Gene mutation spectrum and genotype-phenotype correlation in a cohort of Chinese osteogenesis imperfecta patients revealed by targeted next generation sequencing

The achievement of more accurate diagnosis would greatly benefit the management of patients with osteogenesis imperfecta (OI). In this study, we present the largest OI sample in China as screened by next generation sequencing. In particular, we successfully identified 81 variants, which included 45 novel variants. We further did a genotype-phenotype analysis, which helps make a better understanding of OI.

INTRODUCTION

This study aims to reveal the gene mutation spectrum and the genotype-phenotype relationship among Chinese OI patients by next generation sequencing (NGS).

METHODS

We developed a NGS-based panel for targeted sequencing of all exons of 14 genes related to OI, and performed diagnostic gene sequencing for a cohort of 103 Chinese OI patients from 101 unrelated families. Mutations identified by NGS were further confirmed by Sanger sequencing and co-segregation analysis.

RESULTS

Of the 103 patients from 101 unrelated OI families, we identified 79 mutations, including 43 novel mutations (11 frameshift, 17 missense, 5 nonsense, 9 splice site, and 1 chromosome translocation) in 90 patients (87.4%). Mutations in genes encoding type I collagen, COL1A1 (n = 37), and COL1A2 (n = 29) accounts for 73.3% of all molecularly diagnosed patients, followed by IFITM5 (n = 9, 10%), SERPINF1 (n = 4, 4.4%), WNT1 (n = 4, 4.4%), FKBP10 (n = 3, 3.3%), TMEM38B (n = 3, 3.3%), and PLOD2 (n = 1, 1.1%). This corresponds to 75 autosomal dominant inherited (AD) OI patients and 15 autosomal recessive (AR) inherited patients. Compared with AD inherited OI patients, AR inherited patients had lower bone mineral density (BMD) at spine (P = 0.05) and less frequent blue sclera (P = 0.001). Patients with type I collagen qualitative defects had lower femoral neck BMD Z-score (P = 0.034) and were shorter compared with patients with type I collagen quantitative defects (P = 0.022).

CONCLUSION

We revealed the gene mutation spectrum in Chinese OI patients, and novel mutations identified here expanded the mutation catalog and genotype and phenotype relationships among OI patients.

Association between bone mineral density, muscle strength, and vitamin D status in patients with myasthenia gravis: a cross-sectional study

Myasthenia gravis (MG) patients had low proximal hip BMD, which could be explained by reduced muscle strength, elevated bone resorption markers, vitamin D deficiency, and increased PTH levels in those with MG compared to controls.

INTRODUCTION

Muscle strength is closely correlated with bone mineral density (BMD) and vitamin D status. Here, we evaluated muscle strength, BMD, and vitamin D status in a large sample of Chinese patients with MG.

METHODS

In this cross-sectional survey, 86 patients with MG without glucocorticoid treatment and 86 healthy controls were included. Serum levels of 25-hydroxyvitamin D [25OHD], parathyroid hormone (PTH), bone turnover markers (BTMs), and BMD were measured and compared between the two groups. Grip strength and one-leg standing time (OLST) were also assessed in MG patients.

RESULTS

Low grip strength and short OLST were found in 11 (12.8%) and 12 (14.0%) MG patients, respectively. There were 3 (3.5%) MG patients with low bone mass for chronological age. Serum beta C-terminal telopeptide and PTH levels were higher (p < 0.001 and p = 0.001, respectively), and BMD at the femoral neck and trochanter were lower in MG patients (p < 0.001 and p < 0.001, respectively) compared to healthy controls. In patients with MG, grip strength was positively correlated with BMD. Serum 25OHD levels were lower in MG patients than in healthy controls (17.36 ± 6.64 vs. 22.11 ± 7.28 ng/ml, p < 0.001).

CONCLUSION

Grip strength was positively correlated with BMD in Chinese patients with MG. MG patients tended to have low proximal hip BMD, which may partially be explained by reduced muscle strength, vitamin D deficiency, increased PTH levels, and elevated bone resorption markers compared to controls.

Modeling the Blood-Brain Barrier in a 3D triple co-culture microfluidic system

The need for a blood-brain barrier (BBB) model that accurately mimics the physiological characteristics of the in-vivo situation is well-recognized by researchers in academia and industry. However, there is currently no in-vitro model allowing studies of neuronal growth and/or function influenced by factors from the blood that cross through the BBB. Therefore, we established a 3D triple co-culture microfluidic system using human umbilical vein endothelial cells (HUVEC) together with primary rat astrocytes and neurons. Immunostaining confirmed the successful triple co-culture system consisting of an intact BBB with tight intercellular junctions in the endothelial monolayer. The BBB selective permeability was determined by a fluorescent-based assay using dextrans of different molecular weights. Finally, neuron functionality was demonstrated by calcium imaging.

Abstract P1-06-07: Clinical and molecular relevance of intra-tumor genetic heterogeneity in breast cancer: Integrative analysis of data from The Cancer Genome Atlas

Background: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. Emerging evidence has indicated that the extent of genetic heterogeneity may serve as a clinically useful biomarker. While several studies have suggested the prognostic value of ITH in several cancer types, the clinical significance of genetic ITH and molecular portraits that correlated with different ITH levels were poorly understood in breast cancer. The establishment of algorithms estimating genetic ITH based on sequencing of bulk tumor DNA offered us an opportunity to explore the clinical implication of ITH in large breast cancer cohorts and, for the first time, to use integrative genomic analyses to reveal molecular portraits related to intra-tumor genetic heterogeneity.

Methods: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. Mutant-allele tumor heterogeneity (MATH) values were calculated from whole-exome sequencing data. We used integers nearest to the tertiles of the MATH values as cutoff points to divide the patients into three groups nearly equal in size. The association between MATH value and clinical characteristics was evaluated, followed by survival analyses in these different MATH groups. We then compared the rates of total non-silent somatic mutations among the different MATH groups, and further determined the mutations independently associated with high MATH by logistic regression adjusting for T classification and clinical subtypes. Similar methods, superadding somatic copy number alteration (SCNA) burden in logistic model, were used to evaluate SCNA events that were significantly associated with high MATH level. Gene enrichment between the high and rest MATH groups was analyzed using Gene Set Enrichment Analysis.

Results: The patients were divided into low (MATH value lower than 33), intermediate (MATH between 33 and 46) and high (MATH higher than 46) MATH groups. High T stage, African American race, and triple-negative or basal-like subtype were associated with a higher MATH level (all P&lt;0.001). In hormone receptor-positive and human epidermal growth factor receptor-negative patients, the high MATH group showed a tendency toward a worse overall survival (P=0.052); however, while in triple-negative breast cancer, both high and low MATH indicated a worse outcome (P=0.032). Furthermore, the TP53 mutation rate increased as MATH was elevated (P&lt;0.001), whereas CDH1 mutations were correlated with a lower level of MATH (P=0.002). Several focal and arm-level SCNA events were more common in the high MATH group, including Chr8q24 with only the MYC gene in the “peak” region. Similarly, high MATH was associated with gene set enrichment related to the MYC pathway and proliferation.

Conclusion: Our study extended the knowledge concerning the clinical role of ITH in breast cancer, especially the distinct pattern of prognostic values in different clinical subtypes, which may help promote the clinical utilization of genetic ITH. Our attempt at exploring the molecular features related to ITH might provide clues for the source and consequences of ITH, inspiring subsequent experiments investigating the laws underling tumor heterogeneity.

Citation Format: Ma D, Jiang Y-Z, Liu X-Y, Liu Y-R, Yu K-D, Shao Z-M. Clinical and molecular relevance of intra-tumor genetic heterogeneity in breast cancer: Integrative analysis of data from The Cancer Genome Atlas [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 P1-06-07.

Compacting a Single Flow Diverter versus Overlapping Flow Diverters for Intracranial Aneurysms: A Computational Study

BACKGROUND AND PURPOSE

Locally compacting the mesh of a flow diverter by a dynamic push-pull technique can accelerate intracranial aneurysm healing. We asked how this deployment strategy compares with overlapping 2 flow diverters for aneurysmal flow reduction.

MATERIALS AND METHODS

Using a high-fidelity virtual stent placement method, we simulated 3 flow-diverter strategies (single noncompacted, 2 overlapped, and single compacted) in 3 aneurysms (fusiform, large saccular, and medium saccular). Computational fluid dynamics analysis provided posttreatment hemodynamic parameters, including time-averaged inflow rate, aneurysm-averaged velocity, wall shear stress, total absolute circulation, and turnover time. We examined the relationship between the achieved degree of compaction and aneurysm orifice area.

RESULTS

Flow-diverter compaction resulted in a compaction coverage of 57%, 47%, and 22% over the orifice of the fusiform, large, and medium saccular aneurysm, respectively. Compaction coverage increased linearly with orifice area. In the fusiform aneurysm, the single compacted flow diverter accomplished more aneurysmal flow reduction than the other 2 strategies, as indicated by all 5 hemodynamic parameters. In the 2 saccular aneurysms, the overlapped flow diverters achieved the most flow reduction, followed by the single compacted and the noncompacted flow diverter.

CONCLUSIONS

Compacting a single flow diverter can outperform overlapping 2 flow diverters in aneurysmal flow reduction, provided that the compaction produces a mesh denser than 2 overlapped flow diverters and this denser mesh covers a sufficient portion of the aneurysm orifice area, for which we suggest a minimum of 50%. This strategy is most effective for aneurysms with large orifices, especially fusiform aneurysms.

Structural predictions for curli amyloid fibril subunits CsgA and CsgB

CsgA are the building blocks of curli fibrils.

MR Fingerprinting of Adult Brain Tumors: Initial Experience

BACKGROUND AND PURPOSE

MR fingerprinting allows rapid simultaneous quantification of T1 and T2 relaxation times. This study assessed the utility of MR fingerprinting in differentiating common types of adult intra-axial brain tumors.

MATERIALS AND METHODS

MR fingerprinting acquisition was performed in 31 patients with untreated intra-axial brain tumors: 17 glioblastomas, 6 World Health Organization grade II lower grade gliomas, and 8 metastases. T1, T2 of the solid tumor, immediate peritumoral white matter, and contralateral white matter were summarized within each ROI. Statistical comparisons on mean, SD, skewness, and kurtosis were performed by using the univariate Wilcoxon rank sum test across various tumor types. Bonferroni correction was used to correct for multiple-comparison testing. Multivariable logistic regression analysis was performed for discrimination between glioblastomas and metastases, and area under the receiver operator curve was calculated.

RESULTS

Mean T2 values could differentiate solid tumor regions of lower grade gliomas from metastases (mean, 172 ± 53 ms, and 105 ± 27 ms, respectively; P = .004, significant after Bonferroni correction). The mean T1 of peritumoral white matter surrounding lower grade gliomas differed from peritumoral white matter around glioblastomas (mean, 1066 ± 218 ms, and 1578 ± 331 ms, respectively; P = .004, significant after Bonferroni correction). Logistic regression analysis revealed that the mean T2 of solid tumor offered the best separation between glioblastomas and metastases with an area under the curve of 0.86 (95% CI, 0.69-1.00; P < .0001).

CONCLUSIONS

MR fingerprinting allows rapid simultaneous T1 and T2 measurement in brain tumors and surrounding tissues. MR fingerprinting-based relaxometry can identify quantitative differences between solid tumor regions of lower grade gliomas and metastases and between peritumoral regions of glioblastomas and lower grade gliomas.

Development of an opto-electronic fiber device with multiple nano-probes

We present the fabrication and characterization of an opto-electronic fiber device which can allow for both electromechanical functionality and optical waveguiding capability. The air holes of a photonic crystal fiber are selectively sealed and then pumped with molten metal under pressure. The metal filled holes act as electrodes to which individual carbon nanotubes (CNT) are attached precisely by a laser-welding technique or a focused ion beam assisted pick-and-bond technique. The optical modal profile and the group velocity dispersion of the fabricated device are studied both numerically and experimentally. We also present preliminary experimental proof showing the feasibility of electric actuation of a pair of nanotubes by applying up to 40 V potential difference between the filled electrodes. Furthermore, numerical simulations are carried out which agree with the experimentally observed displacement of the CNT upon electric actuation. The unique aspect of our device is that it provides optical waveguiding and electromechanical nano-probing capability in a single package. Such combined functionality can potentially enable simultaneous electrical and optical manipulation and interrogation at the nanoscale.

Conditioned medium from neural stem cells inhibits glioma cell growth

Malignant glioma is one of the most common brain tumors in the central nervous system. Although the significant progress has been made in recent years, the mortality is still high and 5-year survival rate is still very low. One of the leading causes to the high mortality for glioma patients is metastasis and invasion. An efficient method to control the tumor metastasis is a promising way to treat the glioma. Previous reports indicated that neural stem cells (NSCs) were served as a delivery vector to the anti-glioma therapy. Here, we used the conditioned medium from rat NSCs (NSC-CM) to culture the human glioblastoma cell lines. We found that NSC-CM could inhibit the glioma cell growth, invasion and migration in vitro and attenuate the tumor growth in vivo. Furthermore, this anti-glioma effect was mediated by the inactivation of mitogen activated protein kinase (MAPK) pathway. Above all, this study provided the direct evidence to put forward a simple and efficient method in the inhibition of glioma cells/tumor growth, potentially advancing the anti-glioma therapy.

Clinical application of whole-genome low-coverage next-generation sequencing to detect and characterize balanced chromosomal translocations

Individuals carrying balanced translocations have a high risk of birth defects, recurrent spontaneous abortions and infertility. Thus, the detection and characterization of balanced translocations is important to reveal the genetic background of the carriers and to provide proper genetic counseling. Next-generation sequencing (NGS), which has great advantages over other methods such as karyotyping and fluorescence in situ hybridization (FISH), has been used to detect disease-associated breakpoints. Herein, to evaluate the application of this technology to detect balanced translocations in the clinic, we performed a parental study for prenatal cases with unbalanced translocations. Eight candidate families with potential balanced translocations were investigated using two strategies in parallel, low-coverage whole-genome sequencing (WGS) followed-up by Sanger sequencing and G-banding karyotype coupled with FISH. G-banding analysis revealed three balanced translocations, and FISH detected two cryptic submicroscopic balanced translocations. Consistently, WGS detected five balanced translocations and mapped all the breakpoints by Sanger sequencing. Analysis of the breakpoints revealed that six genes were disrupted in the four apparently healthy carriers. In summary, our result suggested low-coverage WGS can detect balanced translocations reliably and can map breakpoints precisely compared with conventional procedures. WGS may replace cytogenetic methods in the diagnosis of balanced translocation carriers in the clinic.

Single-agent capecitabine as maintenance therapy after induction of XELOX (or FOLFOX) in first-line treatment of metastatic colorectal cancer: randomized clinical trial of efficacy and safety

BACKGROUND

The optimal strategy of maintenance therapy for patients with mCRC is controversial. This study was to evaluate the efficacy and safety of maintenance therapy with capecitabine versus observation following inductive chemotherapy in patients with metastatic colorectal cancer.

PATIENTS AND METHODS

In this randomized, open-label, multicenter, phase III trial, patients who received 18-24 weeks of induction chemotherapy with XELOX or FOLFOX and achieved disease control were randomly assigned centrally (1:1) to receive maintenance therapy of capecitabine or only observation until disease progression. The primary end point was progression-free survival (PFS) from randomization; the secondary end points included overall survival (OS), PFS from induction treatment (PFS2) and safety. Analyses were done by intention to treat. This trial is registered with ClinicalTrials.gov, number NCT02027363.

RESULTS

Between 30 July 2010 and 15 September 2013, 274 patients were enrolled in the study from 11 sites in China and randomly assigned to maintenance group (n = 136) or observation group (n = 138). Clinicopathological characteristics were balanced in two groups. The median follow-up time from randomization was 29.0 months [interquartile range (IQR) 21-36 months]. The primary end point of PFS was statistically significantly longer in capecitabine maintenance group than in observation group {6.43 [95% confidence interval (CI) 5.26-7.71] versus 3.43 (2.83-4.16) months, HR 0.54 (0.42-0.70), P < 0.001}. The median OS of capecitabine maintenance group was longer than that of observation group, but not statistically significant [25.63 (22.46-27.80) versus 23.30 (19.68-26.92) months; HR 0.85 (0.64-1.11), P = 0.2247]. Similar safety profiles were observed in both arms. The most common grade 3 or 4 toxicities in capecitabine maintenance group versus observation group were neutropenia, hand-foot syndrome, and mucositis.

CONCLUSIONS

Maintenance therapy with a single agent of capecitabine can be considered an appropriate option following the induction of XELOX or FOLFOX in mCRC patients with acceptable toxicities.

CLINICAL TRIALS NUMBER

NCT02027363.

Abstract P2-07-03: Nomograms to estimate long-term overall survival and breast cancer-specific survival of patients with luminal breast cancer

Purpose

Luminal breast cancer (estrogen receptor [ER] and/or progesterone receptor [PR] positive) represents approximately two-thirds of all breast cancer. This type of cancer constitutes a group of highly heterogeneous diseases with a sustained high risk of late recurrence. In this study, we aimed to develop comprehensive and practical nomograms for the first time to better estimate the long-term survival of luminal breast cancer. Thus, those patients with high risk of late recurrence and poor prognosis could be screened out and individualized treatments can be applied.

Methods

Patients with luminal breast cancer diagnosed between 1990 and 2006 were retrieved from the Surveillance, Epidemiology, and End Results (SEER) database, and randomly divided into the training (n=87,867) and validation (n=88,215) cohorts. The inclusion criteria we used to identify eligible patients were as follows: female; aged 18 to 79 years old at diagnosis; known time of diagnosis from January 1, 1990, to December 31, 2006; unilateral breast cancer; breast cancer as the first and only cancer diagnosis; diagnosis not obtained from a death certificate or autopsy; surgical treatment with either mastectomy or breast-conserving surgery; pathologic confirmation of invasive carcinoma; AJCC stages I-III; histological grade I-III and known ER and PR statuses. Patients with inflammatory breast cancer or Paget's disease and lack of data on the above inclusion criteria were also excluded. Univariate and multivariate survival analyses were applied to identify prognostic factors for overall survival (OS). The cumulative incidence function (CIF) and a competing-risks model were used to estimate the probability of breast cancer-specific survival (BCSS) and death from other causes. We integrated significant prognostic factors to build nomograms, and subjected the nomograms to bootstrap internal validation and external validation.

Results

We screened 176,082 luminal breast cancer cases. The mean age at diagnosis was 57.5 years, and mean survival time was 107.4 months. By the end of the last follow-up, 36,911 (21.0%) patients had died, including 17,855 (10.1%) died from breast cancer and 19,056 (10.8%) from other causes. The 5- and 10-year probabilities of overall death were 0.089 and 0.202, respectively. The 5- and 10-year probabilities of breast cancer specific-mortality (BCSM) were 0.053 and 0.112, respectively. Independent prognostic factors for both OS and BCSS were integrated to construct the nomograms, including age at diagnosis, race, tumor size, histology, grade, positive lymph nodes, ER/PR status and radiation. The calibration curves for the probabilities of 5- and 10-year OS and BCSS showed excellent agreement between the nomogram prediction and actual observation. The C-indexes of the nomograms were high in both internal validation (0.732 for OS and 0.800 for BCSS) and external validation (0.731 for OS and 0.794 for BCSS).

Conclusion

We established and validated nomograms that accurately predict OS and BCSS of luminal breast cancer based on a large, population-based cohort with long-term follow-up. The nomograms can identify patients with higher risk of late overall mortality and BCSM, helping physicians in facilitating individualized treatment.

Citation Format: Sun W, Jiang Y-Z, Liu Y-R, Ma D, Shao Z-M. Nomograms to estimate long-term overall survival and breast cancer-specific survival of patients with luminal breast cancer. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P2-07-03.