Extracellular Vesicle and Particle Biomarkers Define Multiple Human Cancers.

There is an unmet clinical need for improved tissue and liquid biopsy tools for cancer detection. We investigated the proteomic profile of extracellular vesicles and particles (EVPs) in 426 human samples from tissue explants (TEs), plasma, and other bodily fluids. Among traditional exosome markers, CD9, HSPA8, ALIX, and HSP90AB1 represent pan-EVP markers, while ACTB, MSN, and RAP1B are novel pan-EVP markers. To confirm that EVPs are ideal diagnostic tools, we analyzed proteomes of TE- (n = 151) and plasma-derived (n = 120) EVPs. Comparison of TE EVPs identified proteins (e.g., VCAN, TNC, and THBS2) that distinguish tumors from normal tissues with 90% sensitivity/94% specificity. Machine-learning classification of plasma-derived EVP cargo, including immunoglobulins, revealed 95% sensitivity/90% specificity in detecting cancer. Finally, we defined a panel of tumor-type-specific EVP proteins in TEs and plasma, which can classify tumors of unknown primary origin. Thus, EVP proteins can serve as reliable biomarkers for cancer detection and determining cancer type.

Use of Enzymatically Converted Cell-Free DNA (cfDNA) Data for Copy Number Variation-Linked Fragmentation Analysis Allows for Early Colorectal Cancer Detection.

The use of non-invasive liquid biopsy-based cell-free DNA (cfDNA) analysis is an emerging method of cancer detection and intervention. Different analytical methodologies are used to investigate cfDNA characteristics, resulting in costly and long analysis processes needed for combining different data. This study investigates the possibility of using cfDNA data converted for methylation analysis for combining the cfDNA fragment size with copy number variation (CNV) in the context of early colorectal cancer detection. Specifically, we focused on comparing enzymatically and bisulfite-converted data for evaluating cfDNA fragments belonging to chromosome 18. Chromosome 18 is often reported to be deleted in colorectal cancer. We used counts of short and medium cfDNA fragments of chromosome 18 and trained a linear model (LDA) on a set of 2959 regions to predict early-stage (I-IIA) colorectal cancer on an independent test set. In total, 87.5% sensitivity and 92% specificity were obtained on the enzymatically converted libraries. Repeating the same workflow on bisulfite-converted data yielded lower accuracy results with 58.3% sensitivity, implying that enzymatic conversion preserves the cancer fragmentation footprint in whole genome data better than bisulfite conversion. These results could serve as a promising new avenue for the early detection of colorectal cancer using fragmentation and methylation approaches on the same datasets.

Epigenomic Blood-Based Early Detection of Pancreatic Cancer Employing Cell-Free DNA.

BACKGROUND & AIMS: Early detection of pancreatic cancer (PaC) can drastically improve survival rates. Approximately 25% of subjects with PaC have type 2 diabetes diagnosed within 3 years prior to the PaC diagnosis, suggesting that subjects with type 2 diabetes are at high risk of occult PaC. We have developed an early-detection PaC test, based on changes in 5-hydroxymethylcytosine (5hmC) signals in cell-free DNA from plasma. METHODS: Blood was collected from 132 subjects with PaC and 528 noncancer subjects to generate epigenomic and genomic feature sets yielding a predictive PaC signal algorithm. The algorithm was validated in a blinded cohort composed of 102 subjects with PaC, 2048 noncancer subjects, and 1524 subjects with non-PaCs. RESULTS: 5hmC differential profiling and additional genomic features enabled the development of a machine learning algorithm capable of distinguishing subjects with PaC from noncancer subjects with high specificity and sensitivity. The algorithm was validated with a sensitivity for early-stage (stage I/II) PaC of 68.3% (95% confidence interval [CI], 51.9%-81.9%) and an overall specificity of 96.9% (95% CI, 96.1%-97.7%). CONCLUSIONS: The PaC detection test showed robust early-stage detection of PaC signal in the studied cohorts with varying type 2 diabetes status. This assay merits further clinical validation for the early detection of PaC in high-risk individuals.

Revolutionizing cancer monitoring with carbon-based electrochemical biosensors.

Cancer monitoring plays a critical role in improving patient outcomes by providing early detection, personalized treatment options, and treatment response tracking. Carbon-based electrochemical biosensors have emerged in recent years as a revolutionary technology with the potential to revolutionize cancer monitoring. These sensors are useful for clinical applications because of their high sensitivity, selectivity, rapid response, and compatibility with miniaturized equipment. This review paper gives an in-depth look at the latest developments and the possibilities of carbon-based electrochemical sensors in cancer surveillance. The essential principles of carbon-based electrochemical sensors are discussed, including their structure, operating mechanisms, and critical qualities that make them suited for cancer surveillance. Furthermore, we investigate their applicability in detecting specific cancer biomarkers, evaluating therapy responses, and detecting cancer recurrence early. Additionally, a comparison of carbon-based electrochemical sensor performance measures, including sensitivity, selectivity, accuracy, and limit of detection, is presented in contrast to existing monitoring methods and upcoming technologies. Finally, we discuss prospective tactics, future initiatives, and commercialization opportunities for improving the capabilities of these sensors and integrating them into normal clinical practice. The review highlights the potential impact of carbon-based electrochemical sensors on cancer diagnosis, treatment, and patient outcomes, as well as the importance of ongoing research, collaboration, and validation studies to fully realize their potential in revolutionizing cancer monitoring.

Assessing aneuploidy with repetitive element sequencing.

We report a sensitive PCR-based assay called Repetitive Element AneupLoidy Sequencing System (RealSeqS) that can detect aneuploidy in samples containing as little as 3 pg of DNA. Using a single primer pair, we amplified ∼350,000 amplicons distributed throughout the genome. Aneuploidy was detected in 49% of liquid biopsies from a total of 883 nonmetastatic, clinically detected cancers of the colorectum, esophagus, liver, lung, ovary, pancreas, breast, or stomach. Combining aneuploidy with somatic mutation detection and eight standard protein biomarkers yielded a median sensitivity of 80% in these eight cancer types, while only 1% of 812 healthy controls scored positive.

A NIR Programmable In Vivo miRNA Magnifier for NIR-II Imaging of Early Stage Cancer.

Aberrant expressions of biomolecules occur much earlier than tumor visualized size and morphology change, but their common measurement strategies such as biopsy suffer from invasive sampling process. In vivo imaging of slight biomolecule expression difference is urgently needed for early cancer detection. Fluorescence of rare earth nanoparticles (RENPs) in second near-infrared (NIR-II) region makes them appropriate tool for in vivo imaging. However, the incapacity to couple with signal amplification strategies, especially programmable signal amplification strategies, limited their application in lowly expressed biomarkers imaging. Here we develop a 980/808 nm NIR programmed in vivo microRNAs (miRNAs) magnifier by conjugating activatable DNAzyme walker set to RENPs, which achieves more effective NIR-II imaging of early stage tumor than size monitoring imaging technique. Dye FD1080 (FD1080) modified substrate DNA quenches NIR-II downconversion emission of RENPs under 808 nm excitation. The miRNA recognition region in DNAzyme walker is sealed by a photo-cleavable strand to avoid "false positive" signal in systemic circulation. Upconversion emission of RENPs under 980 nm irradiation activates DNAzyme walker for miRNA recognition and amplifies NIR-II fluorescence recovery of RENPs via DNAzyme catalytic reaction to achieve in vivo miRNA imaging. This strategy demonstrates good application potential in the field of early cancer detection.

AGA Clinical Practice Update on the Diagnosis and Management of Atrophic Gastritis: Expert Review.

DESCRIPTION: The purpose of this Clinical Practice Update Expert Review is to provide clinicians with guidance on the diagnosis and management of atrophic gastritis, a common preneoplastic condition of the stomach, with a primary focus on atrophic gastritis due to chronic Helicobacter pylori infection-the most common etiology-or due to autoimmunity. To date, clinical guidance for best practices related to the diagnosis and management of atrophic gastritis remains very limited in the United States, which leads to poor recognition of this preneoplastic condition and suboptimal risk stratification. In addition, there is heterogeneity in the definitions of atrophic gastritis, autoimmune gastritis, pernicious anemia, and gastric neoplasia in the literature, which has led to confusion in clinical practice and research. Accordingly, the primary objective of this Clinical Practice Update is to provide clinicians with a framework for the diagnosis and management of atrophic gastritis. By focusing on atrophic gastritis, this Clinical Practice Update is intended to complement the 2020 American Gastroenterological Association Institute guidelines on the management of gastric intestinal metaplasia. These recent guidelines did not specifically discuss the diagnosis and management of atrophic gastritis. Providers should recognize, however, that a diagnosis of intestinal metaplasia on gastric histopathology implies the diagnosis of atrophic gastritis because intestinal metaplasia occurs in underlying atrophic mucosa, although this is often not distinctly noted on histopathologic reports. Nevertheless, atrophic gastritis represents an important stage with distinct histopathologic alterations in the multistep cascade of gastric cancer pathogenesis. METHODS: The Best Practice Advice statements presented herein were developed from a combination of available evidence from published literature and consensus-based expert opinion. No formal rating of the strength or quality of the evidence was carried out. These statements are meant to provide practical advice to clinicians practicing in the United States. Best Practice Advice Statements BEST PRACTICE ADVICE 1: Atrophic gastritis is defined as the loss of gastric glands, with or without metaplasia, in the setting of chronic inflammation mainly due to Helicobacter pylori infection or autoimmunity. Regardless of the etiology, the diagnosis of atrophic gastritis should be confirmed by histopathology. BEST PRACTICE ADVICE 2: Providers should be aware that the presence of intestinal metaplasia on gastric histology almost invariably implies the diagnosis of atrophic gastritis. There should be a coordinated effort between gastroenterologists and pathologists to improve the consistency of documenting the extent and severity of atrophic gastritis, particularly if marked atrophy is present. BEST PRACTICE ADVICE 3: Providers should recognize typical endoscopic features of atrophic gastritis, which include pale appearance of gastric mucosa, increased visibility of vasculature due to thinning of the gastric mucosa, and loss of gastric folds, and, if with concomitant intestinal metaplasia, light blue crests and white opaque fields. Because these mucosal changes are often subtle, techniques to optimize evaluation of the gastric mucosa should be performed. BEST PRACTICE ADVICE 4: When endoscopic features of atrophic gastritis are present, providers should assess the extent endoscopically. Providers should obtain biopsies from the suspected atrophic/metaplastic areas for histopathological confirmation and risk stratification; at a minimum, biopsies from the body and antrum/incisura should be obtained and placed in separately labeled jars. Targeted biopsies should additionally be obtained from any other mucosal abnormalities. BEST PRACTICE ADVICE 5: In patients with histology compatible with autoimmune gastritis, providers should consider checking antiparietal cell antibodies and anti-intrinsic factor antibodies to assist with the diagnosis. Providers should also evaluate for anemia due to vitamin B-12 and iron deficiencies. BEST PRACTICE ADVICE 6: All individuals with atrophic gastritis should be assessed for H pylori infection. If positive, treatment of H pylori should be administered and successful eradication should be confirmed using nonserological testing modalities. BEST PRACTICE ADVICE 7: The optimal endoscopic surveillance interval for patients with atrophic gastritis is not well-defined and should be decided based on individual risk assessment and shared decision making. A surveillance endoscopy every 3 years should be considered in individuals with advanced atrophic gastritis, defined based on anatomic extent and histologic grade. BEST PRACTICE ADVICE 8: The optimal surveillance interval for individuals with autoimmune gastritis is unclear. Interval endoscopic surveillance should be considered based on individualized assessment and shared decision making. BEST PRACTICE ADVICE 9: Providers should recognize pernicious anemia as a late-stage manifestation of autoimmune gastritis that is characterized by vitamin B-12 deficiency and macrocytic anemia. Patients with a new diagnosis of pernicious anemia who have not had a recent endoscopy should undergo endoscopy with topographical biopsies to confirm corpus-predominant atrophic gastritis for risk stratification and to rule out prevalent gastric neoplasia, including neuroendocrine tumors. BEST PRACTICE ADVICE 10: Individuals with autoimmune gastritis should be screened for type 1 gastric neuroendocrine tumors with upper endoscopy. Small neuroendocrine tumors should be removed endoscopically, followed by surveillance endoscopy every 1-2 years, depending on the burden of neuroendocrine tumors. BEST PRACTICE ADVICE 11: Providers should evaluate for iron and vitamin B-12 deficiencies in patients with atrophic gastritis irrespective of etiology, especially if corpus-predominant. Likewise, in patients with unexplained iron or vitamin B-12 deficiency, atrophic gastritis should be considered in the differential diagnosis and appropriate diagnostic evaluation pursued. BEST PRACTICE ADVICE 12: In patients with autoimmune gastritis, providers should recognize that concomitant autoimmune disorders, particularly autoimmune thyroid disease, are common. Screening for autoimmune thyroid disease should be performed.

Validation of a Novel Multitarget Blood Test Shows High Sensitivity to Detect Early Stage Hepatocellular Carcinoma.

BACKGROUND & AIMS: Hepatocellular carcinoma (HCC) is a leading cause of cancer-related death worldwide. Although biannual ultrasound surveillance with or without α-fetoprotein (AFP) testing is recommended for at-risk patients, sensitivity for early stage HCC, for which potentially curative treatments exist, is suboptimal. We conducted studies to establish the multitarget HCC blood test (mt-HBT) algorithm and cut-off values and to validate test performance in patients with chronic liver disease. METHODS: Algorithm development and clinical validation studies were conducted with participants in an international, multicenter, case-control study. Study subjects had underlying cirrhosis or chronic hepatitis B virus; HCC cases were diagnosed per the American Association for the Study of Liver Diseases criteria and controls were matched for age and liver disease etiology. Whole blood and serum were shipped to a central laboratory and processed while blinded to case/control status. An algorithm was developed for the mt-HBT, which incorporates methylation biomarkers (HOXA1, TSPYL5, and B3GALT6), AFP, and sex. RESULTS: In algorithm development, with 136 HCC cases (60% early stage) and 404 controls, the mt-HBT showed 72% sensitivity for early stage HCC at 88% specificity. Test performance was validated in an independent cohort of 156 HCC cases (50% early stage) and 245 controls, showing 88% overall sensitivity, 82% early stage sensitivity, and 87% specificity. Early stage sensitivity in clinical validation was significantly higher than AFP at 20 ng/mL or greater (40%; P < .0001) and GALAD (gender, age, Lens culinaris agglutinin-reactive AFP, AFP, and des-γ-carboxy-prothrombin score) of -0.63 or greater (71%; P = .03), although AFP and GALAD at these cut-off values had higher specificities (100% and 93%, respectively). CONCLUSIONS: The mt-HBT may significantly improve early stage HCC detection for patients undergoing HCC surveillance, a critical step to increasing curative treatment opportunities and reducing mortality. ClinicalTrials.gov number NCT03628651.

Unbiased peptoid cell screen identifies a peptoid targeting newly appeared cell surface vimentin on tumor transformed early lung cancer cells.

To identify potential new reagents and biomarkers for early lung cancer detection we combined the use of a novel preclinical isogenic model of human lung epithelial cells comparing non-malignant cells with those transformed to full malignancy using defined oncogenic changes and our on-bead two color (red and green stained cells) (OBTC) peptoid combinatorial screening methodology. The preclinical model used normal parent lung epithelial cells (HBEC3-KT, labeled with green dye) and isogenic fully malignant transformed derivatives (labeled with a red dye) via the sequential introduction of key genetic alterations of p53 knockdown, oncogenic KRAS and overexpression of cMYC (HBEC3p53, KRAS, cMYC). Using the unbiased OBTC screening approach, we tested 100,000 different peptoids and identified only one (named JM3A) that bound to the surface of the HBEC3p53, KRAS, cMYC cells (red cells) but not HBEC3-KT cells (green cells). Using the JM3A peptoid and proteomics, we identified the protein bound as vimentin using multiple validation approaches. These all confirmed the cell surface expression of vimentin (CSV) on transformed (HBEC3p53, KRAS, cMYC) but not on untransformed (HBEC3-KT) cells. JM3A coupled with fluorophores was able to detect and stain cell surface vimentin on very early stage lung cancers but not normal lung epithelial cells in a fashion comparable to that using anti-vimentin antibodies. We conclude: using a combined isogenic preclinical model of lung cancer and two color screening of a large peptoid library, we have identified differential expression of cell surface vimentin (CSV) after malignant transformation of lung epithelial cells, and developed a new peptoid reagent (JM3A) for detection of CSV which works well in staining of early stage NSCLCs. This new, highly specific, easy to prepare, CSV detecting JM3A peptoid provides an important new reagent for identifying cancer cells in early stage tumors as well as a resource for detection and isolating of CSV expressing circulating tumor cells.

Multimodal analysis of ctDNA methylation and fragmentomic profiles enhances detection of nonmetastatic colorectal cancer.

Aims: Early detection of colorectal cancer (CRC) provides substantially better survival rates. This study aimed to develop a blood-based screening assay named SPOT-MAS ('screen for the presence of tumor by DNA methylation and size') for early CRC detection with high accuracy. Methods: Plasma cell-free DNA samples from 159 patients with nonmetastatic CRC and 158 healthy controls were simultaneously analyzed for fragment length and methylation profiles. We then employed a deep neural network with fragment length and methylation signatures to build a classification model. Results: The model achieved an area under the curve of 0.989 and a sensitivity of 96.8% at 97% specificity in detecting CRC. External validation of our model showed comparable performance, with an area under the curve of 0.96. Conclusion: SPOT-MAS based on integration of cancer-specific methylation and fragmentomic signatures could provide high accuracy for early-stage CRC detection.

A novel blood test for early detection of colorectal cancer. Colorectal cancer is a cancer of the colon or rectum, located at the lower end of the digestive tract. The early detection of colorectal cancer can help people with the disease have a higher chance of survival and a better quality of life. Current screening methods can be invasive, cause discomfort or have low accuracy; therefore newer screening methods are needed. In this study we developed a new screening method, called SPOT-MAS, which works by measuring the signals of cancer DNA in the blood. By combining different characteristics of cancer DNA, SPOT-MAS could distinguish blood samples of people with colorectal cancer from those of healthy individuals with high accuracy.

Engaging veteran stakeholders to identify patient-centred research priorities for optimizing implementation of lung cancer screening.

BACKGROUND: Patient engagement in research agenda setting is increasingly being seen as a strategy to improve the responsiveness of healthcare to patient priorities. Implementation of low-dose computed tomography (LDCT) screening for lung cancer is suboptimal, suggesting that research is needed. OBJECTIVES: This study aimed to describe an approach by which a Veteran patient group worked with other stakeholders to develop a research agenda for LDCT screening and to describe the research questions that they prioritized. METHODS: We worked with Veterans organizations to identify 12 Veterans or family members at risk for or having experience with lung cancer to form a Patient Advisory Council (PAC). The PAC met repeatedly from June 2018 to December 2020, both independently and jointly, with stakeholders representing clinicians, health administrators and researchers to identify relevant research topics. The PAC prioritized these topics and then identified questions within these areas where research was needed using an iterative process. Finally, they ranked the importance of obtaining answers to these questions. RESULTS: PAC members valued the co-learning generated by interactions with stakeholders, but emphasized the importance of facilitation to avoid stakeholders dominating the discussion. The PAC prioritized three broad research areas-(1) the impact of insurance on uptake of LDCT; (2) how best to inform Veterans about LDCT; and (3) follow-up and impact of screening results. Using these areas as guides, PAC members identified 20 specific questions, ranking as most important (1) innovative outreach methods, (2) the impact of screening on psychological health, and (3) the impact of outsourcing scans from VA to non-VA providers on completion of recommended follow-up of screening results. The latter two were not identified as high priority by the stakeholder group. CONCLUSIONS: We present an approach that facilitates co-learning between Veteran patients and providers, researchers and health system administrators to increase patient confidence in their ability to contribute important information to a research agenda. The research questions prioritized by the Veterans who participated in this project illustrate that for this new screening technology, patients are concerned about the practical details of implementation (e.g., follow-up) and the technology's impact on quality of life. PATIENT OR PUBLIC CONTRIBUTION: Veterans and Veteran advocates contributed to our research team throughout the entire research process, including conceiving and co-authoring this manuscript.

Making the Rounds: Exploring the Role of Circulating Tumor DNA (ctDNA) in Non-Small Cell Lung Cancer.

Advancements in the clinical practice of non-small cell lung cancer (NSCLC) are shifting treatment paradigms towards increasingly personalized approaches. Liquid biopsies using various circulating analytes provide minimally invasive methods of sampling the molecular content within tumor cells. Plasma-derived circulating tumor DNA (ctDNA), the tumor-derived component of cell-free DNA (cfDNA), is the most extensively studied analyte and has a growing list of applications in the clinical management of NSCLC. As an alternative to tumor genotyping, the assessment of oncogenic driver alterations by ctDNA has become an accepted companion diagnostic via both single-gene polymerase chain reactions (PCR) and next-generation sequencing (NGS) for advanced NSCLC. ctDNA technologies have also shown the ability to detect the emerging mechanisms of acquired resistance that evolve after targeted therapy. Furthermore, the detection of minimal residual disease (MRD) by ctDNA for patients with NSCLC after curative-intent treatment may serve as a prognostic and potentially predictive biomarker for recurrence and response to therapy, respectively. Finally, ctDNA analysis via mutational, methylation, and/or fragmentation multi-omic profiling offers the potential for improving early lung cancer detection. In this review, we discuss the role of ctDNA in each of these capacities, namely, for molecular profiling, treatment response monitoring, MRD detection, and early cancer detection of NSCLC.

Early Melanoma Detection in Primary Care: Clinical Recognition of Melanoma is Not Enough, One Must Also Learn the Basics.

To improve early melanoma detection, educational programs have been developed for general practitioners (GPs). This study aimed to determine whether the adjunct of teaching basic knowledge of pigmented skin lesions (PSL) to the training in melanoma diagnosis improves the GPs' diagnostic accuracy of melanoma. An interventional prospective study was conducted over a 3-month period where GPs attended a 2-h training course. The 1st session taught clinical melanoma recognition and the 2nd session instructed basic knowledge of PSL. Prior to training, after the 1st, and after the 2nd session, GPs were asked to select the malignant or benign nature of 15 clinical images associated to their clinical history. In total, 56 GPs participated in this study. The number of GPs identifying correctly ≥ 50% of the melanomas increased the most after the 1st session from 15 (26.8%; CI = (15.2; 38.4)) to 44 (78.6%; CI = (67.8; 89.3)) GPs (P < 0.001). The number of GPs correctly identifying ≥ 50% of the benign PSL only increased after completing the entire training, going from 10 (17.9%; CI = [(7.8; 27.9)) GPs to 50 (89.3%; CI = (81.2; 97.4)) GPs (P < 0.001). In this study, GPs identified benign PSL most accurately after the 2nd session. This suggested that teaching GPs the basics of PSL would especially improve their diagnostic accuracy for benign PSL, which could reduce unnecessary referrals to dermatologists. Teaching basic knowledge of PSL in addition to melanoma recognition seemed to enable GPs to triage skin lesions more effectively than when they were only trained to recognize melanoma.

[PAPPS Expert Groups. Cancer prevention recommendations: Update 2022]. / Recomendaciones de Prevención del Cáncer. Actualización PAPPS 2022.

Cancer is a major cause of morbidity and mortality. Tobacco use, unhealthy diet, and physical inactivity are some of the lifestyle risk factors that have led to an increase in cancer. This article updates the evidence and includes recommendations for prevention strategies for each of the cancers with the highest incidence. These are based on the reduction of risk factors (primary prevention) and early diagnosis of cancer through screening and early detection of signs and symptoms, in medium-risk and high-risk populations. This update of the 2022 PAPPS has taken into account the vision of the National Health System Cancer Strategy, an update approved by the Interterritorial Council of the National Health System on January 2021 and the European Strategy (Europe's Beating Cancer Plan) presented on 4 February 2021.

Cancer metabolomics: A tool of clinical utility for early diagnosis of gynaecological cancers.

Gynaecological cancers are the major cause of cancer-related deaths in Indian women. The poor prognosis and lack of symptoms in the early stages make early cancer diagnosis difficult. The absence of mandatory screening programmes and the lack of awareness pose to be a real challenge in a developing economy as India. Prompt intervention is required to enhance cancer patient survival statistics and to lessen the social and financial burden. Conventional screening and cytological techniques employed currently have helped to reduce the incidence of cancers considerably. However, these tests offer low sensitivity and specificity and are not widely used for risk assessment, leading to inadequate early-stage cancer diagnosis. The accomplishment of Human Genome Project (HGP) has opened doors to exciting 'omics' platforms. Promising research in genomics and proteomics has revolutionized cancer detection and screening methodologies by providing more insights in the gene expression, protein function and how specific mutation in specific genes corresponds to a particular phenotype. However, these are incompetent to translate the information into clinical applicability. Various factors such as low sensitivity, diurnal variation in protein, poor reproducibility and analytical variables are prime hurdles. Thus the focus has been shifted to metabolomics, which is a much younger platform compared to genomics and proteomics. Metabolomics focuses on endpoint metabolites, which are final products sustained in the response to genetic or environmental changes by a living system. As a result, the metabolome indicates the cell's functional condition, which is directly linked to its phenotype. Metabolic profiling aims to study the changes occurred in metabolic pathways. This metabolite profile is capable of differentiating the healthy individuals from those having cancer. The pathways that a cell takes in turning malignant are exceedingly different, owing to the fact that transformation of healthy cells to abnormal cells is linked with significant metabolic abnormalities. This review is aimed to discuss metabolomics and its potential role in early diagnosis of gynaecological cancers, viz. breast, ovarian and cervical cancer.

Detection of aneuploidy in patients with cancer through amplification of long interspersed nucleotide elements (LINEs).

Aneuploidy is a feature of most cancer cells, and a myriad of approaches have been developed to detect it in clinical samples. We previously described primers that could be used to amplify ∼38,000 unique long interspersed nucleotide elements (LINEs) from throughout the genome. Here we have developed an approach to evaluate the sequencing data obtained from these amplicons. This approach, called Within-Sample AneupLoidy DetectiOn (WALDO), employs supervised machine learning to detect the small changes in multiple chromosome arms that are often present in cancers. We used WALDO to search for chromosome arm gains and losses in 1,677 tumors and in 1,522 liquid biopsies of blood from cancer patients or normal individuals. Aneuploidy was detected in 95% of cancer biopsies and in 22% of liquid biopsies. Using single-nucleotide polymorphisms within the amplified LINEs, WALDO concomitantly assesses allelic imbalances, microsatellite instability, and sample identification. WALDO can be used on samples containing only a few nanograms of DNA and as little as 1% neoplastic content and has a variety of applications in cancer diagnostics and forensic science.

The Potential of Aptamer-Mediated Liquid Biopsy for Early Detection of Cancer.

The early detection of cancer favors a greater chance of curative treatment and long-term survival. Exciting new technologies have been developed that can help to catch the disease early. Liquid biopsy is a promising non-invasive tool to detect cancer, even at an early stage, as well as to continuously monitor disease progression and treatment efficacy. Various methods have been implemented to isolate and purify bio-analytes in liquid biopsy specimens. Aptamers are short oligonucleotides consisting of either DNA or RNA that are capable of binding to target molecules with high specificity. Due to their unique properties, they are considered promising recognition ligands for the early detection of cancer by liquid biopsy. A variety of circulating targets have been isolated with high affinity and specificity by facile modification and affinity regulation of the aptamers. In this review, we discuss recent progress in aptamer-mediated liquid biopsy for cancer detection, its associated challenges, and its future potential for clinical applications.

Inclusion of oral health teams in primary health care promotes early diagnosis of oral and oropharyngeal cancers: a nationwide study.

BACKGROUND: Oral and oropharyngeal cancers are considered important public health problems worldwide. This study aims to analyze the association between late diagnosis of oral and oropharyngeal cancers in Brazil and the contextual indicators of socioeconomic variables and coverage of Primary Health Care (PHC), and to assess the temporal trend of late diagnosis. METHODS: In this cross-sectional observational study, secondary data were evaluated with a time series analysis. All Brazilian cities that reported at least one case of oral and oropharyngeal cancers each year in the period between 2000 and 2013 were included; and the staging was analyzed by calculating the ratio risk for late diagnosis for each municipality. The association between staging and socioeconomic variables and offer of PHC was calculated using multiple linear regression. The time trend of the risk ratio for late-stage diagnosis was calculated using the Prais-Winsten method. RESULTS: One hundred and sixty Brazilian municipalities had at least one annual case of oral and oropharyngeal cancers notified to the INCA hospital system between 2000 and 2013. The adjusted model showed that the higher the Gini value (greater social inequality) and the lower the HDI value (less human development) was, the higher was the number of tumors diagnosed at a late stage, considering the size of the tumor. A greater risk for late diagnosis was identified, as early as at the stage of lymph node involvement, when there was a higher level of social inequality and lower level of coverage by Oral Health Teams (OHT) in PHC. The greater the social inequality, the greater was the risk of late diagnosis, as early as in the stage of metastasis. CONCLUSIONS: We concluded that, during the evaluated period, there was an increase in the number of cases diagnosed at the most advanced stage. Furthermore, there was association between higher levels of social inequality and an increase in the proportion of late diagnosis of oral and oropharyngeal cancers. In addition, the inclusion of Oral Health Teams in Primary Health Care promoted the early diagnosis of these types of cancers.

Single-molecule detection of cancer mutations using a novel PCR-LDR-qPCR assay.

Detection of low-abundance mutations in cell-free DNA is being used to identify early cancer and early cancer recurrence. Here, we report a new PCR-LDR-qPCR assay capable of detecting point mutations at a single-molecule resolution in the presence of an excess of wild-type DNA. Major features of the assay include selective amplification and detection of mutant DNA employing multiple nested primer-binding regions as well as wild-type sequence blocking oligonucleotides, prevention of carryover contamination, spatial sample dilution, and detection of multiple mutations in the same position. Our method was tested to interrogate the following common cancer somatic mutations: BRAF:c.1799T>A (p.Val600Glu), TP53:c.743G>A (p.Arg248Gln), KRAS:c.35G>C (p.Gly12Ala), KRAS:c.35G>T (p.Gly12Val), KRAS:c.35G>A (p.Gly12Asp), KRAS:c.34G>T (p.Gly12Cys), and KRAS:c.34G>A (p.Gly12Ser). The single-well version of the assay detected 2-5 copies of these mutations, when diluted with 10,000 genome equivalents (GE) of wild-type human genomic DNA (hgDNA) from buffy coat. A 12-well (pixel) version of the assay was capable of single-molecule detection of the aforementioned mutations at TP53, BRAF, and KRAS (specifically p.Gly12Val and p.Gly12Cys), mixed with 1,000-2,250 GE of wild-type hgDNA from plasma or buffy coat. The assay described herein is highly sensitive, specific, and robust, and potentially useful in liquid biopsies.

Results of Lung Cancer Screening in the Community.

PURPOSE: To address doubts regarding National Lung Screening Trial (NLST) generalizability, we analyzed over 6,000 lung cancer screenings (LCSs) within a community health system. METHODS: Our LCS program included 10 sites, 7 hospitals (2 non-university tertiary care, 5 community) and 3 free-standing imaging centers. Primary care clinicians referred patients. Standard criteria determined eligibility. Dedicated radiologists interpreted all LCSs, assigning Lung Imaging Reporting and Data System (Lung-RADS) categories. All category 4 Lung-RADS scans underwent multidisciplinary review and management recommendations. Data was prospectively collected from November 2013 through December 2018 and retrospectively analyzed. RESULTS: Of 4,666 referrals, 1,264 individuals were excluded or declined, and 3,402 individuals underwent initial LCS. Second through eighth LCSs were performed on 2,758 patients, for a total of 6,161 LCSs. Intervention rate after LCS was 14.6% (500 individuals) and was most often additional imaging. Invasive interventions (n = 226) were performed, including 141 diagnostic procedures and 85 surgeries in 176 individuals (procedure rate 6.6%). Ninety-five lung cancers were diagnosed: 84 non-small cell (stage 1: 60; stage 2: 7; stage 3: 9; stage 4: 8), and 11 small cell lung cancers. The procedural adverse event rate was 23/226 (10.1%) in 21 patients (0.6% of all screened individuals). Pneumothorax (n = 10) was the most frequent, 6 requiring pleural drainage. There were 2 deaths among 85 surgeries or 2.3% surgical mortality. CONCLUSIONS: Our LCS experience in a community setting demonstrated lung cancer diagnosis, stage shift, intervention frequency, and adverse event rate similar to the NLST. This study confirms that LCS can be performed successfully, safely, and with equivalence to the NLST in a community health care setting.