Selective disruption of an oncogenic mutant allele by CRISPR/Cas9 induces efficient tumor regression

Approximately 15% of non-small cell lung cancer cases are associated with a mutation in the epidermal growth factor receptor (EGFR) gene, which plays a critical role in tumor progression. With the goal of treating mutated EGFR-mediated lung cancer, we demonstrate the use of clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system to discriminate between the oncogenic mutant and wild-type EGFR alleles and eliminate the carcinogenic mutant EGFR allele with high accuracy. We targeted an EGFR oncogene harboring a single-nucleotide missense mutation (CTG > CGG) that generates a protospacer-adjacent motif sequence recognized by the CRISPR/Cas9 derived from Streptococcus pyogenes. Co-delivery of Cas9 and an EGFR mutation-specific single-guide RNA via adenovirus resulted in precise disruption at the oncogenic mutation site with high specificity. Furthermore, this CRISPR/Cas9-mediated mutant allele disruption led to significantly enhanced cancer cell killing and reduced tumor size in a xenograft mouse model of human lung cancer. Taken together, these results indicate that targeting an oncogenic mutation using CRISPR/Cas9 offers a powerful surgical strategy to disrupt oncogenic mutations to treat cancers; similar strategies could be used to treat other mutation-associated diseases.

GW170814: A Three-Detector Observation of Gravitational Waves from a Binary Black Hole Coalescence

On August 14, 2017 at 10∶30:43 UTC, the Advanced Virgo detector and the two Advanced LIGO detectors coherently observed a transient gravitational-wave signal produced by the coalescence of two stellar mass black holes, with a false-alarm rate of ≲1 in 27 000 years. The signal was observed with a three-detector network matched-filter signal-to-noise ratio of 18. The inferred masses of the initial black holes are 30.5_{-3.0}^{+5.7}M_{⊙} and 25.3_{-4.2}^{+2.8}M_{⊙} (at the 90% credible level). The luminosity distance of the source is 540_{-210}^{+130}  Mpc, corresponding to a redshift of z=0.11_{-0.04}^{+0.03}. A network of three detectors improves the sky localization of the source, reducing the area of the 90% credible region from 1160   deg^{2} using only the two LIGO detectors to 60  deg^{2} using all three detectors. For the first time, we can test the nature of gravitational-wave polarizations from the antenna response of the LIGO-Virgo network, thus enabling a new class of phenomenological tests of gravity.

CUT-PCR: CRISPR-mediated, ultrasensitive detection of target DNA using PCR

Circulating tumor DNA (ctDNA) has emerged as a tumor-specific biomarker for the early detection of various cancers. To date, several techniques have been devised to enrich the extremely small amounts of ctDNA present in plasma, but they are still insufficient for cancer diagnosis, especially at the early stage. Here, we developed a novel method, CUT (CRISPR-mediated, Ultrasensitive detection of Target DNA)-PCR, which uses CRISPR endonucleases to enrich and detect the extremely small amounts of tumor DNA fragments among the much more abundant wild-type DNA fragments by specifically eliminating the wild-type sequences. We computed that by using various orthologonal CRISPR endonucleases such as SpCas9 and FnCpf1, the CUT-PCR method would be applicable to 80% of known cancer-linked substitution mutations registered in the COSMIC database. We further verified that CUT-PCR together with targeted deep sequencing enables detection of a broad range of oncogenes with high sensitivity (<0.01%) and accuracy, which is superior to conventional targeted deep sequencing. In the end, we successfully applied CUT-PCR to detect sequences with oncogenic mutations in the ctDNA of colorectal cancer patients’ blood, suggesting that our technique could be adopted for diagnosing various types of cancer at early stages.

GW170104: Observation of a 50-Solar-Mass Binary Black Hole Coalescence at Redshift 0.2

We describe the observation of GW170104, a gravitational-wave signal produced by the coalescence of a pair of stellar-mass black holes. The signal was measured on January 4, 2017 at 10∶11:58.6 UTC by the twin advanced detectors of the Laser Interferometer Gravitational-Wave Observatory during their second observing run, with a network signal-to-noise ratio of 13 and a false alarm rate less than 1 in 70 000 years. The inferred component black hole masses are 31.2_{-6.0}^{+8.4}M_{⊙} and 19.4_{-5.9}^{+5.3}M_{⊙} (at the 90% credible level). The black hole spins are best constrained through measurement of the effective inspiral spin parameter, a mass-weighted combination of the spin components perpendicular to the orbital plane, χ_{eff}=-0.12_{-0.30}^{+0.21}. This result implies that spin configurations with both component spins positively aligned with the orbital angular momentum are disfavored. The source luminosity distance is 880_{-390}^{+450}  Mpc corresponding to a redshift of z=0.18_{-0.07}^{+0.08}. We constrain the magnitude of modifications to the gravitational-wave dispersion relation and perform null tests of general relativity. Assuming that gravitons are dispersed in vacuum like massive particles, we bound the graviton mass to m_{g}≤7.7×10^{-23}  eV/c^{2}. In all cases, we find that GW170104 is consistent with general relativity.

CRISPR/Cas9-mediated gene knockout screens and target identification via whole-genome sequencing uncover host genes required for picornavirus infection

Several groups have used genome-wide libraries of lentiviruses encoding small guide RNAs (sgRNAs) for genetic screens. In most cases, sgRNA expression cassettes are integrated into cells by using lentiviruses, and target genes are statistically estimated by the readout of sgRNA sequences after targeted sequencing. We present a new virus-free method for human gene knockout screens using a genome-wide library of CRISPR/Cas9 sgRNAs based on plasmids and target gene identification via whole-genome sequencing (WGS) confirmation of authentic mutations rather than statistical estimation through targeted amplicon sequencing. We used 30,840 pairs of individually synthesized oligonucleotides to construct the genome-scale sgRNA library, collectively targeting 10,280 human genes (i.e. three sgRNAs per gene). These plasmid libraries were co-transfected with a Cas9-expression plasmid into human cells, which were then treated with cytotoxic drugs or viruses. Only cells lacking key factors essential for cytotoxic drug metabolism or viral infection were able to survive. Genomic DNA isolated from cells that survived these challenges was subjected to WGS to directly identify CRISPR/Cas9-mediated causal mutations essential for cell survival. With this approach, we were able to identify known and novel genes essential for viral infection in human cells. We propose that genome-wide sgRNA screens based on plasmids coupled with WGS are powerful tools for forward genetics studies and drug target discovery.

Abstract P6-09-50: Impact of young age on recurrence and mortality after surgery in breast cancer: 15 years active surveillance

Introduction:Substantial efforts have been made to find factors associated with breast cancer (BC) recurrence and mortality after BC treatment. So far TNM stage, ER, PR, and HER2 status are considered as the major predictive markers of BC recurrence and used for treatment decision. However, most of these factors were evaluated independent from other important confounders such as age, stage, and various anti-cancer treatments because they were mostly derived from clinical trials. In Korea, up to 50% of BC patients are premenopausal women, it is not clear how age at diagnosis affect the progression and outcomes of the disease considering all known prognostic factors including TNM stage, ER, PR, and HER2 status. We aim to evaluate the impact of young age on recurrence and mortality after surgery among Korean women with BC.

Methods: This is a retrospective cohort study conducted using the data from BC registry from 2000 to 2016 at Samsung Medical Cancer, Seoul, Korea. Patients who received curative BC surgery and who had histologically-confirmed invasive BC between 2000 to 2011 were included in the study. Patients who second primary cancer or double primary cancer were excluded. Information local, regional, or distant recurrence and death until May 2016 was collected using electronic medical records and National Health Statistics. Cumulative incidence rates of distant recurrence and morality at 3-years, 5-years and 10-years were calculated using a competing-risk model. Cox proportional hazards analysis were conducted with 3 different models to take into account for potential confounding factors including age, body mass index (BMI), stage and subtype at breast cancer diagnosis, chemotherapy, radiotherapy and hormone therapy.

Results:There were 7360 BC patients with curative BC surgery between 2000 and 2011, and the average follow up duration was 75.4 months. The mean age at diagnosis was 48.4 years old (Standard deviation (SD)=±10), and 6.2% (n=459) was diagnosed younger than 35. Of total, 13.3% were stage III BC and 73.4% of patients had hormone receptor positive BC. The cumulative incidence (95%CI) of recurrence at 3, 5, and 10 years was 4.4% (3.9-4.9), 7.5% (6.8-8.2), and 14.8% (12.9-16.7) respectively. The incidence of mortality at 3, 5, and 10 years was 1.8% (1.5-2.1), 3.8% (3.3-4.3), and 10.2% (9.1-11.5) respectively. Patients who were diagnosed BC under 35 years of age had 2.14 (95% confidence interval (CI):1.74-3.10) and 1.62 (95% CI:1.02-2.56) times higher risk of distant recurrence and mortality compared to patients whose age at diagnosis were between 50 to 60 after adjusting all well-known prognostic factors including stage, subtype, and BMI at diagnosis, chemotherapy, radiotherapy and hormone therapy.

Conclusions: Young age at diagnosis (&lt;35) was the most significant predictor on BC recurrence and mortality independently from BC stage and subtype. Further study is warranted to explain biologic background for the differences in outcomes in young women with BC.

Citation Format: Kim J-Y, Cho J, Kim H, Kang D, Jung HA, Lee S-H, Bae S, Yu JH, Lee SK, Kim SW, Lee JE, Nam SJ, Ahn JS, Im Y-H, Guallar E, Park YH. Impact of young age on recurrence and mortality after surgery in breast cancer: 15 years active surveillance [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-09-50.

Cas-analyzer: an online tool for assessing genome editing results using NGS data

Genome editing with programmable nucleases has been widely adopted in research and medicine. Next generation sequencing (NGS) platforms are now widely used for measuring the frequencies of mutations induced by CRISPR-Cas9 and other programmable nucleases. Here, we present an online tool, Cas-Analyzer, a JavaScript-based implementation for NGS data analysis. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server, a time-consuming step in genome editing analysis. Currently, Cas-Analyzer supports various programmable nucleases, including single nucleases and paired nucleases.

AVAILABILITY AND IMPLEMENTATION

Free access at http://www.rgenome.net/cas-analyzer/ CONTACT: sangsubae@hanyang.ac.kr or jskim01@snu.ac.krSupplementary information: Supplementary data are available at Bioinformatics online.

The experiences of cancer survivors while transitioning from tertiary to primary care

PURPOSE

In current fiscally constrained health care systems, the transition of cancer survivors to primary care from tertiary care settings is becoming more common and necessary. The purpose of our study was to explore the experiences of survivors who are transitioning from tertiary to primary care.

METHODS

One focus group and ten individual telephone interviews were conducted. Data saturation was reached with 13 participants. All sessions were audio-recorded, transcribed verbatim, and analyzed using a qualitative descriptive approach.

RESULTS

Eight categories relating to the main content category of transition readiness were identified in the analysis. Several factors affected participant transition readiness: how the transition was introduced, perceived continuity of care, support from health care providers, clarity of the timeline throughout the transition, and desire for a "roadmap." Although all participants spoke about the effect of their relationships with health care providers (tertiary, transition, and primary care), their relationship with the primary care provider had the most influence on their transition readiness.

CONCLUSIONS

Our study provided insights into survivor experiences during the transition to primary care. Transition readiness of survivors is affected by many factors, with their relationship with the primary care provider being particularly influential. Understanding transition readiness from the survivor perspective could prove useful in ensuring patient-centred care as transitions from tertiary to primary care become commonplace.

DBC2/RhoBTB2 functions as a tumor suppressor protein via Musashi-2 ubiquitination in breast cancer

The gene encoding ‘deleted in breast cancer 2' (DBC2), also referred to as RHOBTB2 (Rho-related BTB domain-containing protein 2), is classified as a tumor suppressor gene. DBC2 is a substrate-specific adaptor protein for a novel class of Cullin-3 (CUL3)-based E3 ubiquitin ligases; however, it is unclear if the substrate adaptor function of DBC2 is required for its tumor suppressor activity. Furthermore, the key substrates of DBC2-mediated ubiquitination have yet to be identified. In the present study, we established a genome-wide human cDNA library-based in vitro ubiquitination target screening assay and identified Musashi-2 (MSI2) as a novel ubiquitination target protein of DBC2. MSI2 directly interacted with DBC2, and this interaction promoted MSI2 polyubiquitination and proteasomal degradation in breast cancer cells. Overexpression and knockdown experiments demonstrated that DBC2 suppressed MSI2-associated oncogenic functions and induced apoptosis. Immunohistochemistry analysis of a breast cancer tissue microarray revealed that DBC2 and MSI2 protein levels are inversely correlated in both normal breast tissues and breast cancer tissues. Taken together, these findings provide evidence that DBC2 suppresses tumorigenesis in breast cancer by ubiquitinating MSI2.

Sensitive Surface Enhanced Raman Scattering-Based Detection of a BIGH3 Point Mutation Associated with Avellino Corneal Dystrophy

Surface enhanced Raman scattering (SERS) is highly useful for sensitive analytical sensing; however, its practical availability for detecting a point mutation associated with disease in clinical sample was rarely proved. Herein, we present a toehold-mediated, DNA displacement-based, SERS sensor for detecting point mutations in the BIGH3 gene associated with the most common corneal dystrophies (CDs) in a clinical setting. To diagnose Avellino corneal dystrophy (ACD), selectivity was ensured by exploring optimal DNA displacement conditions such as length of toehold and hybridization temperature. A SERS-efficient Ag@Au bimetallic nanodendrite was employed to ensure sensitivity. Optimization for a clinical setting showed that discrimination was maximized when toehold length was 6-mer (T6), and hybridization temperature was 36 °C. On the basis of tests that used clinical homozygous and heterozygous CD samples, a single-base mismatched DNA sequence was identifiable within 30 min with a limit of detection (LOD) of 400 fM. From the results, we conclude that our toehold-mediated, DNA displacement-based, SERS sensor allows a rapid and sensitive detection of a BIGH3 gene point mutation associated with Avellino corneal dystrophy, indicating the practical ability of the method to diagnose genetic diseases caused by point mutations.

Structural roles of guide RNAs in the nuclease activity of Cas9 endonuclease

The type II CRISPR-associated protein Cas9 recognizes and cleaves target DNA with the help of two guide RNAs (gRNAs; tracrRNA and crRNA). However, the detailed mechanisms and kinetics of these gRNAs in the Cas9 nuclease activity are unclear. Here, we investigate the structural roles of gRNAs in the CRISPR-Cas9 system by single-molecule spectroscopy and reveal a new conformation of inactive Cas9 that is thermodynamically more preferable than active apo-Cas9. We find that tracrRNA prevents Cas9 from changing into the inactive form and leads to the Cas9:gRNA complex. For the Cas9:gRNA complex, we identify sub-conformations of the RNA-DNA heteroduplex during R-loop expansion. Our single-molecule study indicates that the kinetics of the sub-conformations is controlled by the complementarity between crRNA and target DNA. We conclude that both tracrRNA and crRNA regulate the conformations and kinetics of the Cas9 complex, which are crucial in the DNA cleavage activity of the CRISPR-Cas9 system.

Cas-analyzer: an online tool for assessing genome editing results using NGS data

Summary

Genome editing with programmable nucleases has been widely adopted in research and medicine. Next generation sequencing (NGS) platforms are now widely used for measuring the frequencies of mutations induced by CRISPR-Cas9 and other programmable nucleases. Here, we present an online tool, Cas-Analyzer, a JavaScript-based implementation for NGS data analysis. Because Cas-Analyzer is completely used at a client-side web browser on-the-fly, there is no need to upload very large NGS datasets to a server, a time-consuming step in genome editing analysis. Currently, Cas-Analyzer supports various programmable nucleases, including single nucleases and paired nucleases.

Availability and Implementation

Free access at http://www.rgenome.net/cas-analyzer/.

Supplementary information

Supplementary data are available at Bioinformatics online.

DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins

Microalgae are versatile organisms capable of converting CO₂, H₂O, and sunlight into fuel and chemicals for domestic and industrial consumption. Thus, genetic modifications of microalgae for enhancing photosynthetic productivity, and biomass and bio-products generation are crucial for both academic and industrial applications. However, targeted mutagenesis in microalgae with CRISPR-Cas9 is limited. Here we report, a one-step transformation of Chlamydomonas reinhardtii by the DNA-free CRISPR-Cas9 method rather than plasmids that encode Cas9 and guide RNAs. Outcome was the sequential CpFTSY and ZEP two-gene knockout and the generation of a strain constitutively producing zeaxanthin and showing improved photosynthetic productivity.

DNA-free two-gene knockout in Chlamydomonas reinhardtii via CRISPR-Cas9 ribonucleoproteins

Microalgae are versatile organisms capable of converting CO2, H2O, and sunlight into fuel and chemicals for domestic and industrial consumption. Thus, genetic modifications of microalgae for enhancing photosynthetic productivity, and biomass and bio-products generation are crucial for both academic and industrial applications. However, targeted mutagenesis in microalgae with CRISPR-Cas9 is limited. Here we report, a one-step transformation of Chlamydomonas reinhardtii by the DNA-free CRISPR-Cas9 method rather than plasmids that encode Cas9 and guide RNAs. Outcome was the sequential CpFTSY and ZEP two-gene knockout and the generation of a strain constitutively producing zeaxanthin and showing improved photosynthetic productivity.

Clinical manifestations and coronary artery disease risk factors at diagnosis of systemic lupus erythematosus: data from an international inception cohort

Systemic Lupus International Collaborating Clinics (SLICC) comprises 27 centres from 11 countries. An inception cohort of 918 SLE patients has been assembled according to a standardized protocol between 2000 and 2006. Clinical features, classic coronary artery disease (CAD) risk factors, as well as other potential risk factors were collected. Of the 918 patients 89% were females, and of multi racial origin. Less than half the patients were living in a permanent relationship, 58% had post secondary education and 51% were employed. Eight percent had family history of SLE. At enrolment, with at mean age of diagnosis of 34.5 years, a significant number of patients already had CAD risk factors, such as hypertension (33%) and hypercholesterolemia (36%). Only 15% of the patients were postmenopausal, 16% were current smokers and 3.6% had diabetes at entry to the SLICC-RAS (Registry for Atherosclerosis). A number of patients in this multi-racial, multi-ethnic inception cohort of lupus patients have classic CAD risk factors within a mean of 5.4 months from diagnosis. This cohort will be increased to 1500 patients to be followed yearly for 10 years. This will provide a unique opportunity to evaluate risk factors for accelerated atherosclerosis in SLE. Lupus (2007) 16, 731—735.