Comparison of quantitative whole body PET parameters on [68Ga]Ga-PSMA-11 PET/CT using ordered Subset Expectation Maximization (OSEM) vs. bayesian penalized likelihood (BPL) reconstruction algorithms in men with metastatic castration-resistant prostate cancer.

BACKGROUND: PSMA PET/CT is a predictive and prognostic biomarker for determining response to [177Lu]Lu-PSMA-617 in patients with metastatic castration resistant prostate cancer (mCRPC). Thresholds defined to date may not be generalizable to newer image reconstruction algorithms. Bayesian penalized likelihood (BPL) reconstruction algorithm is a novel reconstruction algorithm that may improve contrast whilst preventing introduction of image noise. The aim of this study is to compare the quantitative parameters obtained using BPL and the Ordered Subset Expectation Maximization (OSEM) reconstruction algorithms. METHODS: Fifty consecutive patients with mCRPC who underwent [68Ga]Ga-PSMA-11 PET/CT using OSEM reconstruction to assess suitability for [177Lu]Lu-PSMA-617 therapy were selected. BPL algorithm was then used retrospectively to reconstruct the same PET raw data. Quantitative and volumetric measurements such as tumour standardised uptake value (SUV)max, SUVmean and Molecular Tumour Volume (MTV-PSMA) were calculated on both reconstruction methods. Results were compared (Bland-Altman, Pearson correlation coefficient) including subgroups with low and high-volume disease burdens (MTV-PSMA cut-off 40 mL). RESULTS: The SUVmax and SUVmean were higher, and MTV-PSMA was lower in the BPL reconstructed images compared to the OSEM group, with a mean difference of 8.4 (17.5%), 0.7 (8.2%) and - 21.5 mL (-3.4%), respectively. There was a strong correlation between the calculated SUVmax, SUVmean, and MTV-PSMA values in the OSEM and BPL reconstructed images (Pearson r values of 0.98, 0.99, and 1.0, respectively). No patients were reclassified from low to high volume disease or vice versa when switching from OSEM to BPL reconstruction. CONCLUSIONS: [68Ga]Ga-PSMA-11 PET/CT quantitative and volumetric parameters produced by BPL and OSEM reconstruction methods are strongly correlated. Differences are proportional and small for SUVmean, which is used as a predictive biomarker. Our study suggests that both reconstruction methods are acceptable without clinical impact on quantitative or volumetric findings. For longitudinal comparison, committing to the same reconstruction method would be preferred to ensure consistency.

Functional Lung Avoidance Planning Using Multicriteria Optimization.

PURPOSE: Functional lung avoidance (FLA) radiation therapy is an evolving field. The aim of FLA planning is to reduce dose to areas of functioning lung, with comparable target coverage and dose to organs at risk. Multicriteria optimization (MCO) is a planning tool that may assist with FLA planning. This study assessed the feasibility of using MCO to adapt radiation therapy plans to avoid functional regions of lung that were identified using a 68Ga-4D-V/Q positron emission tomography/computed tomography. METHODS AND MATERIALS: A prospective clinical trial U1111-1138-4421 was performed in which patients had a 68Ga-4D-V/Q positron emission tomography/computed tomography before radiation treatment. Of the 72 patients enrolled in this trial, 38 patients had stage III non-small cell lung cancer and were eligible for selection into this planning study. Functional lung target volumes HF lung (highly functioning lung) and F lung (functional lung) were defined using the ventilated and perfused lung. Using knowledge-based planning, a baseline anatomic plan was created, and then a functional adapted plan was generated using multicriteria optimization. The primary aim was to spare dose to HF lung. Using the MCO tools, a clinician selected the final FLA plan. Dose to functional lung, target volumes, organs at risk and measures of plan quality were compared using standard statistical methods. RESULTS: The HF lung volume was successfully spared in all patients. The F lung volume was successfully spared in 36 of the 38 patients. There were no clinically significant differences in dose to anatomically defined organs at risk. There were differences in the planning target volume near maximum and minimum doses. Across the entire population, there was a statistically significant reduction in the functional mean lung dose but not in the functional volume receiving 20 Gy. All trade-off decisions were made by the clinician. CONCLUSIONS: Using MCO for FLA was achievable but did result in changes to planning target volume coverage. A distinct advantage in using MCO was that all decisions regarding the cost and benefits of FLA could be made in real time.

Dose-Effect Relationship of Kidney Function After SABR for Primary Renal Cell Carcinoma.

PURPOSE: Stereotactic ablative body radiotherapy (SABR) is a novel option to treat primary renal cell carcinoma. However, a high radiation dose may be received by the treated kidney, which may affect its function posttreatment. This study investigates the dose-effect relationship of kidney SABR with posttreatment renal function. METHODS AND MATERIALS: This was a prespecified secondary endpoint of the multicenter FASTRACK II (Focal Ablative STereotactic RAdiotherapy for Cancers of the Kidney phase II) clinical trial (National Clinical Trial 02613819). Patients received either 26 Gy in a single fraction (SF) for tumors with a maximal diameter of 4 cm or less or 42 Gy in 3 fractions (multifraction [MF]) for larger tumors. To determine renal function change, 99mTc-dimercaptosuccinic acid (DMSA) single-photon emission computed tomography/computed tomography (SPECT/CT) scans were acquired, and the glomerular filtration rate was estimated at baseline, 12, and 24 months posttreatment. Imaging data sets were rigidly registered to the planning CT where kidneys were segmented to calculate dose-response curves. RESULTS: From 71 enrolled patients, 36 (51%) and 26 (37%) patients were included in this study based on availability of posttreatment data at 12 and 24 months, respectively. The ipsilateral kidney glomerular filtration rate decreased from baseline by 42% and 39% in the SF cohort and by 45% and 62% in the MF cohort, at 12 and 24 months, respectively (P < .03). The loss in renal function was 3.6%/Gy ± 0.8%/Gy and 4.5%/Gy ± 1.0%/Gy in the SF cohort and 1.7%/Gy ± 0.1%/Gy and 1.7%/Gy ± 0.2%/Gy in the MF cohort at 12 and 24 months, respectively. The major loss in renal function occurred in high-dose regions, where dose-response curves converged to a plateau. CONCLUSIONS: For the first time in a multicenter study, the dose-effect relationship at 12 and 24 months post-SABR treatment for primary renal cell carcinoma was quantified. Kidney function reduces linearly with dose up to 100 Gy BED3.

Quantitative calibration of Tb-161 SPECT/CT in view of personalised dosimetry assessment studies.

BACKGROUND: Terbium-161 (161Tb)-based radionuclide therapy poses an alternative to current Lutetium-177 (177Lu) approaches with the additional benefit of secondary Auger and conversion electron emissions capable of delivering high doses of localised damage to micro-metastases including single cells. Quantitative single-photon emission computed tomography, paired with computed tomography (SPECT/CT), enables quantitative measurement from post-therapy imaging. In view of dosimetry extrapolations, a Tb-161 sensitivity SPECT/CT camera calibration was performed using a method previously validated for 177Lu. METHODS: Serial imaging of a NEMA/IEC body phantom with Tb-161 was performed on SPECT/CT with low-energy high-resolution collimators employing a photopeak of 75 keV with a 20% width. Quantitative stability and recovery coefficients were investigated over a sequence of 19 scans with buffered 161Tb solution at total phantom activity ranging from 70 to 4990 MBq. RESULTS: Sphere recovery coefficients were 0.60 ± 0.05, 0.52 ± 0.07, 0.45 ± 0.07, 0.39 ± 0.07, 0.28 ± 0.08, and 0.20 ± 0.08 for spheres 37, 28, 22, 17, 13, and 10mm, respectively, when considered across all activity and scan durations with dual-energy window scatter correction. Whole-field reconstructed sensitivity was calculated as 1.42E-5 counts per decay. Qualitatively, images exhibited no visual artefacts and were comparable to 177Lu SPECT/CT. CONCLUSIONS: Quantitative SPECT/CT of 161Tb is feasible over a range of activities enabling dosimetry analogous to 177Lu whilst also producing suitable imaging for clinical review. This has been incorporated into a prospective trial of 161Tb-PSMA for men with metastatic prostate cancer.

Deep Learning Auto-Segmentation Network for Pediatric Computed Tomography Data Sets: Can We Extrapolate From Adults?

PURPOSE: Artificial intelligence (AI)-based auto-segmentation models hold promise for enhanced efficiency and consistency in organ contouring for adaptive radiation therapy and radiation therapy planning. However, their performance on pediatric computed tomography (CT) data and cross-scanner compatibility remain unclear. This study aimed to evaluate the performance of AI-based auto-segmentation models trained on adult CT data when applied to pediatric data sets and explore the improvement in performance gained by including pediatric training data. It also examined their ability to accurately segment CT data acquired from different scanners. METHODS AND MATERIALS: Using the nnU-Net framework, segmentation models were trained on data sets of adult, pediatric, and combined CT scans for 7 pelvic/thoracic organs. Each model was trained on 290 to 300 cases per category and organ. Training data sets included a combination of clinical data and several open repositories. The study incorporated a database of 459 pediatric (0-16 years) CT scans and 950 adults (>18 years), ensuring all scans had human expert ground-truth contours of the selected organs. Performance was evaluated based on Dice similarity coefficients (DSC) of the model-generated contours. RESULTS: AI models trained exclusively on adult data underperformed on pediatric data, especially for the 0 to 2 age group: mean DSC was below 0.5 for the bladder and spleen. The addition of pediatric training data demonstrated significant improvement for all age groups, achieving a mean DSC of above 0.85 for all organs in every age group. Larger organs like the liver and kidneys maintained consistent performance for all models across age groups. No significant difference emerged in the cross-scanner performance evaluation, suggesting robust cross-scanner generalization. CONCLUSIONS: For optimal segmentation across age groups, it is important to include pediatric data in the training of segmentation models. The successful cross-scanner generalization also supports the real-world clinical applicability of these AI models. This study emphasizes the significance of data set diversity in training robust AI systems for medical image interpretation tasks.

Administering [177Lu]Lu-PSMA-617 Prior to Radical Prostatectomy in Men with High-risk Localised Prostate Cancer (LuTectomy): A Single-centre, Single-arm, Phase 1/2 Study.

BACKGROUND: High-risk localised prostate cancer (HRCaP) has high rates of biochemical recurrence; [177Lu]Lu-PSMA-617 is effective in men with advanced prostate cancer. OBJECTIVE: To investigate the dosimetry, safety, and efficacy of upfront [177Lu]Lu-PSMA-617 in men with HRCaP prior to robotic radical prostatectomy (RP). DESIGN, SETTING, AND PARTICIPANTS: In this single-arm, phase I/II trial, we recruited men with HRCaP (any of prostate-specific antigen [PSA] >20 ng/ml, International Society of Urological Pathology (ISUP) grade group [GG] 3-5, and ≥cT2c), with high tumour uptake on [68Ga]Ga-PSMA-11 positron emission tomography/computed tomography (PSMA PET/CT), and scheduled for RP. INTERVENTION: Cohort A (n = 10) received one cycle and cohort B (n = 10) received two cycles of [177Lu]Lu-PSMA-617 (5 GBq) followed by surgery 6 weeks later. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS: The primary endpoint was tumour radiation absorbed dose. Adverse events (AEs; Common Terminology Criteria for Adverse Events (CTCAE) version 5.0), surgical safety (Clavien-Dindo), imaging, and biochemical responses were evaluated (ClinicalTrials.gov: NCT04430192). RESULTS AND LIMITATIONS: Between May 29, 2020 and April 28, 2022, 20 patients were enrolled. The median PSA was 18 ng/ml (interquartile range [IQR] 11-35), Eighteen (90%) had GG ≥3, and six (30%) had N1 disease. The median (IQR) highest tumour radiation absorbed dose after cycle 1 for all lesions was 35.5 Gy (19.5-50.1), with 19.6 Gy (11.3-48.4) delivered to the prostate. Five patients received radiation to lymph nodes. Nine (45%) patients achieved >50% PSA decline. The most common AEs related to [177Lu]Lu-PSMA-617 were grade 1 fatigue in eight (40%), nausea in seven (35%), dry mouth in six (30%), and thrombocytopenia in four (20%) patients. No grade 3/4 toxicities or Clavien 3-5 complications occurred. Limitations include small a sample size. CONCLUSIONS: In men with HRCaP and high prostate-specific membrane antigen (PSMA) expression, [177Lu]Lu-PSMA-617 delivered high levels of targeted radiation doses with few toxicities and without compromising surgical safety. Further studies of [177Lu]Lu-PSMA-617 in this population are worthwhile to determine whether meaningful long-term oncological benefits can be demonstrated. PATIENT SUMMARY: In this study, we demonstrate that up to two cycles of [177Lu]Lu-PSMA-617 given prior to radical prostatectomy in patients with high-risk localised prostate cancer are safe and deliver targeted doses of radiation to tumour-affected tissues. It is tolerated well with minimal treatment-related adverse events, and surgery is safe with a low rate of complications. Activity measured through PSA reduction, repeat PSMA PET/CT, and histological response is promising.

Feasibility of biology-guided radiotherapy for metastatic renal cell carcinoma driven by PSMA PET imaging.

Background: Biology-guided radiotherapy (BgRT) is a novel treatment where the detection of positron emission originating from a volume called the biological tracking zone (BTZ) initiates dose delivery. Prostate-specific membrane antigen (PSMA) positron emission tomography (PET) is a novel imaging technique that may improve patient selection for metastasis-directed therapy in renal cell carcinoma (RCC). This study aims to determine the feasibility of BgRT treatment for RCC. Material and methods: All consecutive patients that underwent PSMA PET/CT scan for RCC staging at our institution between 2014 and 2020 were retrospectively considered for inclusion. GTVs were contoured on the CT component of the PET/CT scan. The tumor-to-background ratio was quantified from the normalized standardized uptake value (nSUV), defined as the ratio between SUVmax inside the GTV and SUVmean inside the margin expansion. Tumors were classified suitable for BgRT if (1) nSUV was greater or equal to an nSUV threshold and (2) if the BTZ was free of any PET-avid region other than the tumor. Results: Out of this cohort of 83 patients, 47 had metastatic RCC and were included in this study. In total, 136 tumors were delineated, 1 to 22 tumors per patient, mostly in lung (40%). Using a margin expansion of 5 mm/10 mm/20 mm and nSUV threshold = 3, 66%/63%/41% of tumors were suitable for BgRT treatment. Uptake originating from another tumor, the kidney, or the liver was typically inside the BTZ in tumors judged unsuitable for BgRT. Conclusions: More than 60% of tumors were found to be suitable for BgRT in this cohort of patients with RCC. However, the proximity of PET-avid organs such as the liver or the kidney may affect BgRT delivery.

Comparison of dual-energy CT with positron emission tomography for lung perfusion imaging in patients with non-small cell lung cancer.

Objective.Functional lung avoidance (FLA) radiotherapy treatment aims to spare lung regions identified as functional from imaging. Perfusion contributes to lung function and can be measured from the determination of pulmonary blood volume (PBV). An advantageous alternative to the current determination of PBV from positron emission tomography (PET) may be from dual energy CT (DECT), due to shorter examination time and widespread availability. This study aims to determine the correlation between PBV determined from DECT and PET in the context of FLA radiotherapy.Approach.DECT and PET acquisitions at baseline of patients enrolled in the HI-FIVE clinical trial (ID: NCT03569072) were reviewed. Determination of PBV from PET imaging (PBVPET), from DECT imaging generated from a commercial software (Syngo.via, Siemens Healthineers, Forchheim, Germany) with its lowest (PBVsyngoR=1) and highest (PBVsyngoR=10) smoothing level parameter value (R), and from a two-material decomposition (TMD) method (PBVTMDL) with variable median filter kernel size (L) were compared. Deformable image registration between DECT images and the CT component of the PET/CT was applied to PBV maps before resampling to the PET resolution. The Spearman correlation coefficient (rs) between PBV determinations was calculated voxel-wise in lung subvolumes.Main results.Of this cohort of 19 patients, 17 had a DECT acquisition at baseline. PBV maps determined from the commercial software and the TMD method were very strongly correlated [rs(PBVsyngoR=1,PBVTMDL=1) = 0.94 ± 0.01 andrs(PBVsyngoR=10,PBVTMDL=9) = 0.94 ± 0.02].PBVPETwas strongly correlated withPBVTMDL[rs(PBVPET,PBVTMDL=28) = 0.67 ± 0.11]. Perfusion patterns differed along the posterior-anterior direction [rs(PBVPET,PBVTMDL=28) = 0.77 ± 0.13/0.57 ± 0.16 in the anterior/posterior region].Significance. A strong correlation between DECT and PET determination of PBV was observed. Streak and smoothing effects in DECT and gravitational artefacts and misregistration in PET reduced the correlation posteriorly.

Value of PET ECG gating in a cross-validation study of cardiac function assessment by PET/MR imaging.

BACKGROUND: This work investigated the impact of different cardiac gating methods on the assessment of cardiac function by FDG-PET in a cross-validation PET/MR study. METHODS AND RESULTS: MR- and PET-based left ventricular end-diastolic, end-systolic volumes, and ejection fraction (EDV, ESV, and EF) were delineated in 30 patients with a PET/MR examination. Cardiac PET imaging was performed using three ECG gating methods: fixed number of gates per beat (STD), STD with a beat acceptance window (STD-BR), and fixed gate duration (FW). High MR-PET correlations were found in all the values. ESVs correlated better than EDVs and EFs: Pearson's r coefficient [0.92, 0.92, 0.92] in ESV vs [0.75, 0.81, 0.80] in EDV and [0.79, 0.91, 0.87] in EF, for each method [STD, STD-BR, FW]. Biases with respect to MRI for all the evaluated PET methods were less than 13% in EDV, 5% in ESV, and 14% in EF, but with wide limits of agreements, in the range (59-68)% in EDV, (65-70)% in ESV, and (49-71)% in EF. STD showed the strongest disagreement, while there were no marked differences between STD-BR and FW. CONCLUSION: Based on these findings, PET- and MR-based cardiac function parameters were highly correlated but in substantial disagreement with variabilities introduced by the selected PET ECG gating method. The most significant differences were associated with the ECG gating method susceptible to highly irregular beats, while similar performance was observed in the methods using uniform adjustment of gates width per beat with the beat acceptance window, and fixed gate width along all the beats. Thus, strict quality controls of R peak detection are needed to minimize its impact on the function assessment.

Fast and Low-GPU-memory abdomen CT organ segmentation: The FLARE challenge.

Automatic segmentation of abdominal organs in CT scans plays an important role in clinical practice. However, most existing benchmarks and datasets only focus on segmentation accuracy, while the model efficiency and its accuracy on the testing cases from different medical centers have not been evaluated. To comprehensively benchmark abdominal organ segmentation methods, we organized the first Fast and Low GPU memory Abdominal oRgan sEgmentation (FLARE) challenge, where the segmentation methods were encouraged to achieve high accuracy on the testing cases from different medical centers, fast inference speed, and low GPU memory consumption, simultaneously. The winning method surpassed the existing state-of-the-art method, achieving a 19× faster inference speed and reducing the GPU memory consumption by 60% with comparable accuracy. We provide a summary of the top methods, make their code and Docker containers publicly available, and give practical suggestions on building accurate and efficient abdominal organ segmentation models. The FLARE challenge remains open for future submissions through a live platform for benchmarking further methodology developments at https://flare.grand-challenge.org/.

Radiation Dosimetry in 177Lu-PSMA-617 Therapy.

Radionuclide therapy using the small molecule PSMA bound to the beta-emitting radionuclide, Lutetium-177 (177Lu-PSMA) has demonstrated efficacy and survival benefit castrate resistant metastatic disease and represents a novel new line of therapy. Whilst dosimetry was critical for early development, it was not incorporated into either the TheraP or VISION randomized studies, highlighting the difficulty of adopting dosimetry in routine clinical practice. Accumulated clinical experience has also shown that the common (and generally low grade) toxicities such as nausea, xerostomia, and cytopenias are not readily predicted on the basis of dosimetry estimates. The majority of dosimetry and clinical literature deals with the radiopharmaceutical 177Lu-PSMA-617 which displays relatively consistent patterns of retention among normal tissues and high specificity for metastatic prostate cancer phenotypes. Population dosimetry incorporating estimates to the kidneys, salivary glands, and bone marrow have been widely reported the typical range of doses is becoming well established. There is growing interest on tumor dosimetry in 177Lu-PSMA-617 therapy as an overall modest side-effect profile from primary organ retention has been observed. A focus away from normal organ dosimetry to whole body tumor dosimetry may enable early prediction of treatment failure. Given the safety of 177Lu-PSMA there is also potential to escalate administered radioactivity to further improve outcomes. Importantly, the variability of uptake between individuals, both to tumor and normal organs, has also been highlighted which provides some rationale for the utility of personalized radiation analysis to optimize treatment based on potential toxicity thresholds or tumor control. Methods to perform dosimetry using serial post treatment imaging may incorporate planar, 3D SPECT, or hybrid datasets. Reliable measurements may be obtained through either method, however, continued developments in computational analysis are better suited to fully 3D imaging; particularly in conjunction with volumetric CT to assist with alignment and contouring. Dose analysis over sequential treatment cycles is vital to understand the radiobiology of these treatments which is unique compared to external beam therapy due to dose rate, fractionation scheme, and potential for intratumoral nonuniformity.

PET/MR Technology: Advancement and Challenges.

When this article was written, it coincided with the 11th anniversary of the installation of our PET/MR device in Munich. In fact, this was the first fully integrated device to be in clinical use. During this time, we have observed many interesting behaviors, to put it kindly. However, it is more critical that in this process, our understanding of the system also improved - including the advantages and limitations from a technical, logistical, and medical perspective. The last decade of PET/MRI research has certainly been characterized by most sites looking for a "key application." There were many ideas in this context and before and after the devices became available, some of which were based on the earlier work with integrating data from single devices. These involved validating classical PET methods with MRI (eg, perfusion or oncology diagnostics). More important, however, were the scenarios where intermodal synergies could be expected. In this review, we look back on this decade-long journey, at the challenges overcome and those still to come.

CT slice alignment to whole-body reference geometry by convolutional neural network.

Volumetric medical imaging lacks a standardised coordinate geometry which links image frame-of-reference to specific anatomical regions. This results in an inability to locate anatomy in medical images without visual assessment and precludes a variety of image analysis tasks which could benefit from a standardised, machine-readable coordinate system. In this work, a proposed geometric system that scales based on patient size is described and applied to a variety of cases in computed tomography imaging. Subsequently, a convolutional neural network is trained to associate axial slice CT image appearance with the standardised coordinate value along the patient superior-inferior axis. The trained neural network showed an accuracy of ± 12 mm in the ability to predict per-slice reference location and was relatively stable across all annotated regions ranging from brain to thighs. A version of the trained model along with scripts to perform network training in other applications are made available. Finally, a selection of potential use applications are illustrated including organ localisation, image registration initialisation, and scan length determination for auditing diagnostic reference levels.

Automated assessment of functional lung imaging with 68Ga-ventilation/perfusion PET/CT using iterative histogram analysis.

PURPOSE: Functional lung mapping from Ga68-ventilation/perfusion (V/Q) PET/CT, which has been shown to correlate with pulmonary function tests (PFTs), may be beneficial in a number of clinical applications where sparing regions of high lung function is of interest. Regions of clumping in the proximal airways in patients with airways disease can result in areas of focal intense activity and artefact in ventilation imaging. These artefacts may even shine through to subsequent perfusion images and create a challenge for quantitative analysis of PET imaging. We aimed to develop an automated algorithm that interprets the uptake histogram of PET images to calculate a peak uptake value more representative of the global lung volume. METHODS: Sixty-six patients recruited from a prospective clinical trial underwent both V/Q PET/CT imaging and PFT analysis before treatment. PET images were normalised using an iterative histogram analysis technique to account for tracer hotspots prior to the threshold-based delineation of varying values. Pearson's correlation between fractional lung function and PFT score was calculated for ventilation, perfusion, and matched imaging volumes at varying threshold values. RESULTS: For all functional imaging thresholds, only FEV1/FVC PFT yielded reasonable correlations to image-based functional volume. For ventilation, a range of 10-30% of adapted peak uptake value provided a reasonable threshold to define a volume that correlated with FEV1/FVC (r = 0.54-0.61). For perfusion imaging, a similar correlation was observed (r = 0.51-0.56) in the range of 20-60% adapted peak threshold. Matched volumes were closely linked to ventilation with a threshold range of 15-35% yielding a similar correlation (r = 0.55-0.58). CONCLUSIONS: Histogram normalisation may be implemented to determine the presence of tracer clumping hotspots in Ga-68 V/Q PET imaging allowing for automated delineation of functional lung and standardisation of functional volume reporting.

Evolution of late-stage metastatic melanoma is dominated by aneuploidy and whole genome doubling.

Although melanoma is initiated by acquisition of point mutations and limited focal copy number alterations in melanocytes-of-origin, the nature of genetic changes that characterise lethal metastatic disease is poorly understood. Here, we analyze the evolution of human melanoma progressing from early to late disease in 13 patients by sampling their tumours at multiple sites and times. Whole exome and genome sequencing data from 88 tumour samples reveals only limited gain of point mutations generally, with net mutational loss in some metastases. In contrast, melanoma evolution is dominated by whole genome doubling and large-scale aneuploidy, in which widespread loss of heterozygosity sculpts the burden of point mutations, neoantigens and structural variants even in treatment-naïve and primary cutaneous melanomas in some patients. These results imply that dysregulation of genomic integrity is a key driver of selective clonal advantage during melanoma progression.

Author Correction: Determination of RNA structural diversity and its role in HIV-1 RNA splicing.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Determination of RNA structural diversity and its role in HIV-1 RNA splicing.

Human immunodeficiency virus 1 (HIV-1) is a retrovirus with a ten-kilobase single-stranded RNA genome. HIV-1 must express all of its gene products from a single primary transcript, which undergoes alternative splicing to produce diverse protein products that include structural proteins and regulatory factors1,2. Despite the critical role of alternative splicing, the mechanisms that drive the choice of splice site are poorly understood. Synonymous RNA mutations that lead to severe defects in splicing and viral replication indicate the presence of unknown cis-regulatory elements3. Here we use dimethyl sulfate mutational profiling with sequencing (DMS-MaPseq) to investigate the structure of HIV-1 RNA in cells, and develop an algorithm that we name 'detection of RNA folding ensembles using expectation-maximization' (DREEM), which reveals the alternative conformations that are assumed by the same RNA sequence. Contrary to previous models that have analysed population averages4, our results reveal heterogeneous regions of RNA structure across the entire HIV-1 genome. In addition to confirming that in vitro characterized5 alternative structures for the HIV-1 Rev responsive element also exist in cells, we discover alternative conformations at critical splice sites that influence the ratio of transcript isoforms. Our simultaneous measurement of splicing and intracellular RNA structure provides evidence for the long-standing hypothesis6-8 that heterogeneity in RNA conformation regulates splice-site use and viral gene expression.

Technical Note: Rapid multiexponential curve fitting algorithm for voxel-based targeted radionuclide dosimetry.

BACKGROUND: Dosimetry in nuclear medicine often relies on estimating pharmacokinetics based on sparse temporal data. As analysis methods move toward image-based three-dimensional computation, it becomes important to interpolate and extrapolate these data without requiring manual intervention; that is, in a manner that is highly efficient and reproducible. Iterative least-squares solvers are poorly suited to this task because of the computational overhead and potential to optimize to local minima without applying tight constraints at the outset. METHODOLOGY: This work describes a fully analytical method for solving three-phase exponential time-activity curves based on three measured time points in a manner that may be readily employed by image-based dosimetry tools. The methodology uses a series of conditional statements and a piecewise approach for solving exponential slope directly through measured values in most instances. The proposed algorithm is tested against a purpose-designed iterative fitting technique and linear piecewise method followed by single exponential in a cohort of ten patients receiving 177 Lu-DOTA-Octreotate therapy. RESULTS: Tri-exponential time-integrated values are shown to be comparable to previously published methods with an average difference between organs when computed at the voxel level of 9.8 ± 14.2% and -3.6 ± 10.4% compared to iterative and interpolated methods, respectively. Of the three methods, the proposed tri-exponential algorithm was most consistent when regional time-integrated activity was evaluated at both voxel- and whole-organ levels. For whole-body SPECT imaging, it is possible to compute 3D time-integrated activity maps in <5 min processing time. Furthermore, the technique is able to predictably and reproducibly handle artefactual measurements due to noise or spatial misalignment over multiple image times. CONCLUSIONS: An efficient, analytical algorithm for solving multiphase exponential pharmacokinetics is reported. The method may be readily incorporated into voxel-dose routines by combining with widely available image registration and radiation transport tools.

Two of a kind: transmissible Schwann cell cancers in the endangered Tasmanian devil (Sarcophilus harrisii).

Devil facial tumour disease (DFTD) comprises two genetically distinct transmissible cancers (DFT1 and DFT2) endangering the survival of the Tasmanian devil (Sarcophilus harrisii) in the wild. DFT1 first arose from a cell of the Schwann cell lineage; however, the tissue-of-origin of the recently discovered DFT2 cancer is unknown. In this study, we compared the transcriptome and proteome of DFT2 tumours to DFT1 and normal Tasmanian devil tissues to determine the tissue-of-origin of the DFT2 cancer. Our findings demonstrate that DFT2 expresses a range of Schwann cell markers and exhibits expression patterns consistent with a similar origin to the DFT1 cancer. Furthermore, DFT2 cells express genes associated with the repair response to peripheral nerve damage. These findings suggest that devils may be predisposed to transmissible cancers of Schwann cell origin. The combined effect of factors such as frequent nerve damage from biting, Schwann cell plasticity and low genetic diversity may allow these cancers to develop on rare occasions. The emergence of two independent transmissible cancers from the same tissue in the Tasmanian devil presents an unprecedented opportunity to gain insight into cancer development, evolution and immune evasion in mammalian species.

Somatic Hypermutation of the YAP Oncogene in a Human Cutaneous Melanoma.

Melanoma is usually driven by mutations in BRAF or NRAS, which trigger hyperactivation of MAPK signaling. However, MAPK-targeted therapies are not sustainably effective in most patients. Accordingly, characterizing mechanisms that co-operatively drive melanoma progression is key to improving patient outcomes. One possible mechanism is the Hippo signaling pathway, which regulates cancer progression via its central oncoproteins YAP and TAZ, although is thought to be only rarely affected by direct mutation. As YAP hyperactivation occurs in uveal melanoma, we investigated this oncogene in cutaneous melanoma. YAP protein expression was elevated in most benign nevi and primary cutaneous melanomas but present at only very low levels in normal melanocytes. In patient-derived xenografts and melanoma cell lines, we observed variable reliance of cell viability on Hippo pathway signaling that was independent of TAZ activity and also of classical melanoma driver mutations such as BRAF and NRAS. Finally, in genotyping studies of melanoma, we observed the first ever hyperactivating YAP mutations in a human cancer, manifest as seven distinct missense point mutations that caused serine to alanine transpositions. Strikingly, these mutate four serine residues known to be targeted by the Hippo pathway and we show that they lead to hyperactivation of YAP. IMPLICATIONS: Our studies highlight the YAP oncoprotein as a potential therapeutic target in select subgroups of melanoma patients, although successful treatment with anti-YAP therapies will depend on identification of biomarkers additional to YAP protein expression.