The Future of Precision Medicine in Oncology. Clin Lab Med. 2016;36:557-573. [PMID: 27514468 DOI: 10.1016/j.cll.2016.05.003]

The Role of the Neurotrophin Network in Skin Squamous Cell Cancer and the Novel Use of the Zebrafish System

Cutaneous squamous cell carcinoma (cSCC) is the second most prevalent form of skin cancer. An increasing number of cSCCs are associated with dysregulation of key molecules that control skin homeostasis. These observations have increased interest in the role of neurotrophins and their receptors in the pathogenesis of cSCC. They have been demonstrated to have a considerable impact on the aggressiveness potential of skin cancer by both in vitro and in vivo models. In this context, mouse models are classically used to dissect proliferation versus differentiation balance, but they have some limitations in terms of time, space, and costs. Recently, zebrafish models have been implemented as a new tool to obtain information regarding the invasive capacity and metastasis of neoplastic cells. By xenotransplantation technique, cSCC cells from a patient's biopsy or cell line can be successfully characterized, with or without the presence of genetic manipulation or treatments. In addition, the evaluation of the immune microenvironment contributes to potentially identifying connections and homologies with humans. In this review, we retrace the role of the neurotrophin network in healthy and pathological skin, particularly in cSCC. We review how zebrafish models can be important tools for studying cSCC development, growth, and potential treatments.

ROS1 kinase inhibition reimagined: identifying repurposed drug via virtual screening and molecular dynamics simulations for cancer therapeutics

Precision medicine has revolutionized modern cancer therapeutic management by targeting specific molecular aberrations responsible for the onset and progression of tumorigenesis. ROS proto-oncogene 1 (ROS1) is a receptor tyrosine kinase (RTK) that can induce tumorigenesis through various signaling pathways, such as cell proliferation, survival, migration, and metastasis. It has emerged as a promising therapeutic target in various cancer types. However, there is very limited availability of specific ROS1 inhibitors for therapeutic purposes. Exploring repurposed drugs for rapid and effective treatment is a useful approach. In this study, we utilized an integrated approach of virtual screening and molecular dynamics (MD) simulations of repurposing existing drugs for ROS1 kinase inhibition. Using a curated library of 3648 FDA-approved drugs, virtual screening identified drugs capable of binding to ROS1 kinase domain. The results unveil two hits, Midostaurin and Alectinib with favorable binding profiles and stable interactions with the active site residues of ROS1. These hits were subjected to stability assessment through all-atom MD simulations for 200 ns. MD results showed that Midostaurin and Alectinib were stable with ROS1. Taken together, the study showed a rational framework for the selection of repurposed Midostaurin and Alectinib with ROS1 inhibitory potential for therapeutic management after further validation.

Overcoming combination fatigue: Addressing high-dimensional effect measure modification and interaction in clinical, biomedical, and epidemiologic research using multilevel analysis of individual heterogeneity and discriminatory accuracy (MAIHDA)

Growing interest in precision medicine, gene-environment interactions, health equity, expanding diversity in research, and the generalizability results, requires researchers to evaluate how the effects of treatments or exposures differ across numerous subgroups. Evaluating combination complexity, in the form of effect measure modification and interaction, is therefore a common study aim in the biomedical, clinical, and epidemiologic sciences. There is also substantial interest in expanding the combinations of factors analyzed to include complex treatment protocols (e.g., multiple study arms or factorial randomization), comorbid medical conditions or risk factors, and sociodemographic and other subgroup identifiers. However, expanding the number of subgroup category combinations creates combination fatigue problems, including concerns over small sample size, reduced power, multiple testing, spurious results, and design and analytic complexity. Creative new approaches for managing combination fatigue and evaluating high-dimensional effect measure modification and interaction are needed. Intersectional MAIHDA (multilevel analysis of individual heterogeneity and discriminatory accuracy) has already attracted substantial interest in social epidemiology, and has been hailed as the new gold standard for investigating health inequities across complex intersections of social identity. Leveraging the inherent advantages of multilevel models, a more general multicategorical MAIHDA can be used to study statistical interactions and predict effects across high-dimensional combinations of conditions, with important advantages over alternative approaches. Though it has primarily been used thus far as an analytic approach, MAIHDA should also be used as a framework for study design. In this article, I introduce MAIHDA to the broader health sciences research community, discuss its advantages over conventional approaches, and provide an overview of potential applications in clinical, biomedical, and epidemiologic research.

Clinical trial considerations for pediatric cancer drug development

Oncology has been one of the most active therapeutic areas in medicinal products development. Despite this fact, few drugs have been approved for use in pediatric cancer patients when compared to the number approved for adults with cancer. This disparity could be attributed to the fact that many oncology drugs have had orphan drug designation and were exempt from Pediatric Research Equity Act (PREA) requirements. On August 18, 2017, the RACE for Children Act, i.e. Research to Accelerate Cures and Equity Act, was signed into law as Title V of the 2017 FDA Reauthorization Act (FDARA) to amend the PREA. Pediatric investigation is now required if the drug or biological product is intended for the treatment of an adult cancer and directed at a molecular target that FDA determines to be "substantially relevant to the growth or progression of a pediatric cancer." This paper discusses the specific considerations in clinical trial designs and statistical methodologies to be implemented in oncology pediatric clinical programs.

Trends and perspectives for improving quality of chronic kidney disease care: conclusions from a Kidney Disease: Improving Global Outcomes (KDIGO) Controversies Conference

Chronic kidney disease (CKD) affects over 850 million people globally, and the need to prevent its development and progression is urgent. During the past decade, new perspectives have arisen related to the quality and precision of care for CKD, owing to the development of new tools and interventions for CKD diagnosis and management. New biomarkers, imaging methods, artificial intelligence techniques, and approaches to organizing and delivering healthcare may help clinicians recognize CKD, determine its etiology, assess the dominant mechanisms at given time points, and identify patients at high risk for progression or related events. As opportunities to apply the concepts of precision medicine for CKD identification and management continue to be developed, an ongoing discussion of the potential implications for care delivery is required. The 2022 KDIGO Controversies Conference on Improving CKD Quality of Care: Trends and Perspectives examined and discussed best practices for improving the precision of CKD diagnosis and prognosis, managing the complications of CKD, enhancing the safety of care, and maximizing patient quality of life. Existing tools and interventions currently available for the diagnosis and treatment of CKD were identified, with discussion of current barriers to their implementation and strategies for improving the quality of care delivered for CKD. Key knowledge gaps and areas for research were also identified.

Combining the amplification refractory mutation system and high-resolution melting analysis for KRAS mutation detection in clinical samples

The success of personalized medicine depends on the discovery of biomarkers that allow oncologists to identify patients that will benefit from a particular targeted drug. Molecular tests are mostly performed using tumor samples, which may not be representative of the tumor's temporal and spatial heterogeneity. Liquid biopsies, and particularly the analysis of circulating tumor DNA, are emerging as an interesting means for diagnosis, prognosis, and predictive biomarker discovery. In this study, the amplification refractory mutation system (ARMS) coupled with high-resolution melting analysis (HRMA) was developed for detecting two of the most relevant KRAS mutations in codon 12. After optimization with commercial cancer cell lines, KRAS mutation screening was validated in tumor and plasma samples collected from patients with pancreatic ductal adenocarcinoma (PDAC), and the results were compared to those obtained by Sanger sequencing (SS) and droplet digital polymerase chain reaction (ddPCR). The developed ARMS-HRMA methodology stands out for its simplicity and reduced time to result when compared to both SS and ddPCR but showing high sensitivity and specificity for the detection of mutations in tumor and plasma samples. In fact, ARMS-HRMA scored 3 more mutations compared to SS (tumor samples T6, T7, and T12) and one more compared to ddPCR (tumor sample T7) in DNA extracted from tumors. For ctDNA from plasma samples, insufficient genetic material prevented the screening of all samples. Still, ARMS-HRMA allowed for scoring more mutations in comparison to SS and 1 more mutation in comparison to ddPCR (plasma sample P7). We propose that ARMS-HRMA might be used as a sensitive, specific, and simple method for the screening of low-level mutations in liquid biopsies, suitable for improving diagnosis and prognosis schemes.

Reversible zwitterionic coordination enables rapid, high-yield, and high-purity isolation of extracellular vesicles from biofluids

Extracellular vesicles (EVs) hold great clinical value as promising diagnostic biomarkers and therapeutic agents. This field, however, is hindered by technical challenges in the isolation of EVs from biofluids for downstream purposes. We here report a rapid (<30 min) isolation method for EV extraction from diverse biofluids with yield and purity exceeding 90%. These high performances are ascribed to the reversible zwitterionic coordination between the phosphatidylcholine (PC) on EV membranes and the "PC-inverse" choline phosphate (CP) decorated on magnetic beads. By coupling this isolation method with proteomics, a set of differentially expressed proteins on the EVs were identified as potential colon cancer biomarkers. Last, we demonstrated that the EVs in various clinically relevant biofluids, such as blood serum, urine, and saliva, can also be isolated efficiently, outperforming the conventional approaches in terms of simplicity, speed, yield, and purity.

Therapeutic Targeting of ALK in Neuroblastoma: Experience of Italian Precision Medicine in Pediatric Oncology

Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. Patients with relapsed/refractory disease have a poor prognosis, and additional therapeutic options are needed. Mutations and amplifications in the ALK (Anaplastic Lymphoma Kinase) gene constitute a key target for treatment. Our goal, within the Italian project of PeRsonalizEdMEdicine (PREME), was to evaluate the genomic status of patients with relapsed/refractory NB and to implement targeted therapies in those with targetable mutations. From November 2018 to November 2021, we performed Whole Exome Sequencing or Targeted Gene Panel Sequencing in relapsed/refractory NB patients in order to identify druggable variants. Activating mutations of ALK were identified in 8(28.57%) of 28 relapsed/refractory NB patients. The mutation p.F1174L was found in six patients, whereas p.R1275Q was found in one and the unknown mutation p.S104R in another. Three patients died before treatment could be started, while five patients received crizotinib: two in monotherapy (one with p.F1174L and the other with p.S104R) and three (with p.F1174L variant) in combination with chemotherapy. All treated patients showed a clinical improvement, and one had complete remission after two cycles of combined treatment. The most common treatment-related toxicities were hematological. ALK inhibitors may play an important role in the treatment of ALK-mutated NB patients.

Assessment of stromal SCD-induced drug resistance of PDAC using 3D-printed zPDX model chips

Lipid metabolism is extensively reprogrammed in pancreatic ductal adenocarcinoma (PDAC). Stearoyl-coenzyme A desaturase (SCD) is a critical lipid regulator that was unexplored in PDAC. Here, we characterized the existence of cancer-associated fibroblasts (CAFs) with high SCD expression, and revealed them as an unfavorable prognostic factor. Therefore, primary CAFs and pancreatic cancer cells were harvested and genetically labeled. The mixture of CAFs and cancer cells were co-injected into scd^-/-; prkdc^-/-, or hIGF1/INS-expressing zebrafish to generate patient-derived xenograft models (zPDX). The models were aligned in 3D-printed chips for semi-automatic drug administration and high-throughput scanning. The results showed that chaperoning of the SCD-high CAFs significantly improved the drug resistance of pancreatic cancer cells against gemcitabine and cisplatin, while the administration of SCD inhibitors neutralized the protective effect. Our studies revealed the prognostic and therapeutic value of stromal SCD in PDAC, and proposed the application of zPDX model chips for drug testing.

Cancer Stem Cell Assay for the Treatment of Platinum-Resistant Recurrent Ovarian Cancer

BACKGROUND

Disease recurrence and progression of ovarian cancer is a common event, which is accompanied by the development of platinum-resistant or refractory disease. The presence of chemo-resistant Cancer Stem Cells (CSCs) contribute to tumor propagation, maintenance, and treatment resistance of this difficult to treat disease. We have developed ChemoID, a cytotoxic synergy assay against CSCs that identifies the most effective chemotherapy treatment from a panel of FDA-approved chemotherapies using fresh cancer biopsies.

PATIENTS AND METHODS

Ascites or interventional radiology biopsies were collected under physician order from 78 consecutive patients affected by 3rd relapsed ovarian cancer. Test results from the assay were used when possible to treat patients with the highest cell kill drugs, taking into consideration their health status and using dose reductions, if needed. A chart analysis and review of CT and PET scans were performed to determine patients' outcomes for tumor response, Progression-Free Survival (PFS), and Overall Survival (OS).

RESULTS

We observed that recurrent ovarian cancer patients treated with high-cell kill chemotherapy agents guided by the CSCs drug response assay had an improvement in their median PFS and OS when compared to historical median PFS and OS and/or when compared to patients who could not receive high cell kill chemotherapies (PFS low cell kill 3.5 months vs. high cell kill 12.0 months; OS low cell kill 6.0 months vs. high cell kill 15.0 months).

CONCLUSION

This data indicates that the drug cytotoxicity assay aimed at targeting CSCs may be a useful tool for optimizing treatment selection when first-line therapy fails, and when there are multiple clinically-acceptable and -equivalent treatments available.

Clinical Impact of Adherence to NCCN Guidelines for Biomarker Testing and First-Line Treatment in Advanced Non-Small Cell Lung Cancer (aNSCLC) Using Real-World Electronic Health Record Data

INTRODUCTION

Although clinical guidelines are broadly available, the relationship between adherence and outcomes is not well studied. This study aimed to assess the association between adherence to National Comprehensive Cancer Network (NCCN) guidelines and clinical outcomes for adult patients with advanced non-small-cell lung cancer (aNSCLC).

METHODS

This was a retrospective cohort study of adult patients with aNSCLC (stages IIIB, IIIC, and IV) from a de-identified real-world database. The objective was accomplished in a two-step analysis process. We first assessed adherence to NCCN recommendations for biomarker testing and overall survival (OS). Next, we assessed adherence to NCCN-recommended first-line therapy and time to treatment discontinuation (TTD). Multivariable Cox regression analyses were conducted to evaluate the association between guideline adherence and patient outcomes. Kaplan-Meier analyses were used to assess median OS and TTD.

RESULTS

A total of 28,784 patients with a diagnosis for aNSCLC between January 1, 2011 and July 31, 2019 met the inclusion criteria for the analysis of NCCN-recommended biomarker testing adherence. Two-thirds of these patients (n = 19,787) had evidence of biomarker testing (adherent). Multivariable Cox models found that testing-adherent patients had a significantly lower risk of mortality [hazard ratio (HR) = 0.89, 95% confidence interval (CI) 0.86, 0.92; p < 0.01]. Median OS was modestly longer in the testing-adherent group compared to the testing-non-adherent group (15.4 vs. 14.2 months; p < 0.01). For the first-line therapy analysis, 15,898 patients met the inclusion criteria, of which 69.9% had evidence of appropriate first-line therapy (first-line-adherent). The multivariable Cox model found that adherent patients had significantly lower risk of treatment discontinuation versus non-adherent patients (HR = 0.60, 95% CI 0.57, 0.62; p < 0.01). First-line-adherent patients had a modest, yet significantly longer median TTD compared to first-line-non-adherent patients (3.45 vs. 2.40 months; p < 0.01).

CONCLUSIONS

Improved clinical outcomes were observed in patients who were adherent to NCCN-recommended biomarker testing and first-line therapy. This study demonstrated the value of following NCCN guideline recommendations and the need to prioritize timely access to biomarker testing and individualized treatment.

Cancer Biology, Epidemiology, and Treatment in the 21st Century: Current Status and Future Challenges From a Biomedical Perspective

Since the second half of the 20th century, our knowledge about the biology of cancer has made extraordinary progress. Today, we understand cancer at the genomic and epigenomic levels, and we have identified the cell that starts neoplastic transformation and characterized the mechanisms for the invasion of other tissues. This knowledge has allowed novel drugs to be designed that act on specific molecular targets, the immune system to be trained and manipulated to increase its efficiency, and ever more effective therapeutic strategies to be developed. Nevertheless, we are still far from winning the war against cancer, and thus biomedical research in oncology must continue to be a global priority. Likewise, there is a need to reduce unequal access to medical services and improve prevention programs, especially in countries with a low human development index.

Germline-focussed analysis of tumour-only sequencing: recommendations from the ESMO Precision Medicine Working Group

It is increasingly common in oncology practice to perform tumour sequencing using large cancer panels. For pathogenic sequence variants in cancer susceptibility genes identified on tumour-only sequencing, it is often unclear whether they are of somatic or constitutional (germline) origin. There is wide-spread disparity regarding both the extent to which systematic 'germline-focussed analysis' is carried out upon tumour sequencing data and for which variants follow-up analysis of a germline sample is carried out. Here we present analyses of paired sequencing data from 17 152 cancer samples, in which 1494 pathogenic sequence variants were identified across 65 cancer susceptibility genes. From these analyses, the European Society of Medical Oncology Precision Medicine Working Group Germline Subgroup has generated (i) recommendations regarding germline-focussed analyses of tumour-only sequencing data, (ii) indications for germline follow-up testing and (iii) guidance on patient information-giving and consent.

Blood-based systems biology biomarkers for next-generation clinical trials in Alzheimer's disease

Alzheimer's disease (AD)-a complex disease showing multiple pathomechanistic alterations-is triggered by nonlinear dynamic interactions of genetic/epigenetic and environmental risk factors, which, ultimately, converge into a biologically heterogeneous disease. To tackle the burden of AD during early preclinical stages, accessible blood-based biomarkers are currently being developed. Specifically, next-generation clinical trials are expected to integrate positive and negative predictive blood-based biomarkers into study designs to evaluate, at the individual level, target druggability and potential drug resistance mechanisms. In this scenario, systems biology holds promise to accelerate validation and qualification for clinical trial contexts of use-including proof-of-mechanism, patient selection, assessment of treatment efficacy and safety rates, and prognostic evaluation. Albeit in their infancy, systems biology-based approaches are poised to identify relevant AD "signatures" through multifactorial and interindividual variability, allowing us to decipher disease pathophysiology and etiology. Hopefully, innovative biomarker-drug codevelopment strategies will be the road ahead towards effective disease-modifying drugs.
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Polyacrylamide/Phytic Acid/Polydopamine Hydrogel as an Efficient Substrate for Electrochemical Enrichment of Circulating Cell-Free DNA from Blood Plasma

A facile method has been developed for the rapid and efficient enrichment of DNAs from different media including synthetic single-strand DNAs (ssDNAs) from buffer solutions and cell-free DNAs (cfDNAs) from blood plasma through electric field-driven adsorption and desorption of DNAs by a polyacrylamide/phytic acid/polydopamine (PAAM/PA/PDA) hydrogel. The as-prepared PAAM/PA/PDA hydrogel possesses regular porosity with a large surface area, strong electric field responsiveness/good conductivity, and a rich aromatic structure, which can be used as an ideal adsorbent for DNA enrichment under a positive electric field. The enriched DNAs can be released efficiently when the positive electric field is converted to a negative electric field. The PAAM/PA/PDA hydrogel-based electrochemical method enables the completion of the process of DNA adsorption and release within 5 min and exhibits reasonable enrichment efficiencies and recovery rates of various DNAs. For instance, the high enrichment sensitivity (0.1 pmol L-1) together with the excellent recovery (>75%) of an ssDNA with 78 nucleotides is obtained. Combined with the PCR amplification technique, the practicability of the as-proposed method is demonstrated by the screening of circulating tumor DNAs (ctDNAs) with a BRAFV600E mutation in cfDNAs from the blood plasma samples of patients with papillary thyroid cancer or thyroid nodule and random patients from a clinical laboratory.

A Model of a Zebrafish Avatar for Co-Clinical Trials

Animal “avatars” and co-clinical trials are being developed for possible use in personalized medicine in oncology. In a co-clinical trial, the cancer cells of the patient’s tumor are xenotransplanted into the animal avatar for drug efficacy studies, and the data collected in the animal trial are used to plan the best drug treatment in the patient trial. Zebrafish have recently been proposed for implementing avatar models, however the lack of a general criterion for the chemotherapy dose conversion from humans to fish is a limitation in terms of conducting co-clinical trials. Here, we validate a simple, reliant and cost-effective avatar model based on the use of zebrafish embryos. By crossing data from safety and efficacy studies, we found a basic formula for estimating the equivalent dose for use in co-clinical trials which we validated in a clinical study enrolling 24 adult patients with solid cancers (XenoZ, NCT03668418).

A New Framework for Patient Engagement in Cancer Clinical Trials Cooperative Group Studies

For the past two decades, the National Cancer Institute (NCI) has supported the involvement of patient advocates in both internal advisory activities and funded research projects to provide a patient perspective. Implementation of the inclusion of patient advocates has varied considerably, with inconsistent involvement of patient advocates in key phases of research such as concept development. Despite this, there is agreement that patient advocates have improved the patient focus of many cancer research studies. This commentary describes our experience designing and pilot testing a new framework for patient engagement at SWOG, one of the largest cancer clinical trial network groups in the United States and one of the four adult groups in the NCI's National Clinical Trials Network (NCTN). Our goal is to provide a roadmap for other clinical trial groups that are interested in bringing the patient voice more directly into clinical trial conception and development. We developed a structured process to engage patient advocates more effectively in the development of cancer clinical trials and piloted the process in four SWOG research committees, including implementation of a new Patient Advocate Executive Review Form that systematically captures patient advocates' input at the concept stage. Based on the positive feedback to our approach, we are now developing training and evaluation metrics to support meaningful and consistent patient engagement across the SWOG clinical trial life cycle. Ultimately, the benefits of more patient-centered cancer trials will be measured in the usefulness, relevance, and speed of study results to patients, caregivers, and clinicians.

Phenotypic Characterization of Circulating Lung Cancer Cells for Clinically Actionable Targets

Objectives: In non-small cell lung cancers (NSCLC), tumour biopsy can often be an invasive procedure. The development of a non-invasive methodology to study genetic changes via circulating tumour cells (CTCs) is an appealing concept. Whilst CTCs typically remain as rare cells, improvements in epitope-independent CTC isolation techniques has given rise to a greater capture of CTCs. In this cross sectional study, we demonstrate the capture and characterization of NSCLC CTCs for the clinically actionable markers epidermal growth factor receptor (EGFR) alterations, anaplastic lymphoma kinase (ALK) rearrangements and programmed death ligand-1 (PD-L1) expression. The study identified CTCs/CTC clusters in 26/35 Stage IV NSCLC patients, and subsequently characterized the CTCs for EGFR mutation, ALK status and PD-L1 status. This pilot study demonstrates the potential of a non-invasive fluid biopsy to determine clinically relevant biomarkers in NSCLC.

Prognositic significance of P-cadherin expression in breast cancer: Protocol for a meta-analysis

BACKGROUND

P-cadherin is a calcium-dependent cell-cell adhesion glycoprotein. It has been implicated in invasiveness and metastasis. However, the clinical prognostic value of overexpression of P-cadherin in patients with breast cancer (BC) remains unsettled.

METHODS

A systematic literature search will be performed in all available databases to quantitatively review eligible studies and identify all relevant data, which could be used to detect the relationship between overexpression of P-cadherin and overall survival (OS), disease-free survival (DFS), and clinicopathological parameters. Hazard ratio and 95% confidence intervals (CIs) or P value will be employed as effect measures to estimate the correlation between P-cadherin and the oncologic outcomes including overall survival (OS), disease-free survival (DFS). Odds ratios (ORs) and the 95% CIs will be evaluated for the pooled analysis of the correlation between P-cadherin expression and clinicopathological features. We will use the Review Manager (Revman) 5.3.5 software (Cochrane Community, London, United Kingdom) and STATA 14 software (version 14.0; Stata Corp, College Station, TX) to perform the meta-analysis to calculate the data.

RESULTS

The review will provide a high-quality synthesis of current evidence of the prognostic role of P-cadherin in BCs. The results will be published in a peer-reviewed journal.

CONCLUSION

We hope that the results of this study will provide significant evidence to assess whether the expression of P-cadherin is associated with poor prognosis in patients with BC.

PROSPERO REGISTRATION NUMBER

This meta-analysis protocol has been registered in the PROSPERO network with registration number: CRD42019119880.

Precision Medicine for CRC Patients in the Veteran Population: State-of-the-Art, Challenges and Research Directions

Colorectal cancer (CRC) accounts for ~9% of all cancers in the Veteran population, a fact which has focused a great deal of the attention of the VA's research and development efforts. A field-based meeting of CRC experts was convened to discuss both challenges and opportunities in precision medicine for CRC. This group, designated as the VA Colorectal Cancer Cell-genomics Consortium (VA4C), discussed advances in CRC biology, biomarkers, and imaging for early detection and prevention. There was also a discussion of precision treatment involving fluorescence-guided surgery, targeted chemotherapies and immunotherapies, and personalized cancer treatment approaches. The overarching goal was to identify modalities that might ultimately lead to personalized cancer diagnosis and treatment. This review summarizes the findings of this VA field-based meeting, in which much of the current knowledge on CRC prescreening and treatment was discussed. It was concluded that there is a need and an opportunity to identify new targets for both the prevention of CRC and the development of effective therapies for advanced disease. Also, developing methods integrating genomic testing with tumoroid-based clinical drug response might lead to more accurate diagnosis and prognostication and more effective personalized treatment of CRC.

Fishing for cures: The alLURE of using zebrafish to develop precision oncology therapies

Zebrafish have proven to be a valuable model to study human cancer biology with the ultimate aim of developing new therapies. Danio rerio are amenable to in vivo imaging, high-throughput drug screening, mutagenesis, and transgenesis, and they share histological and genetic similarities with Homo sapiens. The significance of zebrafish in the field of precision oncology is rapidly emerging. Indeed, modeling cancer in zebrafish has already been used to identify tumor biomarkers, define therapeutic targets and provide an in vivo platform for drug discovery. New zebrafish studies are starting to pave the way to direct individualized clinical applications. Patient-derived cancer cell xenograft models have demonstrated the feasibility of using zebrafish as a real-time avatar of prognosis and drug response to identify the most ideal therapy for an individual patient. Genetic cancer modeling in zebrafish, now facilitated by rapidly evolving genome editing techniques, represents another innovative approach to recapitulate human oncogenesis and develop individualized treatments. Utilizing zebrafish to design customizable precision therapies will improve the clinical outcome of patients afflicted with cancer.

Critical Care and Personalized or Precision Medicine: Who needs whom?

The current paradigm of modern healthcare is a reactive response to patient symptoms, subsequent diagnosis and corresponding treatment of the specific disease(s). This approach is predicated on methodologies first espoused by the Cnidean School of Medicine approximately 2500years ago. More recently escalating healthcare costs and relatively poor disease treatment outcomes have fermented a rethink in how we carry out medical practices. This has led to the emergence of "P-Medicine" in the form of Personalized and Precision Medicine. The terms are used interchangeably, but in fact there are significant differences in the way they are implemented. The former relies on an "N-of-1" model whereas the latter uses a "1-in-N" model. Personalized Medicine is still in a fledgling and evolutionary phase and there has been much debate over its current status and future prospects. A confounding factor has been the sudden development of Precision Medicine, which has currently captured the imagination of policymakers responsible for modern healthcare systems. There is some confusion over the terms Personalized versus Precision Medicine. Here we attempt to define the key differences and working definitions of each P-Medicine approach, as well as a taxonomic relationship tree. Finally, we discuss the impact of Personalized and Precision Medicine on the practice of Critical Care Medicine (CCM). Practitioners of CCM have been participating in Personalized Medicine unknowingly as it takes the protocols of sepsis, mechanical ventilation, and daily awakening trials and applies it to each individual patient. However, the immediate next step for CCM should be an active development of Precision Medicine. This developmental process should break down the silos of modern medicine and create a multidisciplinary approach between clinicians and basic/translational scientists.

Chemoresistance in cancer cells: exosomes as potential regulators of therapeutic tumor heterogeneity

Drug resistance in cancer cells remains a fundamental challenge. Be it nontargeted or targeted drugs, the presence of intrinsic or acquired cancer cell resistance remains a great obstacle in chemotherapy. Conventionally, a spectrum of cellular mechanisms defines drug resistance including overexpression of antiapoptotic proteins and drug efflux pumps, mutations in target and synergistic activation of prosurvival pathways in tumor cells. In addition to these well-studied routes, exosome-induced chemoresistance is emerging as a novel mechanism. Mechanistically, exosomes impart resistance by direct drug export, transport of drug efflux pumps and miRNAs exchange among cells. Moreover, exosome signaling creates ‘therapeutic tumor heterogeneity’ and favorably condition tumor microenvironment. Here, we discuss exosomes’ role in chemoresistance and possibilities of developing novel therapeutic strategies.

Characterization of Patients Who Present With Insomnia: Is There Room for a Symptom Cluster-Based Approach?

STUDY OBJECTIVES

This study examined empirically derived symptom cluster profiles among patients who present with insomnia using clinical data and polysomnography.

METHODS

Latent profile analysis was used to identify symptom cluster profiles of 175 individuals (63% female) with insomnia disorder based on total scores on validated self-report instruments of daytime and nighttime symptoms (Insomnia Severity Index, Glasgow Sleep Effort Scale, Fatigue Severity Scale, Beliefs and Attitudes about Sleep, Epworth Sleepiness Scale, Pre-Sleep Arousal Scale), mean values from a 7-day sleep diary (sleep onset latency, wake after sleep onset, and sleep efficiency), and total sleep time derived from an in-laboratory PSG.

RESULTS

The best-fitting model had three symptom cluster profiles: "High Subjective Wakefulness" (HSW), "Mild Insomnia" (MI) and "Insomnia-Related Distress" (IRD). The HSW symptom cluster profile (26.3% of the sample) reported high wake after sleep onset, high sleep onset latency, and low sleep efficiency. Despite relatively comparable PSG-derived total sleep time, they reported greater levels of daytime sleepiness. The MI symptom cluster profile (45.1%) reported the least disturbance in the sleep diary and questionnaires and had the highest sleep efficiency. The IRD symptom cluster profile (28.6%) reported the highest mean scores on the insomnia-related distress measures (eg, sleep effort and arousal) and waking correlates (fatigue). Covariates associated with symptom cluster membership were older age for the HSW profile, greater obstructive sleep apnea severity for the MI profile, and, when adjusting for obstructive sleep apnea severity, being overweight/obese for the IRD profile.

CONCLUSIONS

The heterogeneous nature of insomnia disorder is captured by this data-driven approach to identify symptom cluster profiles. The adaptation of a symptom cluster-based approach could guide tailored patient-centered management of patients presenting with insomnia, and enhance patient care.

Precision oncology using a limited number of cells: optimization of whole genome amplification products for sequencing applications

Background

Sequencing analysis of circulating tumor cells (CTCs) enables “liquid biopsy” to guide precision oncology strategies. However, this requires low-template whole genome amplification (WGA) that is prone to errors and biases from uneven amplifications. Currently, quality control (QC) methods for WGA products, as well as the number of CTCs needed for reliable downstream sequencing, remain poorly defined. We sought to define strategies for selecting and generating optimal WGA products from low-template input as it relates to their potential applications in precision oncology strategies.

Methods

Single pancreatic cancer cells (HPAF-II) were isolated using laser microdissection. WGA was performed using multiple displacement amplification (MDA), multiple annealing and looping based amplification (MALBAC) and PicoPLEX. Quality of amplified DNA products were assessed using a multiplex/RT-qPCR based method that evaluates for 8-cancer related genes and QC-scores were assigned. We utilized this scoring system to assess the impact of de novo modifications to the WGA protocol. WGA products were subjected to Sanger sequencing, array comparative genomic hybridization (aCGH) and next generation sequencing (NGS) to evaluate their performances in respective downstream analyses providing validation of the QC-score.

Results

Single-cell WGA products exhibited a significant sample-to-sample variability in amplified DNA quality as assessed by our 8-gene QC assay. Single-cell WGA products that passed the pre-analysis QC had lower amplification bias and improved aCGH/NGS performance metrics when compared to single-cell WGA products that failed the QC. Increasing the number of cellular input resulted in improved QC-scores overall, but a resultant WGA product that consistently passed the QC step required a starting cellular input of at least 20-cells. Our modified-WGA protocol effectively reduced this number, achieving reproducible high-quality WGA products from ≥5-cells as a starting template. A starting cellular input of 5 to 10-cells amplified using the modified-WGA achieved aCGH and NGS results that closely matched that of unamplified, batch genomic DNA.

Conclusion

The modified-WGA protocol coupled with the 8-gene QC serve as an effective strategy to enhance the quality of low-template WGA reactions. Furthermore, a threshold number of 5–10 cells are likely needed for a reliable WGA reaction and product with high fidelity to the original starting template.

Electronic supplementary material

The online version of this article (doi:10.1186/s12885-017-3447-6) contains supplementary material, which is available to authorized users.

消化系肿瘤循环微小RNA研究进展

微小RNA(microRNA, miRNA)是一类内源性的、21-25个碱基长度的小分子非编码RNA, 在转录后水平调节靶基因mRNA表达, 并在多种肿瘤的发生和发展中过程中发挥重要的促癌或抑癌作用. 不同肿瘤类型有着各自特异性miRNA表达谱. 近来研究发现游离的miRNA可稳定地存在于血清和血浆中, 并作为一个潜在的非侵入性生物标志物, 该研究领域已成为当前临床研究的热点. 循环中的miRNA作为肿瘤相关生物标志物, 不仅可以反应早期肿瘤的存在, 而且可以检测肿瘤的发展、复发情况以及对药物敏感性. 这种"液体活检"的方法可提供非侵袭性的和持续表达的生物标志物, 并且为肿瘤患者个体化治疗提供一种新的策略. 本文综述了近几年循环miRNA在实体瘤尤其是消化系肿瘤的研究进展, 并探讨了其作为消化系恶性肿瘤潜在的诊断标志物或治疗靶点的发展前景.