The prospect and challenge of liquid biopsy in the diagnosis and treatment of chest malignancy / 中华预防医学杂志

In recent years, the incidence of chest malignant tumors in China has increased year by year, which has seriously threatened the health problems of people. Among them, early screening and intervention of patients with chest malignancies is the key to cancer prevention. Early detection, early diagnosis, and early treatment as the "three early prevention" of clinical practice are conducive to improve the survival rate of tumor patients. As a non-invasive and real-time reflection of tumor status, liquid biopsy has gradually received attention in clinical diagnosis and treatment. Circulating tumor cells (CTCs), circulating tumor DNA (ctDNA) and exosomes as liquid biopsy "Three carriages" are not only widely used in the diagnosis, monitoring and prognostic evaluation of chest malignancies, but also face many unknown challenges. In this article, the application of liquid biopsy in chest malignancies in recent years is elaborated in detail, which provides a reference for the formulation of clinical tumor prevention and diagnosis and treatment strategies.

Utilização de biópsia líquida baseada em detecção de DNA tumoral em urina e plasma em pacientes com carcinoma renal de células claras / Use of liquid biopsy based on detection of tumor DNA in urine and plasma in patients with clear cell renal carcinoma

O carcinoma de células renais (CCR) é o sétimo tipo de câncer mais comum no ocidente e vêm apresentando um aumento em sua prevalência. A classificação histológica dos CCRs é a abordagem mais utilizada para determinar o subtipo da doença, bem como prognosticar o paciente. Cerca de 70-80% dos CCRs é do subtipo células claras (ccRCC), o qual representa o subtipo mais prevalente e agressivo da doença. A escolha do tratamento difere para cada paciente, sendo a ressecção cirúrgica a terapia mais efetiva nos casos de doença localizada. Apesar de ser um tratamento já estabelecido, estudos mostram uma certa heterogeneidade entre massas renais detectadas, onde cerca de 20% apresentam um perfil benigno, 60% são considerados tumores indolentes, sugerindo desta forma que, entender de forma mais detalhada este tumor pode auxiliar na escolha de um tratamento mais direcionado para o paciente. Sendo assim, o presente trabalho buscou selecionar genes potencialmente alterados em CCR com o intuito de customizar um painel multigênico capaz de identificar variantes somáticas, específicas do tumor, e avaliar as variantes específicas do tumor de forma personalizada em amostras de ctDNA (DNA tumoral circulante) extraídas de plasma e dos dois componentes da urina (sedimento e sobrenadante) coletados no momento da cirurgia (baseline). Neste contexto, dentro de nossa proposta, construímos um painel com 28 genes associados com CCR e sequenciamos 89 casos de tumores renais, juntamente com as amostras de leucócitos. Identificamos que dentre os tumores analisados, 59 apresentavam pelo menos uma variante somática, ou seja, o painel customizado apresentou uma sensibilidade para identificar variantes somáticas em 66% dos casos. Com relação aos 45 tumores classificados como ccRCC em 38 casos identificamos pelo menos uma marca tumoral, ou seja, nosso painel foi capaz de detectar variantes somáticas específicas do tumor em 84,4% desses casos. Um total de 105 variantes somáticas foram identificadas, e os genes mais frequentemente mutados nessa coorte de pacientes foram os genes VHL, PBRM1, BAP1, SETD2. Dos 59 casos em que identificamos variante somática, 44 casos foram avaliados as amostras baseline de plasma e 29 casos de urina (sobrenadante e sedimento), e encontramos pelo menos uma marca tumoral em um dos fluidos corpóreos em 11 pacientes, 6 em amostras de plasma e 6 amostras de urina. Através do desenvolvimento deste estudo, confirmamos que o subtipo ccRCC é o CCR mais bem caracterizado genomicamente e que é importante continuar a investigação genômica principalmente nos subtipos não ccRCC. Além disso o estudo demonstra a viabilidade de utilizar biópsia líquida ctDNA tanto no plasma quanto na urina para fins de diagnóstico e prognóstico.

Renal cell carcinoma (RCC) is the seventh most common type of cancer in the West and its prevalence is increasing. The histological classification of RCCs is the most used approach to determine the disease subtype as well as the patient's prognosis. About 70% of RCCs are of the clear cell Renal Cell Carcinoma subtype (ccRCC), which represents the most prevalent and aggressive subtype of the disease. The choice of treatment is different for each patient. Resection is one of the most effective therapies in cases of localized disease. Despite being an established treatment, studies show a certain heterogeneous profile studied. In this profile, up to 20% even present a benign treatment, helping the indolent, thus suggesting that understanding this tumor in detail can help to choose a more targeted treatment for the patient. Therefore, the present work aimed to select potentially altered genes in CCR in order to customize a multigene panel capable of identifying somatic, tumor-specific variants, and to evaluate the tumor-specific variants in a personalized way in ctDNA (circulating tumor DNA) samples extracted from plasma and from two components of urine (sediment and supernatant) collected at the time of surgery (baseline). In this context, within our proposal, we built a panel with 28 genes associated with CCR and sequenced 89 cases of renal tumors, together with leukocyte samples. We identified that among the analyzed tumors, 59 had at least one somatic variant, that is, the customized panel showed sensitivity to identify somatic variants in 66% of cases. Of the 45 classified as ccRCC in 38 cases we identified at least one tumor marker, that is, our panel was able to detect tumor-specific somatic variants in 84.4%. A total of 105 somatic variants were identified, and the genes most frequently mutated in this cohort of patients were the VHL, PBRM1, BAP1, SETD2 genes. Among 59 cases in which we identified somatic variant, 44 cases were evaluated in baseline plasma samples and 29 cases in urine (supernatant and sediment), and we found at least one tumor mark in one of the body fluids in 11 patients, 6 in plasma samples and 6 urine samples. Through the development of this study, we confirm that the ccRCC subtype is the best genomically characterized CCR and that it is important to continue genomic investigation, especially in the non-ccRCC subtypes. Furthermore, the study demonstrates the feasibility of using ctDNA liquid biopsy in both plasma and urine for diagnostic and prognostic purposes.

Consensus of Chinese experts on hot issues in genetic testing of advanced breast cancer (2021 edition) / 中华肿瘤杂志

Advanced breast cancer is a complicated disease with poor prognosis, which is difficult for salvage treatment. Although advanced breast cancer is difficult to cure at present, we can improve the life quality and prolong survival time of patients by applying optimized treatment. In recent years, with the rapid development of molecular biology and gene testing technology, studies on advanced breast cancer continue to deepen. Gene targeted therapy significantly extends the survival time of patients with advanced breast cancer. Gene testing is one of the important means for molecular typing, genetic diagnosis, therapeutic monitoring, drug resistance, and treatment choice of breast cancer, which is of great significance for the selection of targeted drugs and the management plan. In this consensus, the Expert Committee summarized ten hot issues of gene testing for advanced breast cancer and discussed the applicable population, clinical significance, and the application of molecular markers circulating tumor DNA (ctDNA), whole exome sequencing (WES) in different molecular types, and the standardization of next generation sequencing (NGS) technology applied in clinic. This consensus aimed to guide clinicians how to rationally apply the gene testing to know more comprehensive genetic testing information, and formulate more precise treatment strategies for patients with advanced breast cancer.

Application Value of ctDNA-based MRD Dedection in Early Stage Non-small Cell Lung Cancer after Radical Surgery / 中国肺癌杂志

Lung cancer is the most common malignant tumor in the world, among which non-small cell lung cancer (NSCLC) accounts for about 85% of the total number of lung cancers. The 5-year overall survial (OS) of radical surgery NSCLC patients ranged from 92% in stage Ia1 to 26% in stage IIIb, and the continuously decreasing survival time made it a strong clinical need for precise adjuvant therapy to eradicate molecular residual disease (MRD). At present, circulating tumor DNA (ctDNA) as a molecular indicator of MRD has gradually moved from the laboratory to the clinic. The latest consensus proposes that ctDNA with abundance ≥0.02% can be stably detected in the peripheral blood of perioperative NSCLC patients, which is based on the possibility of ctDNA as an MRD indicator. MRD detection technology supports the possibility of monitoring after radical treatment of NSCLC, and ctDNA can predict the recurrence of the disease earlier than the imaging monitoring after treatment of NSCLC, providing valuable time for timely adjustment of adjuvant therapy. In the studies on early postoperative adjuvant therapy of NSCLC, different guidelines differ on whether appropriate adjuvant therapy should be carried out, while MRD can be used as a more accurate predictor to guide postoperative adjuvant therapy, so that patients can benefit from the disease treatment.
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Advances in Clinical Application of Liquid Biopsy in Non-small Cell Lung Cancer / 中国肺癌杂志

Lung cancer, with the highest incidence in China, is the leading cause of death in cancer patients. Of these, about 85% are patients with non-small cell lung cancer (NSCLC). Therefore, the diagnosis and treatment of patients with lung cancer have always been a top priority nowadays. Fluid biopsy has many advantages, such as safety, convenience, repeatability, low trauma and so on, which are not available in traditional invasive biopsy. In recent years, with the rapid progress of molecular biological detection technology, fluid biopsy, as a new technology, has become the focus of attention. What's more, it contributes to the development of precision treatment and individualized treatment of lung cancer. Liquid biopsy mainly detects circulating tumor DNA (ctDNA), circulating tumor cells (CTCs) and exosomes in peripheral blood. We will make an introduce to the detection and clinical applications of ctDNA, CTCs and exocrine in this article, in order that it can provide insights into future clinical treatment for NSCLC.
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Correlation of circulating tumor DNA EGFR mutation levels with clinical outcomes in patients with advanced lung adenocarcinoma / 中华医学杂志(英文版)

BACKGROUND@#Circulating tumor DNA (ctDNA) is a promising biomarker for non-invasive epidermal growth factor receptor mutations (EGFRm) detection in lung cancer patients, but existing methods have limitations in sensitivity and availability. In this study, we used the ΔCt value (mutant cycle threshold [Ct] value-internal control Ct value) generated during the polymerase chain reaction (PCR) assay to convert super-amplification-refractory mutation system (superARMS) from a qualitative method to a semi-quantitative method named reformed-superARMS (R-superARMS), and evaluated its performance in detecting EGFRm in plasma ctDNA in patients with advanced lung adenocarcinoma.@*METHODS@#A total of 41 pairs of tissues and plasma samples were obtained from lung adenocarcinoma patients who had known EGFRm in tumor tissue and were previously untreated. EGFRm in ctDNA was identified by using superARMS. Through making use of ΔCt value generated during the detection process of superARMS, we indirectly transform this qualitative detection method into a semi-quantitative PCR detection method, named R-superARMS. Both qualitative and quantitative analyses of the data were performed. Kaplan-Meier analysis was performed to estimate the progression-free survival (PFS) and overall survival (OS). Fisher exact test was used for categorical variables.@*RESULTS@#The concordance rate of EGFRm in tumor tissues and matched plasma samples was 68.3% (28/41). At baseline, EGFRm-positive patients were divided into two groups according to the cut-off ΔCt value of EGFRm set at 8.11. A significant difference in the median OS (mOS) between the two groups was observed (EGFRm ΔCt ≤8.11 vs. >8.11: not reached vs. 11.0 months; log-rank P = 0.024). Patients were divided into mutation clearance (MC) group and mutation incomplete clearance (MIC) group according to whether the ΔCt value of EGFRm test turned negative after 1 month of treatment. We found that there was also a significant difference in mOS (not reached vs. 10.4 months; log-rank P = 0.021) between MC group and MIC group. Although there was no significant difference in PFS between the two groups, the two curves were separated and the PFS of MC group tended to be higher than the MIC group (not reached vs. 27.5 months; log-rank P = 0.088). Furthermore, EGFRm-positive patients were divided into two groups according to the cut-off of the changes in ΔCt value of EGFRm after 1 month of treatment, which was set at 4.89. A significant difference in the mOS between the two groups was observed (change value of ΔCt >4.89 vs. ≤4.89: not reached vs. 11.0 months; log-rank P = 0.014).@*CONCLUSIONS@#Detecting EGFRm in ctDNA using R-superARMS can identify patients who are more likely sensitive to targeted therapy, reflect the molecular load of patients, and predict the therapeutic efficacy and clinical outcomes of patients.

Clinical Application of Circulating Tumor DNA in Diffuse Large B-Cell Lymphoma--Review / 中国实验血液学杂志

Diffuse large B-cell lymphoma (DLBCL) as an aggressive lymphoma, there has not a good molecular marker to assess the therapeutic efficacy and prognosis of the disease. As compared with the traditional deteation method, it was found that the circulating tumor DNA (ctDNA) can be used as a non-invasive specific biomarker which can dynamically provide the information about the lymphoma. ctDNA in DLBCL can be obtained by dideoxy chain termination method combined with PCR, so as to detect genetic markers, targeted sequences of gene which is related to lymphoma; the digital PCR (dPCR) for lymphoma somatic mutations and the detection of abnormal methylation; ctDNA is closely related to the diagncsis, therapeutic efficiency and prognosis of DLBCL, thus ctDNA can be used for the early detection, mid-term and prognostic monitoring in DLBCL, which makes ctDNA have a broad clinical applied prospect.

Circulating tumor DNA in lung cancer: real-time monitoring of disease evolution and treatment response / 中华医学杂志(英文版)

Lung cancer is one of the leading causes of all cancer-related deaths. Circulating tumor DNA (ctDNA) is released from apoptotic and necrotic tumor cells. Several sensitive techniques have been invented and adapted to quantify ctDNA genomic alterations. Applications of ctDNA in lung cancer include early diagnosis and detection, prognosis prediction, detecting mutations and structural alterations, minimal residual disease, tumor mutational burden, and tumor evolution tracking. Compared to surgical biopsy and radiographic imaging, the advantages of ctDNA are that it is a non-invasive procedure, allows real-time monitoring, and has relatively high sensitivity and specificity. Given the massive research on non-small cell lung cancer, attention should be paid to small cell lung cancer.

Análise de custo-efetividade do painel de sequenciamento de nova geração do DNA circulante tumoral no diagnóstico dos pacientes com câncer de pulmão de não pequenas células não escamoso metastático / Cost-effectiveness analysis of next generation sequencing panel of circulating tumor DNA in the diagnosis of patient with metastatic non-squamous non- small cell lung cancer

Objetivo: Avaliar o impacto clínico e econômico do uso do perfil genômico utilizando Next Generation Sequencing (NGS) em DNA circulante tumoral (ctDNA) na escolha do tratamento de primeira linha (1L) dos pacientes com câncer de pulmão de células não pequenas, não escamoso, metastático e que não apresentam material tecidual suficiente para avaliação das mutações oncogênicas. Métodos: Foi realizada uma análise de custo-efetividade com base em um modelo de árvore de decisão e um modelo de Markov para simular os resultados dos testes diagnósticos e consequentemente o seu impacto clínico e econômico na primeira linha de tratamento. O comparador da análise foi o teste de mutações específicas no gene EGFR por ctDNA. As terapias medicamentosas incluídas na análise foram as terapias-alvo de EGFR e ALK, que estão incorporadas no rol da Agência Nacional de Saúde Suplementar, e a imunoterapia pembrolizumabe combinada à quimioterapia. Os desfechos clínicos foram retirados dos estudos clínicos das terapias avaliadas no modelo. Resultados: O uso do painel de NGS em ctDNA demonstrou uma economia de -R$ 2.076,35 por paciente em um ano, e os resultados de RCEI foram: -R$ 7.652,56 (R$/SLP) e -R$ 33.742,14 (R$/SG). Conclusão: O painel de NGS em ctDNA demonstrou ser uma alternativa dominante em relação ao teste de EGFR em ctDNA.

Objective: The aim of this study was to evaluate the clinical and economic impact of the next generation sequencing (NGS) panel of circulating tumor DNA (ctDNA) in the clinical decision of first line treatment for patients with metastatic non-squamous non-small cell lung cancer who lack of tissue material for evaluation of oncogenic driver mutations. Methods: A cost-effectiveness analysis was performed based on a decision tree model and a Markov model in order to simulate the results of diagnostic tests and therefore its clinical and economic impact in the first line of treatment. The comparators were the single EGFR mutation detection methodologies in ctDNA. The analysis included the anti-EGFR and anti-ALK target therapies; and the combined therapy of pembrolizumab plus chemotherapy. Clinical outcomes were derived from clinical trials of the therapies included in the model. Results: The use of the NGS ctDNA panel showed a saving of -R$ 2,076.35 and the results of the ICER were -R$ 7,652.56 (R$/SLP) and -R$ 33,742.14 (R$/SG). Conclusion: The NGS panel demonstrated to be a dominant alternative in comparison to ctDNA EGFR testing.

Consistency Analysis of Gene Mutation Sites of Bone Marrow Tumor DNA and Circulating Tumor DNA in Patients with Myelodysplastic Syndrome / 中国实验血液学杂志

OBJECTIVE@#To analyze the consistency of gene mutation sites between bone marrow DNA (BM-tDNA) and perepheral plasma circulating tumor DNA (PP-ctDNA) in patients with myelodysplastic syndrome (MDS).@*METHODS@#The simultaneous sampled BM and PP from 19 patients (SBPP) was detected by NGS-127 gene panel, and the consistency of VAF between BM-tDNA and PP-ctDNA was analyzed. The peripheral blood cell tumor DNA (PC-tDNA) of 5 out of 19 patients was detected randomly, the consistency of VAF among PC-tDNA，BM-tDNA and PP-ctDNA was analyzed. The non simultaneous sampled BM and PP from 13 patients (NBPP) was detected, and the difference value of VAF between BM-tDNA and PP-ctDNA in SBPP and NBPP was analyzed.@*RESULTS@#The average concentration of PP-ctDNA in SBPP was 0.59 ng/µl and 0.604 ng/µl in NBPP. The median concentration of PP-ctDNA in SBPP and NBPP was 0.330 ng/µl and 0.338 ng/µl, respectively. The study showed a good consistency of VAF between BM-tDNA and PP-ctDNA in the SBPP (R=0.9693, P<0.05), and the consistency of VAF between BM-tDNA and PP-ctDNA in single base replacement (SNP) sites (R=0.9712) was better than that in insertion deletion (Indel) sites (R=0.6813). The results showed a good consistency of VAF between BM-tDNA and PP-ctDNA both in 12 patients before treatment (R=0.9325, P<0.05) and 5 patients (R=0.9875, P<0.05) after treatment. The results also showed that the VAF of PC-tDNA had a good consistency with the VAF of BM-tDNA (R=0.8783) and PP-ctDNA (R=0.8783) (P<0.05). The difference value of VAF between BM-tDNA and PP-ctDNA in SBPP was significantly lower than that in NBPP (P<0.05).@*CONCLUSION@#PP can replace BM as a biological sample for genes mutation detection in patients with MDS due to its stable concentration, high degree of consistency with bone marrow in clinical significant mutation sites and easy collection.

5-Hydroxymethylome in Circulating Cell-free DNA as A Potential Biomarker for Non-small-cell Lung Cancer / 基因组蛋白质组与生物信息学报·英文版

Non-small-cell lung cancer (NSCLC), the most common type of lung cancer accounting for 85% of the cases, is often diagnosed at advanced stages owing to the lack of efficient early diagnostic tools. 5-Hydroxymethylcytosine (5hmC) signatures in circulating cell-free DNA (cfDNA) that carries the cancer-specific epigenetic patterns may represent the valuable biomarkers for discriminating tumor and healthy individuals, and thus could be potentially useful for NSCLC diagnosis. Here, we employed a sensitive and reliable method to map genome-wide 5hmC in the cfDNA of Chinese NSCLC patients and detected a significant 5hmC gain in both the gene bodies and promoter regions in the blood samples from tumor patients compared with healthy controls. Specifically, we identified six potential biomarkers from 66 patients and 67 healthy controls (mean decrease accuracy >3.2, P < 3.68E-19) using machine-learning-based tumor classifiers with high accuracy. Thus, the unique signature of 5hmC in tumor patient's cfDNA identified in our study may provide valuable information in facilitating the development of new diagnostic and therapeutic modalities for NSCLC.