Single cell transcriptomics reveals early photoreceptor states, cell-specific transcript isoforms, and cancer-predisposing features.

Human cone photoreceptors differ from rods and serve as the retinoblastoma cell-of-origin. Here, we used deep full-length single-cell RNA-sequencing to distinguish post-mitotic cone and rod developmental states and cone-specific features that contribute to retinoblastomagenesis. The analyses revealed early post-mitotic cone- and rod-directed populations characterized by higher THRB or NRL regulon activities, an immature photoreceptor precursor population with concurrent cone and rod gene and regulon expression, and distinct early and late cone and rod maturation states distinguished by maturation-associated declines in RAX regulon activity. Unexpectedly, both L/M cone and rod precursors co-expressed NRL and THRB RNAs, yet they differentially expressed functionally antagonistic NRL isoforms and prematurely terminated THRB transcripts. Early L/M cone precursors exhibited successive expression of lncRNAs along with MYCN, which composed the seventh most L/M-cone-specific regulon, and SYK, which contributed to the early cone precursors' proliferative response to RB1 loss. These findings reveal previously unrecognized photoreceptor precursor states and a role for early cone-precursor-intrinsic SYK expression in retinoblastoma initiation.

Quantitative noninvasive measurement of cerebrospinal fluid flow in shunted hydrocephalus.

OBJECTIVE: Standard MRI protocols lack a quantitative sequence that can be used to evaluate shunt-treated patients with a history of hydrocephalus. The objective of this study was to investigate the use of phase-contrast MRI (PC-MRI), a quantitative MR sequence, to measure CSF flow through the shunt and demonstrate PC-MRI as a useful adjunct in the clinical monitoring of shunt-treated patients. METHODS: The rapid (96 seconds) PC-MRI sequence was calibrated using a flow phantom with known flow rates ranging from 0 to 24 mL/hr. Following phantom calibration, 21 patients were scanned with the PC-MRI sequence. Multiple, successive proximal and distal measurements were gathered in 5 patients to test for measurement error in different portions of the shunt system and to determine intrapatient CSF flow variability. The study also includes the first in vivo validations of PC-MRI for CSF shunt flow by comparing phase-contrast-measured flow rate with CSF accumulation in a collection burette obtained in patients with externalized distal shunts. RESULTS: The PC-MRI sequence successfully measured CSF flow rates ranging from 6 to 54 mL/hr in 21 consecutive pediatric patients. Comparison of PC-MRI flow measurement and CSF volume collected in a bedside burette showed good agreement in a patient with an externalized distal shunt. Notably, the distal portion of the shunt demonstrated lower measurement error when compared with PC-MRI measurements acquired in the proximal catheter. CONCLUSIONS: The PC-MRI sequence provided accurate and reliable clinical measurements of CSF flow in shunt-treated patients. This work provides the necessary framework to include PC-MRI as an immediate addition to the clinical setting in the noninvasive evaluation of shunt function and in future clinical investigations of CSF physiology.

Imputation models and error analysis for phase contrast MR cerebral blood flow measurements.

Cerebral blood flow (CBF) supports brain metabolism. Diseases impair CBF, and pharmacological agents modulate CBF. Many techniques measure CBF, but phase contrast (PC) MR imaging through the four arteries supplying the brain is rapid and robust. However, technician error, patient motion, or tortuous vessels degrade quality of the measurements of the internal carotid (ICA) or vertebral (VA) arteries. We hypothesized that total CBF could be imputed from measurements in subsets of these 4 feeding vessels without excessive penalties in accuracy. We analyzed PC MR imaging from 129 patients, artificially excluded 1 or more vessels to simulate degraded imaging quality, and developed models of imputation for the missing data. Our models performed well when at least one ICA was measured, and resulted in R 2 values of 0.998-0.990, normalized root mean squared error values of 0.044-0.105, and intra-class correlation coefficient of 0.982-0.935. Thus, these models were comparable or superior to the test-retest variability in CBF measured by PC MR imaging. Our imputation models allow retrospective correction for corrupted blood vessel measurements when measuring CBF and guide prospective CBF acquisitions.

Quantitative Susceptibility Mapping: Translating an Investigative Research Tool into High Volume Clinical Diagnostic Imaging.

Quantitative susceptibility mapping (QSM) is an MRI-based technique for iron quantification of targeted tissue. QSM provides information relevant to clinicians in a broad range of diagnostic contexts, including sickle cell disease, inflammatory/demyelinating processes, and neoplasms. However, major MRI vendors do not offer QSM post-processing in a form ready for general use. This work describes a vendor-agnostic approach for scaling QSM analysis from a research technique to a routine diagnostic test. We provide the details needed to seamlessly integrate hardware, software, and clinical systems to provide QSM processing for a busy clinical radiology workflow. This approach can be generalized to other advanced MRI acquisitions and analyses with proven diagnostic utility, yet without crucial MR vendor support.

Effects of B1+ Heterogeneity on Spin Echo-Based Liver Iron Estimates.

BACKGROUND: Liver iron concentration (LIC) measured by MRI has become the clinical reference standard for managing iron overload in chronically transfused patients. Transverse relaxivity (R2 or R2* ) measurements are converted to LIC units using empirically derived calibration curves. HYPOTHESIS: That flip angle (FA) error due to B1+ spatial heterogeneity causes significant LIC quantitation error. B1+ scale (b1 , [FAactual /FAspecified ]) variation is a major problem at 3 T which could reduce the accuracy of transverse relaxivity measurements. STUDY TYPE: Prospective. POPULATION: Forty-seven subjects with chronic transfusional iron overload undergoing clinically indicated LIC assessment. FIELD STRENGTH/SEQUENCE: 5 T/3 T dual-repetition time B1+ mapping sequence ASSESSMENT: We quantified the average/standard deviation b1 in the right and left lobes of the liver from B1+ maps acquired at 1.5 T and 3 T. The impact of b1 variation on spin echo LIC estimates was determined using a Monte Carlo model. STATISTICAL TESTS: Mean, median, and standard deviation in whole liver and right and left lobes; two-sided t-test between whole-liver b1 means. RESULTS: Average b1 within the liver was 99.3% ± 12.3% at 1.5 T versus 69.6% ± 14.6% at 3 T and was independent of iron burden (P < 0.05). Monte Carlo simulations demonstrated that b1 systematically increased R2 estimates at lower LIC (<~25 mg/g at 1.5 T, <~15 mg/g at 3 T) but flattened or even inverted the R2 -LIC relationship at higher LIC (≥~25 mg/g to 1.5 T, ≥~15 mg/g to 3 T); changes in the R2 -LIC relationship were symmetric with respect to over and under excitation and were similar at 1.5 T and 3 T (for the same R2 value). The R2* -LIC relationship was independent of b1 . CONCLUSION: Spin echo R2 measurement of LIC at 3 T is error-prone without correction for b1 errors. The impact of b1 error on current 1.5 T spin echo-based techniques for LIC quantification is large enough to introduce measurable intersubject variability but the in vivo effect size needs a dedicated validation study. TECHNICAL EFFICACY STAGE: 2.

Improving CPMG liver iron estimates with a T 1 -corrected proton density estimator.

PURPOSE: CPMG spin echo acquisitions are attractive for diagnosing and monitoring liver iron concentration in iron overload disorders due to their time efficiency and potential to reveal unique information about tissue iron distribution. Clinical adoption remains low due to the insensitivity of CPMG-based R 2 estimates to liver iron concentration (LIC) when common fitting techniques are applied. In this work, we demonstrate that the inclusion of a proton density estimator (PDE) derived from the CPMG acquisition increase the sensitivity of CPMG R 2 estimates to LIC in both simulated and in-vivo human data. THEORY AND METHODS: CPMG R 2 acquisitions from 50 clinically indicated MRI studies in patients with iron overload were analyzed with and without PDE constraints. Liver regions of interest were fit to monoexpontial and nonexponential signal decay equations. LIC by R 2 ∗ served as the reference standard. The observed calibration between CPMG R 2 values and LIC were compared to results predicted from a previously validated Monte Carlo model. RESULTS: The sensitivity of CPMG-derived R 2 triples when a proton density constraint is applied. When compared with R 2 ∗ -LIC estimates, both monoexponential and nonexponential models were unbiased but demonstrated broad 95% confidence intervals particularly for LIC values below 12 mg/g. Absolute error did not increase with LIC. CONCLUSION: A proton density constraint can increase the sensitivity of CPMG-based models to iron. CPMG acquisitions are time-efficient and could potentially improve the dynamic range of single spin echo techniques as well as providing insight into tissue iron distribution.

Significance of crinoid preservation: Clare Shale Formation (Upper Carboniferous), Fisherstreet Bay, Doolin, County Clare, Ireland.

Some fossils, such as crinoid stems, are not widely appreciated by collectors and researchers, yet can provide unique data regarding taphonomy and palaeoecology. A long crinoid pluricolumnal showing a distinctive pattern of preservation was collected from the Clare Shale Formation (Upper Carboniferous) at Fisherstreet Bay, Doolin, County Clare, western Ireland. The specimen is partly disarticulated and represents the mesistele to mesistele/dististele transition; attachment was by unbranched long, slender radices; pluricolumnal heteromorphic; fragments of pluricolumnal are of multiples of a unit length. This specimen, cladid? sp. indet., slumped to the seafloor after death and started to disarticulate as ligaments rotted. By reference to the broken stick model, the pattern of disarticulation suggests that the noditaxis of the heteromorphic stem was N212.

Ultra-short echo time images quantify high liver iron.

PURPOSE: 1.5T gradient echo-based R2∗ estimates are standard-of-care for assessing liver iron concentration (LIC). Despite growing popularity of 3T, echo time (TE) limitations prevent 3T liver iron quantitation in the upper half of the clinical range (LIC ⪆20 mg/g). In this work, a 3D radial pulse sequence was assessed to double the dynamic range of 3T LIC estimates. THEORY AND METHODS: The minimum TE limits the dynamic range of pulse sequences to estimate R2∗. 23 chronically-transfused human volunteers were imaged with 1.5T Cartesian gradient echo (1.5T-GRE), 3T Cartesian gradient echo (3T-GRE), and 3T ultrashort TE radial (3T-UTE) pulse sequences; minimum TEs were 0.96, 0.76, and 0.19 ms, respectively. R2∗ was estimated with an exponential signal model, normalized to 1.5T equivalents, and converted to LIC. Bland-Altman analysis compared 3T-based estimates to 1.5T-GRE. RESULTS: LIC by 3T-GRE was unbiased versus 1.5T-GRE for LIC ≤ 25 mg/g (sd = 9.6%); 3T-GRE failed to quantify LIC > 25 mg/g. At high iron loads, 3T-UTE was unbiased (sd = 14.5%) compared to 1.5T-GRE. Further, 3T-UTE estimated LIC up to 50 mg/g, exceeding 1.5T-GRE limits. CONCLUSION: 3T-UTE imaging can reliably estimate high liver iron burdens. In conjunction with 3T-GRE, 3T-UTE allows clinical LIC estimation across a wide range of liver iron loads. Magn Reson Med 79:1579-1585, 2018. © 2017 International Society for Magnetic Resonance in Medicine.

Diffusion-relaxation correlation spectroscopic imaging: A multidimensional approach for probing microstructure.

PURPOSE: To propose and evaluate a novel multidimensional approach for imaging subvoxel tissue compartments called Diffusion-Relaxation Correlation Spectroscopic Imaging. THEORY AND METHODS: Multiexponential modeling of MR diffusion or relaxation data is commonly used to infer the many different microscopic tissue compartments that contribute signal to macroscopic MR imaging voxels. However, multiexponential estimation is known to be difficult and ill-posed. Observing that this ill-posedness is theoretically reduced in higher dimensions, diffusion-relaxation correlation spectroscopic imaging uses a novel multidimensional imaging experiment that jointly encodes diffusion and relaxation information, and then uses a novel constrained reconstruction technique to generate a multidimensional diffusion-relaxation correlation spectrum for every voxel. The peaks of the multidimensional spectrum are expected to correspond to the distinct tissue microenvironments that are present within each macroscopic imaging voxel. RESULTS: Using numerical simulations, experiment data from a custom-built phantom, and experiment data from a mouse model of traumatic spinal cord injury, diffusion-relaxation correlation spectroscopic imaging is demonstrated to provide substantially better multicompartment resolving power compared to conventional diffusion- and relaxation-based methods. CONCLUSION: The diffusion-relaxation correlation spectroscopic imaging approach provides powerful new capabilities for resolving the different components of multicompartment tissue models, and can be leveraged to significantly expand the insights provided by MRI in studies of tissue microstructure. Magn Reson Med 78:2236-2249, 2017. © 2017 International Society for Magnetic Resonance in Medicine.

Relaxivity-iron calibration in hepatic iron overload: Predictions of a Monte Carlo model.

PURPOSE: R2* (1/T2*) and single echo R2 (1/T2) have been calibrated to liver iron concentration (LIC) in patients with thalassemia and transfusion-dependent sickle cell disease at 1.5T. The R2*-LIC relationship is linear, whereas that of R2 is curvilinear. However, the increasing popularity of high-field scanners requires generalizing these relationships to higher field strengths. In this study, we tested the hypothesis that numerical simulation can accurately determine the field dependence of iron-mediated transverse relaxation rates. METHODS: We previously replicated the calibration curves between R2 and R2* and iron at 1.5T using Monte Carlo models incorporating realistic liver structure, iron deposit susceptibility, and proton mobility. In this paper, we extend our model to predict relaxivity-iron calibrations at higher field strengths. Predictions were validated by measuring R2 and R2* at 1.5T and 3T in six ß-thalassemia major patients. RESULTS: Predicted R2* increased twofold at 3T from 1.5T, whereas R2 increased by a factor of 1.47. Patient data exhibited a coefficient of variation of 3.6% and 7.2%, respectively, to the best-fit simulated data. Simulations over the range 0.25T-7T showed R2* increasing linearly with field strength, whereas R2 exhibited a concave-downward relationship. CONCLUSION: A model-based approach predicts alterations in relaxivity-iron calibrations with field strength without repeating imaging studies. The model may generalize to alternative pulse sequences and tissue iron distribution.