Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing

Circulating Tumor DNA Profiling Approach Based on In Silico Background Elimination Guides Chemotherapy in Nasopharyngeal Carcinoma

Circulating tumor DNA (ctDNA) analysis increasingly provides a promising minimally invasive alternative to tissue biopsies in precision oncology. However, there are no ctDNA analysis approaches available in nasopharyngeal carcinoma (NPC) and current methods of ctDNA mutation profiling have limited resolution because of the high background noise and false-positive rate caused by benign variants in plasma cell-free DNA (cfDNA), majorly generated during clonal hematopoiesis. Although personalized parallel white blood cell genome sequencing suppresses the noise of clonal hematopoiesis variances, the system cost and complexity restrict its extensive application in clinical settings. We developed Matched WBC Genome sequencing Independent CtDNA profiling (MaGIC) approaches, which synergically integrated a ctDNA capturing panel for a hybrid capture cfDNA deep sequencing, in silico background elimination, and a reliable readout measurement. We profiled the ctDNAs of 80 plasma samples from 40 patients with NPC before and during chemotherapy by MaGICs. In addition, the public cfDNA sequencing data and The Cancer Genome Atlas project data were analyzed by MaGICs to evaluate their application in other scenarios of patient classification. The MaGIC version-2 has the ability to predict the chemosensitivity of patients with NPC with high accuracy by utilizing a single sample of liquid biopsy from each patient prior to a standardized treatment regimen. Moreover, both versions of MaGICs are of ideal performance in the diagnosis of patients with prostate cancer by liquid biopsy and prognosis prediction of multiple cancers by tissue biopsy. This study has the potential to enhance the sensitivity and expand the application scope of ctDNA detection, independently of other paired genome sequencing methods. As a result, it might further increase the clinical utilization of liquid biopsy based on ctDNA.

Interleukins-6 -174G/C (rs1800795) and -572C/G (rs1800796) polymorphisms and prostate cancer risk

Prostate cancer (PCa) is an aggressive cancer influenced by a complex interplay of genetic and environmental factors. Amongst these risk factors, the impact of Interleukin6 (IL6) gene polymorphisms in PCa risk has received a lot of attention. IL-6 is a cytokine that has been implicated in the pathogenesis of several malignancies, including PCa. Two IL-6 gene polymorphisms, - 174 G/C (rs1800795) and - 572 C/G (rs1800796), have received intellectual attention due to their potential role as modulators of prostate cancer risk. The main objective of this research was to comprehensively explore the potential associations between IL-6 rs1800795 and rs1800796 polymorphisms, and their impact on the occurrence of PCa. A case-control study was carried out with a well-defined cohort comprising 110 PCa cases and 110 controls (total n = 220). The genotyping of rs1800795 and rs1800796 was carefully performed using the highly sensitive and accurate Polymerase Chain Reaction-High Resolution Melting Curve (PCR-HRM) technique. The assessment of genetic associations was evaluated using various R packages, such as Haplo-Stats, SNP stat, pheatmap, and LD heatmap. The present study applied odds ratio (OR) analysis to reveal significant evidence of strong associations between the genotypes of rs1800795 and rs1800796 and the susceptibility to PCa. The findings of this study underscore the noteworthy impact of genetic variations in the IL-6 gene on the development of prostate cancer. Specifically, the C/G and G/G genotypes of rs1800795 demonstrated increased PCa risk, with odds ratios (OR) of 1.650 (95% CI = 1.068-2.549, p = 0.032) and 2.475 (95% CI = 1.215-5.043, p < 0.001), respectively. Similarly, the G/C genotype of rs1800796 exhibited an OR of 2.374 (95% CI = 1.363-4.130, p = 0.012) for elevated prostate cancer risk, while the C/C genotype had an OR of 1.81 (95% CI = 1.02-3.22, p = 0.7). Furthermore, our haplotype analysis have revealed an association between haplotype 4 (C-G) and increased risk of PCa (OR = 1.69, 95% CI = 1.05-2.73, p = 0.032). In conclusion, this case-control analysis presents compelling evidence for a significant association between IL-6 variants (rs1800795 and rs1800796) and increased susceptibility to prostate cancer.

Liquid Biopsies for Early Response Evaluation of Radium-223 in Metastatic Prostate Cancer

PURPOSE

Reliable biomarkers for response monitoring during radium-223 treatment in patients with metastatic castration-resistant prostate cancer (mCRPC) are lacking. Circulating tumor cells (CTCs) and circulating tumor DNA (ctDNA), obtained from liquid biopsies, are shown to have prognostic value in mCRPC. The aim of this study was to determine the value of CTCs and ctDNA for response evaluation of radium-223.

METHODS

In this prospective multicenter study, longitudinal blood draws and imaging were performed in 28 patients with mCRPC and predominantly bone disease, who were treated with radium-223. CTCs were counted (CELLSEARCH CTC test), while fraction of ctDNA was estimated by measuring aneuploidy of cell-free DNA (cfDNA; modified Fast Aneuploidy Screening Test-Sequencing System). CTC counts and aneuploidy score (AS) were categorized as low (<5) and high (≥5). Primary and secondary clinical end points were failure-free survival (FFS), and overall survival (OS) and development of extraosseous metastases, respectively. Additionally, CTC count and AS were related to alkaline phosphatase (ALP) and total tumor volume in bone (TTVbone) on positron emission tomography-computed tomography with 68gallium prostate-specific membrane antigen.

RESULTS

FFS was longer in patients with a low CTC count or AS either at baseline or after 12 weeks, whereas for OS, only a significant association with CTC count was observed. Liquid biopsy results correlated well with ALP and TTVbone at baseline, but not with change in both parameters after three cycles of radium-223. AS and CTC count were significantly correlated.

CONCLUSION

CTC count and AS of cfDNA at baseline and during treatment predict clinical response to radium-223 in patients with mCRPC, warranting future evaluation of their value in treatment guidance.

cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA

Cell-free DNA (cfDNA) in blood, viewed as a surrogate for tumor biopsy, has many clinical applications, including diagnosing cancer, guiding cancer treatment and monitoring treatment response. All these applications depend on an indispensable, yet underdeveloped task: detecting somatic mutations from cfDNA. The task is challenging because of the low tumor fraction in cfDNA. Recently, we developed the computational method cfSNV, the first method that comprehensively considers the properties of cfDNA for the sensitive detection of mutations from cfDNA. cfSNV vastly outperformed the conventional methods that were developed primarily for calling mutations from solid tumor tissues. cfSNV can accurately detect mutations in cfDNA even with medium-coverage (e.g., ≥200×) sequencing, which makes whole-exome sequencing (WES) of cfDNA a viable option for various clinical utilities. Here, we present a user-friendly cfSNV package that exhibits fast computation and convenient user options. We also built a Docker image of it, which is designed to enable researchers and clinicians with a limited computational background to easily carry out analyses on both high-performance computing platforms and local computers. Mutation calling from a standard preprocessed WES dataset (~250× and ~70 million base pair target size) can be carried out in 3 h on a server with eight virtual CPUs and 32 GB of random access memory.

Urinary DNA as a Tool for Germline and Somatic Mutation Detection in Castration-Resistant Prostate Cancer Patients

(1) Background: DNA damage response (DDR) pathway gene mutations are detectable in a significant number of patients with metastatic castration-resistant prostate cancer (mCRPC). The study aimed at identification of germline and/or somatic DDR mutations in blood and urine samples from patients with mCRPC for correlation with responses to entire sequence of systemic treatment and survival outcomes. (2) Methods: DDR gene mutations were assessed prospectively in DNA samples from leukocytes and urine sediments from 149 mCRPC patients using five-gene panel targeted sequencing. The impact of DDR status on progression-free survival, as well as treatment-specific and overall survival, was evaluated using Kaplan–Meier curves and Cox regression. (3) Results: DDR mutations were detected in 16.6% of urine and 15.4% of blood samples. BRCA1, BRCA2, CHEK2, ATM and NBN mutations were associated with significantly shorter PFS in response to conventional androgen deprivation therapy and first-line mCRPC therapy with abiraterone acetate. Additionally, BRCA1 and BRCA2 mutation-bearing patients had a significantly worse response to radium-223. However, DDR mutation status was predictive for the favourable effect of second-line abiraterone acetate after previous taxane-based chemotherapy. (4) Conclusions: Our data confirm the benefit of non-invasive urine-based genetic testing for timely identification of high-risk prostate cancer cases for treatment personalization.

The influencing factors of digital health passport adoption and acceptance during COVID-19 in Saudi Arabia

Background

The COVID-19 outbreak has left a destructive trail around the world in terms of deaths, travel restrictions, trade deficits, and an economy that is collapsing, including job losses, real estate, health benefit loss, and a decrease in the quality of access to care and services in almost all sectors, as well as generally in the overall quality of life. The successful development of COVID-19 vaccines may hasten the acceleration of global post-pandemic recovery by vaccinating residents, with a particular focus on important groups, in order to decrease secondary transmission. This will facilitate the easing of enforced restrictions on global and local travel, the tourism industry, education sectors, and other aspects of social life. Vaccinating residents may also help reduce the risk of secondary transmission. The efforts that Saudi Arabia made to control the epidemic were outstanding on all fronts and in all spheres, including the health, education, commerce, and tourism industries, among others.

Objective

The purpose of this research was to investigate the elements that influence a traveler's decision to acquire and use a digital health passport (DHP), which was introduced by the Tawakkalna application in Saudi Arabia at the COVID-19 conference.

Methods

The technology acceptance model (TAM) and the information system success model (ISSM) were the primary theoretical frameworks that guided this investigation. The terms "perceived ease of use" (PEOU), "perceived usefulness" (PU), "information quality" (IQ), "service quality" (SQ), and "net benefit" (NB) were applied in order to investigate the user's acceptance and use of the DHP, as well as how it contributes to the facilitation of traveling and public perception toward using the DHP.

Results

In order to assess the validity of the proposed model and its four assumptions, a survey was sent through social media platforms to get responses from nationals and residents of Saudi Arabia. The SPSS program was used to evaluate a total of 103 replies that were considered valid. Following the completion of the study, the findings revealed that PEOU, PU, IQ, SQ, and NB all had favorable impacts on the use of DHP.

Conclusion

PEOU, PU, IQ, and SQ have a significant relationship with NB that affects the public's acceptance and use of DHP. This study has established validity and reliability while testing the relationship between the variables suggested in the research model.

Genomic Profiling of Prostate Cancer: An Updated Review

Understanding the genomic profiling of prostate cancer is crucial, owing to the emergence of precision medicine to guide therapeutic approaches. Over the last decade, integrative genomic profiling of prostate tumors has provided insights that improve the understanding and treatment of the disease. Minimally invasive liquid biopsy procedures have emerged to investigate cancer-related molecules with the advantage of detecting heterogeneity as well as acquired resistance in cancer. The metastatic castration-resistant prostate cancer (mCRPC) tumors have a highly complex genomic landscape compared to primary prostate tumors; a number of mCRPC harbor clinically actionable molecular alterations, including DNA damage repair (e.g., BRCA1/2 and ATM) and PTEN/phosphoinositide 3-kinase signaling. Heterogeneity in the genomic landscape of prostate cancer has become apparent and genomic alterations of TP53, RB1, AR, and cell cycle pathway are associated with poor clinical outcomes in patients. Prostate cancer with mutant SPOP shows a distinct pattern of genomic alterations, associating with better clinical outcomes. Several genomic profiling tests, which can be used in the clinic, are approved by the U.S. Food and Drug Administration, including MSK-IMPACT, FoundationOne CDx, and FoundationOne Liquid CDx. Here, we review emerging evidence for genomic profiling of prostate cancer, especially focusing on associations between genomic alteration and clinical outcome, liquid biopsy, and actionable molecular alterations.

cfTrack: A Method of Exome-Wide Mutation Analysis of Cell-free DNA to Simultaneously Monitor the Full Spectrum of Cancer Treatment Outcomes Including MRD, Recurrence, and Evolution

PURPOSE

Cell-free DNA (cfDNA) offers a noninvasive approach to monitor cancer. Here we develop a method using whole-exome sequencing (WES) of cfDNA for simultaneously monitoring the full spectrum of cancer treatment outcomes, including minimal residual disease (MRD), recurrence, evolution, and second primary cancers.

EXPERIMENTAL DESIGN

Three simulation datasets were generated from 26 patients with cancer to benchmark the detection performance of MRD/recurrence and second primary cancers. For further validation, cfDNA samples (n = 76) from patients with cancer (n = 35) with six different cancer types were used for performance validation during various treatments.

RESULTS

We present a cfDNA-based cancer monitoring method, named cfTrack. Taking advantage of the broad genome coverage of WES data, cfTrack can sensitively detect MRD and cancer recurrence by integrating signals across known clonal tumor mutations of a patient. In addition, cfTrack detects tumor evolution and second primary cancers by de novo identifying emerging tumor mutations. A series of machine learning and statistical denoising techniques are applied to enhance the detection power. On the simulation data, cfTrack achieved an average AUC of 99% on the validation dataset and 100% on the independent dataset in detecting recurrence in samples with tumor fractions ≥0.05%. In addition, cfTrack yielded an average AUC of 88% in detecting second primary cancers in samples with tumor fractions ≥0.2%. On real data, cfTrack accurately monitors tumor evolution during treatment, which cannot be accomplished by previous methods.

CONCLUSIONS

Our results demonstrated that cfTrack can sensitively and specifically monitor the full spectrum of cancer treatment outcomes using exome-wide mutation analysis of cfDNA.

NucPosDB: a database of nucleosome positioning in vivo and nucleosomics of cell-free DNA

Nucleosome positioning is involved in many gene regulatory processes happening in the cell, and it may change as cells differentiate or respond to the changing microenvironment in a healthy or diseased organism. One important implication of nucleosome positioning in clinical epigenetics is its use in the “nucleosomics” analysis of cell-free DNA (cfDNA) for the purpose of patient diagnostics in liquid biopsies. The rationale for this is that the apoptotic nucleases that digest chromatin of the dying cells mostly cut DNA between nucleosomes. Thus, the short pieces of DNA in body fluids reflect the positions of nucleosomes in the cells of origin. Here, we report a systematic nucleosomics database — NucPosDB — curating published nucleosome positioning datasets in vivo as well as datasets of sequenced cell-free DNA (cfDNA) that reflect nucleosome positioning in situ in the cells of origin. Users can select subsets of the database by a number of criteria and then obtain raw or processed data. NucPosDB also reports the originally determined regions with stable nucleosome occupancy across several individuals with a given condition. An additional section provides a catalogue of computational tools for the analysis of nucleosome positioning or cfDNA experiments and theoretical algorithms for the prediction of nucleosome positioning preferences from DNA sequence. We provide an overview of the field, describe the structure of the database in this context, and demonstrate data variability using examples of different medical conditions. NucPosDB is useful both for the analysis of fundamental gene regulation processes and the training of computational models for patient diagnostics based on cfDNA. The database currently curates ~ 400 publications on nucleosome positioning in cell lines and in situ as well as cfDNA from > 10,000 patients and healthy volunteers. For open-access cfDNA datasets as well as key MNase-seq datasets in human cells, NucPosDB allows downloading processed mapped data in addition to the regions with stable nucleosome occupancy. NucPosDB is available at https://generegulation.org/nucposdb/.

Decoding the evolutionary response to prostate cancer therapy by plasma genome sequencing

BACKGROUND

Investigating genome evolution in response to therapy is difficult in human tissue samples. To address this challenge, we develop an unbiased whole-genome plasma DNA sequencing approach that concurrently measures genomic copy number and exome mutations from archival cryostored plasma samples. This approach is applied to study longitudinal blood plasma samples from prostate cancer patients, where longitudinal tissue biopsies from the bone and other metastatic sites have been challenging to collect.

RESULTS

A molecular characterization of archival plasma DNA from 233 patients and genomic profiling of 101 patients identifies clinical correlations of aneuploid plasma DNA profiles with poor survival, increased plasma DNA concentrations, and lower plasma DNA size distributions. Deep-exome sequencing and genomic copy number profiling are performed on 23 patients, including 9 patients with matched metastatic tissues and 12 patients with serial plasma samples. These data show a high concordance in genomic alterations between the plasma DNA and metastatic tissue samples, suggesting the plasma DNA is highly representative of the tissue alterations. Longitudinal sequencing of 12 patients with 2-5 serial plasma samples reveals clonal dynamics and genome evolution in response to hormonal and chemotherapy. By performing an integrated evolutionary analysis, minor subclones are identified in 9 patients that expanded in response to therapy and harbored mutations associated with resistance.

CONCLUSIONS

This study provides an unbiased evolutionary approach to non-invasively delineate clonal dynamics and identify clones with mutations associated with resistance in prostate cancer.