response data. Median age is 63 (range 22-91), 63% are female, 85% never smokers, 35% East Asian, 24% ECOG PS>1, and 94% have adenocarcinoma. Actionable targets have been identified in 55% of patients using G360 (EGFR/ALK in 38%), and 38% using standard TT profiling. Concordance between TT and LB was high, 84%, with 8 cases each identified by TT or LB but not the other. TT profiling for EGFR/ALK was unsuccessful in 6% of patients (insufficient tissue, failed biopsy, single biomarker tested only). Fifteen patients (15%) had no ctDNA alterations detected by G360 (low disease burden vs. non-shedding). Of 89 patients receiving first-line treatment, 60% received targeted therapy, 26% chemo-immunotherapy combinations, 10% checkpoint inhibitors alone and 4% were observed. Treatment decisions were informed by G360 alone in 40% and by G360+TT results in 28% (by physician report). Among 51 evaluable patients, ORR was 55% (28/51). Using G360, ORR was 75% (18/24) in those with actionable alterations and 37% (10/27) in those without. Using TT, ORR was 64% (16/25) in those with actionable alterations and 46% (12/26) in those without. Mean TAT was 7.7 days (SD+/-1.6) for LB vs 20.8 days (SD+/- 9.8) for TT. LB using G360 identifies actionable targets beyond tissue profiling alone in newly diagnosed lung cancer patients, has faster TAT and yields similar outcomes with targeted and non-targeted therapy.

Updates on liquid biopsy: current trends and future perspectives for clinical application in solid tumors.

Despite advances in screening and therapeutics cancer continues to be one of the major causes of morbidity and mortality worldwide. The molecular profile of tumor is routinely assessed by surgical or bioptic samples, however, genotyping of tissue has inherent limitations: it represents a single snapshot in time and it is subjected to spatial selection bias owing to tumor heterogeneity. Liquid biopsy has emerged as a novel, non-invasive opportunity of detecting and monitoring cancer in several body fluids instead of tumor tissue. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA), RNA (mRNA and microRNA), microvesicles, including exosomes and tumor "educated platelets" were recently identified as a source of genomic information in cancer patients which could reflect all subclones present in primary and metastatic lesions allowing sequential monitoring of disease evolution. In this review, we summarize the currently available information concerning liquid biopsy in breast cancer, colon cancer, lung cancer and melanoma. These promising issues still need to be standardized and harmonized across laboratories, before fully adopting liquid biopsy approaches into clinical practice.

Current Status and Future Perspectives of Liquid Biopsy in Small Cell Lung Cancer.

Approximately 19% of all cancer-related deaths are due to lung cancer, which is the leading cause of mortality worldwide. Small cell lung cancer (SCLC) affects approximately 15% of patients diagnosed with lung cancer. SCLC is characterized by aggressiveness; the majority of SCLC patients present with metastatic disease, and less than 5% of patients are alive at 5 years. The gold standard of SCLC treatment is platinum and etoposide-based chemotherapy; however, its effects are short. In recent years, treatment for SCLC has changed; new drugs have been approved, and new biomarkers are needed for treatment selection. Liquid biopsy is a non-invasive, rapid, repeated and alternative tool to the traditional tumor biopsy that could allow the most personalized medicine into the management of SCLC patients. Circulating tumor cells (CTCs) and cell-free DNA (cfDNA) are the most commonly used liquid biopsy biomarkers. Some studies have reported the prognostic factors of CTCs and cfDNA in SCLC patients, independent of the stage. In this review, we summarize the recent SCLC studies of CTCs, cfDNA and other liquid biopsy biomarkers, and we discuss the future utility of liquid biopsy in the clinical management of SCLC.

Could concurrent biopsy and microwave ablation be reliable? Concordance between frozen section examination and final pathology in CT-guided biopsy of lung cancer

Purpose Microwave ablation combined with concurrent biopsy has been used for lung cancer. Frozen section (FS) diagnosis is an important supplement for the final pathology (FP). Thus, a retrospective study was conducted to evaluate the concordance between FS examination and FP in the computed tomography (CT)-guided biopsy of lung cancer. Materials and methods Patients who underwent percutaneous transthoracic needle lung biopsies and were diagnosed using both intraoperative FS examination and FP were retrospectively enrolled. Concordance between FS findings and FP in the diagnosis of malignant lung cancer and the definitive histology types were recorded. Results Overall, 163 patients were enrolled. The concordance rate in the diagnosis of malignant tumors was 96.3%. The definitive histology types were concordant between FS examinations and FP in 112 patients (68.7%). Lung cancers undefined with FS but diagnosed as adenocarcinoma with FP were the most common type, observed in 18 patients. The concordance in the histology type was lower for those requiring immunohistochemistry for FP diagnoses (47.3 vs. 79.6%, p < 0.000). Concordance rates differed for the different histology types diagnosed using FP (adenocarcinoma vs. squamous cell carcinoma vs. small-cell lung cancer vs. others, 76.6 vs. 56.2 vs. 69.2 vs. 0.0%, p < 0.000). Conclusions FS was inferior to FP in the diagnosis of definitive histology types, but had a high concordance with FP in the diagnosis of malignant lung cancer.

Liquid biopsy in NSCLC: a new challenge in radiation therapy.

Lung cancer is the most common cancer and the leading cause of cancer mortality worldwide. To date, tissue biopsy has been the gold standard for the diagnosis and the identification of specific molecular mutations, to guide choice of therapy. However, this procedure has several limitations. Liquid biopsy could represent a solution to the intrinsic limits of traditional biopsy. It can detect cancer markers such as circulating tumor DNA or RNA (ctDNA, ctRNA), and circulating tumor cells, in plasma, serum or other biological fluids. This procedure is minimally invasive, reproducible and can be used repeatedly. The main clinical applications of liquid biopsy in non-small cell lung cancer (NSCLC) patients are the early diagnosis, stratification of the risk of relapse, identification of mutations to guide application of targeted therapy and the evaluation of the minimum residual disease. In this review, the current role of liquid biopsy and associated markers in the management of NSCLC patients was analyzed, with emphasis on ctDNA and CTCs, and radiotherapy.

Scoping the Problem

Scoping the Problem

Novel Universal Primers to Identify the Expression of MAGE A1-A10 in the Core Biopsy of Lung Cancer

Background: Recent studies have reported that melanoma antigen (MAGE) gene is expressed in a variety of cancers and testicular tissues. The expression of MAGE-A genes could be used for biomarkers with high tumor specificity; however, there is still a lack of data on most solid tumors. The objective of this study was to construct novel universal primers for detecting the mRNA of MAGE A1-10 genes in lung cancer patients. Method: We conducted this cross-sectional study in 2017 at Dr. Soetomo General Academic Hospital, Surabaya, Indonesia. The specimens were a testicular tissue and 15 core biopsies of lung cancer tissues. We designed the universal primers to bind the mRNA of MAGE A1, A2, A2B, A3, A4, A5, A6, A8, A9, A9B, and A10 regions; the assay was performed by nested PCR and continued by direct sequencing. Results: Using the universal primer MAGE A1-10, the PCR was able to detect the MAGE A mRNA of 10 subtypes of MAGE A from testicular and lung cancer tissues. The sequences analysis of individual MAGE A1-10 showed the same homology with MAGE A from GenBank data. Among the 15 lung cancer patients, 13/15 (86.67%) tested positive for GAPDH; subsequently, they were considered for MAGE-A gene detection; while, those testing negative for GAPDH were excluded. The PCR results showed that 12/13 (92.31%) had positive MAGE A1-10 tests and 3/13 (23.08%) tested positive for MAGE A1-6. Conclusion: This finding showed that the novel universal primers could be applied as a new tool for detecting MAGE A1-10 expression in cancer cells.

EGFR mutation testing from liquid biopsy of non-small cell lung cancer at the Institute for Oncology and Radiology of Serbia

EGFR mutation testing from liquid biopsy of non-small cell lung cancer at the Institute for Oncology and Radiology of Serbia

Liquid Biopsy in Small Cell Lung Cancer-A Route to Improved Clinical Care?

Small cell lung cancer (SCLC) has a particularly poor prognosis despite the high initial response to first-line systemic therapy, and there is a well-recognised lack of meaningful treatments beyond the second line. A number of reasons have been put forward to explain this, including a lack of common, easily-druggable genetic mutations in SCLC and rarity of high-quality tissue samples due to late presentation. Liquid biopsies, including circulating tumour cells (CTCs) and circulating tumour DNA (ctDNA) are increasingly used as surrogates for tumour tissue and have the advantage of being easily obtained serially to inform on the biology of disease progression and acquired chemoresistance, and may provide a pathway to improve care in this notoriously refractory disease. Here we discuss the current evidence behind these liquid biopsy methods in SCLC, and how they could be employed in future clinical care.

Contribution of miRNAs, tRNAs and tRFs to Aberrant Signaling and Translation Deregulation in Lung Cancer.

Transcriptomics profiles of miRNAs, tRNAs or tRFs are used as biomarkers, after separate examination of several cancer cell lines, blood samples or biopsies. However, the possible contribution of all three profiles on oncogenic signaling and translation as a net regulatory effect, is under investigation. The present analysis of miRNAs and tRFs from lung cancer biopsies indicated putative targets, which belong to gene networks involved in cell proliferation, transcription and translation regulation. In addition, we observed differential expression of specific tRNAs along with several tRNA-related genes with possible involvement in carcinogenesis. Transfection of lung adenocarcinoma cells with two identified tRFs and subsequent NGS analysis indicated gene targets that mediate signaling and translation regulation. Broader analysis of all major signaling and translation factors in several biopsy specimens revealed a crosstalk between the PI3K/AKT and MAPK pathways and downstream activation of eIF4E and eEF2. Subsequent polysome profile analysis and 48S pre-initiation reconstitution experiments showed increased global translation rates and indicated that aberrant expression patterns of translation initiation factors could contribute to elevated protein synthesis. Overall, our results outline the modulatory effects that possibly correlate the expression of important regulatory non-coding RNAs with aberrant signaling and translation deregulation in lung cancer.

High concordance of programmed death-ligand 1 expression with immunohistochemistry detection between antibody clones 22C3 and E1L3N in non-small cell lung cancer biopsy samples.

BackgroundThe detection of programmed death-ligand 1 (PD-L1) expression can enrich for patients who respond to anti-programmed cell death 1 (PD-1)/PD-L1 therapies. Though, for most laboratories, the cost of PD-L1 22C3 pharmDx is prohibitive for widespread use, whereas the laboratory-developed test (LDT) PD-L1 E1L3N antibody clone is widely available and inexpensive. This study aims to explore the analytical performance of E1L3N on the Dako Autostainer Link-48 platform and further evaluate the concordance of E1L3N and 22C3 expression in non-small cell lung cancer (NSCLC) biopsy samples.MethodsA total of 171 NSCLC biopsy samples were utilized in this study. Cases with less than 100 tumor cells were excluded. Serial sections of representative blocks were used for immunohistochemistry (IHC) staining. The staining protocol was performed according to the standard PD-L1 IHC 22C3 pharmDx package. PD-L1 staining on the tumor cell membrane was detected by immunofluorescence.ResultsAt a 1% cutoff value, PD-L1 was positive in 46.2% of patients using clone 22C3 and 42.1% of patients using E1L3N assays. At a 50% cutoff value, PD-L1 was positive in 16.4% of patients using clone 22C3 and 15.2% of the patients using E1L3N assays. Cohen’s kappa was used to evaluate the concordance of the PD-L1 expression between clone 22C3 and E1L3N. The kappa values were 0.893 [95% confidence interval (CI): 0.826–1] at the 1% cutoff and 0.868 (95% CI: 0.764–1) at the 50% cutoff. An evaluation of the intraclass correlation coefficients (ICCs) between the antibodies was used to quantify the interassay variability for PD-L1 expression in tumor cells. ICCs showed high concordance between the two antibodies (0.955, 95% CI: 0.939–0.967). Cohen’s kappa was also used to assess the consistency of the PD-L1 evaluation between two pathologists. The kappa values were 0.941 and 0.912 at the 1% cutoff, and 0.904 and 0.909 at the 50% cutoff for clone 22C3 and E1L3N expression, respectively.ConclusionsThe results indicated that the clone E1L3N assay has a high concordance with 22C3. The PD-L1 clone E1L3N assay is reliable and cost-effective, and could be used as a primary screening agent for PD-L1 IHC staining in pathological laboratories, especially in a research setting.

Liquid biopsy in lung cancer: tertiary prevention potential

Abstract Background In the era of personalized therapy liquid biopsy is considered an important diagnostic tool in the clinical management of cancer patients. Tissue specimen represents “gold standard” for molecular evaluation of specific gene targets alterations that lead cancer patients to benefit of a “tailed therapy” based on molecular features of the tumor. This innovative source of nucleic acids was introduced in clinical setting only for NSCLC patients to test Epidermal Grow Factor Receptor (EGFR) mutations when tissue is not available or to monitor acquired resistance mutation after a first line of treatment. The study aimed at assessing the diagnostic potential of liquid biopsy in balanced tertiary screening modeling. Methods The cases relating to 5 years of activity regarding to molecular diagnostics performed on liquid biopsy specimens in the Predictive Diagnostic laboratory of AOU Federico II were reviewed. Laboratory data were collected in SPSS. Non parametric analysis were performed in order to test the differences between patients WILD TYPE or not. A multivariate logistic model was performed in order to assess the effect of mutation, age and sex, on the tumor progression. The results of the revision concern 515 total cases (almost of all plasma or peripheral blood) allowed to evaluate the liquid biopsies for women and men. The average age of the Patients is 66.3 years, and the 25 percentile is 59 years. Results The cases are 221 basal and 294 by progression. The cases with mutation, as expected, have an OR 4,15 compared to the basal to have a tumor progression (95% IC: 2,7 - 6,3) regardless of sex and age. The mutations detected were 131 from different types of pulmonary carcinomas. Conclusions Working on case data, specifying the characteristics of the Patients with mutations will drive a further estimate in tertiary prevention screening designs. Key messages In the last five years, the liquid biopsy has been used for different purposes in oncology. To specify the characteristics of the Patients with mutations will drive a further estimate in tertiary prevention screening designs.

Abstract 3338: Intra-tumoral microbes correlate with immune cell fractions in lung cancer biopsies not other cancers

Abstract Exogenous sequences in bacteria have been found in many tumors, but their effect on outcomes remains largely unknown. We hypothesize that intratumoral microbes elicit effects through the recruitment of immune cells, such as CD8+ T-cells that are important for immunotherapy response. Through ORIEN (Oncology Research Information Exchange Network), we obtained RNA-seq data from biopsies of 480 tumors (Melanoma=16, Bladder=104, Colorectal=20 Renal Cell Carcinoma=20, Sarcoma=118, Lung=202) from patients treated at The Ohio State University Comprehensive Cancer Center. Reads were aligned to human and exogenous genomes using TopHat2 and Kraken2/Bracken, respectively. Human gene expression was deconvolved to relative abundances of immune cells using CIBERSORT. Across cancers, an average of 99.87% of reads were aligned to the human reference genome. The immune cell types CD8+ T-cells, activated dendritic cells and M1 macrophages were significantly enriched in lung cancer (p-values &amp;lt;0.0001), and M2 macrophages were significantly enriched in sarcoma (p-values&amp;lt;0.0001). On the other hand, exogenous reads were aligned to 1328 genomes of bacteria, archaea, viruses and fungi. The phyla with the largest average relative abundances were Proteobacteria, Firmicutes and Actinobacteria, with average relative abundances of 39.5%, 20.1%, and 5.16% respectively. In lung cancer, there was a significant positive correlation between the fraction of CD8+ T-cells and Acinetobacter junii (p-value=0.035), and between activated NK cells and Acidipropionibacterium virtanenii (p-value=0.035). This suggests a mechanism by which intratumoral microbes may affect the immune system and thereby cancer outcomes. Citation Format: Xiaokui Mo, Daniel Spakowicz, Rebecca Hoyd. Intra-tumoral microbes correlate with immune cell fractions in lung cancer biopsies not other cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3338.

Abstract 4254: Quality assessment platform for molecular pathology from non small cell lung cancer histopathology images using deep learning: A nationwide study of central laboratory in South Korea

Abstract Molecular testing became the most important part of lung cancer diagnostics. Integration of various molecular testing such as real-time PCR, fluorescent in situ hybridization (FISH) and next-generation sequencing into routine clinical practice and their systemic quality control is challenging to a pathologist and even more in the central laboratory. In this study, we trained a variant of DenseNet, a convolutional neural network model with the highest performance in image classification and suitable for quality assessment. Train dataset is composed of the arbitrarily classified dataset made and assessed by a professional pathologist during routine molecular test using whole-slide tissue images and molecular profiles including DNA density and the signal intensity of FISH obtained from 15,000 tests from lung cancer biopsies and resections, which were sent to the central laboratory for molecular studies from 45 hospitals nationwide. The performance of our platform is tested and compared to the quality assessment dataset made from each a general pathologist and a technician. The performance of our method for classifying DNA concentration and the signal intensity of FISH is comparable to that of a general pathologist and we are under improving its average area under the curve (AUC) over 0.95. This result suggests that deep learning model based on a convolutional neural network can assist pathologists for rigorous assessing quality of tissue morphology and signal of FISH for tissue samples with various molecular quality before or during the molecular test and, furthermore, can be applied to quality control of lung cancer molecular testing in a central laboratory. Citation Format: Tae-Jung Kim, Ho Chul Kang, Yonggeun Lee, Seokman Seo, Donghwan Kim. Quality assessment platform for molecular pathology from non small cell lung cancer histopathology images using deep learning: A nationwide study of central laboratory in South Korea [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4254.