Predictive Factors for Response to Adaptive Therapy in Thoracic Stereotactic Ablative Radiotherapy

PURPOSE/OBJECTIVE(S)

Online adaptive radiotherapy (ART) has been increasingly adopted for clinical use. However, ART for thoracic malignancies has lagged beyond its implementation for other primary cancers. Efforts are needed to identify optimal patients for ART by finding trends for changes in tumor position, shape, or proximity to OARs are needed. We hypothesized tumor size, histology, pre-RT SUV value, and intrathoracic location could influence how tumors change during cone beam computed tomography (CBCT)-based ART Stereotactic Ablative Radiotherapy (SAbR) for thoracic disease.

MATERIALS/METHODS

Data was collected from a prospective registry of patients who received CBCT-ART and SAbR for primary and secondary lung tumors. Dosimetry data was obtained from the simulation planning and the daily adaptive workflow. Central lung tumors were defined as those located within 2 cm of the bronchial tree. Plans were either delivered as per simulation or through the online adaptive workflow delivery (AD). Change in planning tumor volumes (PTV) were calculated between initial and final fractions (ΔPTV).

RESULTS

A total of 42 patients with a median age of 67 (range 17-90) and median 8.3 months follow up, treated between June 2021 and December 2022 were included. Most patients had NSCLC or presumed NSCLC (73.85%, 31/42), and most lesions were peripheral (61.9%, 26/42) versus central (31%, 13/42) or apical (7.1%, 3/42). Mean dose and median fractions were 52.5 Gy (SD 8.07) and 5 (range 3-5) while median initial (i) PTV was 31.75 cm3 (IQR 42.3 cm3). On average, ΔPTV decreased by 4.9% (SD 21) and volume shrunk by 5 cm3 (SD 14.5). AD improved per fraction PTV coverage and conformality while esophageal, cardiac, and spinal cord dose were significantly decreased (all p < 0.05), and most fractions were delivered with AD (73.4%, 138/188). AD was aborted most often for small iPTVs. ΔPTV grew >10% for two lesions though their iPTV were < 10 cm3. 12/42 ΔPTV were >10% smaller by the end of RT and corresponded to larger iPTVs. Age, lung primary, metastatic disease, smoking status, and tumor location were not predictive for >10% decrease in ΔPTV. Among 24 biopsy-proven NSCLC ΔPTV was >10% smaller in 6/12 patients (50%) with adenocarcinoma and only in 2/12 (16.7%) with SCC, although this was not significant on χ2 testing (p = 0.08). There were no differences in local, regional, distant failure or death comparing those with a ΔPTV of >10% vs <10% (all p > 0.1). Comparing pre-treatment PET SUV and tumor response, lower SUVs appear to be associated with more PTV shrinkage, with no significant PTV change plateauing at SUV 20. However, this analysis was limited by the number of patients with high SUV values.

CONCLUSION

CBCT-ART SAbR is associated with improved PTV coverage, target conformality, and reduced OAR dose. Large iPTV and adenocarcinomas were more likely to decrease >10%. High metabolic activity appeared predictive for a lack of significant ΔPTV. Further clinical and radiographic features should be explored to predict response to ART.

Racial Difference in Outcomes in Breast Cancer Patients with Residual Nodal Disease after Neoadjuvant Chemotherapy

PURPOSE/OBJECTIVE(S)

African Americans (AA) requiring neoadjuvant chemotherapy (NAC) have been associated with worse outcomes. Residual nodal disease (ypN+) after NAC represents a highly unfavorable risk factor. We hypothesized that even within this unfavorable subgroup, that racial differences in outcome would persist.

MATERIALS/METHODS

An IRB-approved retrospective review of breast cancer (BC) patients in a multi-institutional study was performed between 2005-2018 to identify ypN+ patients (excluding metastatic or inflammatory BC). Clinico-pathologic parameters stratified by race were collected and analyzed. For molecular subtype analyses, patients were stratified into triple negative (TN), hormone receptor (HR)+/HER2-, and HR+/HER2+, and HR-/HER2+ subtypes. Overall survival (OS), disease free survival (DFS) and recurrence outcomes were obtained, and univariate and multivariate (MVA) logistic regression models were constructed and analyzed.

RESULTS

Among 404 ypN+ patients, 107 (26%) were AA, and 297 (74%) were non-AA. Median follow-up for the non-AA group was 3.8 years (y) (IQR 2.4-6.3) and 3.5y (IQR 2.0-6.2) for the AA group. Clinical and pathologic patient characteristics (age, molecular subtypes, BRCA status, histology, grade, smoking status, primary surgery type, axillary/reconstruction surgery rates, margin status, stage) were without significant statistical differences between the non-AA and AA group, except the non-AA group had proportionally more cN3 disease (10.5% vs. 5.1%; p = .01). Despite this, AA demonstrated worse OS and DFS outcomes (Table). AA also had significantly worse local (15% vs. 6.7%, p = .02), regional (11.2% vs. 5.1%, p = .05) and distant recurrences (32.7% vs. 22.6%, p = .05) compared to non-AA. On MVA for OS and DFS, HR+ status, clinical stage, and AA race (HR 2.1 (CI 1.3-3.4), p = .004 and HR 1.7 (CI 1.1-2.6), p = .01 respectively) remained significant. Molecular subtype analysis demonstrated that AA with HR+/HER2- but not the TN subtypes demonstrated significantly worse outcomes (Table). Utilization of endocrine therapy was not different between AA and non-AA patients (94% vs. 97%, p = 0.3) to explain this discrepancy. Worse outcomes in HER2 subtype for AA group was suggested but could not be statistically verified due to insufficient sample size. There was no discernible difference in chemotherapy and radiation therapy regimen or compliance between the AA and non-AA groups.

CONCLUSION

AA patients who fail to achieve nodal clearance with NAC had higher local, regional and distant recurrence, and worse survival compared to non-AA, particularly those with non-TN status. These differences could not be readily explained by therapeutic disparity, or compliance. These hypothesis generating findings suggest need to explore biological implications, and alternative therapeutic strategies for this unfavorable subgroup.

Predicted Cardiac Toxicity in Daily Cone-Beam CT-Based Online Adaptive Stereotactic Partial Breast Irradiation with Decreased PTV Margins

PURPOSE/OBJECTIVE(S)

Partial breast irradiation (PBI) targets a smaller volume over less time compared to whole breast radiation, but the organ-at-risk (OAR) sparing allowed by its large (up to 1 cm) PTV can be improved. The heart is sensitive to low doses with conventional fractionation and NTCP models have been created for heart substructures. We hypothesized that daily online adaptive stereotactic PBI (A-SPBI) IMRT with 3-mm PTV improves dosimetry and predicted cardiac toxicity risk.

MATERIALS/METHODS

Patients treated with daily CBCT-based online A-SPBI IMRT were excluded if the minimum heart dose was <1 Gy. IMRT radiation plans with 3-mm PTV margins were recreated with 1-cm margins per the Florence APBI IMRT trial planning guideline. Dose statistics were converted to the equivalent doses in 2-Gy fractions (EQD2) using α/β = 3 for use in NTCP models and for comparison using paired t tests, with differences considered significant if p≤0.05.

RESULTS

The table details heart, left anterior descending artery (LAD), and left (LV) and right ventricle (RV) EQD2 statistics for 4 left-sided and 4 right-sided 3-mm PTV plans and their 1-cm PTV replans. For 2 patients with non-zero LV V5, 9-year excess cumulative risk of acute coronary event was <0.001% for both margin sizes. No plan reached thresholds for increased risk of non-cardiac death, major adverse cardiac event, or >10% decrease in LV ejection fraction.

CONCLUSION

Given the established relationship between low MHD and cardiac events, the significant decrease in MHD revealed in comparisons of 3-mm and 1-cm PTV A-SPBI plans of our first 8 patients is promising; we expect the forthcoming larger sample size to show significant differences in substructure doses. NTCP models created for non-IMRT breast plans and targets with higher heart exposure did not predict clinically-relevant differences in cardiac risk. NTCP model development for the low heart dose achieved with A-SPBI would define expected benefit in these patients; in their absence, daily adaptation should be considered in patients with unfavorable anatomy or cardiac risk factors.

Assessment of Cardiac Radiation Dose in the Co-60 Prone Based Stereotactic Partial Breast Irradiation (CP-sPBI) Using the Distance from the Heart to the Planning Treatment Volume as a Surrogate Marker

PURPOSE/OBJECTIVE(S)

Irradiation of the breast has shown to provide sharp dose gradients using Co-60 prone based stereotactic partial breast irradiation (CP-sPBI), a contemporary device for stereotactic radiotherapy for breast cancer (BC) for accelerated partial breast irradiation (APBI). In addition, the precise setup of CP-sPBI permits a small planning treatment volume (PTV) margin of 3 mm creating a greater distance from PTV to organs at risk. However, to date the factors that influence dose gradients and subsequent cardiac doses of ionizing radiation using CP-sPBI have not been well-studied. Here we evaluate distance of the heart to the lumpectomy PTV cavity and how this effects cardiac dose.

MATERIALS/METHODS

A retrospective database of 113 consecutive patients treated by CP-sPBI for APBI from March 2019 to February 2023 who were treated with 30 Gy in 5 fractions were queried for analysis. The minimum distance from the heart to the PTV (hP) was measured in either the axial or sagittal view. A group of 28 patient cases were randomly selected to achieve an even distribution of 28 cases with hP < 2.75 cm and hP ≥ 2.75 cm to compare cardiac toxicities based on hP. Descriptive analyses were performed to evaluate various cardiac dosimetric parameters based on laterality of BC and hP, using the student's t test.

RESULTS

The mean (range) hP was 4.58 cm (0.80-12.23) for all cases. The subgroup analyses of 28 patient cases with cardiac parameters showed the heart mean (range) dose of 1.20 Gy (0.01-2.11). The mean and max heart dose to the left-sided BC were similar to those to the right-sided BC (mean dose: 1.20 vs. 1.19 Gy; P = 0.97 and max dose: 10.47 vs. 5.66 Gy; P = 0.06). An inverse correlation between hP and mean heart dose was shown with the correlation coefficient of -0.81. Using a cutoff of 2.75 cm hP, the differences between hP < 2.75 and hP ≥ 2.75 cm for all cardiac dosimetric evaluations were all statistically significant, including mean (1.67 vs. 0.79 Gy; p<0.01) and maximal heart dose (14.48 vs. 4.11 Gy; p<0.01) CONCLUSION: CP-sPBI treatment delivery system was able to achieve acceptable clinically relevant heart dosimetric parameters when delivering 5 fraction APBI with a mean heart dose of 1.20 Gy for all locations of PTV cavity volume in the breast. Due to CP-sPBIs excellent dose fall-off characteristics, APBI using CP-SPBI showed clinically acceptable cardiac dosimetric parameters, particularly for PTVs located > 2.75 cm from the heart.

Observed and Predicted Toxicity in Daily Cone-Beam CT-Based Online Adaptive Stereotactic Partial Breast Irradiation with Decreased PTV Margins

PURPOSE/OBJECTIVE(S)

Accelerated partial breast irradiation (APBI) delivers smaller radiation volumes over less time compared to whole breast irradiation (WBI), but the organ-at-risk (OAR) sparing allowed by its large (up to 1 cm) planning target volume (PTV) can be improved. PTV can be decreased with daily online adaptive planning, which we hypothesized yields low rates of adverse events observed and predicted by normal tissue complication probability (NTCP) models.

MATERIALS/METHODS

Intensity-modulated (IMRT) cone-beam CT (CBCT)-based daily online adaptive stereotactic PBI (A-SPBI) plans with 3-mm PTV from 8 patients were recreated with 1-cm PTV per the Florence APBI IMRT trial planning guideline. Dose statistics with evidence for association with toxicity were compared. Documented toxicities were collected for patients treated with A-SPBI with a minimum follow-up of 3.5 months and Common Terminology Criteria for Adverse Events (CTCAE) v.5.0 grade was assigned. Using α/β = 3 for breast and lung, dose statistics were converted to equivalent doses in 2-Gy fractions (EQD2) for use in NTCP models and for comparison using paired t tests, with differences considered significant if p≤0.05.

RESULTS

The table details EQD2 dose statistics for breast, lung, and cosmetic toxicity for A-SPBI plans with 3-mm PTV and their 1-cm PTV re-plans in 8 patients. PTV volume, mean lung dose (MLD), and lung V5, V20, and V30 were significantly lower in 1-cm plans. Acute, subacute (3-6 months), and late toxicities were collected for 30 patients followed for a median of 8 months (range 4-13 months). Radiation dermatitis was the most common acute toxicity (n = 16, 53%), followed by hyperpigmentation (n = 12, 40%), fibrosis (n = 9, 30%), and fatigue (n = 9, 30%). One grade 3 radiation dermatitis was the only grade ≥3 toxicity. Six patients (20%) acutely developed breast or axillary edema: 4 (13.3%) resolved, and 2 (6.7%) developed acutely and persist at last follow-up, >6 months after RT. No patient had a lung V20, V30, or MLD meeting thresholds for radiation-induced lung injury, radiation pneumonitis, or symptomatic or imaging-based pneumonitis models, respectively. The breast V55 model predicted a median risk of unfavorable cosmesis of 33% (range 26-44%) for A-SBPI plans and 35% (range 28-51) for 1-cm PTV plans (p = 0.28).

CONCLUSION

Observed acute toxicities are tolerable and rarely persist in patients treated with A-SPBI with 3-mm PTV margins with daily CBCT-based online adaptation. NTCP modeling predicts similar cosmetic outcome to 1-cm margins. The significant reduction in ipsilateral lung dose with a 3-mm PTV in our first 8 patients especially supports daily adaptation in low-risk breast cancer patients with smoking history and/or lung comorbidity.

Principal Component Analysis to Design Planning Target Volume in Oropharyngeal Cancers

PURPOSE/OBJECTIVE(S)

Standard translational shifts of the Clinical Target volume (CTV) to generate the Planning Target Volume (PTV) do not account for rotations. Head and neck positional misalignments derive in large part from rotations due to cervical spine arching and twisting in Cone Beam Computed Tomography (CBCT). Translational expansions do not track rotations, yielding coverage envelopes that unnecessarily overlap with adjacent structures. This work examines whether principal component analysis of the motion along all 6 degrees of freedom may be used to produce a more favorable PTV.

MATERIALS/METHODS

Seventy-five CBCTs of ten oropharyngeal cases were included. The records of couch shifts needed to align individual bony structures (C1-5, mandible and mastoid) between the planning image and CBCTs were recorded. A Principal Component Analysis of the shifts was used to generate an ellipsoid inflation of each CTV vertex along 6 degrees of freedom. The result was compared to a 3D ellipsoid based translational expansion, and to a described ellipsoid based vertex expansion along 6 degrees of freedom, with axes oriented in parallel to the treatment reference frame.

RESULTS

Themean (x, y) shifts in mm needed to align individually bodies C1 - C5 were respectively (-0.4, 0.5), (+.5, -0.2), (+-0.2, -0.2), (-0.2, +0.4), and (-0.5, +0.7), the monophasic pattern showing acquired curvature along both axes during treatment and demanding a PTV for coverage. A PTV was constructed using a described 6D ellipsoidal based boundary point expansion aligned along the reference frame axis or using a new theory to align against the principal components of the motion. A cyclical one-out method was used to validate the PTV models. Selected confidence intervals yielded complete coverage in >80% weeks in 80% cases. Validation testing disclosed similar complete coverage in 83-86% weekly CBCTs in the test cases with either method. The PCA 6D PTV could yield less normal structure overlap. A one out method was used to test overlap avoidance from PTVs constructed from a population of weekly CBCTs drawn from seven cases with one excluded. PTVs were drawn around target and constrictors on an extraneous case and imaged on a CT slice. Both a rolling 'ball' expansion of the vertices that applies a 3D translational ellipsoid and a PTV constructed using a 6D ellipsoid aligned against the standard reference frame overlapped with all or nearly all the constrictors in all but one trial (1/7). The 6D ellipsoid aligned against the principal motion components spared >70% of a constrictor in all trials (7/7).

CONCLUSION

PTVs remain needed to ensure target coverage in head and neck radiotherapy even with daily CT accuracy because of acquired spinal curvatures resulting in rotational displacements. A described 6D ellipsoid oriented to the reference frame can yield good coverage, but with unneeded constrictor coverage. A PCA analysis yields a PTV with equally good coverage but able to spare 70% of a constrictor.

Dosimetric Comparison of Adaptive Radiotherapy Modalities for Stereotactic Partial Breast Irradiation

PURPOSE/OBJECTIVE(S)

An increase in the availability of adaptive radiotherapy (ART) platforms have proven to be effective in the treatment of a variety of sites. In this study, we aim to evaluate the effectiveness of non-adaptive RT and 3 different ART platforms: (1) CBCT-based, (2) CT-based, and (3) MRI-based for stereotactic partial breast irradiation (SPBI).

MATERIALS/METHODS

Data were collected from 32 patients (16 left and 16 right breast) treated at a single institution. 16 patients (8 left and 8 right) treated using the non-ART platform were re-planned onto two different ART platforms, CBCT- and MRI-based. The remaining 16 patients treated using CT-based adaptive platform were not re-planned due to the prone patient treatment position (others systems supine). All cases were planned to 30 Gy in 5 fractions. Plan quality was evaluated based on pre-defined planning goals to the OARS: ipsilateral and contralateral lungs (Dmean, Dmax, V20 Gy, V9 Gy), ipsilateral (V15 Gy, V30 Gy) and contralateral breasts (Dmax), heart (Dmean, Dmax, V3 Gy, V1.5 Gy), skin (Dmax, V36.5 Gy), and rib (Dmax, V30 Gy). Target goals were defined by Dmax, Dmin, gradient index, and paddock conformality index. Re-planned cases were compared within the cohort using a paired t-test and a 2-sided t-test was used comparing to the CT-based platform.

RESULTS

Comparing the left and right breast cohort across all platforms, the CT-based ART system showed a signification dose reduction in Dmean (p<0.001 for all platforms), Dmax (p<0.001 for left breast, p<0.03 for right breast) and V9 Gy (p<0.004 for left breast, p<0.001 for right breast) to the ipsilateral lung, V15 Gy (p<0.004 for left breast cohort) to the ipsilateral breast, and Dmax to the contralateral breast (p<0.001) and ribs (p = 0.01, p<0.001, p = 0.01 for CBCT-ART, MRI-ART, and non-ART for left breast cohort only). On average, the MR-Linac platform showed the least degree of OAR sparing across nearly all dosimetric parameters evaluated when compared to all modalities, especially for contralateral lung Dmean and Dmax (p<0.05 for all dosimetric parameters for all platforms) and contralateral breast Dmax (p<0.003 for all platforms). The CBCT-based platform showed superior dose reduction in contralateral lung mean (p<0.03 for all platforms) and heart Dmean (p = 0.065, p<0.001, p = 0.045 for non-adaptive, MRI-ART, and CT-ART for left breast and p<0.008 for right breast). PTV coverage was comparable across all platforms, averaging at approximately 95%. The CT-based ART platform showed a significantly reduced gradient index relative to the CBCT- and MRI-based platforms (p<0.001).

CONCLUSION

For SPBI treatments, the CT-based ART platforms displayed a higher degree of OAR sparing for many of the dosimetric parameters recorded relative to the other ART and non-ART platforms presented. The MRI-based system typically showed less reduced OAR sparing; however, the advantage of the system is shown if soft tissue contrast is needed. PTV coverage remained comparable across all platforms.

Combination of BET Inhibition with Radiation Induces Anti-Tumor Immune Response in Pre-Clinical Models of ER-Positive Breast Cancer

PURPOSE/OBJECTIVE(S)

Despite advances in multidisciplinary care, the risk of late recurrence in Estrogen Receptor-positive (ER+) breast cancer (BC) patients following standard-of-care treatment ranges from 20-52% at 20 years. While immune checkpoint inhibitors (CPI), have shown enormous potential in inducing long term remission in some cases, patients with ER+ BC show poor response to these agents. The objective of this study is to develop effective radiation therapy (RT)-based combination regimens that induce anti-tumor immunity against immunologically cold ER+ breast tumors.

BACKGROUND

We have previously shown that pharmacological inhibition of bromodomain and extraterminal domain (BET) family of epigenetic regulator proteins overcomes both endocrine therapy resistance and radiation resistance in pre-clinical models of ER+ BC by reversing pathological reprogramming of transcriptional and DNA repair pathways, respectively. In this study, we explore the potential of RT+BET inhibition combination to elicit anti-tumor immunity against ER+ BC.

MATERIALS/METHODS

A unique ER+ BC model, MXT+, was used to generate tumors in female, BDF1 mice. PD-L1 expression following RT or RT+OTX015 (a BET inhibitor) was assessed by Western blot analysis. Comet assay was used to assess the degree of unrepaired DNA damage following treatment with RT alone, OTX015 alone and RT+OTX015. Multiplex IHC was used to assess changes in tumor microenvironment after various treatments. Tumor growth characteristics were established following treatment with vehicle, RT alone (8 Gy x 3), OTX015 alone (100 mg/kg x 3 days) and RT+OTX015.

RESULTS

Using murine ER+ BC model, MXT+, we show that RT is a potent inducer of PD-L1 expression. Combination of RT+OTX015 completely ablated RT-mediated PD-L1 induction at the transcription level. OTX015 also accentuated RT-induced DNA damage through inhibition of NHEJ pathway, resulting in increased micronuclei formation (which activate cGAS/STING pathway, a critical bridge between innate and adaptive immunity). Combination of OTX015 with RT also caused a statistically significant (on unpaired t test) increase tumor infiltrating lymphocytes. In in vivo therapeutic studies, combination of OTX015 with RT (8 Gy x 3) resulted in extraordinary synergy and caused complete inhibition of long-term tumor growth. Treatment with RT alone (8 Gy x 3) or OTX015 alone (on 3 consecutive days) only caused modest inhibition of tumor growth. ANOVA with Dunnett's test was used to adjust for multiple comparisons and showed statistically significant difference in tumor growth between OTX015+RT arm and OTX alone as well as OTX015+RT arm and RT alone.

CONCLUSION

Patients with ER+ BC face high risk of late recurrence after definitive treatment and show poor response to immune CPIs. We show that combination of BET inhibition with RT induces anti-tumor immunity and completely prevents tumor growth. Clinical validation of this regimen is warranted to prevent late recurrences in ER+ BC patients.

The Changing Profile of Academic Radiation Oncology Leaders: Updates over the Past Decade

PURPOSE/OBJECTIVE(S)

To report objective characteristics of program directors (PDs) and chairpersons and examine contemporary trends of their demographic and academic profiles from 2013 to 2023. We hypothesize that there are significant changes in the profiles of our radiation oncology leaders over the past decade.

MATERIALS/METHODS

A total of 89 PDs and 85 chairpersons in the Accreditation Council for Graduate Medical Education (ACGME)-approved residency programs in the U.S were queried for analysis. Demographic data on race, ethnicity, post graduate training, years in practice were obtained from publicly available online resources (e.g., institutional websites and online networking services for physicians). Variables on academic productivity and professional accolades included Hirsh-index, National Institute of Health (NIH) research grant (R), the ASTRO fellowship designation, and leadership positions in professional society meetings. Descriptive analyses, including Fisher's exact tests, were performed to compare findings from the published article in 2013 on this topic (Wilson LD et al. IJROBP 2013).

RESULTS

A total of 36 out of 89 PDs (40.4%) and 11 out of 85 chairpersons (12.8%) were females, revealing higher proportion of females from the initial analysis: 40.4 vs. 24.1% for PDs (p = 0.025) and 12.8 vs. 9.2% for chairpersons (p = 0.618). 29 out of 89 (32.6%) PDs and 30 out of 85 (35.3%) chairpersons were non-White. The median length of practice for PDs and chairpersons were 11 and 29 years, respectively. 38 out of 89 PDs (42.7%) and 11 out of 85 (12.9%) chairpersons were employed at the institution of their training. 7 out of 89 (7.9%) for PDs and 51 out of 85 (60.0%) for chairpersons were awarded FASTRO designation. Median H-index showed increasing trends for PDs (14.5 vs 9) and chairpersons (40 vs 29) from the initial analysis.

CONCLUSION

While most PDs and chairpersons are males, female representation has increased in radiation oncology leadership in the last 10 years, most notably among PDs. Academic productivity among our leaders has also increased. These trends highlight the changes in the landscape of our leadership characteristics.

Evolution of an adenine base editor into a small, efficient cytosine base editor with low off-target activity

Cytosine base editors (CBEs) are larger and can suffer from higher off-target activity or lower on-target editing efficiency than current adenine base editors (ABEs). To develop a CBE that retains the small size, low off-target activity and high on-target activity of current ABEs, we evolved the highly active deoxyadenosine deaminase TadA-8e to perform cytidine deamination using phage-assisted continuous evolution. Evolved TadA cytidine deaminases contain mutations at DNA-binding residues that alter enzyme selectivity to strongly favor deoxycytidine over deoxyadenosine deamination. Compared to commonly used CBEs, TadA-derived cytosine base editors (TadCBEs) offer similar or higher on-target activity, smaller size and substantially lower Cas-independent DNA and RNA off-target editing activity. We also identified a TadA dual base editor (TadDE) that performs equally efficient cytosine and adenine base editing. TadCBEs support single or multiplexed base editing at therapeutically relevant genomic loci in primary human T cells and primary human hematopoietic stem and progenitor cells. TadCBEs expand the utility of CBEs for precision gene editing.

Base editing rescue of spinal muscular atrophy in cells and in mice

Spinal muscular atrophy (SMA), the leading genetic cause of infant mortality, arises from survival motor neuron (SMN) protein insufficiency resulting from SMN1 loss. Approved therapies circumvent endogenous SMN regulation and require repeated dosing or may wane. We describe genome editing of SMN2, an insufficient copy of SMN1 harboring a C6>T mutation, to permanently restore SMN protein levels and rescue SMA phenotypes. We used nucleases or base editors to modify five SMN2 regulatory regions. Base editing converted SMN2 T6>C, restoring SMN protein levels to wild type. Adeno-associated virus serotype 9-mediated base editor delivery in Δ7SMA mice yielded 87% average T6>C conversion, improved motor function, and extended average life span, which was enhanced by one-time base editor and nusinersen coadministration (111 versus 17 days untreated). These findings demonstrate the potential of a one-time base editing treatment for SMA.

Efficient C•G-to-G•C base editors developed using CRISPRi screens, target-library analysis, and machine learning

Programmable C•G-to-G•C base editors (CGBEs) have broad scientific and therapeutic potential, but their editing outcomes have proved difficult to predict and their editing efficiency and product purity are often low. We describe a suite of engineered CGBEs paired with machine learning models to enable efficient, high-purity C•G-to-G•C base editing. We performed a CRISPR interference (CRISPRi) screen targeting DNA repair genes to identify factors that affect C•G-to-G•C editing outcomes and used these insights to develop CGBEs with diverse editing profiles. We characterized ten promising CGBEs on a library of 10,638 genomically integrated target sites in mammalian cells and trained machine learning models that accurately predict the purity and yield of editing outcomes (R = 0.90) using these data. These CGBEs enable correction to the wild-type coding sequence of 546 disease-related transversion single-nucleotide variants (SNVs) with >90% precision (mean 96%) and up to 70% efficiency (mean 14%). Computational prediction of optimal CGBE-single-guide RNA pairs enables high-purity transversion base editing at over fourfold more target sites than achieved using any single CGBE variant.

Determinants of Base Editing Outcomes from Target Library Analysis and Machine Learning

Although base editors are widely used to install targeted point mutations, the factors that determine base editing outcomes are not well understood. We characterized sequence-activity relationships of 11 cytosine and adenine base editors (CBEs and ABEs) on 38,538 genomically integrated targets in mammalian cells and used the resulting outcomes to train BE-Hive, a machine learning model that accurately predicts base editing genotypic outcomes (R ≈ 0.9) and efficiency (R ≈ 0.7). We corrected 3,388 disease-associated SNVs with ≥90% precision, including 675 alleles with bystander nucleotides that BE-Hive correctly predicted would not be edited. We discovered determinants of previously unpredictable C-to-G, or C-to-A editing and used these discoveries to correct coding sequences of 174 pathogenic transversion SNVs with ≥90% precision. Finally, we used insights from BE-Hive to engineer novel CBE variants that modulate editing outcomes. These discoveries illuminate base editing, enable editing at previously intractable targets, and provide new base editors with improved editing capabilities.

Continuous evolution of SpCas9 variants compatible with non-G PAMs

The targeting scope of Streptococcus pyogenes Cas9 (SpCas9) and its engineered variants is largely restricted to protospacer-adjacent motif (PAM) sequences containing G bases. Here we report the evolution of three new SpCas9 variants that collectively recognize NRNH PAMs (where R is A or G and H is A, C or T) using phage-assisted non-continuous evolution, three new phage-assisted continuous evolution strategies for DNA binding and a secondary selection for DNA cleavage. The targeting capabilities of these evolved variants and SpCas9-NG were characterized in HEK293T cells using a library of 11,776 genomically integrated protospacer-sgRNA pairs containing all possible NNNN PAMs. The evolved variants mediated indel formation and base editing in human cells and enabled A•T-to-G•C base editing of a sickle cell anemia mutation using a previously inaccessible CACC PAM. These new evolved SpCas9 variants, together with previously reported variants, in principle enable targeting of most NR PAM sequences and substantially reduce the fraction of genomic sites that are inaccessible by Cas9-based methods.

Author Correction: Predictable and precise template-free CRISPR editing of pathogenic variants

In this Article, a data processing error affected Fig. 3e and Extended Data Table 2; these errors have been corrected online.

Self-Cloning CRISPR

CRISPR/Cas9-gene editing has emerged as a revolutionary technology to easily modify specific genomic loci by designing complementary sgRNA sequences and introducing these into cells along with Cas9. Self-cloning CRISPR/Cas9 (scCRISPR) uses a self-cleaving palindromic sgRNA plasmid (sgPal) that recombines with short PCR-amplified site-specific sgRNA sequences within the target cell by homologous recombination to circumvent the process of sgRNA plasmid construction. Through this mechanism, scCRISPR enables gene editing within 2 hr once sgRNA oligos are available, with high efficiency equivalent to conventional sgRNA targeting: >90% gene knockout in both mouse and human embryonic stem cells and cancer cell lines. Furthermore, using PCR-based addition of short homology arms, we achieve efficient site-specific knock-in of transgenes such as GFP without traditional plasmid cloning or genome-integrated selection cassette (2% to 4% knock-in rate). The methods in this paper describe the most rapid and efficient means of CRISPR gene editing. © 2016 by John Wiley & Sons, Inc.

Cloning-free CRISPR

We present self-cloning CRISPR/Cas9 (scCRISPR), a technology that allows for CRISPR/Cas9-mediated genomic mutation and site-specific knockin transgene creation within several hours by circumventing the need to clone a site-specific single-guide RNA (sgRNA) or knockin homology construct for each target locus. We introduce a self-cleaving palindromic sgRNA plasmid and a short double-stranded DNA sequence encoding the desired locus-specific sgRNA into target cells, allowing them to produce a locus-specific sgRNA plasmid through homologous recombination. scCRISPR enables efficient generation of gene knockouts (∼88% mutation rate) at approximately one-sixth the cost of plasmid-based sgRNA construction with only 2 hr of preparation for each targeted site. Additionally, we demonstrate efficient site-specific knockin of GFP transgenes without any plasmid cloning or genome-integrated selection cassette in mouse and human embryonic stem cells (2%–4% knockin rate) through PCR-based addition of short homology arms. scCRISPR substantially lowers the bar on mouse and human transgenesis.

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scCRISPR circumvents the need to clone sgRNAs or knockin homology constructs

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A self-cleaving palindromic plasmid recombines to produce a locus-specific sgRNA

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scCRISPR targets via state-of-the-art efficiency for a fraction of the time and cost

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scCRISPR benefits throughput of functional genomic screens and generation of reporter lines

DAZL regulates Tet1 translation in murine embryonic stem cells

Embryonic stem cell (ESC) cultures display a heterogeneous gene expression profile, ranging from a pristine naïve pluripotent state to a primed epiblast state. Addition of inhibitors of GSK3β and MEK (so-called 2i conditions) pushes ESC cultures toward a more homogeneous naïve pluripotent state, but the molecular underpinnings of this naïve transition are not completely understood. Here, we demonstrate that DAZL, an RNA-binding protein known to play a key role in germ-cell development, marks a subpopulation of ESCs that is actively transitioning toward naïve pluripotency. Moreover, DAZL plays an essential role in the active reprogramming of cytosine methylation. We demonstrate that DAZL associates with mRNA of Tet1, a catalyst of 5-hydroxylation of methyl-cytosine, and enhances Tet1 mRNA translation. Overexpression of DAZL in heterogeneous ESC cultures results in elevated TET1 protein levels as well as increased global hydroxymethylation. Conversely, null mutation of Dazl severely stunts 2i-mediated TET1 induction and hydroxymethylation. Our results provide insight into the regulation of the acquisition of naïve pluripotency and demonstrate that DAZL enhances TET1-mediated cytosine hydroxymethylation in ESCs that are actively reprogramming to a pluripotent ground state.

A multi-parametric flow cytometric assay to analyze DNA-protein interactions

Interactions between DNA and transcription factors (TFs) guide cellular function and development, yet the complexities of gene regulation are still far from being understood. Such understanding is limited by a paucity of techniques with which to probe DNA–protein interactions. We have devised magnetic protein immobilization on enhancer DNA (MagPIE), a simple, rapid, multi-parametric assay using flow cytometric immunofluorescence to reveal interactions among TFs, chromatin structure and DNA. In MagPIE, synthesized DNA is bound to magnetic beads, which are then incubated with nuclear lysate, permitting sequence-specific binding by TFs, histones and methylation by native lysate factors that can be optionally inhibited with small molecules. Lysate protein–DNA binding is monitored by flow cytometric immunofluorescence, which allows for accurate comparative measurement of TF-DNA affinity. Combinatorial fluorescent staining allows simultaneous analysis of sequence-specific TF-DNA interaction and chromatin modification. MagPIE provides a simple and robust method to analyze complex epigenetic interactions in vitro.

Pathways of parasympathetic and sensory cerebrovascular nerves in monkeys

Using immunohistochemistry, we studied the origins and pathways of parasympathetic and sensory nerve fibers to the pial arteries in four squirrel monkeys. Following its application to the surface of the middle cerebral artery, the retrograde axonal tracer True Blue accumulated in parasympathetic neurons of the sphenopalatine ganglion and the internal carotid ganglion. The latter is strategically located where the internal carotid artery enters the cranium. Fibers from the sphenopalatine ganglion reach the internal carotid artery in the cavernous sinus region after running as rami orbitales. Before reaching the internal carotid artery, the fibers bypass aberrant sphenopalatine ganglia, with the most distant, the cavernous ganglion, being located in the cavernous sinus region. True Blue also accumulated in sensory neurons of the ophthalmic and maxillary divisions of the trigeminal ganglion and in sensory neurons of the internal carotid ganglion. Fibers from the ophthalmic division of the trigeminal ganglion reach the internal carotid artery as a branch through the cavernous sinus, bypassing the cavernous ganglion. Fibers from the maxillary division also bypass the cavernous ganglion after reaching it via a recurrent branch of the orbitociliary nerve. Thus, the cavernous ganglion forms a confluence zone for parasympathetic and sensory fibers in the region. In addition, parasympathetic and sensory fibers leave the confluence zone to follow the abducent and trochlear nerves backward to the basilar artery and tentorium cerebelli, respectively. Clinical implications are discussed.