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Detection and localization of surgically resectable cancers with a multi-analyte blood test
Abstract
SEEK and you may find cancer earlier
Many cancers can be cured by surgery and/or systemic therapies when detected before they have metastasized. This clinical reality, coupled with the growing appreciation that cancer's rapid genetic evolution limits its response to drugs, have fueled interest in methodologies for earlier detection of the disease. Cohen et al. developed a noninvasive blood test, called CancerSEEK that can detect eight common human cancer types (see the Perspective by Kalinich and Haber). The test assesses eight circulating protein biomarkers and tumor-specific mutations in circulating DNA. In a study of 1000 patients previously diagnosed with cancer and 850 healthy control individuals, CancerSEEK detected cancer with a sensitivity of 69 to 98% (depending on cancer type) and 99% specificity.
Science , this issue p. 926 ; see also p. 866
... Another pan-cancer screening test, CancerSEEK, combines ctDNA detection with proteomic analysis 48 . It screens for eight prevalent cancers, including breast cancer, and looks at an amplicon-based targeted NGS of 16 genes involved in cancer together with eight cancer-specific proteins in the blood via an immunoassay 48 . ...
... Another pan-cancer screening test, CancerSEEK, combines ctDNA detection with proteomic analysis 48 . It screens for eight prevalent cancers, including breast cancer, and looks at an amplicon-based targeted NGS of 16 genes involved in cancer together with eight cancer-specific proteins in the blood via an immunoassay 48 . In an observational study involving 1005 patients with untreated early cancer and 812 healthy controls, median sensitivity was 70% for detection of early cancer in the eight included tumor types while maintaining a specificity over 99% 48 . ...
... However, there was a huge discrepancy in detection between tumor sites. Similar to Galleri TM , the detection rate for early BC was low: 33% compared to 98% detection for ovarian cancer 48 . Furthermore, in DETECT-A, a prospective interventional study using a modified version of CancerSEEK and further steps to reduce the interferences of CHIPs (N = 10,006 women aged 65-75 years old), almost all BC (26/27) were diagnosed using another method mostly routine screening mammogram 75 . ...
Circulating free tumor DNA (ctDNA) analysis is gaining popularity in precision oncology, particularly in metastatic breast cancer, as it provides non-invasive, real-time tumor information to complement tissue biopsies, allowing for tailored treatment strategies and improved patient selection in clinical trials. Its use in early breast cancer has been limited so far, due to the relatively low sensitivity of available techniques in a setting characterized by lower levels of ctDNA shedding. However, advances in sequencing and bioinformatics, as well as the use of methylome profiles, have led to an increasing interest in the application of ctDNA analysis in early breast cancer, from screening to curative treatment evaluation and minimal residual disease (MRD) detection. With multiple prospective clinical trials in this setting, ctDNA evaluation may become useful in clinical practice. This article reviews the data regarding the analytical validity of the currently available tests for ctDNA detection and the clinical potential of ctDNA analysis in early breast cancer.
... cancers), a test with very high specificity is important because high false positive rates result in many healthy individuals undergoing unnecessary clinical procedure (Arash Jamshidi, 2022) (E. Klein, 2021) (Joshua Cohen, 2018). Prioritizing specificity is key to building trust and maximizing the benefits of these tests. ...
... The real data is for the Colorectal Cancer individuals, before receiving any chemotherapy. There was not also any sign of metastasis at the time of blood collection (Joshua Cohen, 2018). The synthetic data was created such that one of the features has high sensitivity and the other one has the low sensitivity, at the high value for specificity, so we can evaluate the performance of our methods at different prespecified values for specificity. ...
... ;https://doi.org/10.1101https://doi.org/10. /2024 The dataset is from published study of (Joshua Cohen, 2018) Here, we focus only on these 16 proteins. The file can be downloaded from the supplementary material of (Joshua Cohen, 2018) as well as out GitHub repository. ...
Logistic regression has demonstrated its utility in classifying binary labeled datasets through the maximum likelihood approach. However, in numerous biological and clinical contexts, the aim is often to determine coefficients that yield the highest sensitivity at the pre-specified specificity or vice versa. Therefore, the application of logistic regression is limited in such settings. To this end, we have developed an improved regression framework, SMAGS, for binary classification that, for a given specificity, finds the linear decision rule that yields the maximum sensitivity. Furthermore, we employed the method for feature selection to find the features that are satisfying the sensitivity maximization goal. We compared our method with normal logistic regression by applying it to real clinical data as well as synthetic data. In the real application data (colorectal cancer dataset), we found 14% improvement of sensitivity at 98.5% specificity.
Availability and implementation
Software is made available in Python ( https://github.com/smahmoodghasemi/SMAGS )
... Liquid biopsy has the potential to revolutionize cancer diagnosis as a less invasive and innovative approach [3][4][5][6][7][8]. This technique provides valuable insights into tumors' genetic makeup by evaluating circulating biomarkers (i.e. ...
... The recent Pathfinder study aimed to evaluate methylated cfDNA of cancer patients further, providing new insights on test applications in real-world data [35]. Another promising, clinically available diagnostic test is CancerSEEK reported by Cohen et al. [6]. The latter platform would combine protein biomarker concentrations and mutations in cfDNA, reaching a remarkable 70% sensitivity at a 98% specificity level. ...
Liquid biopsy demonstrates excellent potential in patient management by providing a minimally invasive and cost‐effective approach to detecting and monitoring cancer, even at its early stages. Due to the complexity of liquid biopsy data, machine‐learning techniques are increasingly gaining attention in sample analysis, especially for multidimensional data such as RNA expression profiles. Yet, there is no agreement in the community on which methods are the most effective or how to process the data. To circumvent this, we performed a large‐scale study using various machine‐learning techniques. First, we took a closer look at existing datasets and filtered out some patients to assert data collection quality. The final data collection included platelet RNA samples acquired from 1397 cancer patients (17 types of cancer) and 354 asymptomatic, presumed healthy, donors. Then, we assessed an array of different machine‐learning models and techniques (e.g., feature selection of RNA transcripts) in pan‐cancer detection and multiclass classification. Our results show that simple logistic regression performs the best, reaching a 68% cancer detection rate at a 99% specificity level, and multiclass classification accuracy of 79.38% when distinguishing between five cancer types. In summary, by revisiting classical machine‐learning models, we have exceeded the previously used method by 5% and 9.65% in cancer detection and multiclass classification, respectively. To ease further research, we open‐source our code and data processing pipelines (https://gitlab.com/jopekmaksym/improving‐platelet‐rna‐based‐diagnostics), which we hope will serve the community as a strong baseline.
... Early detection relies heavily on minimally invasive tests using blood samples, urine, saliva, or other biological fluids, so-called liquid biopsies [10,11]. Multiple cancer blood tests using known protein cancer biomarkers [12], circulating tumor DNA shed from tumors [13,14], and DNA methylation profiles [15], are currently being tested in large trials to replace exploratory invasive tissue biopsies and support clinical decisions in symptomatic subjects. Even asymptomatic individuals, especially those aged >60 years, with or without a family history of cancer, are worried about having cancer. ...
... Within the accuracy of this technology, these five samples provided statistically indistinguishable let-7b copy numbers. To simplify the comparison, copy numbers were normalized to the H6914 1 st lot RNA content of 16.0 ng/L (reference), and then divided by the let-7b copy number (12,150) from this reference sample to give the HL number posted in the last column of Table 3. These five numbers (1.00, 1.07, 0.72, 1.00 and 0.67) ...
We developed a technology for detecting and quantifying trace nucleic acids using a bracketing protocol designed to yield a copy number with approximately ± 20% accuracy across all concentrations. The microRNAs (miRNAs) let-7b, miR-15b, miR-21, miR-375 and miR-141 were measured in serum and urine samples from healthy subjects and patients with breast, prostate, or pancreatic cancer. Detection and quantification were amplification-free and enabled using osmium-tagged probes and MinION, a nanopore array detection device. Combined serum from healthy men (Sigma‒Aldrich #H6914) was used as a reference. Total RNA isolated from biospecimens using commercial kits was used as the miRNA source. The unprecedented ± 20% accuracy led to the conclusion that miRNA copy numbers must be normalized to the same RNA content, which in turn illustrates (i) independence from age, sex, and ethnicity, as well as (ii) equivalence between serum and urine. miR-21, miR-375 and miR-141 copies in cancers were 1.8-fold overexpressed, exhibited zero overlap with healthy samples and had a p value of 1.6x10 ⁻²² , tentatively validating each miRNA as a cancer biomarker. miR-15b was confirmed to be cancer-independent, whereas let-7b appeared to be a cancer biomarker for prostate and breast cancer, but not for pancreatic cancer.
... Advanced next-generation sequencing (NGS) technologies have been developed to detect ctDNA with high sensitivity [13][14][15][16] , surpassing dropletdigital PCR (ddPCR) approaches [17][18][19][20][21] . Yet, their clinical application is complicated by the need for patient-specific panels and intensive sequencing processes. ...
... We detected ctDNA in 90.47% of the samples. This detection percentage is superior to previous studies 14,17,18,26,27 . In addition to ctDNA, we also investigated the detection of CTCs using ddPCR in pre-treatment blood samples. ...
Early breast cancer patients often experience relapse due to residual disease after treatment. Liquid biopsy is a methodology capable of detecting tumor componentsin blood, but low concentrations at early stages pose challenges. To detect them, next-generation sequencing has promise but entails complex processes. Exploring larger blood volumes could overcome detection limitations. Herein, a total of 282 high-volume plasma and blood-cell samples were collected for dual ctDNA/CTCs detection using a single droplet-digital PCR assay per patient. ctDNA and/or CTCs were detected in 100%of pre-treatment samples. On the other hand, post-treatment positive samples exhibited a minimumvariantallelefrequencyof0.003%forctDNAandminimumcellnumberof0.069CTCs/mLof blood,surpassingpreviousinvestigations.Accuratepredictionofresidualdiseasebeforesurgerywas achieved in patients without a complete pathological response. A model utilizing ctDNA dynamics achieved an area under the ROC curve of 0.92 for predicting response. We detected disease recurrence in blood in the three patients who experienced a relapse, anticipating clinical relapse by 34.61, 9.10, and 7.59 months. This methodology provides an easily implemented alternative for ultrasensitive residual disease detection in early breast cancer patient
... The sensitivity for stage II was 73 %, which decreased to 43 % for stage I cases. The overall sensitivity for GC detection was 72 % at 99 % specificity [101]. ...
... [131]. Similarly, an improvement was observed using a combination of ctDNAs and proteinbased biomarkers [101]. Regarding this strategy, it is important to identify the most efficient markers to be included in the assay. ...
... Since the publication of the first MCED clinical study in 2018 [3], dozens of MCED tests are being developed internationally, including Galleri, CancerSEEK, PanSeer, DELFI and others. The majority of these tests primarily identify alterations in cell-free DNA (cfDNA), including DNA methylation, mutations, fragmentation patterns, etc., and are often combined with other biomarkers such as proteins, cell-free RNA, and cancer metabolites. ...
... Current studies indicate that MCED tests have high diagnostic specificity (usually over 98%), but sensitivity varies across different cancer clinical stages [2]. For instance, CancerSEEK (Exact Sciences), with a specificity of 99%, demonstrates greater sensitivity for stage III cancers (80%) compared to stage I cancers (40%) [3]. The sensitivity of MCED in diagnosing early-stage tumors is further influenced by the cancer type. ...
... An approach involving the analysis of body fluids other than blood might help by increasing the sensitivity of tumor DNA detection. For instance, a tumor-specific liquid biopsy as uterine cavity lavage could provide higher fractions of tumor material [48,49]. ...
Ovarian cancer (OC) is the most lethal gynecologic malignancy worldwide. Due to the lack of effective screening and early detection strategies, many patients with OC are diagnosed with advanced disease, where treatment is rarely curative. Moreover, OC is characterized by high intratumor heterogeneity, which represents a major barrier to the development of effective treatments. Conventional tumor biopsy and blood-based biomarkers, such as cancer antigen 125 (CA125), have different limitations. Liquid biopsy has recently emerged as an attractive and promising area of investigation in oncology, due to its minimally invasive, safe, comprehensive, and real-time dynamic nature. Preliminary evidence suggests a potential role of liquid biopsy to refine OC management, by improving screening, early diagnosis, assessment of response to treatment, detection, and profiling of drug resistance. The current knowledge and the potential clinical value of liquid biopsy in OC is discussed in this review to provide an overview of the clinical settings in which its use might support and improve diagnosis and treatment.
... While clinical and community interest continues to grow, with MCED tests being discussed as the "holy grail" for cancer detection [50], it is still unclear whether the benefits outweigh the harms. Although MCED tests have been shown in early small-scale studies to increase cancer detection and are designed to have high specificity, that is, reduce false-positive results [51][52][53][54], there are valid concerns surrounding overdiagnosis [55]. There are clinical trials [56,57] underway internationally to assess the performance and use of the tests. ...
Background
In recent years, social media have emerged as important spaces for commercial marketing of health tests, which can be used for the screening and diagnosis of otherwise generally healthy people. However, little is known about how health tests are promoted on social media, whether the information provided is accurate and balanced, and if there is transparency around conflicts of interest.
Objective
This study aims to understand and quantify how social media is being used to discuss or promote health tests with the potential for overdiagnosis or overuse to generally healthy people.
Methods
Content analysis of social media posts on the anti-Mullerian hormone test, whole-body magnetic resonance imaging scan, multicancer early detection, testosterone test, and gut microbe test from influential international social media accounts on Instagram and TikTok. The 5 tests have been identified as having the following criteria: (1) there are evidence-based concerns about overdiagnosis or overuse, (2) there is evidence or concerns that the results of tests do not lead to improved health outcomes for generally healthy people and may cause harm or waste, and (3) the tests are being promoted on social media to generally healthy people. English language text-only posts, images, infographics, articles, recorded videos including reels, and audio-only posts are included. Posts from accounts with <1000 followers as well as stories, live videos, and non-English posts are excluded. Using keywords related to the test, the top posts were searched and screened until there were 100 eligible posts from each platform for each test (total of 1000 posts). Data from the caption, video, and on-screen text are being summarized and extracted into a Microsoft Excel (Microsoft Corporation) spreadsheet and included in the analysis. The analysis will take a combined inductive approach when generating key themes and a deductive approach using a prespecified framework. Quantitative data will be analyzed in Stata SE (version 18.0; Stata Corp).
Results
Data on Instagram and TikTok have been searched and screened. Analysis has now commenced. The findings will be disseminated via publications in peer-reviewed international medical journals and will also be presented at national and international conferences in late 2024 and 2025.
Conclusions
This study will contribute to the limited evidence base on the nature of the relationship between social media and the problems of overdiagnosis and overuse of health care services. This understanding is essential to develop strategies to mitigate potential harm and plan solutions, with the aim of helping to protect members of the public from being marketed low-value tests, becoming patients unnecessarily, and taking resources away from genuine needs within the health system.
International Registered Report Identifier (IRRID)
DERR1-10.2196/56899
... However, due to their limited sensitivity and specificity for the early diagnosis of cancer, clinical guidelines do not recommend them as standalone diagnostic tests for cancer. [3][4][5][6][7] Some TMs that are currently used in clinical practice include carcinoembryonic antigen )CEA(, cancer antigen 125 )CA 125(, and cancer antigen 15-3 )CA 15-3(. Cancer antigen 125, also known as mucin 16, is a TM primarily associated with ovarian, lung, and endometrial cancers. ...
... Blood-based liquid biopsy tests for multicancer detection are the focus of this research. Commercially available blood-based MCED tests include Galleri (GRAIL) and OneTest [28], with several in development, including Cancerguard (Exact Sciences) [29], CancerSEEK [30], and others [31][32][33][34]. MCED tests are typically developed to convey high specificity and variable sensitivity, which translates to low false positive rates, typically with the compromise of high false negative rates. ...
Current United States Preventive Services Task Force (USPSTF) recommendations include routine screening for breast, cervical, colorectal, and lung cancer; however, two out of every three cancer cases occur in other indications, leading to diagnoses in advanced stages of the disease and a higher likelihood of mortality. Blood-based multi-cancer early detection (MCED) tests can impact cancer screening and early detection by monitoring for multiple different cancer types at once, including indications where screening is not performed routinely today. We conducted a survey amongst healthcare providers (HCPs), payers, and patients within the U.S. health system to understand the current utilization of cancer screening tests and the anticipated barriers to widespread adoption of blood-based MCED tests. The results indicated that the community favors the adoption of blood-based MCED tests and that there is broad agreement on the value proposition. Despite this recognition, the survey highlighted that there is limited use today due to the perceived lack of clinical accuracy and utility data, high out-of-pocket patient costs, and lack of payer coverage. To overcome the hurdles for future widespread adoption of blood-based MCED tests, increased investment in data generation, education, and implementation of logistical support for HCPs will be critical.
... Cell-free circulating tumor DNA (ctDNA) can be used for the detection of somatic point mutations, rearrangements, copy number variations and methylation markers in tumor cells, thus having utility for non-invasive detection of cancer, monitoring treatment responses and disease progression, and tracking intratumoral heterogeneity and evolution [62,66,67]. Some recent studies have suggested the potential of ctDNA analysis for the detection of gastric cancer with high accuracy, including early-stage cancer [68,69]. The potential of the methylation markers for early detection of gastric cancer has been recently reviewed by Xue et al. [70]. ...
Purpose of Review
Non-invasive markers for gastric disease are highly useful, ideally allowing to diagnose a disease or a condition in a simple and convenient way. Such markers could also be of importance in population-based screening.
Recent Findings
This review provides an overview of non-invasive markers for H.pylori gastritis, autoimmune gastritis, gastric precancerous conditions and lesions, as well as gastric cancer. Traditionally used markers, such as non-invasive tests for H.pylori, pepsinogen and gastrin tests for atrophic gastritis, anti-parietal cell and anti- intrinsic factor antibodies for autoimmune gastritis, as well as newer tests are discussed. Current key guidelines on the routinely used tests are summarized.
A brief insight is provided to the status of volatile breath markers, plasma metabolic fingerprinting, as well as the use of circulating tumor cells, circulating tumor DNA, cell-free RNA, and extracellular vesicles in gastric cancer testing.
Summary
There is still a clear unmet need for perfect non-invasive markers in early gastric cancer and precancer lesion detection. Additional research is required to justify the available test application in clinical practice.
... 10 In the past decade, various studies have focused on exploring the diagnostic utility of circulating tumor DNA (ctDNA). [11][12][13][14][15] ctDNA is a subclass of short cell-free DNA (cfDNA) with an average size of 167 bp that is released from tumor cells mainly via apoptosis and necrosis. 16 Only a small amount of ctDNA is released into the blood circulation during the early stage of disease. ...
Ovarian cancer (OC) is a major cause of cancer mortality in women worldwide. Due to the occult onset of OC, its nonspecific clinical symptoms in the early phase, and a lack of effective early diagnostic tools, most OC patients are diagnosed at an advanced stage. In this study, shallow whole‐genome sequencing was utilized to characterize fragmentomics features of circulating tumor DNA (ctDNA) in OC patients. By applying a machine learning model, multiclass fragmentomics data achieved a mean area under the curve (AUC) of 0.97 (95% CI 0.962–0.976) for diagnosing OC. OC scores derived from this model strongly correlated with the disease stage. Further comparative analysis of OC scores illustrated that the fragmentomics‐based technology provided additional clinical benefits over the traditional serum biomarkers cancer antigen 125 (CA125) and the Risk of Ovarian Malignancy Algorithm (ROMA) index. In conclusion, fragmentomics features in ctDNA are potential biomarkers for the accurate diagnosis of OC.
... Its sensitivity for detecting ovarian cancer was reported to be 98%, with a specificity exceeding 99%. [14] Surgical prevention ...
Individuals with BRCA1 and BRCA2 mutations face significantly heightened likelihood of developing breast and ovarian cancers. Besides some lifestyle recommendations, like maintaining physical activity, healthy BMI, possibly early parenthood and breastfeeding, the management of BRCA1/2 mutation carriers includes gene mutation early-detection, screening, risk-reducing surgeries, and chemoprevention. Various prevention strategies exist, all aimed at monitoring patients and mitigating the cancer risks. However, even with the existence of national and international guidelines to direct prevention efforts, there is no ideal protocol that would be universally applicable for all individuals with mutated BRCA gene. This article aims to delve into the currently available surveillance and preventive strategies and explore the potential future avenues for early detection and risk reduction in BRCA mutation carriers.
... Various types of cfDNA isolated from human blood for diagnostic and screening purposes include circulating tumor DNA, mitochondrial DNA, and fetal DNA. With the continuous accumulation and support of clinical research, it has found wide applications in liquid biopsy, non-invasive prenatal screening (NIPT), medication guidance, and diagnosis of infectious diseases [41][42][43][44][45][46][47][48] . ...
Urinary tract infection (UTI) constitutes a pervasive health concern. UTIs are dichotomously classified into upper and lower strata, and further categorized as either complicated or uncomplicated. Upper UTIs predominantly afflict the renal and ureteral domains, typified by conditions exemplified in pyelonephritis, whereas lower UTIs manifest within the confines of the urethra and bladder. The conventional diagnosis of UTIs relies upon clinical manifestations and urine culture. Common symptoms encompass dysuria, frequent micturition, hematuria, and suprapubic discomfort. Urine culture serves to identify the specific pathogens instigating the infection and assess their antibiotic susceptibility. However, this procedural protocol generally necessitates an approximate duration of 24 h, coupled with an additional 24‐h interval for antibiotic susceptibility testing. In contradistinction, the detection of cell‐free DNA (cfDNA) in the circulatory system presents a potential avenue for non‐invasive diagnostic modalities. Notwithstanding, cfDNA emanates from deteriorating cells, affording insights into the extant cellular demise within the organism. Extensive scholarly inquiry has established a positive correlation between cfDNA concentration in the bloodstream and the incidence of cell death in conditions, such as severe traumas, sepsis, aseptic inflammation, myocardial infarction, and stroke. However, limited investigative effort has been devoted to elucidating the diagnostic potential of cfDNA in the context of UTIs. Consequently, the concentration and constitution of plasma cfDNA harbor substantial promise for non‐invasively diagnosing UTIs. In summation, the utilization of cfDNA in UTI diagnosis remains an incipient area of scholarly pursuit, underscoring the imperative for further research to elucidate the prospective role of plasma cfDNA in non‐intrusively discerning UTIs.
... The discovery of variant-specific KRAS inhibitors is a major breakthrough, yet clinical trial data has revealed that only a subset of indicated KRAS mutant patients respond to treatment (Fakih et al, 2022;Skoulidis et al, 2021), highlighting the need to find novel combination treatments to improve efficacy and overcome resistance mechanisms. Significant improvements in early-stage cancer detection using lowdose computed tomography (LDCT) (Jonas et al, 2021) and blood-based detection assays (Cohen et al, 2018;Lennon et al, 2020) will ultimately result in more patients being diagnosed, increasing the demand for early-stage therapeutics. To address these gaps, we sought to identify transcriptional dynamics downstream of activation of oncogenic KRAS expression in AT2 cells. ...
Glycine-12 mutations in the GTPase KRAS (KRAS G12 ) are an initiating event for development of lung adenocarcinoma (LUAD). KRAS G12 mutations promote cell-intrinsic rewiring of alveolar type-II progenitor (AT2) cells, but to what extent such changes interplay with lung homeostasis and cell fate pathways is unclear. Here, we generated single-cell RNA-seq (scRNA-seq) profiles from AT2-mesenchyme organoid co-cultures, mice, and stage-IA LUAD patients, identifying conserved regulators of AT2 transcriptional dynamics and defining the impact of KRAS G12D mutation with temporal resolution. In AT2 WT organoids, we found a transient injury/plasticity state preceding AT2 self-renewal and AT1 differentiation. Early-stage AT2 KRAS cells exhibited perturbed gene expression dynamics, most notably retention of the injury/plasticity state. The injury state in AT2 KRAS cells of patients, mice, and organoids was distinguishable from AT2 WT states via altered receptor expression, including co-expression of ITGA3 and SRC. The combination of clinically relevant KRAS G12D and SRC inhibitors impaired AT2 KRAS organoid growth. Together, our data show that an injury/plasticity state essential for lung repair is co-opted during AT2 self-renewal and LUAD initiation, suggesting that early-stage LUAD may be susceptible to interventions that target specifically the oncogenic nature of this cell state.
... It is already being r outinel y implemented in cancer ther a gnostics, for example in the detection of EGFR mutations in lung cancer. It also has significant potential for r esearc hers and clinicians in many other areas of cancer management care, including the detection of minimal residual disease ( MRD ) [5][6][7], treatment monitoring [ 8 , 9 ], cancer recurrence surveillance [ 6 , 7 ], and e v en cancer scr eening [10][11][12][13]. ...
Objectives
Elevated circulating DNA (cirDNA) concentrations were found to be associated with trauma or tissue damage which suggests involvement of inflammation or cell death in post-operative cirDNA release. We carried out the first prospective, multicenter study of the dynamics of cirDNA and neutrophil extracellular trap (NETs) markers during the perioperative period from 24 h before surgery up to 72 h after curative surgery in cancer patients.
Methods
We examined the plasma levels of two NETs protein markers [myeloperoxidase (MPO) and neutrophil elastase (NE)], as well as levels of cirDNA of nuclear (cir-nDNA) and mitochondrial (cir-mtDNA) origin in 29 colon, prostate, and breast cancer patients and in 114 healthy individuals (HI).
Results
The synergistic analytical information provided by these markers revealed that: (i) NETs formation contributes to post-surgery conditions; (ii) post-surgery cir-nDNA levels were highly associated with NE and MPO in colon cancer [r = 0.60 (P < 0.001) and r = 0.53 (P < 0.01), respectively], but not in prostate and breast cancer; (iii) each tumor type shows a specific pattern of cir-nDNA and NETs marker dynamics, but overall the pre- and post-surgery median values of cir-nDNA, NE, and MPO were significantly higher in cancer patients than in HI.
Conclusion
Taken as a whole, our work reveals the association of NETs formation with the elevated cir-nDNA release during a cancer patient's perioperative period, depending on surgical procedure or cancer type. By contrast, cir-mtDNA is poorly associated with NETs formation in the studied perioperative period, which would appear to indicate a different mechanism of release or suggest mitochondrial dysfunction.
... Most advanced cancers can be accurately diagnosed using cfDNA biomarkers (Ref. 143), however, early-stage cancers generate lower levels of detectable tumour mutations limiting cfDNA-based biomarker sensitivity. Considering that transcriptional dysregulations are more prevalent than genomic alterations, cf-mRNA appears to be a well-suited vehicle for earlystage, non-invasive cancer biomarkers (Ref. ...
Despite gene-expression profiling being one of the most common methods to evaluate molecular dysregulation in tissues, the utilization of cell-free messenger RNA (cf-mRNA) as a blood-based non-invasive biomarker analyte has been limited compared to other RNA classes. Recent advancements in low-input RNA-sequencing and normalization techniques, however, have enabled characterization as well as accurate quantification of cf-mRNAs allowing direct pathological insights. The molecular profile of the cell-free transcriptome in multiple diseases has subsequently been characterized including, prenatal diseases, neurological disorders, liver diseases and cancers suggesting this biological compartment may serve as a disease agnostic platform. With mRNAs packaged in a myriad of extracellular vesicles and particles, these signals may be used to develop clinically actionable, non-invasive disease biomarkers. Here, we summarize the recent scientific developments of extracellular mRNA, biology of extracellular mRNA carriers, clinical utility of cf-mRNA as disease biomarkers, as well as proposed functions in cell and tissue pathophysiology.
... The study by Jiang et al [12] showed that cancer-related end coordinates in plasma cfDNA can be applied to liver cancer early detection. Using plasma cfDNA and protein markers, Cohen et al [18] developed CancerSEEK, which can detect eight common cancers of the lung, colorectum, liver, stomach, esophagus, pancreas, breast, or ovary. In my previous studies [20,21], suggesting that cfDNA has prognostic potential. ...
With the rapid development of science and technology, cell-free DNA (cfDNA) is rapidly becoming an important biomarker for tumor diagnosis, monitoring and prognosis, and this cfDNA-based liquid biopsy technology has great potential to become an important part of precision medicine. cfDNA is the total amount of free DNA in the systemic circulation, including DNA fragments derived from tumor cells and all other somatic cells. Tumor cells release fragments of DNA into the bloodstream, and this source of cfDNA is called circulating tumor DNA (ctDNA). cfDNA detection has become a major focus in the field of tumor research in recent years, which provides a new opportunity for non-invasive diagnosis and prognosis of cancer. In this paper, we discuss the limitations of the study on the origin and dynamics analysis of ctDNA, and how to solve these problems in the future. Although the future faces major challenges, it also contains great potential.
Glycosylation is the most common post‐translational modification of proteins and regulates a myriad of fundamental biological processes under normal, and pathological conditions. Altered protein glycosylation is linked to malignant transformation, showing distinct glycopatterns that are associated with cancer initiation and progression by regulating tumor proliferation, invasion, metastasis, and therapeutic resistance. The glycopatterns of small extracellular vesicles (sEVs) released by cancer cells are promising candidates for cancer monitoring since they exhibit glycopatterns similar to their cell‐of‐origin. However, the clinical application of sEV glycans is challenging due to the limitations of current analytical technologies in tracking the trace amounts of sEVs specifically derived from tumors in circulation. Herein, a sEV GLYcan PHenotype (EV‐GLYPH) assay that utilizes a microfluidic platform integrated with surface‐enhanced Raman scattering for multiplex profiling of sEV glycans in non‐small cell lung cancer is clinically validated. For the first time, the EV‐GLYPH assay effectively identifies distinct sEV glycan signatures between non‐transformed and malignantly transformed lung cells. In a clinical study evaluated on 40 patients, the EV‐GLYPH assay successfully differentiates patients with early‐stage malignant lung nodules from benign lung nodules. These results reveal the potential to profile sEV glycans for noninvasive diagnostics and prognostics, opening up promising avenues for clinical applications and understanding the role of sEV glycosylation in lung cancer.
Importance
Uninterrupted targeted therapy until disease progression or intolerable toxic effects is currently the routine therapy for advanced non−small cell lung cancer (NSCLC) involving driver gene variations. However, drug resistance is inevitable.
Objective
To assess the clinical feasibility of adaptive de-escalation tyrosine kinase inhibitor (TKI) treatment guided by circulating tumor DNA (ctDNA) for achieving complete remission after local consolidative therapy (LCT) in patients with advanced NSCLC.
Design, Setting, and Participants
This prospective nonrandomized trial was conducted at a single center from June 3, 2020, to July 19, 2022, and included 60 patients with advanced NSCLC with driver variations without radiologically detectable disease after TKI and LCT. The median (range) follow-up time was 19.2 (3.8-29.7) months. Data analysis was conducted from December 15, 2022, to May 10, 2023.
Intervention
Cessation of TKI treatment and follow-up every 3 months. Treatment was restarted in patients with progressive disease (defined by the Response Evaluation Criteria in Solid Tumors 1.1 criteria), detectable ctDNA, or elevated carcinoembryonic antigen (CEA) levels, whichever manifested first, and treatment ceased if all indicators were negative during follow-up surveillance.
Main Outcomes and Measures
Progression-free survival (PFS). Secondary end points were objective response rate, time to next treatment, and overall survival.
Results
Among the total study sample of 60 participants (median [range] age, 55 [21-75] years; 33 [55%] were female), the median PFS was 18.4 (95% CI, 12.6-24.2) months and the median (range) total treatment break duration was 9.1 (1.5-28.1) months. Fourteen patients (group A) remained in TKI cessation with a median (range) treatment break duration of 20.3 (6.8-28.1) months; 31 patients (group B) received retreatment owing to detectable ctDNA and/or CEA and had a median PFS of 20.2 (95% CI, 12.9-27.4) months with a median (range) total treatment break duration of 8.8 (1.5-20.6) months; and 15 patients (group C) who underwent retreatment with TKIs due to progressive disease had a median PFS of 5.5 (95% CI, 1.5-7.2) months. For all participants, the TKI retreatment response rate was 96%, the median time to next treatment was 29.3 (95% CI, 25.3-35.2) months, and the data for overall survival were immature.
Conclusions and Relevance
The findings of this nonrandomized trial suggest that this adaptive de-escalation TKI strategy for patients with NSCLC is feasible in those with no lesions after LCT and a negative ctDNA test result. This might provide a de-escalation treatment strategy guided by ctDNA for the subset of patients with advanced NSCLC.
Trial Registration
ClinicalTrials.gov Identifier: NCT03046316
This review summarizes insights into colorant selection and signal mechanisms for the development of colorimetric sensing and POC sensors.
Background Profiling circulating cell-free DNA (cfDNA) has become a fundamental practice in cancer medicine, but the effectiveness of cfDNA at elucidating tumor-derived molecular features has not been systematically compared to standard single-lesion tumor biopsies in prospective cohorts of patients. The use of plasma instead of tissue to guide therapy is particularly attractive for patients with small cell lung cancer (SCLC), a cancer whose aggressive clinical course making it exceedingly challenging to obtain tumor biopsies.
Methods Here, a prospective cohort of 49 plasma samples obtained before, during, and after treatment from 20 patients with recurrent SCLC, we study cfDNA low pass whole genome (0.1X coverage) and exome (130X) sequencing in comparison with time-point matched tumor, characterized using exome and transcriptome sequencing.
Results Direct comparison of cfDNA versus tumor biopsy reveals that cfDNA not only mirrors the mutation and copy number landscape of the corresponding tumor but also identifies clinically relevant resistance mechanisms and cancer driver alterations not found in matched tumor biopsies. Longitudinal cfDNA analysis reliably tracks tumor response, progression, and clonal evolution. Genomic sequencing coverage of plasma DNA fragments around transcription start sites shows distinct treatment-related changes and captures the expression of key transcription factors such as NEUROD1 and REST in the corresponding SCLC tumors, allowing prediction of SCLC neuroendocrine phenotypes and treatment responses. Conclusions These findings have important implications for non-invasive stratification and subtype-specific therapies for patients with SCLC, now treated as a single disease.
Lung cancer is the most common cancer in the world and has a consistently high mortality rate, with the majority of patients being diagnosed at an advanced stage. This study aimed to identify potential biomarkers through metabolomics to provide clues for the diagnosis and treatment of early-stage non-small cell lung cancer (NSCLC). We enrolled two prospective cohorts with a total of 180 patients (115 patients with I-II a NSCLC and 65 healthy controls) and tested serum samples for tumour markers, cytokines, and 306 metabolites by ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry (UPLC‒MS/MS). In both the discovery and validation cohorts, there were 57 differentially abundant metabolites in the serum between patients with early-stage NSCLC and healthy controls, which were concentrated in the fatty acid metabolic pathway and amino acid metabolic pathway. Finally, three metabolites with significant differences were screened as isoleucine, 5Z-dodecenoic acid and 9E-tetradecenoic acid. The AUC of centralized combined diagnosis reached 0.95. This study provides new evidence that abnormalities in valine, leucine, and isoleucine metabolism and dysregulation of fatty acid synthesis may play important roles in the development of NSCLC.
Liver cancer, primarily hepatocellular carcinoma, remains a global health challenge with rising incidence and limited therapeutic options. Genetic factors play a pivotal role in the development and progression of liver cancer. This state-of-the-art paper provides a comprehensive review of the current landscape of genetic screening strategies for liver cancer. We discuss the genetic underpinnings of liver cancer, emphasizing the critical role of risk-associated genetic variants, somatic mutations, and epigenetic alterations. We also explore the intricate interplay between environmental factors and genetics, highlighting how genetic screening can aid in risk stratification and early detection via using liquid biopsy, and advancements in high-throughput sequencing technologies. By synthesizing the latest research findings, we aim to provide a comprehensive overview of the state-of-the-art genetic screening methods for liver cancer, shedding light on their potential to revolutionize early detection, risk assessment, and targeted therapies in the fight against this devastating disease.
Multi-Cancer Early Detection tests:
• Distinguish tumor informative from tumor agnostic assays as they may have different uses and stage dependent test performance;
• Cancer prevalence excludes feasibility of screening in low prevalent cancers (although there is an unmet need);
• Proposed potentially implementation and use for MCEDs:
• As a targeted test in population screening for prevalent cancers,
• As a complementary test in current population screening,
• In hospital settings, to distinguish between indolent and aggressive cancer types.
BACKGROUND: FAM170B-AS1 is usually expressed low in all organs except for testicular tissues. No study was performed to explore its role in breast cancer (BC). Contradictory results were reported about hsa-miR-1202 and hsa-miR-146a-5p in BC. OBJECTIVE: The present study aimed to explore the involvement of FAM170B-AS1 in BC using bioinformatics predictive tools, followed by a practical validation besides exploring the impact of hsa-miR-1202 and hsa-miR-146a-5p in BC. METHODS: This study enrolled 96 female patients with BC, 30 patients with benign breast diseases (BBD), and 25 control subjects. The expressions of circulating FAM170B-AS1, hsa-miR-1202, and hsa-miR-146a-5p were quantified using qRT-PCR. These ncRNAs' associations, predictive, and diagnostic roles in BC were statistically tested. The underlying miRNA/mRNA targets of FAM170B-AS1 in BC were bioinformatically predicted followed by confirmation based on the GEPIA and TCGA databases. RESULTS: The expression of FAM170B-AS1 was upregulated in sera of BC patients and hsa-miR-1202 was upregulated in sera of BBD and BC patients while that of hsa-miR-146a-5p was downregulated in BC. These FAM170B-AS1 was significantly associated with BC when compared to BBD. FAM170B-AS1 and hsa-miR-1202 were statistically associated with the BC's stage, grade, and LN metastasis. FAM170B-AS1 and hsa-miR-146a-5p gave the highest specificity and sensitivity for BC. KRAS and EGFR were predicted to be targeted by FAM170B-AS1 through interaction with hsa-miR-143-3p and hsa-miR-7-5p, respectively. Based on the TCGA database, cancer patients having mutations in FAM170B show good overall survival. CONCLUSIONS: The present study reported that for the first time, FAM170B-AS1 may be a potential risk factor, predictive, and diagnostic marker for BC. In addition, FAM170B-AS1 might be involved in BC by interacting with hsa-miR-143-3p/KRAS and hsa-miR-7-5p/EGFR through enhancement or repression that may present a new therapeutic option for BC.
The advent of single-cell sequencing techniques has not only revolutionized the investigation of biological processes but also significantly contributed to unraveling cellular heterogeneity at unprecedented levels. Among the various methods, single-cell transcriptome sequencing stands out as the best established, and has been employed in exploring many physiological and pathological activities. The recently developed single-cell epigenetic sequencing techniques, especially chromatin accessibility sequencing, have further deepened our understanding of gene regulatory networks. In this review, we summarize the recent breakthroughs in single-cell transcriptome and chromatin accessibility sequencing methodologies. Additionally, we describe current bioinformatic strategies to integrate data obtained through these single-cell sequencing methods and highlight the application of this analysis strategy on a deeper understanding of tumorigenesis and tumor progression. Finally, we also discuss the challenges and anticipated developments in this field.
Cell-free DNA (cfDNA) in the blood is a less-invasive tool to reveal genomic profiles in pancreatic and bile tract cancers (PC and BTC); however, its utility is limited owing to its small amount and fragmentation of DNA for integrated sequences. This study evaluated the quality of in bile juice to clarify the potential of genome profiling for precision treatment. We collected data from 13 patients with pancreatic-biliary tumors invading the bile duct and subsequently underwent surgical resection: 7 cholangiocarcinomas, 1 gallbladder carcinoma, 3 ampullary carcinomas, 1 pancreatic cancer, and 1 intraductal papillary mucinous carcinoma. Whole-exome sequencing-based extracted DNA from resected samples revealed pathogenic alterations of TP53, ABCA8, BRCA2, FGFR2, APC, SMAD4 and NRAS. Of the 13 patients, nine pairs of cfDNA from bile and plasma were analyzed. Bile contained more (and longer fragments) cfDNAs compared with plasma. The most representative alterations in TP53, KRAS, PIK3CA, BRAF and NRAS were detected in bile cfDNA. Thus, bile cfDNA indicated better quality and quantity for sequence analysis and reflected tumor-derived genetic variation. Bile cfDNA is a useful tool for liquid biopsy in genomic profiling and precision medicine.
DNA methylation is an important mechanism in epigenetics, which can change the transcription ability of genes and is closely related to the pathogenesis of ovarian cancer (OC). We hypothesize that DNA methylation is significantly different in OCs compared to controls. Specific DNA methylation status can be used as a biomarker of OC, and targeted drugs targeting these methylation patterns and DNA methyltransferase may have better therapeutic effects. Studying the key DNA methylation sites of immune-related genes (IRGs) in OC patients and studying the effects of these methylation sites on the immune microenvironment may provide a new method for further exploring the pathogenesis of OC, realizing early detection and effective monitoring of OC, identifying effective biomarkers of DNA methylation subtypes and drug targets, improving the efficacy of targeted drugs or overcoming drug resistance, and better applying it to predictive diagnosis, prevention, and personalized medicine (PPPM; 3PM) of OC.
Hypermethylated subtypes (cluster 1) and hypomethylated subtypes (cluster 2) were established in OCs based on the abundance of different methylation sites in IRGs. The differences in immune score, immune checkpoints, immune cells, and overall survival were analyzed between different methylation subtypes in OC samples. The significant pathways, gene ontology (GO), and protein-protein interaction (PPI) network of the identified methylation sites in IRGs were enriched. In addition, the immune-related methylation signature was constructed with multiple regression analysis. A methylation site model based on IRGs was constructed and verified.
A total of 120 IRGs with 142 differentially methylated sites (DMSs) were identified. The DMSs were clustered into a high-level methylation group (cluster 1) and a low-level methylation group (cluster 2). The significant pathways and GO analysis showed many immune-related and cancer-associated enrichments. A methylation site signature based on IRGs was constructed, including RORC|cg25112191, S100A13|cg14467840, TNF|cg04425624, RLN2|cg03679581, and IL1RL2|cg22797169. The methylation sites of all five genes showed hypomethylation in OC, and there were statistically significant differences among RORC|cg25112191, S100A13|cg14467840, and TNF|cg04425624 (p < 0.05). This prognostic model based on low-level methylation and high-level methylation groups was significantly linked to the immune microenvironment as well as overall survival in OC.
This study provided different methylation subtypes for OC patients according to the methylation sites of IRGs. In addition, it helps establish a relationship between methylation and the immune microenvironment, which showed specific differences in biological signaling pathways, genomic changes, and immune mechanisms within the two subgroups. These data provide ones to deeply understand the mechanism of immune-related methylation genes on the occurrence and development of OC. The methylation-site signature is also to establish new possibilities for OC therapy. These data are a precious resource for stratification and targeted treatment of OC patients toward an advanced 3PM approach.
Objectives:
About 17% of patients with human papillomavirus (HPV)-positive head and neck squamous cell carcinoma (HNSCC), which is mainly comprised of oropharyngeal SCC (OPSCC), will experience disease recurrence, which is often considered incurable when manifested at a metastatic and/or recurrent stage. We conducted a critical qualitative systematic review. Our objectives were to provide an overview of the molecular landscape of recurrent/metastatic HPV-positive HNSCC as well as novel molecular biomarkers.
Design:
A literature review was conducted to identify studies reporting on the molecular characteristics of recurrent/metastatic HPV-positive HNSCC, novel molecular biomarkers and treatment options. The reviews of abstracts, full articles, and revision of the included studies, followed by data extraction and quality assessment were performed by three independent assessors. All primary literature, such as retrospective, prospective, and clinical trials as well as basic research studies were considered, and the final search was conducted at the end of February 2023. The level of evidence was rated using the guidelines published by the Oxford Centre for Evidence-based Medicine and quality was assessed using the Newcastle-Ottawa Scale criteria.
Results and conclusions:
The literature search resulted in the identification of 1991 articles. A total of 181 full articles were screened, and 66 articles were included in this analysis. Several studies reported that recurrent/metastatic HPV-positive HNSCC had higher rates of TP53 mutation and were genomically similar to HPV-negative HNSCC. The detection of circulating tumour tissue-modified HPV DNA (ctHPVDNA) as a specific biomarker has shown promising results for monitoring treatment response and recurrence in the subset of HPV-positive HNSCC. In addition, evidence for targeted therapy in recurrent/metastatic HPV-positive HNSCC has emerged, including agents that inhibit overexpressed EGFR. Studies of combination immunotherapy are also underway. Our review outlines the latest evidence on the distinct molecular profiles of recurrent/metastatic HPV-positive HNSCC as well as the clinical potential of ctHPVDNA testing in routine practice. More controlled and longitudinal studies are needed to identify additional molecular targets and to assess the performance and benefits of novel molecular biomarkers in clinical practice.
Background
The literature suggests that the medical community needs musicians to provide an insider’s perspective to understand the physical and psychological dimensions of playing an instrument, and healthcare providers need to understand musicians’ experiences in order to develop coping strategies. Compared with professional pianists, student pianists are a neglected group. However, student and professional pianists both want to maintain their playing careers and have the experience of giving up playing because of playing-related musculoskeletal disorder (PRMD). There are a few studies conducted on student pianists’ experiences with PRMD, but none have been conducted in the Chinese context. Given the distinctive characteristics of higher music education in China and Chinese piano students, this study aims to investigate the lived experiences of tertiary student pianists with PRMD.
Methods
Phenomenology is the most suitable qualitative method for investigating lived experiences. This study employed a transcendental phenomenological approach to investigate the experiences of student pianists, collecting data through one-on-one interviews and focus group discussions. Since phenomenological research emphasizes the homogeneity of research subjects, all 25 participants in this study are tertiary student pianists from seven Chinese higher education institutions.
Results
Four themes and ten sub-themes were identified in this study. They are as follows: Theme one, Perceptions of PRMD, with sub-themes of body perceptions, negative thought, and emotional changes; Theme two, Complex Identity, with sub-themes of future pianists’ identity, nuanced identity of student pianists, and the dual identity between student pianist and patient; Theme three, Coping Strategies, with sub-themes of self-regulation and actively seek help from social relations; Theme four, Influences and Meanings, with sub-themes of negative influences of PRMD and positive meanings of PRMD.
Conclusion
This study explores the experiences of tertiary student pianists with PRMD, including their subjective thoughts and feelings. It also highlights the importance of understanding tertiary student pianists’ experiences in developing health education and healthcare measures tailored to them.
b> Background: Lung cancer screening is still in an early phase compared to other cancer screening programs, despite its high lethality particularly when diagnosed late. Achieving early diagnosis is crucial to obtain optimal outcomes. Summary: In this review, we will address the current evidence on lung cancer screening through low-dose computed tomography (LDCT) and its impact on mortality reduction, existing screening recommendations, patient eligibility criteria, screening frequency and duration, benefits and harms, cost-effectiveness and some insights on lung cancer screening implementation and adoption. Additionally, new non-imaging, noninvasive biomarkers with high diagnostic potential are also briefly highlighted. Key Messages: LDCT screening in a prespecified population based on age and smoking history proved to reduce lung cancer mortality. Optimization of the target population and management of LDCT pitfalls can further improve lung cancer screening efficiency and cost-effectiveness. Novel screening technologies and biomarkers being studied can potentially be game-changers in lung cancer screening and diagnosis.
Over a billion people across the world experience a high rate of missed disease diagnosis, an issue that highlights the need for diagnostic tools showing increased accuracy and affordability. In addition, such tools could be used in ecologically fragile and energy-limited regions, pointing to the need for developing solutions that can maximize health gains under limited resources for enhanced sustainability. Metabolic diagnosis holds promise but faces challenges due to the applicability of biospecimens and limited robustness of analytical tools. Here we present a diagnostic method coupling dried serum spots (DSS) and nanoparticle-enhanced laser desorption/ionization mass spectrometry (NPELDI MS). Our approach allows diagnosis of multiple cancers within minutes at affordable cost, environmental friendliness, serum-equivalent precision and user-friendly protocol. Our assessment shows that the implementation of this tool in less-developed regions could reduce the estimated proportion of undiagnosed cases of colorectal cancer from 84.30% to 29.20%, gastric cancer from 77.57% to 57.22% and pancreatic cancer from 34.56% to 9.30%—an overall reduction in the range of 20.35–55.10%. This work provides insights into delivering more sustainable metabolic diagnosis with maximum health gains.
Background
Recent advances in circulating tumor DNA (ctDNA) analysis offer a promising approach for diagnosing and monitoring hepatocellular carcinoma (HCC). This study focused on the potential clinical role of ctDNA analysis in HCC management.
Materials and methods:
Thirty patients with HCC and 10 with non-malignant liver disease were enrolled in this study. Circulating free nucleic acids, germline DNA, and tumor DNA (tDNA) from both blood samples and paraffin-embedded tumor biopsies were analyzed by a panel targeting 100 common HCC-related genes.
Results
The ctDNA mutations were identified in 66.6% of HCC patients. New ctDNA mutations were identified, among them NCOR2 having the highest frequency (13%), the same with classical mutation CTNNB1. Gene sets composed of several mutations in ctDNA have the potential to predict the prognosis of HCC. A higher proportion of concordant mutations was also detected in HCC patients with tumor vascular invasion (p=0.045). Combining the ctDNA mutations and the Alpha-fetoprotein (AFP) level revealed more diagnostic accuracy than either the mutations or AFP alone, with p-values of 0.028 and 0.009, respectively.
Conclusion
Liquid biopsy-based analysis of ctDNA mutations may offer considerable benefits to diagnostic systems for HCC.
Introduction:
Oral Squamous Cell Carcinoma (OSCC), the sixth most widespread malignancy in the world, accounts for 90% of all cases of oral cancer. The primary risk factors are tobacco chewing, alcohol consumption, viral infection, and genetic modifications. OSCC has a high morbidity rate due to the lack of early diagnostic methods. Nowadays, liquid biopsy plays a vital role in the initial diagnosis of oral cancer. ctNAs extracted from saliva and serum/plasma offer meaningful insights into tumor genetics and dynamics. The interplay of these elements in saliva and serum/plasma showcases their significance in advancing noninvasive, effective OSCC detection and monitoring.
Areas covered:
This review mainly focused on the role of liquid biopsy as an emerging point in the diagnosis and prognosis of OSCC and the current advancements and challenges associated with liquid biopsy.
Expert opinion:
Liquid biopsy is regarded as a new, minimally invasive, real-time monitoring tool for cancer diagnosis and prognosis. Many biomolecules found in bodily fluids, including ctDNA, ctRNA, CTCs, and EVs, are significant biomarkers to identify cancer in its early stages. Despite these groundbreaking strides, challenges persist. Standardization of sample collection, isolation, processing, and detection methods is imperative for ensuring result reproducibility across diverse studies.
In solid tumors, targeted treatments can lead to dramatic regressions, but responses are often short-lived because resistant cancer cells arise. The major strategy proposed for overcoming resistance is combination therapy. We present a mathematical model describing the evolutionary dynamics of lesions in response to treatment. We first studied 20 melanoma patients receiving vemurafenib. We then applied our model to an independent set of pancreatic, colorectal, and melanoma cancer patients with metastatic disease. We find that dual therapy results in long-term disease control for most patients, if there are no single mutations that cause cross-resistance to both drugs; in patients with large disease burden, triple therapy is needed. We also find that simultaneous therapy with two drugs is much more effective than sequential therapy. Our results provide realistic expectations for the efficacy of new drug combinations and inform the design of trials for new cancer therapeutics.
Background
The presence of circulating cell-free DNA from tumours in blood (ctDNA) is of major importance to those interested in early cancer detection, as well as to those wishing to monitor tumour progression or diagnose the presence of activating mutations to guide treatment. In 2014, the UK Early Cancer Detection Consortium undertook a systematic mapping review of the literature to identify blood-based biomarkers with potential for the development of a non-invasive blood test for cancer screening, and which identified this as a major area of interest. This review builds on the mapping review to expand the ctDNA dataset to examine the best options for the detection of multiple cancer types.
Methods
The original mapping review was based on comprehensive searches of the electronic databases Medline, Embase, CINAHL, the Cochrane library, and Biosis to obtain relevant literature on blood-based biomarkers for cancer detection in humans (PROSPERO no. CRD42014010827). The abstracts for each paper were reviewed to determine whether validation data were reported, and then examined in full. Publications concentrating on monitoring of disease burden or mutations were excluded.
Results
The search identified 94 ctDNA studies meeting the criteria for review. All but 5 studies examined one cancer type, with breast, colorectal and lung cancers representing 60% of studies. The size and design of the studies varied widely. Controls were included in 77% of publications. The largest study included 640 patients, but the median study size was 65 cases and 35 controls, and the bulk of studies (71%) included less than 100 patients. Studies either estimated cfDNA levels non-specifically or tested for cancer-specific mutations or methylation changes (the majority using PCR-based methods).
Conclusion
We have systematically reviewed ctDNA blood biomarkers for the early detection of cancer. Pre-analytical, analytical, and post-analytical considerations were identified which need to be addressed before such biomarkers enter clinical practice. The value of small studies with no comparison between methods, or even the inclusion of controls is highly questionable, and larger validation studies will be required before such methods can be considered for early cancer detection.
Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction sequencing (TEC-Seq) that allows ultrasensitive direct evaluation of sequence changes in circulating cell-free DNA using massively parallel sequencing. We have used this approach to examine 58 cancer-related genes encompassing 81 kb. Analysis of plasma from 44 healthy individuals identified genomic changes related to clonal hematopoiesis in 16% of asymptomatic individuals but no alterations in driver genes related to solid cancers. Evaluation of 200 patients with colorectal, breast, lung, or ovarian cancer detected somatic mutations in the plasma of 71, 59, 59, and 68%, respectively, of patients with stage I or II disease. Analyses of mutations in the circulation revealed high concordance with alterations in the tumors of these patients. In patients with resectable colorectal cancers, higher amounts of preoperative circulating tumor DNA were associated with disease recurrence and decreased overall survival. These analyses provide a broadly applicable approach for noninvasive detection of early-stage tumors that may be useful for screening and management of patients with cancer.
This portion of the NCCN Guidelines for Colon Cancer focuses on the use of systemic therapy in metastatic disease. Considerations for treatment selection among 32 different monotherapies and combination regimens in up to 7 lines of therapy have included treatment history, extent of disease, goals of treatment, the efficacy and toxicity profiles of the regimens, KRAS/NRAS mutational status, and patient comorbidities and preferences. Location of the primary tumor, the BRAF mutation status, and tumor microsatellite stability should also be considered in treatment decisions.
The early detection of relapse following primary surgery for non-small cell lung cancer and the characterization of emerging subclones seeding metastatic sites might offer new therapeutic approaches to limit tumor recurrence. The potential to non-invasively track tumor evolutionary dynamics in ctDNA of early-stage lung cancer is not established. Here we conduct a tumour-specific phylogenetic approach to ctDNA profiling in the first 100 TRACERx (TRAcking non-small cell lung Cancer Evolution through therapy (Rx)) study participants, including one patient co-recruited to the PEACE (Posthumous Evaluation of Advanced Cancer Environment) post-mortem study. We identify independent predictors of ctDNA release and perform tumor volume limit of detection analyses. Through blinded profiling of post-operative plasma, we observe evidence of adjuvant chemotherapy resistance and identify patients destined to experience recurrence of their lung cancer. Finally, we show that phylogenetic ctDNA profiling tracks the subclonal nature of lung cancer relapse and metastases, providing a new approach for ctDNA driven therapeutic studies.
COSMIC, the Catalogue of Somatic Mutations in Cancer (http://cancer.sanger.ac.uk) is a high-resolution resource for exploring targets and trends in the genetics of human cancer. Currently the broadest database of mutations in cancer, the information in COSMIC is curated by expert scientists, primarily by scrutinizing large numbers of scientific publications. Over 4 million coding mutations are described in v78 (September 2016), combining genome-wide sequencing results from 28 366 tumours with complete manual curation of 23 489 individual publications focused on 186 key genes and 286 key fusion pairs across all cancers. Molecular profiling of large tumour numbers has also allowed the annotation of more than 13 million non-coding mutations, 18 029 gene fusions, 187 429 genome rearrangements, 1 271 436 abnormal copy number segments, 9 175 462 abnormal expression variants and 7 879 142 differentially methylated CpG dinucleotides. COSMIC now details the genetics of drug resistance, novel somatic gene mutations which allow a tumour to evade therapeutic cancer drugs. Focusing initially on highly characterized drugs and genes, COSMIC v78 contains wide resistance mutation profiles across 20 drugs, detailing the recurrence of 301 unique resistance alleles across 1934 drug-resistant tumours. All information from the COSMIC database is available freely on the COSMIC website.
Mass spectrometry (MS) -based proteomics has become an indispensable tool with broad applications in systems biology and biomedical research. With recent advances in liquid chromatography (LC) and MS instrumentation, LC-MS is making increasingly significant contributions to clinical applications, especially in the area of cancer biomarker discovery and verification. To overcome challenges associated with analyses of clinical samples (for example, a wide dynamic range of protein concentrations in bodily fluids and the need to perform high throughput and accurate quantification of candidate biomarker proteins), significant efforts have been devoted to improve the overall performance of LC-MS-based clinical proteomics platforms. Reviewed here are the recent advances in LC-MS and its applications in cancer biomarker discovery and quantification, along with the potentials, limitations and future perspectives.
A substantial fraction of disease-causing mutations are pathogenic through aberrant splicing. Although genome profiling studies have identified somatic single-nucleotide variants (SNVs) in cancer, the extent to which these variants trigger abnormal splicing has not been systematically examined. Here we analyzed RNA sequencing and exome data from 1,812 patients with cancer and identified ∼900 somatic exonic SNVs that disrupt splicing. At least 163 SNVs, including 31 synonymous ones, were shown to cause intron retention or exon skipping in an allele-specific manner, with ∼70% of the SNVs occurring on the last base of exons. Notably, SNVs causing intron retention were enriched in tumor suppressors, and 97% of these SNVs generated a premature termination codon, leading to loss of function through nonsense-mediated decay or truncated protein. We also characterized the genomic features predictive of such splicing defects. Overall, this work demonstrates that intron retention is a common mechanism of tumor-suppressor inactivation.
To explore the potential of tumor-specific DNA as a biomarker for head and neck squamous cell carcinomas (HNSCC), we queried DNA from saliva or plasma of 93 HNSCC patients. We searched for somatic mutations or human papillomavirus genes, collectively referred to as tumor DNA. When both plasma and saliva were tested, tumor DNA was detected in 96% of 47 patients. The fractions of patients with detectable tumor DNA in early- and late-stage disease were 100% (n = 10) and 95% (n = 37), respectively. When segregated by site, tumor DNA was detected in 100% (n = 15), 91% (n = 22), 100% (n = 7), and 100% (n = 3) of patients with tumors of the oral cavity, oropharynx, larynx, and hypopharynx, respectively. In saliva, tumor DNA was found in 100% of patients with oral cavity cancers and in 47 to 70% of patients with cancers of the other sites. In plasma, tumor DNA was found in 80% of patients with oral cavity cancers, and in 86 to 100% of patients with cancers of the other sites. Thus, saliva is preferentially enriched for tumor DNA from the oral cavity, whereas plasma is preferentially enriched for tumor DNA from the other sites. Tumor DNA in saliva was found postsurgically in three patients before clinical diagnosis of recurrence, but in none of the five patients without recurrence. Tumor DNA in the saliva and plasma appears to be a potentially valuable biomarker for detection of HNSCC.
Copyright © 2015, American Association for the Advancement of Science.
This study used case reports to review the role of systemic chemotherapy in oligometastatic colorectal cancer (CRC) and to suggest ways to integrate clinical research findings into the interdisciplinary management of this potentially curable subset of patients.
This educational review discusses the role of chemotherapy in the management of oligometastatic metastatic CRC.
In initially resectable oligometastatic CRC, the goal of chemotherapy is to eradicate micrometastatic disease. Perioperative 5-fluorouracil and oxaliplatin together with surgical resection can result in 5-year survival rates as high as 57 %. With the development of increasingly successful chemotherapy regimens, attention is being paid to chemotherapy used to convert patients with initially unresectable metastasis to patients with a chance of surgical cure. The choice of chemotherapy regimen requires consideration of the goals for therapy and assessment of both tumor- and patient-specific factors.
This report discusses the choice and timing of chemotherapy in patients with initially resectable and borderline resectable metastatic CRC. Coordinated multidisciplinary care of such patients can optimize survival outcomes and result in cure for patients with this otherwise lethal disease.
Background:
The incidence of hematologic cancers increases with age. These cancers are associated with recurrent somatic mutations in specific genes. We hypothesized that such mutations would be detectable in the blood of some persons who are not known to have hematologic disorders.
Methods:
We analyzed whole-exome sequencing data from DNA in the peripheral-blood cells of 17,182 persons who were unselected for hematologic phenotypes. We looked for somatic mutations by identifying previously characterized single-nucleotide variants and small insertions or deletions in 160 genes that are recurrently mutated in hematologic cancers. The presence of mutations was analyzed for an association with hematologic phenotypes, survival, and cardiovascular events.
Results:
Detectable somatic mutations were rare in persons younger than 40 years of age but rose appreciably in frequency with age. Among persons 70 to 79 years of age, 80 to 89 years of age, and 90 to 108 years of age, these clonal mutations were observed in 9.5% (219 of 2300 persons), 11.7% (37 of 317), and 18.4% (19 of 103), respectively. The majority of the variants occurred in three genes: DNMT3A, TET2, and ASXL1. The presence of a somatic mutation was associated with an increase in the risk of hematologic cancer (hazard ratio, 11.1; 95% confidence interval [CI], 3.9 to 32.6), an increase in all-cause mortality (hazard ratio, 1.4; 95% CI, 1.1 to 1.8), and increases in the risks of incident coronary heart disease (hazard ratio, 2.0; 95% CI, 1.2 to 3.4) and ischemic stroke (hazard ratio, 2.6; 95% CI, 1.4 to 4.8).
Conclusions:
Age-related clonal hematopoiesis is a common condition that is associated with increases in the risk of hematologic cancer and in all-cause mortality, with the latter possibly due to an increased risk of cardiovascular disease. (Funded by the National Institutes of Health and others.).
The development of noninvasive methods to detect and monitor tumors continues to be a major challenge in oncology. We used digital polymerase chain reaction-based technologies to evaluate the ability of circulating tumor DNA (ctDNA) to detect tumors in 640 patients with various cancer types. We found that ctDNA was detectable in >75% of patients with advanced pancreatic, ovarian, colorectal, bladder, gastroesophageal, breast, melanoma, hepatocellular, and head and neck cancers, but in less than 50% of primary brain, renal, prostate, or thyroid cancers. In patients with localized tumors, ctDNA was detected in 73, 57, 48, and 50% of patients with colorectal cancer, gastroesophageal cancer, pancreatic cancer, and breast adenocarcinoma, respectively. ctDNA was often present in patients without detectable circulating tumor cells, suggesting that these two biomarkers are distinct entities. In a separate panel of 206 patients with metastatic colorectal cancers, we showed that the sensitivity of ctDNA for detection of clinically relevant KRAS gene mutations was 87.2% and its specificity was 99.2%. Finally, we assessed whether ctDNA could provide clues into the mechanisms underlying resistance to epidermal growth factor receptor blockade in 24 patients who objectively responded to therapy but subsequently relapsed. Twenty-three (96%) of these patients developed one or more mutations in genes involved in the mitogen-activated protein kinase pathway. Together, these data suggest that ctDNA is a broadly applicable, sensitive, and specific biomarker that can be used for a variety of clinical and research purposes in patients with multiple different types of cancer.
Purpose:
Genetic alterations of KRAS, CDKN2A, TP53, and SMAD4 are the most frequent events in pancreatic cancer. We determined the extent to which these 4 alterations are coexistent in the same carcinoma, and their impact on patient outcome.
Experimental design:
Pancreatic cancer patients who underwent an autopsy were studied (n = 79). Matched primary and metastasis tissues were evaluated for intragenic mutations in KRAS, CDKN2A, and TP53 and immunolabeled for CDKN2A, TP53, and SMAD4 protein products. The number of altered driver genes in each carcinoma was correlated to clinicopathologic features. Kaplan-Meier estimates were used to determine median disease free and overall survival, and a Cox proportional hazards model used to compare risk factors.
Results:
The number of genetically altered driver genes in a carcinoma was variable, with only 29 patients (37%) having an alteration in all 4 genes analyzed. The number of altered driver genes was significantly correlated with disease free survival (P = 0.008), overall survival (P = 0.041), and metastatic burden at autopsy (P = 0.002). On multivariate analysis, the number of driver gene alterations in a pancreatic carcinoma remained independently associated with overall survival (P = 0.046). Carcinomas with only 1 to 2 driver alterations were enriched for those patients with the longest survival (median 23 months, range 1 to 53).
Conclusions:
Determinations of the status of the 4 major driver genes in pancreatic cancer, and specifically the extent to which they are coexistent in an individual patients cancer, provides distinct information regarding disease progression and survival that is independent of clinical stage and treatment status.
Massively parallel sequencing of cell-free, maternal plasma DNA was recently demonstrated to be a safe and effective screening method for fetal chromosomal aneuploidies. Here, we report an improved sequencing method achieving significantly increased throughput and decreased cost by replacing laborious sequencing library preparation steps with PCR employing a single primer pair designed to amplify a discrete subset of repeated regions. Using this approach, samples containing as little as 4% trisomy 21 DNA could be readily distinguished from euploid samples.
The early detection of cancers through analysis of circulating DNA could have a substantial impact on morbidity and mortality. To achieve this goal, it is essential to determine the number of mutant molecules present in the circulation of cancer patients and to develop methods that are sufficiently sensitive to detect these mutations. Using a modified version of a recently developed assay for this purpose, we found that patients with advanced colorectal cancers consistently contained mutant adenomatous polyposis coli (APC) DNA molecules in their plasma. The median number of APC DNA fragments in such patients was 47,800 per ml of plasma, of which 8% were mutant. Mutant APC molecules were also detected in >60% of patients with early, presumably curable colorectal cancers, at levels ranging from 0.01% to 1.7% of the total APC molecules. These results have implications for the mechanisms through which tumor DNA is released into the circulation and for diagnostic tests based on this phenomenon.
• colorectal cancer
• plasma DNA
• tumor suppressor gene
• circulating DNA
• diagnosis
We show that the times separating the birth of benign, invasive, and metastatic tumor cells can be determined by analysis of the mutations they have in common. When combined with prior clinical observations, these analyses suggest the following general conclusions about colorectal tumorigenesis: (i) It takes ≈17 years for a large benign tumor to evolve into an advanced cancer but <2 years for cells within that cancer to acquire the ability to metastasize; (ii) it requires few, if any, selective events to transform a highly invasive cancer cell into one with the capacity to metastasize; (iii) the process of cell culture ex vivo does not introduce new clonal mutations into colorectal tumor cell populations; and (iv) the rates at which point mutations develop in advanced cancers are similar to those of normal cells. These results have important implications for understanding human tumor pathogenesis, particularly those associated with metastasis.
• cancer genetics
• colorectal cancer
• metastasis
• stem cells
Significance
Few patients with pancreatic cancer survive longer than 5 y, in part because most patients are identified only after their disease has progressed to an advanced stage. In this study, we show how combining mutations in circulating tumor DNA (ctDNA) with protein markers can result in a screening test with improved sensitivity while retaining specificity. The combination of the ctDNA and protein markers was superior to any single marker. Moreover, the combination detected nearly two-thirds of pancreatic cancers that had no evidence of distant metastasis at the time of surgical resection. The strategy may represent an approach to detect cancers of many types at an earlier stage.
The use of circulating DNA(ctDNA) to provide a non-invasive, personalised genomic snapshot of a patients' tumour has huge potential. Over the past five years this area of research has gained huge momentum. A number of studies in metastatic breast cancer have shown the potential of ctDNA to predict prognosis and treatment response using ctDNA. Further developments have included deeper sequencing using whole exome and shallow whole genome approaches which has the potential to identify new mutations and chromosomal copy number changes which appear upon resistance to treatment. In early breast cancer, recent work utilising personalised digital PCR probes has shown huge potential in predicting disease relapse and the detection of micrometastatic disease which could lead to improved treatment and outcome for these patients. Specific pathways of resistance can also be monitored and liquid biopsy approaches for the detection of ESR1 mutations have been used which could identify patients who have become resistant to particular endocrine therapies. The identification of PIK3CA mutations in plasma has also been shown to predict a higher response rate to specific PI3K inhibitors and could be used as a non-invasive screening tool prior to treatment. Further work on the detection of exosomal miRNA and hypermethylated DNA in plasma have shown promise in terms of specificity for early breast cancer detection and could be used to monitor treatment response. This review will focus on technological advances in the field, early detection of relapse and the detection of tumour-specific genomic alterations which could predict treatment response and resistance in patients with breast cancer.
Despite the success of monotherapies based on blockade of programmed cell death 1 (PD-1) in human melanoma, most patients do not experience durable clinical benefit. Pre-existing T-cell infiltration and/or the presence of PD-L1 in tumours may be used as indicators of clinical response; however, blood-based profiling to understand the mechanisms of PD-1 blockade has not been widely explored. Here we use immune profiling of peripheral blood from patients with stage IV melanoma before and after treatment with the PD-1-targeting antibody pembrolizumab and identify pharmacodynamic changes in circulating exhausted-phenotype CD8 T cells (Tex cells). Most of the patients demonstrated an immunological response to pembrolizumab. Clinical failure in many patients was not solely due to an inability to induce immune reinvigoration, but rather resulted from an imbalance between T-cell reinvigoration and tumour burden. The magnitude of reinvigoration of circulating Tex cells determined in relation to pretreatment tumour burden correlated with clinical response. By focused profiling of a mechanistically relevant circulating T-cell subpopulation calibrated to pretreatment disease burden, we identify a clinically accessible potential on-treatment predictor of response to PD-1 blockade.
Controversy continues to roil around the role of PSA screening in prostate cancer. The authors review the available data and its quality and conclude that the evidence does not indicate that the benefits outweigh the harms.
The inherent molecular heterogeneity of metastatic tumors and the ability of cancer genomes to dynamically evolve are not properly captured by tissue specimens. Analysis of cell-free DNA and circulating tumor cells has the potential to change clinical practice by exploiting blood rather than tissue as a source of information. Liquid biopsies are already used to monitor disease response and track the emergence of drug resistance. The suitability of blood-based molecular profiles for early detection and monitoring minimal residual disease is being evaluated. In this review, we address open questions in this fast-evolving field of research.
The extent of heterogeneity among driver gene mutations present in naturally occurring metastases—that is, treatment-naive metastatic disease—is largely unknown. To address this issue, we carried out 60× whole-genome sequencing of 26 metastases from four patients with pancreatic cancer. We found that identical mutations in known driver genes were present in every metastatic lesion for each patient studied. Passenger gene mutations, which do not have known or predicted functional consequences, accounted for all intratumoral heterogeneity. Even with respect to these passenger mutations, our analysis suggests that the genetic similarity among the founding cells of metastases was higher than that expected for any two cells randomly taken from a normal tissue. The uniformity of known driver gene mutations among metastases in the same patient has critical and encouraging implications for the success of future targeted therapies in advanced-stage disease.
Each year, the American Cancer Society estimates the numbers of new cancer cases and deaths that will occur in the United States in the current year and compiles the most recent data on cancer incidence, mortality, and survival. Incidence data were collected by the Surveillance, Epidemiology, and End Results Program; the National Program of Cancer Registries; and the North American Association of Central Cancer Registries. Mortality data were collected by the National Center for Health Statistics. In 2017, 1,688,780 new cancer cases and 600,920 cancer deaths are projected to occur in the United States. For all sites combined, the cancer incidence rate is 20% higher in men than in women, while the cancer death rate is 40% higher. However, sex disparities vary by cancer type. For example, thyroid cancer incidence rates are 3-fold higher in women than in men (21 vs 7 per 100,000 population), despite equivalent death rates (0.5 per 100,000 population), largely reflecting sex differences in the "epidemic of diagnosis." Over the past decade of available data, the overall cancer incidence rate (2004-2013) was stable in women and declined by approximately 2% annually in men, while the cancer death rate (2005-2014) declined by about 1.5% annually in both men and women. From 1991 to 2014, the overall cancer death rate dropped 25%, translating to approximately 2,143,200 fewer cancer deaths than would have been expected if death rates had remained at their peak. Although the cancer death rate was 15% higher in blacks than in whites in 2014, increasing access to care as a result of the Patient Protection and Affordable Care Act may expedite the narrowing racial gap; from 2010 to 2015, the proportion of blacks who were uninsured halved, from 21% to 11%, as it did for Hispanics (31% to 16%). Gains in coverage for traditionally underserved Americans will facilitate the broader application of existing cancer control knowledge across every segment of the population. CA Cancer J Clin 2017. © 2017 American Cancer Society.
Focusing on driver-gene mutations and the pathways they control has rendered complex cancer-genome landscapes intelligible. In solid tumors of adults, alterations in as few as three driver genes appear to suffice for a cell to evolve into an advanced cancer.
Objective: To determine the effectiveness of two adjuvant therapy regimens in improving surgical cure rates in stage III (Dukes stage C) colon cancer. Design: Randomized, concurrently controlled clinical trial. Setting: Major cancer centers, universities, and community clinics affiliated with the North Cancer Treatment Group, the Southwest Oncology Group, and the Eastern Cooperative Oncology Group. Patients: Those who had had curative-intent resections of stage III colon cancer in the previous 1 to 5 weeks. Intervention: Patients were assigned to observation only, to levamisole alone (50 mg orally three times/d for 3 days, repeated every 2 weeks for 1 year), or to this regimen of levamisole plus fluorouracil (450 mg/m 2 body surface area intravenously daily for 5 days and then, beginning at 28 days, weekly for 48 weeks). Measurements: Rates of cancer recurrence and death. Early- and late-treatment side effects. Results: With all 929 eligible patients able to be followed for 5 years or more (median follow-up, 6.5 years), fluorouracil plus levamisole reduced the recurrence rate by 40% (P<0.0001) and the death rate by 33% (P=0.0007). Levamisole reduced the recurrence rate by only 2% and the death rate by only 6%. With few exceptions, toxicity was mild and patient compliance was excellent. No evidence of late side effects was seen. Conclusion: Fluorouracil plus levamisole is tolerable adjuvant therapy to surgery; it has been confirmed to substantially increase cure rates for patients with high-risk (stage III) colon cancer. It should be considered standard treatment for all such patients not entered into clinical trials
Unlabelled:
The ability to study nonhematologic cancers through noninvasive sampling of blood is one of the most exciting and rapidly advancing fields in cancer diagnostics. This has been driven both by major technologic advances, including the isolation of intact cancer cells and the analysis of cancer cell-derived DNA from blood samples, and by the increasing application of molecularly driven therapeutics, which rely on such accurate and timely measurements of critical biomarkers. Moreover, the dramatic efficacy of these potent cancer therapies drives the selection for additional genetic changes as tumors acquire drug resistance, necessitating repeated sampling of cancer cells to adjust therapy in response to tumor evolution. Together, these advanced noninvasive diagnostic capabilities and their applications in guiding precision cancer therapies are poised to change the ways in which we select and monitor cancer treatments.
Significance:
Recent advances in technologies to analyze circulating tumor cells and circulating tumor DNA are setting the stage for real-time, noninvasive monitoring of cancer and providing novel insights into cancer evolution, invasion, and metastasis.
Over the past decade, comprehensive sequencing efforts have revealed the genomic landscapes of common forms of human cancer.
For most cancer types, this landscape consists of a small number of “mountains” (genes altered in a high percentage of tumors)
and a much larger number of “hills” (genes altered infrequently). To date, these studies have revealed ~140 genes that, when
altered by intragenic mutations, can promote or “drive” tumorigenesis. A typical tumor contains two to eight of these “driver
gene” mutations; the remaining mutations are passengers that confer no selective growth advantage. Driver genes can be classified
into 12 signaling pathways that regulate three core cellular processes: cell fate, cell survival, and genome maintenance.
A better understanding of these pathways is one of the most pressing needs in basic cancer research. Even now, however, our
knowledge of cancer genomes is sufficient to guide the development of more effective approaches for reducing cancer morbidity
and mortality.
Background:
The management of metastatic breast cancer requires monitoring of the tumor burden to determine the response to treatment, and improved biomarkers are needed. Biomarkers such as cancer antigen 15-3 (CA 15-3) and circulating tumor cells have been widely studied. However, circulating cell-free DNA carrying tumor-specific alterations (circulating tumor DNA) has not been extensively investigated or compared with other circulating biomarkers in breast cancer.
Methods:
We compared the radiographic imaging of tumors with the assay of circulating tumor DNA, CA 15-3, and circulating tumor cells in 30 women with metastatic breast cancer who were receiving systemic therapy. We used targeted or whole-genome sequencing to identify somatic genomic alterations and designed personalized assays to quantify circulating tumor DNA in serially collected plasma specimens. CA 15-3 levels and numbers of circulating tumor cells were measured at identical time points.
Results:
Circulating tumor DNA was successfully detected in 29 of the 30 women (97%) in whom somatic genomic alterations were identified; CA 15-3 and circulating tumor cells were detected in 21 of 27 women (78%) and 26 of 30 women (87%), respectively. Circulating tumor DNA levels showed a greater dynamic range, and greater correlation with changes in tumor burden, than did CA 15-3 or circulating tumor cells. Among the measures tested, circulating tumor DNA provided the earliest measure of treatment response in 10 of 19 women (53%).
Conclusions:
This proof-of-concept analysis showed that circulating tumor DNA is an informative, inherently specific, and highly sensitive biomarker of metastatic breast cancer. (Funded by Cancer Research UK and others.).
We propose the elastic net, a new regularization and variable selection method. Real world data and a simulation study show that the elastic net often outperforms the lasso, while enjoying a similar sparsity of representation. In addition, the elastic net encourages a grouping effect, where strongly correlated predictors tend to be in or out of the model together. The elastic net is particularly useful when the number of predictors (p) is much bigger than the number of observations (n). By contrast, the lasso is not a very satisfactory variable selection method in the p≫n case. An algorithm called LARS-EN is proposed for computing elastic net regularization paths efficiently, much like algorithm LARS does for the lasso.
Plasma of cancer patients contains cell-free tumor DNA that carries information on tumor mutations and tumor burden. Individual mutations have been probed using allele-specific assays, but sequencing of entire genes to detect cancer mutations in circulating DNA has not been demonstrated. We developed a method for tagged-amplicon deep sequencing (TAm-Seq) and screened 5995 genomic bases for low-frequency mutations. Using this method, we identified cancer mutations present in circulating DNA at allele frequencies as low as 2%, with sensitivity and specificity of >97%. We identified mutations throughout the tumor suppressor gene TP53 in circulating DNA from 46 plasma samples of advanced ovarian cancer patients. We demonstrated use of TAm-Seq to noninvasively identify the origin of metastatic relapse in a patient with multiple primary tumors. In another case, we identified in plasma an EGFR mutation not found in an initial ovarian biopsy. We further used TAm-Seq to monitor tumor dynamics, and tracked 10 concomitant mutations in plasma of a metastatic breast cancer patient over 16 months. This low-cost, high-throughput method could facilitate analysis of circulating DNA as a noninvasive "liquid biopsy" for personalized cancer genomics.
The identification of mutations that are present in a small fraction of DNA templates is essential for progress in several areas of biomedical research. Although massively parallel sequencing instruments are in principle well suited to this task, the error rates in such instruments are generally too high to allow confident identification of rare variants. We here describe an approach that can substantially increase the sensitivity of massively parallel sequencing instruments for this purpose. The keys to this approach, called the Safe-Sequencing System ("Safe-SeqS"), are (i) assignment of a unique identifier (UID) to each template molecule, (ii) amplification of each uniquely tagged template molecule to create UID families, and (iii) redundant sequencing of the amplification products. PCR fragments with the same UID are considered mutant ("supermutants") only if ≥95% of them contain the identical mutation. We illustrate the utility of this approach for determining the fidelity of a polymerase, the accuracy of oligonucleotides synthesized in vitro, and the prevalence of mutations in the nuclear and mitochondrial genomes of normal cells.
Currently, a blood test for lung cancer does not exist. Serum biomarkers that could aid clinicians in making case management decisions would be enormously valuable. We used two proteomic platforms and a literature search to select candidate serum markers for the diagnosis of lung cancer.
We initially assayed six serum proteins, four discovered by proteomics and two previously known to be cancer associated, on a training set of sera from 100 patients (50 with a new diagnosis of lung cancer and 50 age- and sex-matched controls). Classification and Regression Tree (CART) analysis selected a panel of four markers that most efficiently predicted which patients had lung cancer. An independent, blinded validation set of sera from 97 patients (49 lung cancer patients and 48 matched controls) determined the accuracy of the four markers to predict which patients had lung cancer.
Four serum proteins-carcinoembryonic antigen, retinol binding protein, alpha1-antitrypsin, and squamous cell carcinoma antigen-were collectively found to correctly classify the majority of lung cancer and control patients in the training set (sensitivity, 89.3%; specificity, 84.7%). These markers also accurately classified patients in the independent validation set (sensitivity, 77.8%; specificity, 75.4%). Remarkably, 90% of patients who fell into any one of three groupings in the CART analysis had lung cancer.
This panel of four serum proteins is valuable in suggesting the diagnosis of lung cancer. These data may be useful for treating patients with an indeterminate pulmonary lesion, and potentially in predicting individuals at high risk for lung cancer.
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