Application Of Precision Medicine Research Articles

Current State of Personalized Genitourinary Cancer Radiotherapy in the Era of Precision Medicine.

Radiation therapy plays a crucial role for the management of genitourinary malignancies, with technological advancements that have led to improvements in outcomes and decrease in treatment toxicities. However, better risk-stratification and identification of patients for appropriate treatments is necessary. Recent advancements in imaging and novel genomic techniques can provide additional individualized tumor and patient information to further inform and guide treatment decisions for genitourinary cancer patients. In addition, the development and use of targeted molecular therapies based on tumor biology can result in individualized treatment recommendations. In this review, we discuss the advances in precision oncology techniques along with current applications for personalized genitourinary cancer management. We also highlight the opportunities and challenges when applying precision medicine principles to the field of radiation oncology. The identification, development and validation of biomarkers has the potential to personalize radiation therapy for genitourinary malignancies so that we may improve treatment outcomes, decrease radiation-specific toxicities, and lead to better long-term quality of life for GU cancer survivors.

Transperineal Parallel Biopsy of the Prostate: A New Approach of Tissue Sampling for Precision Medicine.

PurposeThrough an observational study to present a new approach for obtaining high-quality samples for the targeted therapy of prostate cancer.Patients and MethodsParallel biopsy, which was defined as collecting the tissue from the same site by two biopsies, was performed on patients with elevated PSA. Each tissue was stained by ink to identify the pathological characteristics, including Gleason score and tumor tissue ratio. Kendall tau-b test and intraclass correlation coefficient test were used to compare the consistency between each paired sample. Then, based on the pathology of the biopsies, high-quality tissues would be selected for sequencing, and PyClone model was used to track the clonal evolution.ResultsIn total, 252 pairs of biopsies were collected. The consistency of Gleason score between each paired biopsy is 0.777 (p<0.01), and the consistency of tumor tissue ratio is 0.853 (p<0.01). With the application of parallel biopsy, on average five nonsynonymous mutations could be identified in patients with castration-resistant prostate cancer. Six out of eight had at least one biology-relevant alteration in patients, guiding further treatment. Meanwhile, clonal evolution was constructed to investigate the progress of tumor.ConclusionParallel biopsy is a reliable approach to collect high-quality tissue and shows potential application in precision medicine.

Personalizing the Care and Treatment of Alzheimer's Disease: An Overview.

Alzheimer’s disease (AD) is a progressive, complex, and multifactorial neurodegenerative disorder, still without effective and stable therapeutic strategies. Currently, available medications for AD are based on symptomatic therapy, which include acetylcholinesterase (AChE) inhibitors and N-methyl-D-aspartate (NMDA) receptor antagonist. Additionally, medications such as antipsychotic drugs, antidepressants, sedative, and hypnotic agents, and mood stabilizers are used for the management of behavioral and psychological symptoms of dementia (BPSD). Clinical research has been extensively investigated treatments focusing on the hallmark pathology of AD, including the amyloid deposition, tau hyperphosphorylation, neuroinflammation, and vascular changes; however, so far without success, as all new potential drugs failed to show significant clinical benefit. The underlying heterogeneous etiology and diverse symptoms of AD suggest that a precision medicine strategy is required, which would take into account the complex genetic, epigenetic, and environmental landscape of each AD patient. The article provides a comprehensive overview of the literature on AD, the current and potential therapy of both cognitive symptoms as well as BPSD, with a special focus on gut microbiota and epigenetic modifications as new emerging drug targets. Their specific patterns could represent the basis for novel individually tailored approaches aimed to optimize precision medicine strategies for AD prevention and treatment. However, the successful application of precision medicine to AD demands a further extensive research of underlying pathological processes, as well as clinical and biological complexity of this multifactorial neurodegenerative disorder.

Real-life survey of pitfalls and successes of precision medicine in genetic epilepsies

ObjectiveThe term ‘precision medicine’ describes a rational treatment strategy tailored to one person that reverses or modifies the disease pathophysiology. In epilepsy, single case and small cohort reports document nascent...

A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population.

The ethnic composition of the population of a country contributes to the uniqueness of each national DNA sequencing project and, ideally, individual reference genomes are required to reduce the confounding nature of ethnic bias. This work represents a representative Whole Genome Sequencing effort of an understudied population. Specifically, high coverage consensus sequences from 120 whole genomes and 33 whole exomes were used to construct the first ever population specific major allele reference genome for the United Arab Emirates (UAE). When this was applied and compared to the archetype hg19 reference, assembly of local Emirati genomes was reduced by ∼19% (i.e., some 1 million fewer calls). In compiling the United Arab Emirates Reference Genome (UAERG), sets of annotated 23,038,090 short (novel: 1,790,171) and 137,713 structural (novel: 8,462) variants; their allele frequencies (AFs) and distribution across the genome were identified. Population-specific genetic characteristics including loss-of-function variants, admixture, and ancestral haplogroup distribution were identified and reported here. We also detect a strong correlation between FST and admixture components in the UAE. This baseline study was conceived to establish a high-quality reference genome and a genetic variations resource to enable the development of regional population specific initiatives and thus inform the application of population studies and precision medicine in the UAE.

The fourth scientific discovery paradigm for precision medicine and healthcare: Challenges ahead.

With the progression of modern information techniques, such as next generation sequencing (NGS), Internet of Everything (IoE) based smart sensors, and artificial intelligence algorithms, data-intensive research and applications are emerging as the fourth paradigm for scientific discovery. However, we face many challenges to practical application of this paradigm. In this article, 10 challenges to data-intensive discovery and applications in precision medicine and healthcare are summarized and the future perspectives on next generation medicine are discussed.

Ampullary carcinoma of the duodenum: current clinical issues and genomic overview

Ampullary carcinomas of the duodenum are uncommon. Moreover, the diversity in the clinical outcomes of these patients makes it difficult to interpret previous studies and clinical trial results. The difficulty in proper staging of ampullary carcinomas, especially with regard to the T category of the tumor in the TNM system, reflects the anatomic complexity and non-uniform histopathologic subtypes. One major reason for this difficulty in interpretation is that the tumors may arise from any of the three epithelia (duodenal, biliary, or pancreatic) that converge at this location. Generally, ampullary carcinomas are classified into intestinal and pancreaticobiliary types based on morphology and immunohistochemical features. While many studies have described their specific characteristics and clinical impact, the prognostic value of these subtypes is controversial. In recent years, whole-exome sequencing analyses have advanced our understanding of the genomic overview of ampullary carcinoma. Gene mutations serve as prognostic and predictive biomarkers for this disease. Therefore, basic knowledge of the genomic profile of ampullary carcinomas is required for surgeons to understand how best to apply precision medicine as well as surgery and adjuvant therapies. This review provides an overview of the current basic and clinical issues of ampullary carcinoma.

Evaluation of structured data from electronic health records to identify clinical classification criteria attributes for systemic lupus erythematosus

ObjectiveOur objective was to develop algorithms to identify lupus clinical classification criteria attributes using structured data found in the electronic health record (EHR) and determine whether they could be used...

Evolving Paradigm of Precision Medicine in Cardiovascular Disease.

In the year 1892, Sir William Osler, the legendary Canadian physician and one of the four founding professors of Johns Hopkins Hospital, said “If it were not for the great variability among individuals, medicine might as well be a science and not an art”. It is this heterogeneity among patients with seemingly homogenous medical conditions, that form the basis of what we today refer to as precision medicine. The fundamental of precision medicine is based on the tenets of ‘The right drug for the right patient at the right time’. Personalized or precision medicine found immense popularity in oncology. With the completion of Human Genome Project and the advent of genomics, big data and artificial intelligence, 21st century saw rapid progress of precision medicine in predicting, diagnosing and treating cancer. However, the same has not happened to cardiovascular diseases, the biggest killer of humanity. In this review article, we aim to address the concepts, components, outcomes and applications of precision medicine in general, and to review the evolving paradigm of how precision medicine is shaping the management of cardiovascular diseases. We delve deep into the aspects of risk prediction, preventative measures, and targeted therapeutic approaches for cardiovascular diseases. We also look at the recent trends and current applications of precision medicine in this area, the problems they solve and the challenges they possess, and what is in store for the future. Finally, we review the application of artificial intelligence specific to cardiovascular diseases, and the role of precision medicine in interventional cardiology.

Multi‐Responsive Biodegradable Cationic Nanogels for Highly Efficient Treatment of Tumors

AbstractThe facile preparation, modular design, and multi‐responsiveness are extremely critical for developing pervasive nanoplatforms to meet heterogeneous applications. Here, cationic nanogels (NGs) are modularly engineered with tunable responsiveness, versatility, and biodegradation. Cationic PVCL‐based NGs with core/shell structure are fabricated by facile one‐step synthesis. The formed PVCL‐NH2 NGs exhibit uniform size, thermal/pH dual‐responsive behaviors, and redox‐triggered degradation. Moreover, the NGs can be employed to modify or/and load with various functional agents to construct multipurpose nanoplatforms in a modular manner. Notably, the novel hybrid structure with copper sulfide (CuS) NPs loaded in the NGs shell is prepared, which leads to higher photothermal conversion efficiency (31.1%) than other CuS randomly loaded NGs reported. By personalized tailoring, these functionalized NGs display fluorescent property, r1 relaxivity, strong near‐infrared (NIR) absorption, good biocompatibility, and targeting specificity. The superior photothermal effect of hybrid NGs (CuS@NGs‐LA) is presented under NIR II over NIR I. Importantly, hybrid NGs encapsulated doxorubicin (CuS@NGs‐LA/DOX) show endogenous pH/redox and exogenous NIR multi‐triggered drug release for efficient photothermal‐chemotherapy, which can completely eliminate advanced tumors and effectively inhibit recurrence. Overall, the pervasive nanoplatforms based on intelligent cationic NGs with tunable responsiveness, versatility, and biodegradation are developed by engineered modular strategy for precision medicine applications.

Impact of sex and pathophysiology on optimal drug choice in hypertensive rats: Quantitative insights for precision medicine

SummaryLess than half of all hypertensive patients receiving treatment are successful in normalizing their blood pressure. Despite the complexity and heterogeneity of hypertension, the current antihypertensive guidelines are not tailored to the individual patient. As a step toward individualized treatment, we develop a quantitative systems pharmacology model of blood pressure regulation in the spontaneously hypertensive rat (SHR) and generate sex-specific virtual populations of SHRs to account for the heterogeneity between the sexes and within the pathophysiology of hypertension. We then used the mechanistic model integrated with machine learning tools to study how variability in these mechanisms leads to differential responses in rodents to the four primary classes of antihypertensive drugs. We found that both the sex and the pathophysiological profile of the individual play a major role in the response to hypertensive treatments. These results provide insight into potential areas to apply precision medicine in human primary hypertension.

The promise of public health ethics for precision medicine: the case of newborn preventive genomic sequencing

Precision medicine aims to tailor medical treatment to match individual characteristics and to stratify individuals to concentrate benefits and avoid harm. It has recently been joined by precision public health-the application of precision medicine at population scale to decrease morbidity and optimise population health. Newborn preventive genomic sequencing (NPGS) provides a helpful case study to consider how we should approach ethical questions in precision public health. In this paper, I use NPGS as a case in point to argue that both precision medicine and precision public health need public health ethics. I make this argument in two parts. First, I claim that discussions of ethics in precision medicine and NPGS tend to focus on predominantly individualistic concepts from medical ethics such as autonomy and empowerment. This highlights some deficiencies, including overlooking that choice is subject to constraints and that an individual's place in the world might impact their capacity to 'be responsible'. Second, I make the case for using a public health ethics approach when considering ethics and NPGS, and thus precision public health more broadly. I discuss how precision public health needs to be construed as a collective enterprise and not just as an aggregation of individual interests. I also show how analysing collective values and interests through concepts such as solidarity can enrich ethical discussion of NPGS and highlight previously overlooked issues. With this approach, bioethics can contribute to more just and more appropriate applications of precision medicine and precision public health, including NPGS.

Cerebral Expression of Metabotropic Glutamate Receptor Subtype 5 in Idiopathic Autism Spectrum Disorder and Fragile X Syndrome: A Pilot Study.

Multiple lines of evidence suggest that dysfunction of the metabotropic glutamate receptor subtype 5 (mGluR5) plays a role in the pathogenesis of autism spectrum disorder (ASD). Yet animal and human investigations of mGluR5 expression provide conflicting findings about the nature of dysregulation of cerebral mGluR5 pathways in subtypes of ASD. The demonstration of reduced mGluR5 expression throughout the living brains of men with fragile X syndrome (FXS), the most common known single-gene cause of ASD, provides a clue to examine mGluR5 expression in ASD. We aimed to (A) compare and contrast mGluR5 expression in idiopathic autism spectrum disorder (IASD), FXS, and typical development (TD) and (B) show the value of positron emission tomography (PET) for the application of precision medicine for the diagnosis and treatment of individuals with IASD, FXS, and related conditions. Two teams of investigators independently administered 3-[18F]fluoro-5-(2-pyridinylethynyl)benzonitrile ([18F]FPEB), a novel, specific mGluR5 PET ligand to quantitatively measure the density and the distribution of mGluR5s in the brain regions, to participants of both sexes with IASD and TD and men with FXS. In contrast to participants with TD, mGluR5 expression was significantly increased in the cortical regions of participants with IASD and significantly reduced in all regions of men with FXS. These results suggest the feasibility of this protocol as a valuable tool to measure mGluR5 expression in clinical trials of individuals with IASD and FXS and related conditions.

Anticlogging Hemofiltration Device for Mass Collection of Circulating Tumor Cells by Ligand-Free Size Selection.

A new hemofiltration system was developed to continuously capture circulating tumor cells (CTCs) from a large volume of whole blood using a column that was packed with antifouling zwitterionized silica microspheres. The silica microspheres were modified with sulfobetaine silane (SBSi) to inhibit fouling, resist clogging, and give a high surface wettability and prolonged operation time. Packed microspheres with different diameters formed size-controllable interstitial pores that effectively captured CTCs by ligand-free size selection. For optimized performance of the hemofiltration system, operational factors, including the size of microspheres, flow rate, and cross-sectional area of the column, were considered with respect to the removal rate for colorectal cancer cells and the retention rate for white blood cells and red blood cells. The captured CTCs were collected from the column by density sedimentation. A large quantity of colorectal cancer cells was spiked into sheep blood, and the sample was circulated for 5 h with a total operational volume of 2 L followed by collection and culture in vitro. The results showed that the proposed hemofiltration device selectively removed abundant CTCs from in vitro circulatory blood. The viable cells were harvested for amplification and potential applications for precision medicine.

Nonparametric machine learning for precision medicine with longitudinal clinical trials and Bayesian additive regression trees with mixed models.

Precision medicine is an active area of research that could offer an analytic paradigm shift for clinical trials and the subsequent treatment decisions based on them. Clinical trials are typically analyzed with the intent of discovering beneficial treatments if the same treatment is applied to the entire population under study. But, such a treatment strategy could be suboptimal if subsets of the population exhibit varying treatment effects. Identifying subsets of the population experiencing differential treatment effect and forming individualized treatment rules is a task well-suited to modern machine learning methods such as tree-based ensemble predictive models. Specifically, Bayesian additive regression trees (BART) has shown promise in this regard because of its exceptional performance in out-of-sample prediction. Due to the unique inferential needs of precision medicine for clinical trials, we have proposed the BART extensions explicated here. We incorporate random effects for longitudinal repeated measures and subject clustering within medical centers. The addition of a novel interaction detection prior to identify treatment heterogeneity among clinical trial patients and its association with patient characteristics. These extensions are unified under a framework that we call mixedBART. Simulation studies and applications of precision medicine based on real randomized clinical trials data examples are presented.

Abstract IA-23: Multi-scale modeling of cancer patients

Abstract Recently biomedical analysis in both imaging and non-imaging data has advanced rapidly aided by the modeling power of deep learning networks. Complex diseases such as cancer may reveal different aspects of disease characteristics in different data modalities, and thus integrating imaging with non-imaging biomarkers and clinical data has the potential to discover information that is not obvious in any single data modality. We are developing methods for integrating image, genomic and clinical data to improve precision medicine applications for cancer patients. Our results suggest that the integration strategies achieve improved prediction results than using each single data modality alone. We further show that information is transferrable across age groups or tumor subtypes under the data fusion framework. Citation Format: Olivier Gevaert. Multi-scale modeling of cancer patients [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr IA-23.

Whole genome sequencing in the Middle Eastern Qatari population identifies genetic associations with 45 clinically relevant traits

Clinical laboratory tests play a pivotal role in medical decision making, but little is known about their genetic variability between populations. We report a genome-wide association study with 45 clinically relevant traits from the population of Qatar using a whole genome sequencing approach in a discovery set of 6218 individuals and replication in 7768 subjects. Trait heritability is more similar between Qatari and European populations (r = 0.81) than with Africans (r = 0.44). We identify 281 distinct variant-trait-associations at genome wide significance that replicate known associations. Allele frequencies for replicated loci show higher correlations with European (r = 0.94) than with African (r = 0.85) or Japanese (r = 0.80) populations. We find differences in linkage disequilibrium patterns and in effect sizes of the replicated loci compared to previous reports. We also report 17 novel and Qatari-predominate signals providing insights into the biological pathways regulating these traits. We observe that European-derived polygenic scores (PGS) have reduced predictive performance in the Qatari population which could have implications for the translation of PGS between populations and their future application in precision medicine.

In vitro biomimetic models for glioblastoma-a promising tool for drug response studies.

The poor response of glioblastoma to current treatment protocols is a consequence of its intrinsic drug resistance. Resistance to chemotherapy is primarily associated with considerable cellular heterogeneity, and plasticity of glioblastoma cells, alterations in gene expression, presence of specific tumor microenvironment conditions and blood-brain barrier. In an attempt to successfully overcome chemoresistance and better understand the biological behavior of glioblastoma, numerous tri-dimensional (3D) biomimetic models were developed in the past decade. These novel advanced models are able to better recapitulate the spatial organization of glioblastoma in a real time, therefore providing more realistic and reliable evidence to the response of glioblastoma to therapy. Moreover, these models enable the fine-tuning of different tumor microenvironment conditions and facilitate studies on the effects of the tumor microenvironment on glioblastoma chemoresistance. This review outlines current knowledge on the essence of glioblastoma chemoresistance and describes the progress achieved by 3D biomimetic models. Moreover, comprehensive literature assessment regarding the influence of 3D culturing and microenvironment mimicking on glioblastoma gene expression and biological behavior is also provided. The contribution of the blood-brain barrier as well as the blood-tumor barrier to glioblastoma chemoresistance is also reviewed from the perspective of 3D biomimetic models. Finally, the role of mathematical models in predicting 3D glioblastoma behavior and drug response is elaborated. In the future, technological innovations along with mathematical simulations should create reliable 3D biomimetic systems for glioblastoma research that should facilitate the identification and possibly application in preclinical drug testing and precision medicine.

InContext: curation of medical context for drug indications

Accurate and precise information about the therapeutic uses (indications) of a drug is essential for applications in drug repurposing and precision medicine. Leading online drug resources such as DrugCentral and DrugBank provide rich information about various properties of drugs, including their indications. However, because indications in such databases are often partly automatically mined, some may prove to be inaccurate or imprecise. Particularly challenging for text mining methods is the task of distinguishing between general disease mentions in drug product labels and actual indications for the drug. For this, the qualifying medical context of the disease mentions in the text should be studied. Some examples include contraindications, co-prescribed drugs and target patient qualifications. No existing indication curation efforts attempt to capture such information in a precise way. Here we fill this gap by presenting a novel curation protocol for extracting indications and machine processable annotations of contextual information about the therapeutic use of a drug. We implemented the protocol on a reference set of FDA-approved drug product labels on the DailyMed website to curate indications for 150 anti-cancer and cardiovascular drugs. The resulting corpus - InContext - focuses on anti-cancer and cardiovascular drugs because of the heightened societal interest in cancer and heart disease. In order to understand how InContext relates with existing reputable drug indication databases, we analysed it’s overlap with a state-of-the-art indications database - LabeledIn - as well as a reputable online drug compendium - DrugCentral. We found that 40% of indications sampled from DrugCentral (and 23% from LabeledIn) respectively, could not be accounted for in InContext. This raises questions about the veracity of indications not appearing in InContext. The additional contextual information curated by InContext about disease mentions in drug SPLs provides a foundation for more precise, structured and formal representations of knowledge related to drug therapeutic use, in order to increase accuracy and agreement of drug indication extraction methods for in silico drug repurposing.

Response in Immune Repertoires

The immune repertoire responds to a wide variety of pathogenic threats. Immune repertoire sequencing experiments give us insight into the composition of these repertoires. Since the functioning of the repertoire relies on statistical properties, statistical analysis is needed to identify responding clones. Using such methods I will describe the repertoire level response to the SARS-CoV-2, among other perturbations. More generally, I will show how immune repertoires provide a unique fingerprint reflecting the immune history of individuals, with potential applications in precision medicine.