Citations

GPR15 expression is promoted by Ahr in an evolutionarily conserved manner via cooperation with Foxp3 but inhibited by RORγt.

e19013 Background: Mutation profiling to assess for potentially druggable mutations in NSCLC is being offered at an increasing number of cancer centers throughout North America and internationally. Although data continue to accumulate for the potential value of mutation testing in designing chemotherapeutic regimens, the treatment impact of obtaining information beyond assessment of EGFR and ALK status remains unclear. How best to obtain and clinically utilize these data, including information from exome and whole genome sequencing, also remains unclear. Methods: Patients were reviewed electronically in a multidisciplinary conference regarding indications for testing and results of mutation profiling from various methods, including the mass-spec based LungCarta test, targeted NexGen sequencing, exome, and whole genome sequencing. Outcomes of the multidisciplinary review were communicated back to treating physicians. Results: Mutation testing was performed on 200 patients using a variety of approaches. The majority (>150) were surgically resected stage I and II tumors. Mutations in at least 1 major cancer driver gene, including EGFR, KRAS, MET, BRAF and PIK3CA, were found in 47% of all patients tested. EGFR mutations were present in 14.8% of patients tested, KRAS 21.3%, BRAF 2.6%, PIK3CA 3.2%, and MET 4.5%. A total of 8 patients underwent either exome or whole genome sequencing. A limited number of patients (<10) had mutation results that impacted treatment decisions from this cohort. Conclusions: Mutation profiling can influence treatment decisions in NSCLC, but at a low frequency. The role of exome and or whole genome sequencing for patients with NSCLC is evolving and remains undefined.

Background Low tube potential-high tube current computed tomography (CT) imaging allows reduction in iodine-based contrast dose and may extend the benefit of routine contrast-enhanced CT exams to patients at risk of nephrotoxicity. Purpose To determine the ability of an iodine contrast reduction algorithm to maintain diagnostic image quality for contrast-enhanced abdominal CT. Material and Methods CT exams with iodine contrast reduction were prescribed for patients at risk for renal dysfunction. The iodine contrast reduction algorithm combines weight-based contrast volume reduction with patient width-based low tube potential selection and bolus-tracking. Control exams with routine iodine dose were selected based on weight, width, and scan protocol. Three radiologists evaluated image quality and diagnostic confidence using a 4-point scale (<2 acceptable). Another radiologist assessed contrast reduction indications and measured portal vein and liver contrast-to-noise ratios. Results Forty-six contrast reduction algorithm and control exams were compared (mean creatinine 1.6 vs. 1.2 mg/dL, P ≤ 0.0001). Thirty-nine contrast reduction patients had an eGFR <60 mL/min/1.73m 2 and 15 had single or transplanted kidney. Mean iodine contrast dose was lower in the contrast reduction group (20.9 vs. 39.4 g/mL, P < 0.0001). Diagnostic confidence was rated as acceptable in 95% (131/138) of contrast reduction and 100% of control exams (1.18–1.28 vs. 1.02–1.13, respectively; P > 0.06). Liver attenuation and contrast-to-noise ratio (CNR) were similar ( P = 0.08), but portal vein attenuation and CNR were lower with contrast-reduction (mean 176 vs. 198 HU, P = 0.02; 13 vs. 16, P = 0.0002). Conclusion This size-based contrast reduction algorithm using low kV and bolus tracking reduced iodine contrast dose by 50%, while achieving acceptable image quality in 95% of exams.

PurposeFiltering measured projections with a particular convolutional kernel is an essential step in analytic reconstruction of computed tomography (CT) images. A tradeoff between noise and spatial resolution exists for different choices of reconstruction kernel. In a clinical setting, this often requires producing multiple images reconstructed with different kernels for a single CT exam, which increases the burden of computation, networking, archival, and reading. We address this problem by training a deep convolutional neural network (CNN) to synthesize multiple input images into a single output image which exhibits low noise while also preserving features in images reconstructed with the sharpest kernels.MethodsA CNN architecture consisting of repeated blocks of residual units containing a total of 20 convolutional layers was used to combine features. The CNN inputs consisted of two images produced with different reconstruction kernels, one smooth and one sharp, which were stacked in the channel dimension. The network was trained using supervised learning with both full‐dose and simulated quarter‐dose abdominal CT images. After training, the performance was evaluated using a reserved set of full‐dose scans that were not used for network optimization. Noise reduction performance was measured by comparing root mean square (RMS) measurements in uniform regions. Spatial resolution was compared using line profiles of anatomic features.ResultsFor the regions tested, the synthetic images feature noise levels slightly below those of the smooth input images, while maintaining the resolution of anatomic details found in the sharp input images.ConclusionsA deep CNN can be used combine features from CT images reconstructed with different kernels to produce a single synthesized image series that exhibits both low noise and high spatial resolution. This approach has implications for improving image quality, reducing radiation dose, and simplifying the clinical workflow for CT imaging.

PurposeTo evaluate the quantitative accuracy and dose efficiency of simultaneous imaging of two contrast agents using dual‐energy computed tomography (DECT), two imaging tasks each representing one potential clinical application were investigated in a phantom study: biphasic liver imaging with iodine and gadolinium, and small bowel imaging with iodine and bismuth.MethodsTo separate and quantify mixtures of two contrast agents using a single DECT scan, mixed iodine and gadolinium samples were prepared with the contrast enhancement values corresponding to the late arterial (iodine) and the portal‐venous (gadolinium) phase for biphasic liver imaging. Mixed iodine and bismuth samples were prepared mimicking the arterial (iodine) and the enteric (bismuth) enhancement for small bowel imaging. For comparison to the reference condition of performing two single‐energy CT (SECT) scans, contrast samples were prepared separately to mimic separate scans in the arterial/venous phase and arterial/enteric enhancement. Samples were placed in a 35 cm wide water tank and scanned using a third‐generation dual‐source DECT scanner with three tube potential pairs: 80/Sn150, 90/Sn150, and 100/Sn150 kV, all with default dose partitioning between two x‐ray beams to acquire DECT data. The same scanner operated in a single‐energy mode acquired SECT data (120 kV). Total radiation dose (CTDIvol) was matched for the single‐scan DECT and the two‐scan SECT protocols. The DECT protocol was followed by a generic image‐based three‐material decomposition method to determine the material‐specific images, based on which concentrations of each basis material were quantified and noise levels were measured. To compare with the SECT images directly acquired with the SECT protocol, the concentration values in each contrast‐specific image were converted to CT numbers at 120 kV (i.e., virtual SECT (vSECT) images). The noise level and noise power spectra differences between the SECT and vSECT images were compared to evaluate the dose efficiency of the single‐scan DECT protocol. The impact of dose partitioning in the DECT protocol on quantitative dual‐contrast imaging performance was also studied.ResultsFor each imaging task, contrast materials were accurately quantified against the nominal concentrations using the DECT data with strong correlation (R2 ≥ 0.98 for both imaging tasks). Compared to the SECT protocol, the DECT protocol was not dose efficient. With the optimal x‐ray tube potential pair 80/Sn150 kV, the noise level in vSECT images increased by 401%/488% (arterial/portal‐venous) for the biphasic liver imaging task and by 10%/41% (arterial/enteric) for the small bowel imaging task compared to that in SECT images. The corresponding radiation dose increase is 2410%/3357% for the biphasic liver imaging task and 21%/99% for the small bowel imaging task, respectively, to achieve the same noise as that in SECT images. This could be improved by adjusting the dose partitioning in DECT.ConclusionsDECT can be used to simultaneously separate and quantify two contrast materials. However, compared to a two‐scan SECT protocol, much higher radiation dose is needed in a single‐scan DECT protocol to achieve the same image noise, especially for tasks involving the dual contrast of iodine and gadolinium.

Abstract DNA methylation at cytosine position 5 (5mC) is a genetic modification that regulates gene expression and is critical for cancer initiation and development. The methylcytosine dioxygenase TET2 participates in active DNA demethylation by converting 5mC to 5-hydroxymethylcytosine (5hmC) and its subsequent intermediates thereby regulating gene expression. TET2 gene is frequently mutated in hematological disorders, including 15-25% of myelodysplastic syndrome (MDS) cases. Loss of TET2 function leads to DNA hypermethylation and subsequent dysregulated gene expression in hematopoietic stem cells, and has been considered as an initial step of myeloid malignant transformation including MDS and acute myeloid leukemia (AML). While enzymatic activity of TET2 is well studied, little is known about post-translational modifications (PTMs) that regulate its activity in hematopoietic cells. Lysine acetylation, one of the most crucial PTMs, occurs in a variety of proteins and modulates protein-protein or protein-nucleic acids interactions. Here, we first observed that ectopic expression of histone acetyltransferase EP300 or CREB binding protein (CBP) increased the endogenous TET2 acetylation in 293T cells. Mass spectrometry analysis of TET2 identified several conserved acetylated lysine residues located on the exterior surface of its catalytic domain (CD), which is predicted to be essential for the interaction of TET2 with DNA. Modeling of TET2/DNA interaction using x-ray crystal structure (PDB code: 4NM6) indicates acetylated TET2 interferes with DNA binding thereby impairing the catalytic activity of the enzyme. Like other acetylated proteins, TET2 modification is reversible, since ectopic expression of the protein deacetylase Sirtuin1 (SIRT1) significantly decreases acetylation of TET2. A domain mapping analysis revealed that SIRT1 preferentially interacts with TET2 CD, further supporting the regulatory role of SIRT1 on TET2. To explore the role of SIRT1 mediated deacetylaion of TET2 in more physiological condition, SIRT1 knockdown (KD) MDS-L cells as well as SIRT1 knockout (KO) murine hematopoietic c-kit+ cells were used. In MDS-L cells derived from a MDS patient, SIRT1 KD promoted hyperacetylation of endogenous TET2 which is associated with 50% decrease in 5hmC levels compared to control (p=0.03, n=3). Similarly, SIRT1 KO murine c-Kit+ cells showed TET2 hyperacetylation and 62% decrease in 5hmC compared to wildtype (WT) counterpart (p=0.009, n=5). Phenotypically, the transforming ability of SIRT1 shRNA transduced MDS-L cells was evaluated in vitro through serial replating assay. In contrast to first plating which showed no difference between two groups, the number of colonies derived from SIRT1 KD cells was 2.39 fold higher than that from the control shRNA transduced group after two rounds of replating (p=0.0002, n=3). Importantly, we tested the in-vivo effect of SIRT1 KD on MDS-L cells engrafted in immunodeficient NSGS mice. SIRT1 KD significantly enhanced MDS-L cell engraftment compared to control shRNA (50±5% of human CD45+ cells in SIRT1 KD group vs. 19±4% human CD45+ cells in control group, p=0.003, n=6). Interestingly, increased transformation capacity of SIRT1 KD MDS-L cells was associated with decreased expression of TET2 regulated tumor suppressor genes. For example, expression levels of Mtss1 and Dusp6 were significantly decreased in SIRT1 KD MDS-L cells compared to control shRNA counterpart (Mtss1, 49±5% decrease compared to control, p=0.005; Dusp6, 25±2% decrease compared to control, p=0.01). Similar results were observed in SIRT1 KO cells. The validation of physical binding of TET2 to its targets is ongoing. Moreover, the effect of an SIRT1 allosteric activator-SRT1720 in MDS-L cells is similar to that of Vitamin C, a known TET2 activator. Specifically, SRT1720 significantly increased Mtss1 expression in MDSL cells (p=0.0005, n=3), indicating that SIRT1 agonist may lead to activation of TET2 downstream tumor suppressor genes. In summary, our data demonstrate that TET2 activity can be functionally modified by acetylation and may be enhanced in MDS patients that do not harbor loss-of-function mutations through the SIRT1 mediated deacetylation. These results support further exploration of molecular mechanisms inducing TET2 acetylation, and evaluation of SIRT1 activation as a potential therapeutic approach in MDS. Disclosures No relevant conflicts of interest to declare.