RNA-triggered protein cleavage and cell growth arrest by the type III-E CRISPR nuclease-protease

The type III-E CRISPR-Cas7-11 effector binds a CRISPR RNA (crRNA) and the putative protease Csx29 and catalyzes crRNA-guided RNA cleavage. We report cryo-electron microscopy structures of the Cas7-11-crRNA-Csx29 complex with and without target RNA (tgRNA), and demonstrate that tgRNA binding induces conformational changes in Csx29. Biochemical experiments revealed tgRNA-dependent cleavage of the accessory protein Csx30 by Csx29. Reconstitution of the system in bacteria showed that Csx30 cleavage yields toxic protein fragments that cause growth arrest, which is regulated by Csx31. Csx30 binds Csx31 and the associated sigma factor RpoE (RNA polymerase, extracytoplasmic E), suggesting that Csx30-mediated RpoE inhibition modulates the cellular response to infection. We engineered the Cas7-11-Csx29-Csx30 system for programmable RNA sensing in mammalian cells. Overall, the Cas7-11-Csx29 effector is an RNA-dependent nuclease-protease.

Structure of the IscB-ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9

Transposon-encoded IscB family proteins are RNA-guided nucleases in the OMEGA (obligate mobile element-guided activity) system, and likely ancestors of the RNA-guided nuclease Cas9 in the type II CRISPR-Cas adaptive immune system. IscB associates with its cognate ωRNA to form a ribonucleoprotein complex that cleaves double-stranded DNA targets complementary to an ωRNA guide segment. Although IscB shares the RuvC and HNH endonuclease domains with Cas9, it is much smaller than Cas9, mainly due to the lack of the α-helical nucleic-acid recognition lobe. Here, we report the cryo-electron microscopy structure of an IscB protein from the human gut metagenome (OgeuIscB) in complex with its cognate ωRNA and a target DNA, at 2.6-Å resolution. This high-resolution structure reveals the detailed architecture of the IscB-ωRNA ribonucleoprotein complex, and shows how the small IscB protein assembles with the ωRNA and mediates RNA-guided DNA cleavage. The large ωRNA scaffold structurally and functionally compensates for the recognition lobe of Cas9, and participates in the recognition of the guide RNA-target DNA heteroduplex. These findings provide insights into the mechanism of the programmable DNA cleavage by the IscB-ωRNA complex and the evolution of the type II CRISPR-Cas9 effector complexes.

Structure and engineering of the type III-E CRISPR-Cas7-11 effector complex

The type III-E CRISPR-Cas effector Cas7-11, with dual RNase activities for precursor CRISPR RNA (pre-crRNA) processing and crRNA-guided target RNA cleavage, is a new platform for bacterial and mammalian RNA targeting. We report the 2.5-Å resolution cryoelectron microscopy structure of Cas7-11 in complex with a crRNA and its target RNA. Cas7-11 adopts a modular architecture comprising seven domains (Cas7.1-Cas7.4, Cas11, INS, and CTE) and four interdomain linkers. The crRNA 5' tag is recognized and processed by Cas7.1, whereas the crRNA spacer hybridizes with the target RNA. Consistent with our biochemical data, the catalytic residues for programmable cleavage in Cas7.2 and Cas7.3 neighbor the scissile phosphates before the flipped-out fourth and tenth nucleotides in the target RNA, respectively. Using structural insights, we rationally engineered a compact Cas7-11 variant (Cas7-11S) for single-vector AAV packaging for transcript knockdown in human cells, enabling in vivo Cas7-11 applications.

Structure of the type V-C CRISPR-Cas effector enzyme

RNA-guided CRISPR-Cas nucleases are widely used as versatile genome-engineering tools. Recent studies identified functionally divergent type V Cas12 family enzymes. Among them, Cas12c2 binds a CRISPR RNA (crRNA) and a trans-activating crRNA (tracrRNA) and recognizes double-stranded DNA targets with a short TN PAM. Here, we report the cryo-electron microscopy structures of the Cas12c2-guide RNA binary complex and the Cas12c2-guide RNA-target DNA ternary complex. The structures revealed that the crRNA and tracrRNA form an unexpected X-junction architecture, and that Cas12c2 recognizes a single T nucleotide in the PAM through specific hydrogen-bonding interactions with two arginine residues. Furthermore, our biochemical analyses indicated that Cas12c2 processes its precursor crRNA to a mature crRNA using the RuvC catalytic site through a unique mechanism. Collectively, our findings improve the mechanistic understanding of diverse type V CRISPR-Cas effectors.

Comparison of clinical effect of living alone between urban area and rural area in patient with acute coronary syndrome

Background and objective

Living alone is reported as an independent risk factor for worse clinical outcomes after percutaneous coronary intervention (PCI) for acute coronary syndrome (ACS). Manifestations of psychological stress such as depression and anxiety in patients living alone is thought to be associated with subsequent cardiovascular events. The impact of living alone on the psychological factors of patients may be differ depending on their living environment. However, comparison of the effects of living alone in different living environment on the prognosis of patients with ACS has not been reported.

Purpose

The aim of the present study was to compare the clinical effect of living alone on clinical outcomes in patients with ACS between urban area and rural area.

Methods

Data from a multi-center, observational study of consecutive patients who underwent emergency PCI for ACS between January 2012 and December 2016 were analyzed. The primary endpoint was major adverse cardiac and cerebrovascular events (MACCE). MACCE was defined as composite of cardiovascular death, ACS, and stroke.

Results

In this study, 1349 patients were enrolled and divided into two population according to their living environment: urban area population (n=417), and rural area population (n=932). In urban area population, 87 patients (20.9%) were living alone, and 330 (79.1%) were living together. In rural area population, 169 (18.1%) were living alone, and 763 (81.9%) were living together. There are no significant differences in baseline characteristics between the living alone group and the living together group in both urban area population and rural area population. During a median follow-up period of 2.1 years, Kaplan-Meier curves showed the living alone group had higher risk of MACCE than the living together group in urban area population (log-rank, p=0.01). On the other hands, there are no significant differences in the incidences of MACCE between two groups in rural area population (p=0.86). After adjustment for other covariates, the living alone was significantly associated with MACCE (hazard ratio [HR], 2.83; 95% confidential interval [CI], 1.16–6.91; p=0.02) compared with the living together group in urban area population. However, in rural area population, the living alone group was not significantly associated with MACCE (HR, 1.02; 95% CI, 0.66–1.57; p=0.92) compared with the living together group.

Conclusion

Living alone was significantly associated with worse clinical outcomes after emergency PCI of ACS in urban area but not in rural area.

Funding Acknowledgement

Type of funding sources: None. Figure 1

Comparison of clinical outcomes between percutaneous coronary intervention for the de novo lesion versus in-stent restenosis lesion

Background and objective

Percutaneous coronary intervention (PCI) with metallic coronary stent (bare-metal stents [BMS] and drug-eluting stents [DES]) implantation is most frequently performed therapeutic procedures for coronary artery disease. In-stent restenosis (ISR) is a critical drawback of metallic coronary stents. Incidence of ISR has been reported in up to 30% after BMS implantation. The use of DES has greatly reduced the proportion of restenosis compared with the BMS. However, ISR still remains the primary concern after PCI even in the contemporary DES era, and thought to be associated with worse clinical outcomes. However, comparative data on ISR and de novo lesions are rare.

Purpose

The aim of the present study was to compare the clinical outcomes after PCI for the de novo lesion and the ISR lesion.

Methods

We performed a retrospective analysis of patients who underwent PCI between 2013 and 2020. The incidences of major adverse cardiac and cerebrovascular events (MACCE) and all-cause death were evaluated. MACCE was defined as composite of cardiovascular death, non-fatal myocardial infarction, and stroke.

Results

In this study, 1538 patients were enrolled and divided into two groups: PCI for de novo lesion group (n=1258, 81.8%), and PCI for ISR lesion group (n=280, 18.2%). Patients in the ISR lesion group were significantly older and had higher prevalence of hypertension, diabetes mellitus, dyslipidemia and chronic kidney disease than patients in the de novo lesion group. During a median follow-up period of 1.9 years, Kaplan-Meier curves showed no significant differences in the incidences of MACCE (log-rank, p=0.86) and all-cause death (p=0.84) between two groups. After adjustment for other covariates, PCI for ISR lesion were not significantly associated with MACCE (hazard ratio [HR], 1.10; 95% confidential interval [CI], 0.61–1.97; p=0.76) and all-cause death (HR, 0.93; 95% CI, 0.56–1.56; p=0.79)

Conclusion

PCI for the ISR lesion was not associated with worse clinical outcomes compared with PCI for the de novo lesion.

Funding Acknowledgement

Type of funding sources: None.

Optimal measurement location of on-site based CT-derived FFR on midterm prognosis

Background

Fractional Flow Reserve (FFR) derived from coronary computed tomography angiography (CCTA) enables anatomical and hemodynamical assessment of coronary artery disease. CT-FFR, which can be acquired on-site workstation using fluid structure interaction during the multiple optimal diastolic phase, has an incremental diagnostic value over conventional CCTA. However, few studies are focused on investigating the appropriate measurement location of CT-FFR, considering the prognosis, using CCTA as a standalone modality.

Purpose

The aim of this study is to assess the clinical impact on CT-FFR with an appropriate measurement.

Methods

A total of 370 consecutive patients who underwent CCTA in a single-heartbeat scan with a phase window of 70% to 99% of the R-R interval, showing 50–90% stenosis of at least one major epicardial vessel measuring ≥1.8 mm in diameter on CCTA were retrospectively analyzed and followed during a median follow up 2.9 years. CT-FFR values were measured at three points: 1, 2 cm distal to a target lesion (CT-FFR1cm, 2cm) and the vessel terminus (CT-FFRlowest), and a CT-FFR value ≤0.80 was considered abnormal. The endpoint was MACE, a composite of cardiac death, non-fatal MI, and unplanned revascularization.

Results

The incidence of MACE occurred in 8.4% (31/370) of the whole patients, including four cardiac deaths, ten all cause deaths, two non-fatal MI, and twenty unplanned revascularization. The Kaplan-Meier survival analysis demonstrated a significantly higher cumulative MACE rate in patients with positive CT-FFR1cm and 2cm than those with negative CT-FFR1cm and 2cm, while there was no significant difference between negative and positive in CT-FFRlowest, among patients with negative CT-FFR1cm and 2cm (Figure 1). Among 221 patients, who did not perform early revascularization within 90 days from CCTA, there was no significant difference in CT-FFRlowest in the incidence of MACE. In contrast, the risk of MACE was significantly higher in both positive CT-FFR1cm and CT-FFR2cm (Figure 2).

Conclusion

From a view point of clinical outcome for patients with moderate to severe stenosis on CCTA, a CT-FFR value when measured at 1-to-2 cm distal to a target lesion could be feasible for the deferral of unnecessary invasive coronary angiography safely. Moreover, CT-FFR1–2cm showed better risk stratification measurement rather than CT-FFRlowest, based on future adverse cardiac event.

Funding Acknowledgement

Type of funding sources: Private company. Main funding source(s): Canon Medical Systems Corporation Kaplan-Meier 1Kaplan-Meier 2

The relationship among extent of lipid-rich plaque, factors associated with a reduction of lipid-rich plaque and late lumen loss: a near-infrared spectroscopy and intravascular ultrasound study

Background

Near-infrared spectroscopy (NIRS) and intravascular ultrasound (IVUS) are useful imaging modalities to identify lipid-rich plaque (LRP) which is associated with an increased risk of future cardiovascular events in individuals undergoing PCI. Pathological studies have raised concerns that treating LRP with stents may impair vascular healing. However, the impact of stent implantation to LRP lesions was less known. Moreover, little information is available about changes in the extent of LRP at before and after PCI.

Purpose

The aim of this study was to investigate changes in LRP by NIRS between pre- and post-stent implantation, and to evaluate an association among impact of LRP by NIRS at pre- and post-stenting and late lumen loss (LLL) by angiography.

Methods

We studied 175 lesions in 149 patients who underwent PCI under NIRS-IVUS guidance and follow-up angiography at 8-month later from 2017 to 2020. Plaque characteristics on IVUS, the extent of LRP [defined as a long segment with a 4-mm maximum lipid core burden index (maxLCBI4mm)] on NIRS, and quantitative coronary angiography measurements were analyzed. We evaluated a change of the extent of LRP between pre- and post-stenting at index PCI procedure, and association between the extent of LRP and a 8-month LLL at follow-up coronary angiography. A large LRP was defined as maxLCBI4mm>400 at pre-stenting.

Results

Mean age was 64.5 years old, and 123 (82%) patients were male. The prevalence of large LRP was 51% and median plaque burden at minimum lumen area was 81%. The extent of LRP at culprit lesion significantly decreased from pre- to post-stenting (median maxLCBI4mm [interquartile range (IQR)]: 407 [199, 580] to 133 [13, 319], p<0.001) (Figure 1). In multivariable liner regression analysis, independent predictors for the reduction of LRP were a pre-stenting LRP (β coefficient = −57.0, 95% confidence interval (CI) [−65.1 to −48.8], p<0.001) and plaque burden (β coefficient = −30.0, 95% CI [−56.6 to −3.4], p<0.001), respectively. On the other hands, patient comorbidities, lipid profile and inflammatory markers were not associated with the reduction of LRP (all p>0.05). Median LLL at follow-up angiogram was 0.17 [0.07–0.35] mm. Both the extent of pre- and post-stenting LRP were not associated with LLL (r=0.018, p=0.80 and r=0.022, p=0.76, respectively) (Figure 2). In addition, there was no significant difference in LLL between the post-stenting large and non-large LRP (median [IQR] 0.18 [0.08–0.35] vs. 0.17 [0.07–0.35]; P=0.95).

Conclusions

This study showed coronary stent implantation significantly reduced the NIRS-derived LRP in patients undergoing PCI. Although the extent of pre-stenting LRP and IVUS plaque burden predicted the reduction of LRP, the extent of pre- and post-stenting LRP were not associated with LLL. These findings suggest that stent implantation for LRP, even in a large LRP, is safe and does not affect LLL.

Funding Acknowledgement

Type of funding sources: None. Figure 1. Scatter plotsFigure 2. CENTRAL Figure

Coronary lipid-rich plaque characteristics with acute coronary syndrome and chronic coronary syndrome: a near infrared spectroscopy and intravascular ultrasound study

Background

Asians have a much lower incidence of adverse coronary events than Caucasians, and the characteristics of vulnerable plaque might be different among the ethnics.

Purpose

The aim of this study was to investigate the clinical characteristics of lipid-rich plaque (LRP) in the Asian population and we also aimed to distinguish the characteristics of an acute coronary syndrome (ACS) culprit lesion and a chronic coronary syndrome (CCS) culprit lesion. Furthermore, we evaluated the association between lipid core burden index (LCBI) and cardiovascular risk factors, lipid profiles, and inflammatory biomarkers, as determined in vivo by near infrared spectroscopy intravascular ultrasound (NIRS-IVUS) imaging in patients undergoing percutaneous coronary intervention (PCI).

Methods

We evaluated 207 patients (ACS, n=75; CCS, n=132) who underwent PCI under NIRS-IVUS. Plaque characteristics and the extent of LRP [defined as a long segment with a 4-mm maximum LCBI (maxLCBI4mm)] on NIRS in de-novo culprit and non-culprit segments were analyzed.

Results

The mean age was 65 years old and 82% of patients were male. The ACS culprit lesions had a significantly higher maxLCBI4mm (median [interquartile range (IQR)]: 533 [385–745] vs. 361 [174–527], p<0.001) than the CCS culprit lesions. Whereas, no significant difference was seen in maxLCBI4mm between ACS and CCS non-culprit lesion segments (246 [53, 342] vs. 185 [37, 350], p=0.47) (Figure 1). Receiver-operating characteristic analysis showed that the NIRS maxLCBI4mm could distinguish the ACS culprit segment from the CCS culprit segment, with a sensitivity of 73% and a specificity of 69% (c-statistic = 0.69; p<0.001, cut-off value of max LCBI4mm = 408) (Figure 2). On multivariate logistic analysis, a large LRP (defined as maxLCBI4mm ≥400) was the strongest independent predictor of the ACS culprit segment (odds ratio, 3.87; 95% confidence interval, 1.95–8.02). In non-culprit segments, 19.8% of patients had at least one large LRP without a small lumen. No significant correlation was found between the extent of LRP and circulating lipid profiles and inflammatory makers biomarkers (hs-CRP, IL-6, TNF-α) in both the culprit and non-culprit lesion segments, whereas the extent of LRP was positively correlated with IVUS plaque burden (r=0.24, p<0.001).

Conclusions

We confirmed that NIRS-IVUS plaque assessment could be useful to differentiate ACS from CCS culprit lesions, and that a threshold maxLCBI4mm ≥400 was clinically suitable in Japanese patients. No systemic surrogate markers were found to be associated with the extent of LRP by NIRS in culprit and non-culprit segments. Consequently, we believe that direct intravascular evaluation of coronary plaque characteristics remains important for identification of high-risk LRP.

Funding Acknowledgement

Type of funding sources: None. Figure 1. The difference of maxLCBI4mmFigure 2. ROC curve

Structure of the miniature type V-F CRISPR-Cas effector enzyme

RNA-guided DNA endonucleases derived from CRISPR-Cas adaptive immune systems are widely used as powerful genome-engineering tools. Among the diverse CRISPR-Cas nucleases, the type V-F Cas12f (also known as Cas14) proteins are exceptionally compact and associate with a guide RNA to cleave single- and double-stranded DNA targets. Here, we report the cryo-electron microscopy structure of Cas12f1 (also known as Cas14a) in complex with a guide RNA and its target DNA. Unexpectedly, the structure revealed that two Cas12f1 molecules assemble with the single guide RNA to recognize the double-stranded DNA target. Each Cas12f1 protomer adopts a different conformation and plays distinct roles in nucleic acid recognition and DNA cleavage, thereby explaining how the miniature Cas12f1 enzyme achieves RNA-guided DNA cleavage as an "asymmetric homodimer." Our findings augment the mechanistic understanding of diverse CRISPR-Cas nucleases and provide a framework for the development of compact genome-engineering tools critical for therapeutic genome editing.

Combined impact of residual inflammatory risk and chronic kidney disease on long-term clinical outcomes in patients undergoing percutaneous coronary intervention

Background

Inflammatory status pre-percutaneous coronary intervention (PCI) and post-PCI has been reported not only associated with poor prognosis, but also to impair renal function. Statins reduce cardiovascular events by lowering lipids and have anti-inflammatory impacts, but residual inflammatory risk (RIR) exists. It remains unclear that the synergistic effect of RIR and chronic kidney disease (CKD) on long-term clinical outcome in stable coronary artery disease (CAD) patients undergoing PCI in statin era.

Aim

The aim of this study was to investigate the long-term combined impact of RIR evaluating hs-CRP at follow-up and CKD among stable CAD patients undergoing PCI in statin era.

Methods

This is a single-center, observational, retrospective cohort study assessing consecutive 2,984 stable CAD patients who underwent first PCI from 2000 to 2016. We analyzed 2,087 patients for whom hs-CRP at follow-up (6–9 months later) was available. High residual inflammatory risk was defined as hs-CRP >0.6 mg/L according to the median value at follow up. Patients were assigned to four groups as Group1 (high RIR and CKD), Group2 (low RIR and CKD), Group3 (high RIR and non-CKD) or Group4 (low RIR and non-CKD). We evaluated all-cause death and major adverse cardiac events (MACE), defined as a composite of cardiovascular (CV) death, non-fatal myocardial infarction (MI) and non-fatal stroke.

Results

Of patients (83% men; mean age 67 years), there were 299 (14.3%) patients in group 1, 201 (9.6%) patients in group 2, 754 (36.1%) patients in group 3, and 833 (39.9%) patients in group 4. The median follow-up period was 5.2 years (IQR, 1.9–9.9 years). In total, 189 (frequency, 16.1%) cases of all-cause death and 128 (11.2%) MACE were identified during follow-up, including 53 (4.6%) CV deaths, 27 (2.4%) MIs and 52 (4.8%) strokes. The rate of all-cause death and MACE in group 1 was significantly higher than other groups (p<0.001, respectively). There was a stepwise increase in the incidence rates of all-cause death and MACE. After adjustment for important covariates, the presence of high RIR and/or CKD were independently associated with higher incidence of MACE and higher all-cause mortality. (shown on figure).

Conclusion

The presence of both high RIR and CKD conferred a synergistic adverse effect on the risk for long-term adverse cardiac events in patients undergoing PCI.

Kaplan-Meier curve

Funding Acknowledgement

Type of funding source: None

The effect of underweight on mid-term outcome following transcatheter aortic valve implantation: an insight from multicenter registry

Background

Obesity has the adverse prognostic impact in the general population, whereas paradoxical effect of obesity has been reported in patients with heart failure. Several studies have suggested the same obesity paradox in patients undergoing transcatheter aortic valve implantation (TAVI), however, they included limited number of underweight patients.

Purpose

The aim of this study was to clarify the effect of underweight on outcome following TAVI.

Methods

We retrospectively analyzed consecutive 1,027 patients undergoing TAVI between April 2010 and June 2019. The patients were categorized according to body mass index (BMI) as follows: underweight (<18.5 kg/m2, n=150), normal weight (18.5 to 25 kg/m2, n=657), and overweight (>25 kg/m2, n=220). BMI was defined as body weight (kg) divided by the square of body height (m) measured at the hospital admission. We compared the short- and mid-term outcome after TAVI among three groups, and all clinical events were accordance with Valve Academic Research Consortium-2 criteria.

Results

Underweight patients were more often female, and had a higher prevalence of hypertension, dyslipidemia, peripheral artery disease, anemia, and hypoalbuminemia. They also presented lower ejection fraction, smaller aortic valve area, and higher surgical risk score. In procedural findings, device unsuccess and major vascular complication more occurred in underweight patients, but 30-day mortality was equivalent among three groups. The mid-term survival of the underweight was inferior to the other two groups (figure).In the multivariate analysis, female (hazard ratio [HR] 0.52, 95% confidence interval [CI] 0.37–0.73, P=0.0002), atrial fibrillation (HR 2.22, 95% CI 1.56–3.17, P<0.0001), albumin value (HR 0.37 per 1-g/dl increase, 95% CI 0.25–0.55, P<0.0001), Society of Thoracic Surgeons score (HR 1.06 per 1% increase, 95% CI 1.02–1.06, P=0.0039), 30-day combined endpoint (HR 2.12, 95% CI 1.33–3.38, P=0.0017), and underweight (HR 1.59, 95% CI 1.04–2.37, P=0.026) were associated with the survival after TAVI.

Conclusion

The underweight had a worse mid-term prognosis, representing the obesity paradox in the TAVI population.

Kaplan-Meier curves

Funding Acknowledgement

Type of funding source: None

P6173Plaque characteristics on coronary CT angiography in case of discordance between fractional flow reserve (FFR) and instantaneous wave-free ratio (IFR)

Background

The usefulness of fractional flow reserve (FFR) and instantaneous wave-free ratio (iFR) evaluation has been confirmed in the determination of revascularization of coronary artery disease. When FFR≤0.8 and iFR≤0.89 were regarded as the criteria for positivity, the discordance was noted in approximately 20%, but this cause has not been well established.

Purpose

The purpose of this study was to investigate the patient background and features on coronary CT angiography (CCTA) showing the discordance between FFR≤0.8 and iFR≤0.89.

Methods

The subjects were consecutive 85 cases with 108 vessels in which stenosis of 30–90% was detected at one vessel of at least 2mm or more in the major epicardial vessels and FFR and iFR was performed within subsequent 90 days, among suspected cases of coronary arterial diseases which underwent CCTA. The factors showing the discordance between FFR and iFR (patient background, coronary artery calcification score, high risk plaque features on CCTA (positive remodeling, low attenuation plaque), plaque characteristics by a plaque analysis software using a new algorithm called labeling method (vessel volume, plaque volume, lumen volume, plaque length, maximum plaque burden, necrotic core area, fibrous area and calcium area) were evaluated using logistic regression analysis on per-patient and per-vessel basis.

Results

There were no significant both FFR and iFR positive definite factors on per-patient basis. The lumen volume/vessel volume (OR: 0.93, 95% CI: 0.88–0.98, P=0.0032) (OR: 0.90, 95% CI: 0.85–0.95, P<0.0001),minimum lumen area (MLA) (OR: 0.59, 95% CI: 0.41–0.85, P=0.0006) (OR: 0.64, 95% CI: 0.44–0.92, P=0.0047), the plaque volume/vessel volume (OR: 1.05, 95% CI: 1.01–1.10, P=0.0114) (OR: 1.09, 95% CI: 1.04–1.15, P=0.0002) and maximum plaque burden (OR: 1.08, 95% CI: 1.01–1.15, P=0.0095) (OR: 1.06, 95% CI: 1.00–1.13, P=0.0406) were significant both FFR and iFR positive definite factors on per-vessels basis. Discordance between FFR≤0.8 and iFR≤0.89 was observed in 23 vessels (21.3%) of 19 patients. In FFR positive and iFR negative group (15 vessels, 13.9%), positive remodeling (PR) (OR: 4.38, 95% CI: 1.13–17.00, P=0.0294) was only significant predictor. In FFR negative and iFR positive group, there was no significant predictors.

Conclusions

In both FFR and iFR, only lumen volume /vessel volume, MLA, plaque volume/vessel volume and plaque burden were significant positive definite factors. As for the discordance between FFR and iFR, PR is significant predictor in FFR positive and iFR negative group.

Engineered CRISPR-Cas9 nuclease with expanded targeting space

The RNA-guided endonuclease Cas9 cleaves its target DNA and is a powerful genome-editing tool. However, the widely used Streptococcus pyogenes Cas9 enzyme (SpCas9) requires an NGG protospacer adjacent motif (PAM) for target recognition, thereby restricting the targetable genomic loci. Here, we report a rationally engineered SpCas9 variant (SpCas9-NG) that can recognize relaxed NG PAMs. The crystal structure revealed that the loss of the base-specific interaction with the third nucleobase is compensated by newly introduced non-base-specific interactions, thereby enabling the NG PAM recognition. We showed that SpCas9-NG induces indels at endogenous target sites bearing NG PAMs in human cells. Furthermore, we found that the fusion of SpCas9-NG and the activation-induced cytidine deaminase (AID) mediates the C-to-T conversion at target sites with NG PAMs in human cells.

Genetic variants of DNA repair-related genes predict efficacy of TAS-102 in patients with refractory metastatic colorectal cancer

Background

Tri-phosphorylated trifluridine (FTD) incorporation into DNA is TAS-102's main anti-tumor action. We tested whether genetic polymorphisms in homologous recombination (HR) and cell cycle checkpoint pathway for DNA repair is associated with outcomes in refractory metastatic colorectal cancer (mCRC) patients treated with TAS-102.

Patients and methods

We analyzed genomic DNA extracted from 233 samples of three cohorts: an evaluation cohort of 52 patients receiving TAS-102, a validation cohort of 129 patients receiving TAS-102 and a control cohort of 52 patients receiving regorafenib. Single nucleotide polymorphisms of genes involved in HR (ATM, BRCA1, BRCA2, XRCC3, FANCD2, H2AX, RAD51) and cell cycle checkpoint (ATR, CHEK1, CHEK2, CDKN1A, TP53, CHE1, PIN1, PCNA) were analyzed by PCR-based direct sequencing.

Results

In univariate analysis for the evaluation cohort, patients with any G allele in ATM rs609429 had longer overall survival (OS) than those with the C/C variant (8.7 vs. 4.4 months, HR 0.37, 95% CI: 0.14-0.99, P = 0.022). Patients carrying any A allele in XRCC3 rs861539 had significantly longer progression-free survival (PFS) (3.8 vs. 2.3 months, HR 0.44, 95% CI: 0.21-0.92, P = 0.024) and OS (15.6 vs. 6.3 months, HR 0.25, 95% CI: 0.08-0.79, P = 0.012) than those with the G/G variant. In multivariable analysis, ATM rs609429 remained significant for OS (P = 0.020). In the validation cohort, patients having ATM rs609429 with any G allele showed longer OS and PFS; the G/A variant in XRCC3 rs861539 showed longer OS, though without statistical significance.

Conclusion

Genetic variants in the HR pathway may predict clinical outcome in mCRC patients receiving TAS-102.

Long-term clinical impact of serum albumin in coronary artery disease patients with preserved renal function

BACKGROUND AND AIMS

Low serum albumin level is reportedly associated with worse clinical outcomes in patients with chronic kidney disease (CKD). However, associations between decreased serum albumin level and outcomes in non-CKD patients with coronary artery disease (CAD) remain unclear. Therefore, we aimed to evaluate the prognostic value of serum albumin concentrations in stable CAD patients with preserved renal function.

METHODS AND RESULTS

We studied 1316 patients with CAD and preserved renal function (estimated glomerular filtration rate ≥60 mL/min/1.73 m²) who underwent their first PCI between 2000 and 2011 and had data available for pre-procedural serum albumin. Patients were assigned to quartiles based on pre-procedural albumin concentrations. The incidence of major adverse cardiac events (MACE), including all-cause death and non-fatal myocardial infarction, was evaluated. Mean albumin concentration was 4.1 ± 0.4 g/dL. During the median follow-up of 7.5 years, 181 events occurred (13.8%). Kaplan-Meier curves revealed that patients with decreased serum albumin concentrations showed a higher event rate for MACE (log-rank, p < 0.0001). Using the highest tertiles (>4.3 g/dL) as reference, adjusted hazard ratios were 1.97 (95% CI, 1.12-3.55), 1.77 (95% CI, 0.99-3.25), and 1.19 (95% CI, 0.68-2.15) for serum albumin concentrations of <3.9, 3.9-4.0, and 4.1-4.3 g/dL, respectively. Decreased serum albumin concentration was associated with MACE even after adjusting for other independent variables (HR, 2.21 per 1-g/dL decrease; 95% CI, 1.37-3.56, p = 0.001).

CONCLUSION

Decreased serum albumin concentration independently predicted worse long-term prognosis in non-CKD patients after PCI. Pre-procedural serum albumin concentration could offer a useful predictor for patients with CAD and preserved renal function.

Impact of genetic variations in the MAPK signaling pathway on outcome in metastatic colorectal cancer patients treated with first-line FOLFIRI and bevacizumab: data from FIRE-3 and TRIBE trials

BACKGROUND

The MAPK-interacting kinase 1 (MKNK1) is localized downstream of the RAS/RAF/ERK and the MAP3K1/MKK/p38 signaling pathway. Through phosphorylation MKNK1 regulates the function of eukaryotic translation initiation factor 4E, a key player in translational control, whose expression is often upregulated in metastatic colorectal cancer patients (mCRC). Preclinical data suggest that MKNK1 increases angiogenesis by upregulating angiogenic factors. We therefore hypothesize that variations in the MKNK1 gene predict outcome in mCRC patients treated with first-line FOLFIRI and bevacizumab (bev).

PATIENTS AND METHODS

A total of 567 patients with KRAS wild-type mCRC in the randomized phase III FIRE-3 and TRIBE trials treated with first-line FOLFIRI/bev (discovery and validation cohorts) or FOLFIRI and cetuximab (cet) (control cohort) were included in this study. Five single-nucleotide polymorphisms in the MAPK signaling pathway were analyzed.

RESULTS

AA genotype carriers of the MKNK1 rs8602 single-nucleotide polymorphism treated with FOLFIRI/bev in the discovery cohort (FIRE-3) had a shorter progression-free survival (PFS) than those harboring any C (7.9 versus 10.3 months, Hazard ratio (HR) 1.73, P = 0.038). This association could be confirmed in the validation cohort (TRIBE) in multivariable analysis (PFS 9.0 versus 11.0 months, HR 3.04, P = 0.029). Furthermore, AA carriers in the validation cohort had a decreased overall response rate (25% versus 66%, P = 0.049). Conversely, AA genotype carriers in the control group receiving FOLFIRI/cet did not show a shorter PFS. By combining both FOLFIRI/bev cohorts the worse outcome among AA carriers became more significant (PFS 9.0 versus 10.5 months) in univariable (HR 1.74, P = 0.015) and multivariable analysis (HR 1.76, P = 0.022). Accordingly, AA carriers did also exhibit an inferior overall response rate compared with those harboring any C (36% versus 65%, P = 0.005).

CONCLUSION

MKNK1 polymorphism rs8602 might serve as a predictive marker in KRAS wild-type mCRC patients treated with FOLFIRI/bev in the first-line setting. Additionally, MKNK1 might be a promising target for drug development.

The Biomarker Salivary SP-D May Indicate Small Airway Inflammation and Asthma Exacerbation

BACKGROUND

Noninvasive and child-friendly biomarkers are important tools for understanding the various phenotypes of childhood asthma. Objective: The aim of this study was to examine the usefulness of salivary surfactant protein (SP) D in assessing the pathophysiology of childhood asthma.

METHODS

We measured salivary concentrations of SP-D and forced oscillation technique (FOT) indexes in 19 healthy controls and 21 asthmatic children. Regression equations for the predictive values of FOT indexes were generated from healthy controls. We analyzed the correlations between salivary SP-D concentration and percentages of the predictive values of FOT indexes, as well as the severity of exacerbation.

RESULTS

We found that salivary SP-D levels were higher in asthmatic children than in healthy controls. In the asthmatic children, salivary SP-D levels correlated with the percentages of predicted differences in resistance between 5 Hz and 20 Hz (%R5-R20), which represented the resistance of peripheral airways, and with the severity of asthma exacerbation.

CONCLUSIONS

Salivary SP-D may reflect asthmatic inflammation in peripheral small airways and may be a useful marker for monitoring the degree of exacerbation in childhood asthma.

Prognostic impact of FOXF1 polymorphisms in gastric cancer patients

A recent genome-wide association study identified seven single-nucleotide polymorphisms (SNPs) in region 16q24, near the Forkhead box-F1 (FOXF1) gene, which confer susceptibility to esophageal adenocarcinoma. We examined whether these SNPs are associated with clinical outcomes in gastric cancer (GC) patients in Japan and the United States. A total of 362 patients were included in this study: 151 Japanese GC patients treated with first-line S1 plus CDDP (training cohort) and 211 GC patients from Los Angeles County (LAC; validation cohort). Genomic DNA was isolated from whole blood or tumor tissue and analyzed by PCR-based direct DNA sequencing. Cox proportional hazard regression analyses were used to assess relationships between FOXF1 SNPs and progression-free survival (PFS) and overall survival (OS). FOXF1 rs3950627 was significantly associated with survival in both the training and validation cohorts. Japanese patients with the C/C genotype had a longer PFS (median 8.2 vs 5.3 months, hazard ratio (HR) 1.44, P=0.037) and OS (median 16.4 vs 12.2 months, HR 1.44, P=0.043) compared to patients with any A allele. Similarly, LAC patients with the C/C genotype had improved OS (3.9 vs 2.3 years, HR 1.5, P=0.022). Subgroup analyses showed these associations were specific to male patients and primary tumor subsite. Our findings suggest that FOXF1 rs3950627 might be a promising prognostic marker in GC patients.

A genetic variant in Rassf1a predicts outcome in mCRC patients treated with cetuximab plus chemotherapy: results from FIRE-3 and JACCRO 05 and 06 trials

The Hippo pathway is involved in colorectal cancer (CRC) development and progression. The Hippo regulator Rassf1a is also involved in the Ras signaling cascade. In this work, we tested single nucleotide polymorphisms within Hippo components and their association with outcome in CRC patients treated with cetuximab. Two cohorts treated with cetuximab plus chemotherapy were evaluated (198 RAS wild-type (wt) patients treated with first-line FOLFIRI plus Cetuximab within the FIRE-3 trial and 67 Ras wt patients treated either with first-line mFOLFOX6 or SOX plus Cetuximab). In these two populations, Rassf1a rs2236947 was associated with overall survival, as patients with a CC genotype had significantly longer OS compared to those with CA or AA genotypes. This association was stronger in patients with left-side CRC [HR: 1.79 (1.01–3.14); P=0.044 and HR: 2.83 (1.14–7.03); P=0.025, for Fire 3 and JACCRO cohorts, respectively]. Rassf1a rs2236947 is a promising biomarker for patients treated with cetuximab plus chemotherapy.

Clinical relevance of EMT and stem-like gene expression in circulating tumor cells of metastatic colorectal cancer patients

Using approved methods, circulating tumor cells (CTCs) are only isolated from blood in 30%-50% of metastatic colorectal cancer (mCRC) patients. We previously validated a technique to isolate circulating tumor cells (CTCs) in a cohort of mCRC patients by combining immunomagnetic enrichment of EpCAM⁺/CD45^- cells with qRT-PCR amplification of CK20 and survivin expression. Here, we examined the prognostic utility of CTC epithelial-mesenchymal transition (EMT) and stem cell gene expression. An 8 ml blood sample was collected from 78 consecutive mCRC patients before treatment with investigational and standard chemotherapeutics. The mRNA expression of EMT (PI3Kα, Akt-2, Twist1) and stem cell (ALDH1) markers was measured. Associations between CTC gene expression and progression-free survival (PFS) and overall survival (OS) were determined using Cox regression models. Among patients without CK20 or survivin-expressing CTCs (n=17), 55% had expression of ALDH1, PI3Kα and/or Akt-2. Patients with positive CTC Akt-2 expression had a significantly shorter median PFS (3.0 versus 4.0 months) compared with those without CTC Akt-2 expression in univariable (hazard ratio (HR)=1.61; log-rank P=0.034) and multivariable analyses (HR=1.70; adjusted P=0.041). In univariable analysis, CTC ALDH1 expression was associated with shorter OS (10.0 versus 38.6 months; HR=2.04, P=0.021). Patients with CTCs expressing ALDH1, PI3Kα and/or Akt-2 had a significantly inferior PFS (3.0 versus 7.7 months; HR=1.88, P=0.015) and OS (10.0 versus 26.8+ months; HR=2.25, P=0.050) in univariable, but not multivariable, analysis.

CONCLUSIONS

CTC Akt-2 expression may serve as a clinically useful prognostic marker in mCRC patients and warrants further evaluation in prospective trials.

TRPV1, ASICs and P2X2/3 expressed in bone cells simultaneously regulate bone metabolic markers in ovariectomized mice

OBJECTIVES

Nociceptors are expressed at peripheral terminals of neurons. Recent studies have shown that TRPV1, a nociceptor, is expressed in bone tissue and regulates bone metabolism. We have demonstrated that a TRPV1 antagonist improved pain-like behavior in ovariectomized (OVX) mice. The aim of this study was to determine whether nociceptors, including TRPV1, acid-sensing ion channel (ASIC) and P2X2/3 are expressed in bone cells, and to examine the effects of nociceptor antagonists on bone metabolism.

METHODS

The expression of nociceptors in femoral bone tissue and cultured bone marrow cells in OVX and sham-operated mice were examined. The effects of nociceptor antagonists on the up-regulated expression of bone metabolic markers, Runx2, Osterix, osteocalcin and RANKL, were also examined.

RESULTS

TRPV1, ASIC 2 and 3, and P2X2 and 3, were expressed in bone tissue and bone marrow cells, and the expression levels of ASIC1 and 2, and P2X2 were significantly increased in OVX mice in comparison with those in sham mice. Treatment with nociceptor antagonists significantly inhibited the expression of bone metabolic markers in OVX mice.

CONCLUSION

An array of nociceptors, TRPV1, ASICs and P2X2/3, could simultaneously regulate not only increases in skeletal pain but also bone turnover in OVX mice.

Interleukin-6, interleukin-6 receptor gene variant, small-vessel disease and incident dementia

BACKGROUND AND PURPOSE

Mixed neurogenerative and vascular dementia has emerged as the leading cause of dementia in the elderly. Inflammation is implicated in atherosclerosis, cerebral small-vessel disease (SVD) as well as cognitive impairment. However, longitudinal data on the predictive value of circulating inflammatory markers including gene variants and magnetic resonance imaging (MRI) findings in incident dementia are scarce. It was investigated whether circulating interleukin-6 (IL-6), C-reactive protein (CRP) and gene variants increase dementia risk.

METHODS

In a cohort of Japanese participants with vascular risk factors in an observational study from 2001, the association between baseline IL-6, CRP levels, gene variants [interleukin-6 receptor (IL-6R), rs2228145; IL-6, rs2097677; CRP, rs3093059] and incident all-cause dementia was evaluated. Baseline MRI was used to determine SVD (lacuna, white matter hyperintensities) and atrophy (medial-temporal lobe atrophy, bicaudate ratio). Cox proportional hazards analyses were performed for predictors of dementia, adjusting for age, sex, apolipoprotein Eε4, education, cerebrovascular events, vascular risk factors and MRI findings.

RESULTS

Of 803 subjects (mean 67.0 ± 8.5 years, males 59%), during a mean of 7.5 ± 3.2 years follow-up, 60 incident dementia patients (Alzheimer's disease 31; vascular dementia 17; mixed-type six; other six) were diagnosed. In multivariable analyses adjusted for age, sex, cerebrovascular events, MRI findings and IL-6R variant (rs2228145), IL-6 levels (relative risk 1.68, P = 0.048) or highest tertile (relative risk 2.38, P = 0.031) for all-cause dementia remained significant. Although subjects with rs2228145 carrier had significantly higher IL-6 levels, a significant association between rs2228145 and dementia was not observed. Conversely, CRP and remaining gene variants were not associated with dementia.

CONCLUSIONS

The deleterious effect of higher IL-6 on dementia remains consistent irrespective of conventional risk factors, MRI findings and IL-6R variant.

Serum high-molecular-weight adiponectin level and incident dementia in patients with vascular risk factors

BACKGROUND AND PURPOSE

The involvement of metabolic factors in the development of dementia has received much attention. However, previous studies have yielded conflicting results regarding how blood adipocytokine level impacts cognitive decline and dementia. This study aimed to clarify whether serum high-molecular-weight (HMW) adiponectin level is related to incident dementia.

METHODS

Data were from 466 patients (mean age 67.8 years, male 57%)--who had normal cognitive function and received brain magnetic resonance imaging--from amongst the 1106 patients in the Osaka Follow-up Study for Carotid Atherosclerosis, Part 2, a prospective cohort study of cardiovascular events and dementia amongst patients with vascular risk factors enrolled between 2001 and 2009. Baseline HMW adiponectin levels were measured using frozen serum. Dementia occurrence was examined in June 2013.

RESULTS

Serum HMW adiponectin level was 4.33 ± 2.95 μg/ml; the levels were lower in men than in women and negatively correlated with body mass index. During the follow-up period (median 6.9 years), 47 patients had incident dementia including Alzheimer's disease dementia (27), vascular dementia (13), mixed dementia (four), other dementia (three). Risks of dementia in patients with high versus low HMW adiponectin levels were almost identical (P = 0.689). No association was found between adiponectin levels and Alzheimer's disease dementia or vascular dementia in the whole group or amongst men and women separately.

CONCLUSIONS

This study demonstrated that serum HMW adiponectin level has little association with future dementia. Determination of metabolic factors involved in dementia requires evaluation of other biomarkers or parameters.

Variations in genes regulating tumor-associated macrophages (TAMs) to predict outcomes of bevacizumab-based treatment in patients with metastatic colorectal cancer: results from TRIBE and FIRE3 trials

BACKGROUND

Tumor-associated macrophages (TAMs) with the M2-like phenotype are regulated by mainly NF-kB pathway including TBK1, which can influence tumor progression by secretion of proangiogenic factors such as vascular endothelial growth factor. The CCL2/CCR2 axis, histidine-rich glycoprotein (HRG), and placenta growth factor (PIGF) play a critical role in the polarization of M1/M2 phenotypes and the recruitment of TAMs to tumor microenvironment. We therefore hypothesized that variations in genes involved in regulating TAMs may predict clinical outcomes of bevacizumab treatment in patients with metastatic colorectal cancer (mCRC).

PATIENTS AND METHODS

We analyzed genomic DNA extracted from samples of patients receiving bevacizumab plus FOLFIRI as a first-line treatment using PCR-based direct sequencing. Twelve functional single-nucleotide polymorphisms in eight genes (CCL2, CCR2, HRG, PIGF, NFKB1, TBK1, CCL18, and IRF3) were tested for associations with clinical outcomes in a discovery cohort of 228 participants in TRIBE trial (NCT00719797), then validated in 248 KRAS exon2 (KRAS) wild-type participants in FIRE3 trial (NCT00433927). FIRE3-cetuximab cohort served as a negative control.

RESULTS

TBK1 rs7486100 was significantly associated with overall survival in 95 KRAS wild-type patients of TRIBE cohort in univariate analysis and had a strong trend in multivariable analysis; furthermore, the association of the T allele was observed for progression-free survival (PFS) in both univariate and multivariable analyses in FIRE3-bevacizumab but not cetuximab cohort. CCL2 rs4586, CCL18 rs14304, and IRF3 rs2304205 had univariate and multivariable correlations with PFS in KRAS mutant patients of the TRIBE cohort, whereas they had no correlations in KRAS wild-type patients of the TRIBE cohort. No association was seen in control cohort.

CONCLUSIONS

Our study demonstrates for the first time that variations in genes regulating TAMs-related functions are significantly associated with clinical outcomes in mCRC patients treated with bevacizumab-containing chemotherapy. These results also suggest that some TAM-related gene variations may predict outcomes of bevacizumab treatment in KRAS status-dependent manner.