CRISPR PERSIST-On enables heritable and fine-tunable human gene activation

Current technologies for upregulation of endogenous genes use targeted artificial transcriptional activators but stable gene activation requires persistent expression of these synthetic factors. Although general "hit-and-run" strategies exist for inducing long-term silencing of endogenous genes using targeted artificial transcriptional repressors, to our knowledge no equivalent approach for gene activation has been described to date. Here we show stable gene activation can be achieved by harnessing endogenous transcription factors ( EndoTF s) that are normally expressed in human cells. Specifically, EndoTFs can be recruited to activate endogenous human genes of interest by using CRISPR-based gene editing to introduce EndoTF DNA binding motifs into a target gene promoter. This Precision Editing of Regulatory Sequences to Induce Stable Transcription-On ( PERSIST-On ) approach results in stable long-term gene activation, which we show is durable for at least five months. Using a high-throughput CRISPR prime editing pooled screening method, we also show that the magnitude of gene activation can be finely tuned either by using binding sites for different EndoTF or by introducing specific mutations within such sites. Our results delineate a generalizable framework for using PERSIST-On to induce heritable and fine-tunable gene activation in a hit-and-run fashion, thereby enabling a wide range of research and therapeutic applications that require long-term upregulation of a target gene.

MOSAIC enables in situ saturation mutagenesis of genes and CRISPR prime editing guide RNA optimization in human cells

CRISPR prime editing offers unprecedented versatility and precision for the installation of genetic edits in situ . Here we describe the development and characterization of the Multiplexing Of Site-specific Alterations for In situ Characterization ( MOSAIC ) method, which leverages a non-viral PCR-based prime editing method to enable rapid installation of thousands of defined edits in pooled fashion. We show that MOSAIC can be applied to perform in situ saturation mutagenesis screens of: (1) the BCR-ABL1 fusion gene, successfully identifying known and potentially new imatinib drug-resistance variants; and (2) the IRF1 untranslated region (UTR), re-confirming non-coding regulatory elements involved in transcriptional initiation. Furthermore, we deployed MOSAIC to enable high-throughput, pooled screening of hundreds of systematically designed prime editing guide RNA ( pegRNA ) constructs for a large series of different genomic loci. This rapid screening of >18,000 pegRNA designs identified optimized pegRNAs for 89 different genomic target modifications and revealed the lack of simple predictive rules for pegRNA design, reinforcing the need for experimental optimization now greatly simplified and enabled by MOSAIC. We envision that MOSAIC will accelerate and facilitate the application of CRISPR prime editing for a wide range of high-throughput screens in human and other cell systems.

Parieto-Occipital Injury on Diffusion MRI Correlates with Poor Neurologic Outcome following Cardiac Arrest

BACKGROUND AND PURPOSE

MR imaging of the brain provides unbiased neuroanatomic evaluation of brain injury and is useful for neurologic prognostication following cardiac arrest. Regional analysis of diffusion imaging may provide additional prognostic value and help reveal the neuroanatomic underpinnings of coma recovery. The purpose of this study was to evaluate global, regional, and voxelwise differences in diffusion-weighted MR imaging signal in patients in a coma after cardiac arrest.

MATERIALS AND METHODS

We retrospectively analyzed diffusion MR imaging data from 81 subjects who were comatose for >48 hours following cardiac arrest. Poor outcome was defined as the inability to follow simple commands at any point during hospitalization. ADC differences between groups were evaluated across the whole brain, locally by using voxelwise analysis and regionally by using ROI-based principal component analysis.

RESULTS

Subjects with poor outcome had more severe brain injury as measured by lower average whole-brain ADC (740 [SD, 102] × 10-6 mm2/s versus 833 [SD, 23] × 10-6 mm2/s, P < .001) and larger average volumes of tissue with ADC below 650 × 10-6 mms/s (464 [SD, 469] mL versus 62 [SD, 51] mL, P < .001). Voxelwise analysis showed lower ADC in the bilateral parieto-occipital areas and perirolandic cortices for the poor outcome group. ROI-based principal component analysis showed an association between lower ADC in parieto-occipital regions and poor outcome.

CONCLUSIONS

Brain injury affecting the parieto-occipital region measured with quantitative ADC analysis was associated with poor outcomes after cardiac arrest. These results suggest that injury to specific brain regions may influence coma recovery.

Sensory Over-responsivity and Aberrant Plasticity in Cerebellar Cortex in a Mouse Model of Syndromic Autism

Background

Patients with autism spectrum disorder often show altered responses to sensory stimuli as well as motor deficits, including an impairment of delay eyeblink conditioning, which involves integration of sensory signals in the cerebellum. Here, we identify abnormalities in parallel fiber (PF) and climbing fiber (CF) signaling in the mouse cerebellar cortex that may contribute to these pathologies.

Methods

We used a mouse model for the human 15q11-13 duplication (patDp/+) and studied responses to sensory stimuli in Purkinje cells from awake mice using two-photon imaging of GCaMP6f signals. Moreover, we examined synaptic transmission and plasticity using in vitro electrophysiological, immunohistochemical, and confocal microscopic techniques.

Results

We found that spontaneous and sensory-evoked CF-calcium transients are enhanced in patDp/+ Purkinje cells, and aversive movements are more severe across sensory modalities. We observed increased expression of the synaptic organizer NRXN1 at CF synapses and ectopic spread of these synapses to fine dendrites. CF-excitatory postsynaptic currents recorded from Purkinje cells are enlarged in patDp/+ mice, while responses to PF stimulation are reduced. Confocal measurements show reduced PF+CF-evoked spine calcium transients, a key trigger for PF long-term depression, one of several plasticity types required for eyeblink conditioning learning. Long-term depression is impaired in patDp/+ mice but is rescued on pharmacological enhancement of calcium signaling.

Conclusions

Our findings suggest that this genetic abnormality causes a pathological inflation of CF signaling, possibly resulting from enhanced NRXN1 expression, with consequences for the representation of sensory stimuli by the CF input and for PF synaptic organization and plasticity.

Malignant Glomus Tumor of the Kidney: A Case Report and Review of the Literature

Introduction/Objective

Glomus tumors are rare neoplasms arising from the glomus body which is a specialized arteriovenous anastomosis that has a role in temperature regulation of the skin. They account for less than 2% of soft tissue tumors and typically manifest as painful nodules in the extremities, most commonly in the subungual region of the fingers and dermis of the wrist, forearm, and foot. They rarely arise in visceral organs as they lack glomus bodies. There are rare case reports of benign glomus tumors arising in the kidney, and malignant renal glomus tumors are exceedingly rare.

Methods/Case Report

We present a case of a 32-year-old man who was found to have a right renal mass incidentally after being involved in a motor vehicle accident. Computed tomography of the abdomen revealed a 5.3 cm enhancing mass in the posterior aspect of the inferior pole of the right kidney. Histological examination revealed a solid neoplasm composed of a pleomorphic population of cells with densely eosinophilic to pale cytoplasm, centrally located round to oval nuclei with fine nuclear chromatin and relatively inconspicuous nucleoli. Prominent lymphovascular invasion and 1 mitotic figure per 10 high power fields were also present. Areas composed of necrosis, sclerosis, hemosiderin deposition and calcification were identified. Immunohistochemical stains revealed the neoplastic cells to be positive for CD34, vimentin, smooth muscle actin, caldesmon, with focal reticulin staining around the tumor cells. Cells were negative for desmin, high and low molecular weight cytokeratins, synaptophysin, chromogranin, PAX8, and GATA3. The morphology and immunoprofile of the mass are consistent with the diagnosis of glomus tumor.

Results (if a Case Study enter NA)

NA

Conclusion

Although very rare, the presence of prominent vascular invasion, increased mitotic activity as well as necrosis are consistent with malignant behavior and support the classification as a malignant glomus tumor.

PrimeDesign software for rapid and simplified design of prime editing guide RNAs

Prime editing (PE) is a versatile genome editing technology, but design of the required guide RNAs is more complex than for standard CRISPR-based nucleases or base editors. Here we describe PrimeDesign, a user-friendly, end-to-end web application and command-line tool for the design of PE experiments. PrimeDesign can be used for single and combination editing applications, as well as genome-wide and saturation mutagenesis screens. Using PrimeDesign, we construct PrimeVar, a comprehensive and searchable database that includes candidate prime editing guide RNA (pegRNA) and nicking sgRNA (ngRNA) combinations for installing or correcting >68,500 pathogenic human genetic variants from the ClinVar database. Finally, we use PrimeDesign to design pegRNAs/ngRNAs to install a variety of human pathogenic variants in human cells.

Utility of 18F-fluoroestradiol (18F-FES) PET/CT imaging as a pharmacodynamic marker in patients with refractory estrogen receptor-positive solid tumors receiving Z-endoxifen therapy

BACKGROUND

Z-endoxifen is the most potent of the metabolites of tamoxifen, and has the potential to be more effective than tamoxifen because it bypasses potential drug resistance mechanisms attributable to patient variability in the expression of the hepatic microsomal enzyme CYP2D6. ¹⁸F-FES is a positron emission tomography (PET) imaging agent which selectively binds to estrogen receptor alpha (ER-α) and has been used for non-invasive in vivo assessment of ER activity in tumors. This study utilizes ¹⁸F-FES PET imaging as a pharmacodynamic biomarker in patients with ER+ tumors treated with Z-endoxifen.

METHODS

Fifteen patients were recruited from a parent therapeutic trial of Z-endoxifen and underwent imaging with ¹⁸F-FES PET at baseline. Eight had positive lesions on the baseline scan and underwent follow-up imaging with ¹⁸F-FES 1-5 days post administration of Z-endoxifen.

RESULTS

Statistically significant changes (p = 0.0078) in standard uptake value (SUV)-Max were observed between the baseline and follow-up scans as early as 1 day post drug administration.

CONCLUSION

F-FES PET imaging could serve as a pharmacodynamic biomarker for patients treated with ER-directed therapy.

Creutzfeldt-Jakob disease with mixed transcortical aphasia: insights into echolalia

Aphasia is a common manifestation of Creutzfeldt-Jakob disease (CJD), and investigation of the linguistic disorders of CJD patients may provide insights into the neurobiological mechanisms of language and aphasia. We report an autopsy-confirmed case of CJD in which the presenting symptom was change in language abilities. The patient ultimately evidenced mixed transcortical aphasia (MTA) with echolalia. Disruption of frontal-subcortical circuits with environmental dependency accounts for the symptoms in MTA, including intact repetition and echolalia. Observation in this patient and a review of the literature suggest that frontal-subcortical circuit dysfunction may contribute to the syndrome of echolalia. This hypothesis offers an alternative explanation to "isolation" of the speech area as the cause of MTA.

Distinct long-term neurocognitive outcomes after equipotent sevoflurane or isoflurane anaesthesia in immature rats

BACKGROUND

Many anaesthetics when given to young animals cause cell death and learning deficits that persist until much later in life. Recent attempts to compare the relative safety or toxicity between different agents have not adequately controlled for the relative dose of anaesthetic given, thereby making direct comparisons difficult.

METHODS

Isoflurane or sevoflurane were given at 1 minimum alveolar concentration (MAC) for 4 h to postnatal day 7 (P7) rat pups. Beginning at P75 these animals underwent fear conditioning and at P83 Morris water maze testing to assess working memory, short-term memory and early long-term memory using delays of 1 min, 1 h, and 4 h.

RESULTS

No difference between groups was seen in fear conditioning experiments. Morris water maze learning was equivalent between groups, and no difference was seen in working memory. Sevoflurane-treated animals had a deficit in early long-term memory, and isoflurane-treated animals had a deficit in both short-term and early long-term memory.

CONCLUSIONS

Both isoflurane and sevoflurane delivered at 1 MAC for 4 h to immature rats caused a deficit in long-term memory. Isoflurane also caused a deficit in short-term memory. Isoflurane might be more detrimental than sevoflurane in very young animals.

SU-E-T-19: Fitting a Multiple Source Photon Model for Monte Carlo Treatment Plan Verification

PURPOSE

To assess and reduce the difficulty of fitting a multiple source photon model for monte carlo treatment plan verification.

METHODS

The EGS4 user code MCSIM, from Fox Chase Cancer Center, was chosen for its support of a multiple source photon model, of which the point and secondary (extrafocal) photon sources were utilized. A described method of fitting the secondary source to in-air output factors was implemented. Additionally, a method to fit the point source to a single large field dose distribution was explored. The point source fitter utilizes a database of pre-simulated mono-energetic fanlines to build distributions from arbitrary spectra. Perturbations are made to fanline spectra to reduce the errors along them. In this study the energy spectrum for each fanline has been limited to the log-normal distribution, which reduces the number of parameters for each to two.

RESULTS

It was found that one spectral parameter could be set to a constant for all fanlines and the other restricted to linearity with respect to off-axis position. The model matched the outputs and distributions in non-superficial areas to within 2% for 6MV and 15MV Varian iX field sizes between 4 and 40 cm. Various types of treatment plans were then successfully verified, including 3D, VMAT, IMRT, and an iPlan Monte Carlo stereotactic lung to within 3% (tumor dose).

CONCLUSION

With such tools it is practical for a non-research physicist to fit a two source photon model for the purpose of monte carlo treatment plan verification. The only commissioning data needed are in-air output factors, a single large field dose distribution, and the usual machine parameters provided by LINAC vendors for clinical second check programs. Even when only photons are simulated and spectra are greatly simplified it is possible to achieve acceptable results for non-superficial tumors. Furthermore, this is achieved without proprietary machine specifications.

Quality of life in advanced non-small cell lung cancer patients receiving first-line gefitinib monotherapy

9614

Background: Gefitinib is a potential first-line treatment option for patients with advanced non-small cell lung cancer (NSCLC), especially for patients with activating mutations in the EGFR gene. However, little is known about patient-reported health-related quality of life (HRQOL) in this patient population. The aims of this study were to explore the prognostic values of baseline HRQOL for time-to-treatment failure (TTF), as well as the predictors of repeatedly measured posttreatment HRQOL, in advanced NSCLC patients receiving first-line gefitinib. Methods: A total of 106 chemonaive patients with advanced NSCLC were enrolled in a phase II trial. Gefitinib was given at a dose of 250 mg/d. HRQOL was assessed monthly with the EuroQoL instrument (EQ-5D) and the Lung Cancer Symptom Scale (LCSS) questionnaire. Baseline HRQOL and clinical/molecular predictors of TTF were jointly examined by multiple Cox's proportional hazards model. The associations between the clinical/molecular factors and repeatedly measured posttreatment HRQOL were analyzed by fitting marginal linear regression model using the generalized estimating equations (GEE) method. Results: In this prospective study, HRQOL data were obtained from 94 patients. Baseline EQ-5D index (estimated hazard ratio = 0.286, 95% C.I.: 0.135–0.603, p = 0.001) and the presence of L858R EGFR mutation in adenocarcinoma (estimated hazard ratio = 0.520, 95% C.I.: 0.307–0.880, p = 0.015) were retained as independent prognostic factors in the final multiple Cox's proportional hazards model for TTF. According to preliminary GEE analysis of repeatedly measured posttreatment HRQOL, the patients with wild-type EGFR consistently had worse HRQOL in EQ-5D index (p < 0.0001), EQ-5D VAS score (p = 0.0002), and LCSS global score (p < 0.0001), respectively. Conclusions: In advanced NSCLC patients receiving first-line gefitinib, better baseline EQ-5D index and L858R EGFR mutation in adenocarcinoma predict longer TTF. In addition, patients with wild-type EGFR had worse posttreatment HRQOL.

No significant financial relationships to disclose.

Phase II randomized trial of erlotinib versus vinorelbine in chemotherapy-naive patients with advanced non-small-cell lung cancer (NSCLC) aged ≥70 years in Taiwan

8051

Background: Epidermal growth factor receptor (EGFR) tyrosine-kinase inhibitors, such as erlotinib, are effective against NSCLC, especially in East Asian patients. Single-agent chemotherapy, such as vinorelbine, is an appropriate treatment choice for elderly patients. Oral vinorelbine is more convenient for elderly patients than intravenous vinorelbine. The primary objective of this study was to compare the response rate of chemo-naïve, elderly patients with advanced NSCLC treated with daily erlotinib versus oral vinorelbine. Methods: Chemo-naïve Taiwanese patients aged ≥70 years with advanced NSCLC were enrolled and randomized (stratified by histology, smoking status, ECOG performance status, and gender) to receive either oral erlotinib 150mg/day or oral vinorelbine (60mg/m2 on days 1 and 8 of the first cycle and subsequently increased to 80mg/m2 every 3 weeks in the absence of grade 2 adverse events). From February 2007 to July 2008, 116 patients were enrolled. Results: By October 2008, 77 enrolled patients (n = 37 for erlotinib; n = 40 for vinorelbine) had completed 6 cycles of study treatment and were available for efficacy and safety analyses. Objective response rates were 21.6% (8/37) with erlotinib and 12.8% (5/39) with vinorelbine [95% CI -0.09–0.24 for the difference in response rate between arms]. Disease control rate was 70.3% with erlotinib and 56.4% with vinorelbine [95% CI -0.09–0.34 for the difference in disease control rate between arms; p = 0.216). Median time to disease progression was 4.4 months [95% CI 4.1–5.4] with erlotinib, compared with 3.9 months [95% CI 2.4–6.9] with vinorelbine, p = 0.6069. The most common treatment-related toxicities were skin rash and diarrhea with erlotinib, and diarrhea and nausea with vinorelbine. Conclusions: Erlotinib is effective and well tolerated compared with oral vinorelbine in elderly, chemo-naïve, Taiwanese patients with NSCLC. Updated efficacy and safety data will be presented.

[Table: see text]

A phase II study of BIBW 2992, a novel irreversible dual EGFR and HER2 tyrosine kinase inhibitor (TKI), in patients with adenocarcinoma of the lung and activating EGFR mutations after failure of one line of chemotherapy (LUX-Lung 2)

8013

Background: EGFR mutations are associated with exquisite sensitivity to EGFR TKIs in NSCLC. A phase II trial evaluating the efficacy of BIBW 2992 (Tovok), a novel, potent, irreversible, dual EGFR and HER2 TKI with preclinical activity in cell lines harboring activating (H3255, IC50=0.7 nM) and resistant (H1975, IC50=99 nM) EGFR mutations, is reported. Methods: Objective response rate is the primary endpoint of this 2-stage trial. Based on 16 or more unconfirmed PRs in an interim analysis of the first 40 2nd line patients (pts) completing 1 course (28 days), accrual will continue to a total of 120 1st and 2nd line pts (expected completion of accrual by May 2009. Data on 2nd line pts only are presented). Eligible pts have stage IIIB/IV lung adenocarcinoma, EGFR mutation in exons 18–21 (tested by direct sequencing), measurable disease, ECOG PS 0–2 and adequate end organ function. Pts receive 50 mg BIBW 2992 qd until progression. Tumor assessments are performed every 4 weeks for 12 weeks, then every 8 weeks. Results: Since Oct 2007, samples from 289 pts (222 from Taiwan and 67 from the US) have been sequenced. 100 had detectable EGFR mutations including del19 (n=39), L858R (n=45) and others (n=16). 69 pts have started treatment. The trial was moved to stage 2 after 21 of the first 38 treated pts had objective response at 28 days. Of 55 evaluable 2nd line pts, 29 (53%) had PR, and 23 (42%) had SD. Median follow up is 5.1 months. Most common related AEs were diarrhea and skin-related AEs, reported in 87% and 88% of pts, respectively. 27 pts (42.9 %) had dose reduction to 40 mg and 7 pts (11%) to 30 mg but only 1 pt permanently discontinued due to AEs. Diarrhea and rash were main causes of dose reduction. Conclusions: In the 2nd line setting, BIBW 2992 shows efficacy in NSCLC harboring EGFR activating mutations. Diarrhea and skin disorders, the most frequently observed AEs, are manageable with supportive care and dose reduction. Updated response and disease control rates and preliminary progression-free survival data will be presented. An international Phase III trial program investigating BIBW 2992 in NSCLC, LUX-Lung, is now recruiting.

[Table: see text]