Identification of functional sgRNA mutants lacking canonical secondary structure using high-throughput FACS screening

Coexpressing multiple identical single guide RNAs (sgRNAs) in CRISPR-dependent engineering triggers genetic instability and phenotype loss. To provide sgRNA derivatives for efficient DNA digestion, we design a high-throughput digestion-activity-dependent positive screening strategy and astonishingly obtain functional nonrepetitive sgRNA mutants with up to 48 out of the 61 nucleotides mutated, and these nonrepetitive mutants completely lose canonical secondary sgRNA structure in simulation. Cas9-sgRNA complexes containing these noncanonical sgRNAs maintain wild-type level of digestion activities in vivo, indicating that the Cas9 protein is compatible with or is able to adjust the secondary structure of sgRNAs. Using these noncanonical sgRNAs, we achieve multiplex genetic engineering for gene knockout and base editing in microbial cell factories. Libraries of strains with rewired metabolism are constructed, and overproducers of isobutanol or 1,3-propanediol are identified by biosensor-based fluorescence-activated cell sorting (FACS). This work sheds light on the remarkable flexibility of the secondary structure of functional sgRNA.

River valley urban network and morphology: A study on the urban morphology evolution of Lanzhou

The present study investigates the dynamic evolution characteristics of urban spatial morphology by analyzing real road network data from 2000, 2010, and 2020, along with nighttime lighting data employing spatial analysis methods and spatial syntax models. Accordingly, two separate dimensions of urban morphology: internal and external, are covered. First, the integration and synergy of interior morphology features are analyzed using spatial syntactic modeling. Subsequently, the spatial compactness, fractal dimension, and level of center of gravity shift of the city are assessed by combining the nighttime lighting data with the earlier dataset. This analysis facilitated the deep exploration of the spatiotemporal evolution of the city's external morphology. Building upon this foundation, the interaction between the "internal and external" domains was analyzed further. The main findings of the study reveal a synchronous pattern of urban expansion throughout the evolution of urban spatial morphology. Furthermore, the urban form was observed to undergo a progressive transformation, transitioning from a "single core" morphology to a "primary and secondary double core" morphology. Over time, this development progressed and evolved into a "belt-like multi-core" structure. Additionally, the coupling characteristics further validate the relationship between the structure of the road network and the urban morphology in river valley-type cities. In particular, accessibility of dense and horizontally distributed transportation network was found to significantly influence the spatial development of these cities. As observed, the findings provides valuable insights into understanding the characteristics of internal and external associations regarding urban spatial patterns.

Synthesis of cerium-based flame retardant containing phosphorus and its impact on the flammability of polylactic acid

The synthesis and characterization of [Ce2(PPPA)4(OH)2]·4H2O, wherein PPPA denotes 3-(hydroxy(phenyl)phosphoryl)propanoate, were conducted. Its potential as a flame-retardant additive for poly(L-lactic acid) (PLA) in conjunction with ammonium polyphosphate (APP) was investigated. Remarkably, with just incorporation of the 1 % Ce-complex and 4 % APP, the resulting PLA composite (PLA-8) meets the V-0 standard, exhibiting an impressive limiting oxygen index (LOI) of 29.4 %. Moreover, the introduction of the Ce-complex leads to a significant extension of ignition time (TTI), a significant 24.1 % decrease in total heat release (THR) compared to pure PLA, and a notable increase in residual carbon rate from 0.3 % to 3.51 %. Although PLA-8 exhibits a minor decline of 8.7 % in tensile strength and 3.4 % in elongation at break, respectively, compared to pure PLA, there is a substantial improvement of 32.2 % in Young's modulus and 29.9 % in impact resistance. These results emphasise the potential of cerium-based phosphorus-containing flame retardants, with cerium playing a key role in enhancing the flammability characteristics of PLA. This study contributes to the development of sustainable and fire-resistant materials in polymer chemistry.

Intelligently Quantifying the Entire Irregular Dental Structure

Quantitative analysis of irregular anatomical structures is crucial in oral medicine, but clinicians often typically measure only several representative indicators within the structure as references. Deep learning semantic segmentation offers the potential for entire quantitative analysis. However, challenges persist, including segmentation difficulties due to unclear boundaries and acquiring measurement landmarks for clinical needs in entire quantitative analysis. Taking the palatal alveolar bone as an example, we proposed an artificial intelligence measurement tool for the entire quantitative analysis of irregular dental structures. To expand the applicability, we have included lightweight networks with fewer parameters and lower computational demands. Our approach finally used the lightweight model LU-Net, addressing segmentation challenges caused by unclear boundaries through a compensation module. Additional enamel segmentation was conducted to establish a measurement coordinate system. Ultimately, we presented the entire quantitative information within the structure in a manner that meets clinical needs. The tool achieved excellent segmentation results, manifested by high Dice coefficients (0.934 and 0.949), intersection over union (0.888 and 0.907), and area under the curve (0.943 and 0.949) for palatal alveolar bone and enamel in the test set. In subsequent measurements, the tool visualizes the quantitative information within the target structure by scatter plots. When comparing the measurements against representative indicators, the tool's measurement results show no statistically significant difference from the ground truth, with small mean absolute error, root mean squared error, and errors interval. Bland-Altman plots and intraclass correlation coefficients indicate the satisfactory agreement compared with manual measurements. We proposed a novel intelligent approach to address the entire quantitative analysis of irregular image structures in the clinical setting. This contributes to enabling clinicians to swiftly and comprehensively grasp structural features, facilitating the design of more personalized treatment plans for different patients, enhancing clinical efficiency and treatment success rates in turn.

Application of deep learning in radiation therapy for cancer

In recent years, with the development of artificial intelligence, deep learning has been gradually applied to clinical treatment and research. It has also found its way into the applications in radiotherapy, a crucial method for cancer treatment. This study summarizes the commonly used and latest deep learning algorithms (including transformer, and diffusion models), introduces the workflow of different radiotherapy, and illustrates the application of different algorithms in different radiotherapy modules, as well as the defects and challenges of deep learning in the field of radiotherapy, so as to provide some help for the development of automatic radiotherapy for cancer.

Multi-locus genome-wide association studies reveal the dynamic genetic architecture of flowering time in chrysanthemum

KEY MESSAGE

The dynamic genetic architecture of flowering time in chrysanthemum was elucidated by GWAS. Thirty-six known genes and 14 candidate genes were identified around the stable QTNs and QEIs, among which ERF-1 was highlighted. Flowering time (FT) adaptation is one of the major breeding goals in chrysanthemum, a multipurpose ornamental plant. In order to reveal the dynamic genetic architecture of FT in chrysanthemum, phenotype investigation of ten FT-related traits was conducted on 169 entries in 2 environments. The broad-sense heritability of five non-conditional FT traits, i.e., budding (FBD), visible coloring (VC), early opening (EO), full-bloom (OF) and decay period (DP), ranged from 56.93 to 84.26%, which were higher than that of the five derived conditional FT traits (38.51-75.13%). The phenotypic variation coefficients of OF_EO and DP_OF were relatively large ranging from 30.59 to 36.17%. Based on 375,865 SNPs, the compressed variance component mixed linear model 3VmrMLM was applied for a multi-locus genome-wide association study (GWAS). As a result, 313 quantitative trait nucleotides (QTNs) were identified for the non-conditional FT traits in single-environment analysis, while 119 QTNs and 67 QTN-by-environment interactions (QEIs) were identified in multi-environment analysis. As for the conditional traits, 343 QTNs were detected in single-environment analysis, and 119 QTNs and 83 QEIs were identified in multi- environment analysis. Among the genes around stable QTNs and QEIs, 36 were orthologs of known FT genes in Arabidopsis and other plants; 14 candidates were mined by combining the transcriptomics data and functional annotation, including ERF-1, ACA10, and FOP1. Furthermore, the haplotype analysis of ERF-1 revealed six elite accessions with extreme FBD. Our findings contribute to the understanding of dynamic genetic architecture of FT and provide valuable resources for future chrysanthemum molecular breeding programs.

HSP90β regulates EAAT2 expression and participates in ischemia‑reperfusion injury in rats

Cerebrovascular diseases (CVDs) have become a global public health problem and ischemia‑reperfusion injury, the major cause of neurological impairment exacerbation, is closely related to excitotoxicity. The present study aimed to investigate the effects of changes in heat shock protein (HSP)90β expression and verify whether HSP90β regulates EAAT2 expression in a cerebral ischemia‑reperfusion injury model. Healthy adult Sprague‑Dawley (SD) male rats were used to establish a control group, sham‑operated group, middle cerebral artery occlusion (MCAO) group, empty virus group and lentivirus group. A model of cerebral ischemia‑reperfusion was established using the MCAO method. Lentivirus construction and injection were used to interfere with the expression of HSP90β. The modified neurological severity score was used to assess neurological deficits. Triphenyltetrazolium chloride staining was used to detect infarct areas. Immunofluorescence was used to detect HSP90β expression localization and the expression levels of HSP90β and EAAT2 were determined using western blotting and reverse transcription‑quantitative PCR. An MCAO model was successfully established and it was found that HSP90β, but not HSP90α, was upregulated after MCAO. HSP90β expression coincided with astrocyte markers in the ischemic penumbra area, while no expression was observed in microglia. Inhibition of HSP90β expression improved neurological deficits and alleviated brain injury by increasing EAAT2 expression. These results suggested that HSP90β is involved in the process of cerebral ischemia‑reperfusion injury in rats and that inhibition of HSP90β expression increases EAAT2 levels, conferring a neuroprotective effect in MCAO model rats.

Green and economic flame retardant prepared by the one-step method for polylactic acid

Resolving the flammability of poly(L-lactic acid) (PLA) while ensuring its environmental friendliness and preserving key flame retardancy and mechanical properties represents a critical challenge. We have successfully developed a highly efficient and environmentally friendly flame retardant called Hexamethylenediamine tetramethylene phosphonic acid amine (HDME). The flame retardancy of PLA/HDME composites was significantly improved, as indicated by the LOI value of 29.1 % and UL-94 V-0 rating for PLA/3.5 HDME with only 3.5 % HDME addition. The results show a 23.4 % reduction in the total heat release (THR), a 40.0 % increase in the time to ignition (TTI), and a 21.2 % increase in the flame propagation index (FPI) compared to original PLA. Flame retardant mechanism of HDME involves the gas phase, condensed phase, and interrupted heat exchange effects. The HDME also preserved the original mechanical properties of PLA, with the elongation at break and tensile strength retention of PLA/3.5 HDME reaching 93.05 % and 89.65 %. This work provides a simple and efficient method for flame retardant modification of PLA, which can expand its application scope.

[Seroprevalence of the specific antibody against Toxoplasma gondii among patients with hematological diseases]

OBJECTIVE

To investigate the seroprevalence of Toxoplasma gondii infections among patients with hematological diseases, so as to provide insights into improving the prognosis and quality of life among patients with hematological diseases.

METHODS

A total of 240 patients with hematological diseases (including 170 patients with hematological tumors and 70 patients with non-tumor hematological diseases) admitted to The Affiliated Hospital of Putian University during the period from January 1, 2021 through October 10, 2023 and 500 healthy volunteers in the hospital during the same period were enrolled. Subjects' demographics and serum samples were collected, and serum specific IgG and IgM antibodies against T. gondii were detected using the chemiluminescence assay, with any of a positive IgG or IgM antibody defined as a positive T. gondii infection. The seroprevalence of specific IgG and IgM antibodies against T. gondii was compared between patients with hematological diseases and healthy volunteers.

RESULTS

The mean age (F = 2.034, P > 0.05) and gender distribution (χ2 = 0.462, P > 0.05) were comparable among patients with hematological tumors, patients with non-tumor hematological diseases and healthy volunteers, and there was no significant difference in the proportion of history of cat or dog contacts between patients with hematological diseases and healthy volunteers (χ2 = 0, P > 0.05). The seroprevalence of anti-T. gondii antibody was significantly higher among patients with hematological diseases than among healthy volunteers (15.8% vs. 0.6%; χ2 = 71.902, P < 0.01), and there was a significant difference in the seroprevalence of anti-T. gondii antibody among patients with hematological tumors (18.2%), patients with non-tumor hematological diseases (10.0%) and healthy volunteers (χ2 = 78.327, P < 0.01). The seroprevalence of anti-T. gondii antibody was significantly higher among patients with hematological tumors and non-tumor hematological diseases than among healthy volunteers (both P values < 0.05), while no significant difference was seen in the seroprevalence of anti-T. gondii antibody between patients with hematological tumors and non-tumor hematological diseases (P > 0.05). In addition, the proportion of history of cat or dog contacts was significantly higher among patients with hematological diseases that were positive for serum anti-T. gondii anti-body than among those negative for serum anti-T. gondii antibody (21.1% vs. 5.4%; χ2 = 8.653, P < 0.05).

CONCLUSIONS

There is a high seroprevalene rate of T. gondii infections among hematological diseases, which is significantly greater than that among healthy volunteers.

Energy-Efficient ReS2-Based Optoelectronic Synapse for 3D Object Reconstruction and Recognition

The neuromorphic vision system (NVS) equipped with optoelectronic synapses integrates perception, storage, and processing and is expected to address the issues of traditional machine vision. However, owing to their lack of stereo vision, existing NVSs focus on 2D image processing, which makes it difficult to solve problems such as spatial cognition errors and low-precision interpretation. Consequently, inspired by the human visual system, an NVS with stereo vision is developed to achieve 3D object recognition, depending on the prepared ReS2 optoelectronic synapse with 12.12 fJ ultralow power consumption. This device exhibits excellent optical synaptic plasticity derived from the persistent photoconductivity effect. As the cornerstone for 3D vision, color planar information is successfully discriminated and stored in situ at the sensor end, benefiting from its wavelength-dependent plasticity in the visible region. Importantly, the dependence of the channel conductance on the target distance is experimentally revealed, implying that the structure information on the object can be directly captured and stored by the synapse. The 3D image of the object is successfully reconstructed via fusion of its planar and depth images. Therefore, the proposed 3D-NVS based on ReS2 synapses for 3D objects achieves a recognition accuracy of 97.0%, which is much higher than that for 2D objects (32.6%), demonstrating its strong ability to prevent 2D-photo spoofing in applications such as face payment, entrance guard systems, and others.

Multi-locus genome-wide association study and genomic prediction for flowering time in chrysanthemum

MAIN CONCLUSION

Multi-locus GWAS detected several known and candidate genes responsible for flowering time in chrysanthemum. The associations could greatly increase the predictive ability of genome selection that accelerates the possible application of GS in chrysanthemum breeding. Timely flowering is critical for successful reproduction and determines the economic value for ornamental plants. To investigate the genetic architecture of flowering time in chrysanthemum, a multi-locus genome-wide association study (GWAS) was performed using a collection of 200 accessions and 330,710 single-nucleotide polymorphisms (SNPs) via 3VmrMLM method. Five flowering time traits including budding (FBD), visible colouring (VC), early opening (EO), full-bloom (OF) and senescing (SF) stages, plus five derived conditional traits were recorded in two environments. Extensive phenotypic variations were observed for these flowering time traits with coefficients of variation ranging from 6.42 to 38.27%, and their broad-sense heritability ranged from 71.47 to 96.78%. GWAS revealed 88 stable quantitative trait nucleotides (QTNs) and 93 QTN-by-environment interactions (QEIs) associated with flowering time traits, accounting for 0.50-8.01% and 0.30-10.42% of the phenotypic variation, respectively. Amongst the genes around these stable QTNs and QEIs, 21 and 10 were homologous to known flowering genes in Arabidopsis; 20 and 11 candidate genes were mined by combining the functional annotation and transcriptomics data, respectively, such as MYB55, FRIGIDA-like, WRKY75 and ANT. Furthermore, genomic selection (GS) was assessed using three models and seven unique marker datasets. We found the prediction accuracy (PA) using significant SNPs identified by GWAS under SVM model exhibited the best performance with PA ranging from 0.90 to 0.95. Our findings provide new insights into the dynamic genetic architecture of flowering time and the identified significant SNPs and candidate genes will accelerate the future molecular improvement of chrysanthemum.

Effects of lysolecithins on performance, egg quality, blood profiles and liver histopathology in late-phase laying hens

1. This study investigated the effects of lysolecithins (LL) on performance, egg quality, blood profiles, relative organ weight and liver histopathology in laying hens.2. A total of 480 healthy 65-week-old Lohmann laying hens were randomly allocated into four treatments in a 2 × 2 factorial arrangement design with two levels of energy (AMEn, 11.08 MJ/kg and 12.94 MJ/kg) and two levels of LL (0 and 0.05%).3. Birds fed high energy diets had lower (P < 0.05) average daily intake and feed conversion rate during weeks 0-4, 5-8 and 0-8, but higher (P < 0.05) average egg weight (AEW) during trial weeks 0-4. There was an interaction in (P < 0.05) AEW during trial weeks 0-14 and 0-8 for energy and LL. The high energy diets increased yolk colour at the end of weeks 2 and 4, while addition of LL increased albumen height at the end of week 2. There was an interaction (P < 0.05) in yolk colour between energy and LL at the end of week 2. There was an interaction (P < 0.05) in serum superoxide dismutase and LDL-C throughout the experiment.4. The high energy diets increased (P < 0.05) the relative weight of abdominal fat compared with low energy diets. The high energy diets increased (P < 0.05) liver ether extract content and liver pathological injury score compared with low energy diets at the end of week 8, while the addition of LL decreased (P < 0.05) liver pathological injury score.5. The supplementation of LL in high energy diets could alleviate some negative effects on liver injury in late laying hens.

Developing flexible models for genetic evaluations in smallholder crossbred dairy farms

The productivity of smallholder dairy farms is very low in developing countries. Important genetic gains could be realized using genomic selection, but genetic evaluations need to be tailored for lack of pedigree information and very small farm sizes. To accommodate this situation, we propose a flexible Bayesian model for the genetic evaluation of milk yield, which allows us to simultaneously account for nongenetic random effects for farms and varying SNP variance (BayesR model). First, we used simulations based on real genotype data from Indian crossbred dairy cattle to demonstrate that the proposed model can separate the true genetic and nongenetic parameters even for small farm sizes (2 cows on average) although with high standard errors in scenarios with low heritability. The accuracy of genomic genetic evaluation increased until farm size was approximately 5. We then applied the model to real data from 4,655 crossbred cows with 106,109 monthly test day milk records and 689,750 autosomal SNPs. We estimated a heritability of 0.16 (0.04) for milk yield and using cross-validation, a genomic estimated breeding value (GEBV) accuracy of 0.45 and bias (regression of phenotype on GEBV) of 1.04 (0.26). Estimated genetic parameters were very similar using BayesR, BayesC, and genomic BLUP approaches. Candidate genes near the top variants, IMMP2L and ARHGEF2, have been previously associated with milk protein composition, mastitis resistance, and milk cholesterol content. The estimated heritability and GEBV accuracy for milk yield are much lower than those from intensive or pasture-based systems in many countries. Further increases in the number of phenotyped and genotyped animals in farms with at least 2 cows (preferably 3-5, to allow for dropout of cows) are needed to improve the estimation of genetic effects in these smallholder dairy farms.

Prostate Advanced Radiation Technologies Investigating Quality of Life (PARTIQoL): A Phase III Randomized Clinical Trial of Proton Therapy vs. IMRT for Low or Intermediate Risk Prostate Cancer

PURPOSE/OBJECTIVE(S)

Prostate cancer is the most common non-cutaneous cancer diagnosed among men in the United States, and the majority of patients are diagnosed with localized disease. Men with localized prostate cancer have several treatment options including external beam radiotherapy with either photons or protons. Proton beam therapy (PBT) has certain dosimetric advantages and the potential to reduce treatment-associated morbidity and improve oncologic outcomes, but current PBT is significantly more costly than intensity-modulated radiotherapy (IMRT). The PARTIQoL trial (NCT01617161) is the first multicenter phase 3 randomized trial comparing protons to photons in the treatment of localized prostate cancer.

MATERIALS/METHODS

Patients with low or intermediate risk prostate cancer (Stage T1c-T2c, PSA < 20, Gleason score ≤ 7) are randomized to receive either PBT or IMRT, with targeted recruitment efforts for minority populations. A companion registry study has concurrently enrolled patients who declined randomization or whose insurance denied coverage for PBT. Patients are stratified by clinical site, age, use of rectal spacer, and fractionation schedule (conventional fractionation: 79.2 Gy in 44 fractions vs moderate hypofractionation: 70.0 Gy in 28 fractions). Participants are followed longitudinally to assess patient-reported outcomes (PROs) of bowel, urinary, and erectile function for 60 months after completion of radiotherapy (with an option for additional follow up through 10 years). Participants may also participate in correlative studies, including serial CT imaging during treatment and analyses of biopsy tissue, blood and urine specimens. The primary objective is to compare PROs of bowel function using the EPIC score at 24 months following completion of radiation. Secondary objectives are to assess treatment-related differences in urinary and erectile functions, adverse events, efficacy endpoints (biochemical control, metastasis-free survival, disease-specific survival, and overall survival), health state utilities, perceptions of care, late effects, cost-effectiveness, association between radiotherapy dose distribution and PROs, and to identify biomarkers of radiation response and toxicity.

RESULTS

The randomized trial has completed accrual, with 450 patients enrolled at 27 sites between June 2012 and November 2021. 20.3% of patients enrolled are non-white. Accrual on the companion registry is active, with 354 patients enrolled as of February 2023.

CONCLUSION

Follow-up for the primary endpoint on the randomized trial will be reached in 2024. The PARTIQoL randomized clinical trial will rigorously assess the clinical benefits of PBT relative to IMRT and results will inform decision making by patients, providers, policymakers, and payers.

Proton Radiation Therapy for Stage IIA/IIB Testicular Seminoma

PURPOSE/OBJECTIVE(S)

Testicular seminoma affects young men and is associated with very favorable prognosis. The evolution in treatment paradigm has focused on minimizing acute and especially late toxicities. Following orchiectomy, while surveillance is favored in Stage I patients, radiotherapy (RT) is a standard treatment option for de novo or relapsed stage IIA or select non-bulky stage IIB disease. Despite low doses, standard RT fields to paraaortic and pelvic lymphatics using x-rays exposes a large volume of uninvolved normal tissue/viscera to excess dose. This young patient population is especially vulnerable to risks of late RT toxicities including secondary malignancy. Proton beam therapy (PBT) has dosimetric advantage over x-ray-based RT due to lack of exit dose, and comparative dosimetric/modeling studies show significant sparing of uninvolved abdominal/pelvic organs. However, there is scant reported clinical data at this time for PBT. We review our early institutional outcomes with PBT for testicular seminoma.

MATERIALS/METHODS

Single institution retrospective review from a tertiary care center of patients treated with PBT from 2013-2022 for testicular seminoma. Recurrence free (RFS) and overall survival (OS) were calculated from the completion of PBT. Toxicities were graded (Gr) using CTCAE v5.0.

RESULTS

Four patients underwent PBT, median age 39 (range 36-47). All were Stage I at diagnosis (pT1b n = 3; pT2 n = 1) and were treated for recurrent stage II disease (IIA n = 3; IIB n = 1) at a median of 34 months from orchiectomy (range 3 - 74 months). Nodal extent included 2 with multiple paraaortic nodes, 1 with solitary paraaortic node and 1 with solitary pelvic node. PBT was delivered with pencil-beam scanning, treating paraaortic + ipsilateral pelvic fields (20 Gy in 10 fractions), then sequential boost to involved nodes (10 -16 Gy in 5-8 fractions). Typically, PA or posterior oblique fields were used to minimize dose to out-of-field abdominal/pelvic viscera. Treatment was well tolerated with minimal acute toxicities: fatigue Gr 1 (n = 3), nausea Gr 1 (n = 3). No Gr 2 or higher acute toxicities or significant late toxicities were observed. At median follow up of 30 months (range 3 - 54), no recurrences were observed, and RFS and OS were 100%. Two patients are without evidence of disease > 4 years post-treatment.

CONCLUSION

In this case series, PBT for retroperitoneal and pelvic metastases in Stage IIA/IIB testicular seminoma was associated with oncologic efficacy with minimal toxicity. PBT reduces unnecessary dose to abdominal/pelvic organs compared to x-ray techniques, which is advantageous in young patients who have anticipated long-term survival. This is one of the few series reporting clinical outcomes of PBT in the management of seminoma. Randomized comparisons with x-ray approaches are impractical given the relatively low volume of patients receiving RT in modern seminoma management, so it is essential to report and track longitudinal outcomes across institutions to validate this approach.

Treatment of Thymoma and Thymic Carcinoma with Proton Beam Therapy: Outcomes from the Proton Collaborative Group Prospective Registry

PURPOSE/OBJECTIVE(S)

Given the generally long natural history of thymic malignancies, proton beam therapy (PBT) is advocated to minimize the risk of long-term toxicities to mediastinal organs. Adverse events (AE) and long-term clinical outcomes for this population have not been well-characterized.

MATERIALS/METHODS

The Proton Collaborative Group registry (NCT01255748), a multi-institutional prospective database of academic and community proton centers in the US, was queried for patients with thymomas and thymic carcinomas treated with PBT. Patients with recurrent/metastatic disease, non-thymic histology, received either prior or palliative radiotherapy (dose < 40 Gy RBE) were excluded. Overall survival (OS) and local control (LC) were estimated using Kaplan-Meier methods.

RESULTS

A total of 97 patients were identified in the PCG registry. After applying relevant exclusion criteria, 70 patients from 12 proton centers treated from 2011-2021 were included for analysis. Median follow-up length was 16 months. Median age was 58.5 years (IQR 46-63), and 60% were female. 81.4% had a diagnosis of thymoma, and 18.6% thymic carcinoma. 59 patients underwent surgical resection. 11 were treated with definitive PBT, of which 5 received concurrent chemotherapy. Median dose was 54 Gy RBE (range 41.4 - 70 Gy RBE), median number of fractions was 30 (range 21 - 38). 73.4% received pencil beam scanning and 23% uniform scanning PBT. Treatment was overall well-tolerated: a single patient developed grade 4 pneumonitis. Grade 3 AEs were seen in 3 patients - dyspnea, anorexia, and heart failure. Highest grade toxicity experienced was grade 2 for 47.1% and grade 1 for 42.9% of patients. 3-year overall survival (OS) was 82.6% for the entire cohort. 3-year OS was 94% for resected/adjuvant cohort and 35.6% in the non-surgical/definitive cohort. 3-year local control (LC) was 91.7% for the entire cohort. By surgery/margin status, 3-year LC was 96.8% in patients with close or negative margins (a single failure in a patient with close margins), whereas 3-year LC was 55.1% for patients with positive margins/unresectable disease.

CONCLUSION

Thymic malignancies treated with PBT appear to have favorable outcomes, especially in the adjuvant setting, in this cohort representing the largest series of such patients.

Multi-Institutional Experience of Proton Therapy for Rhabdomyosarcoma and Ewing Sarcoma in the Proton Collaborative Group (PCG) Prospective Registry

PURPOSE/OBJECTIVE(S)

To report on outcomes, acute toxicities, and the use of dose-escalation with proton therapy (PT) in patients with rhabdomyosarcoma and Ewing sarcoma in a prospective multi-institutional registry (PCG).

MATERIALS/METHODS

Data on patients with primary rhabdomyosarcoma and Ewing sarcoma treated with definitive PT (defined as ≥45 Gy) were queried from the PCG registry. A similar query was performed of our institutional database with IRB approval. Overall survival rates were calculated by Kaplan-Meier. Toxicities were scored using CTCAE v4.0.

RESULTS

A total of 354 patients across 10 institutions (203 rhabdomyosarcoma, 151 Ewing sarcoma) met the eligibility criteria. Median age was 9 years (Interquartile Range: 5-15). Median dose was 50.4 GyRBE for rhabdomyosarcoma patients (Range: 45-66 GyRBE) and 55.8 GyRBE for Ewing sarcoma patients (Range: 45-66 GyRBE). Median follow-up was 2.4 years (Range 0.3-12.3 years). Two-year overall survival rates were 81.1% (95% CI: 73.7%-88.5%) for rhabdomyosarcoma and 79.1% (95% CI: 71.7%-86.2%) for Ewing sarcoma. The Table lists the prescription doses delivered by tumor histology; 28.1% of rhabdomyosarcoma and 21.9% of Ewing sarcoma patients, respectively, received dose-escalated radiotherapy (defined as >50.4 Gy for rhabdomyosarcoma and >55.8 Gy for Ewing sarcoma). Excluding alopecia and skin desquamation, 153 patients (43.2%) developed any acute grade 2+ non-hematologic toxicity, while 49 patients (13.8%) developed one or more grade 3 toxicities. The most common grade 3 toxicities were anorexia/weight loss (7.3%), pain (7.3%) mucositis/esophagitis (4.8%), and nausea/vomiting (3.1%). One grade 4 toxicity (esophagitis) and no deaths were reported during treatment.

CONCLUSION

In this multi-institutional prospective registry, 28.1% of rhabdomyosarcoma and 21.9% of Ewing sarcoma patients received dose-escalated PT, with 13.8% of patients developing grade 3 toxicities. Long-term outcomes for disease control and late toxicity and anticipated cooperative group trial results are needed to fully assess the benefits and risks of dose-escalated radiotherapy for these tumors.

Adaptation of a Clinical Proton Pencil Beam Scanning System for FLASH Experiments

PURPOSE/OBJECTIVE(S)

To characterize a proton pencil beam scanning system for ultra-high dose rate (UHDR) irradiations and validate it with FLASH preclinical experiments.

MATERIALS/METHODS

After modifications to the beamline to maximize the beam current at isocenter in our gantry room, we characterized the UHDR beam in terms of: 1) Size and shape of the beam spot in three configurations; pristine beam, 75 mm water-equivalent-thickness (WET) range shifter (RS), and custom-built 135 mm WET RS mounted 310 mm upstream of the aperture in the snout housing. These configurations were analyzed to determine which one achieved the highest dose rate; 2) Beam transport efficiency and beam output. We compared the signal in the monitor chambers of the proton system with a Faraday cup and plane parallel ionization chamber (PPC05, IBA dosimetry) for beam current at the cyclotron from 7.5 nA to 800 nA; 3) Dose homogeneity, beam penumbra, and dose rate for the fields to be used in preclinical irradiations. All measurements were performed at isocenter, in air or at 1 cm depth in solid water, using the highest energy (about 230 MeV), which corresponded to a nominal range of 32.9 cm in water. We modeled the UHDR beam in our treatment planning system (TPS) to optimize the dose homogeneity and lateral penumbra of the irradiation fields. We performed the preclinical experiments in single fractions of 19 Gy (RBE), 21 Gy (RBE) and 23 Gy (RBE) (RBE = 1.1), targeting the pelvis of C57BL/6 mice and using survival as the endpoint. Each arm included 6-10 mice. The proton beam was used in transmission mode, positioning the center of the mouse pelvis at isocenter, and irradiating the pelvis with a 2x6 cm^2 field. Apertures were placed at 9cm from the isocenter to sharpen the lateral penumbra.

RESULTS

The range measurements with a multi-layer ionization chamber were consistent within 1 mm with the nominal range. In UHDR mode, the spot size at the isocenter varied from 4.5 mm for the pristine beam to 9.2 mm for the 135 mm RS. The spot size at isocenter remained constant when the beam intensity varied from 7.5 nA to 800 nA at the cyclotron exit. By employing the configuration with the 135 mm RS and optimizing the fields in the TPS, we achieved a dose rate of 1 Gy (RBE)/s for the conventional regime and 75(RBE) Gy/s for the UHDR regime. The monitor chambers of the proton system were affected by recombination at high dose rates: we observed about 35% higher output for the same number of monitor units delivered at 800 nA vs 7.5 nA. The delivered dose was determined with the PPC05 for each field, as this detector did not show recombination effects. When preclinical irradiations were independently monitored, the delivered dose was typically within 1% of the intended value. In three independent experiments, a dose of 21 Gy (RBE) or higher was associated with an increased survival in the UHDR arm compared to the conventional arm.

CONCLUSION

We adapted a clinical proton system for preclinical irradiations at UHDR. Our results confirm the presence of the FLASH effect.

Multi-Institutional Experience of Proton Therapy for Osteosarcoma in the Proton Collaborative Group (PCG) Prospective Registry

PURPOSE/OBJECTIVE(S)

To report on the utilization of dose-escalated radiotherapy, acute toxicities, and survival following definitive proton therapy (PT) for osteosarcoma patients in a prospective multi-institutional study.

MATERIALS/METHODS

Data on patients with osteosarcoma treated with definitive intent PT were queried from the Proton Collaborative Group (PCG) prospective registry. A similar query was performed on an institutional database with IRB approval. Overall survival rates were calculated by Kaplan-Meier. Toxicities were scored using CTCAE v4.0.

RESULTS

Forty osteosarcoma patients across 9 institutions received definitive intent PT between 2011-2021 and met the eligibility criteria. Median age was 32 years (Range: 6-86 years). Median PT dose was 66.6 GyRBE (Range: 50.4-80.0 GyRBE); 38 patients received proton therapy alone, whereas 2 received combined proton/photon therapy. Seventeen (42.5%) patients received doses ≥70 GyRBE. Median follow-up was 3.1 years (Range: 0.9-10.5 years). One-year and three-year overall survival rates were 83.5% and 59.1%, respectively, with 14 deaths due to disease. Excluding skin desquamation and alopecia, 22 patients (55.0%) developed any acute grade 2+ toxicity, and 5 patients (12.5%) developed any grade 3 toxicities. No acute grade 4-5 toxicities were reported. The most frequent grade 2+ non-skin toxicities were fatigue (37.5%), anorexia/weight loss (17.5%), mucositis/esophagitis (22.5%), pain (20.0%), and nausea/vomiting (10.0%). The most frequent grade 3 toxicities were anorexia/weight loss (5.0%), mucositis/esophagitis (5.0%), and neurologic symptoms (5.0%).

CONCLUSION

In this multi-institutional study, 42.5% of osteosarcoma patients treated with PT received doses between 70-80 Gy, with 12.5% experiencing any grade 3 toxicity. Long-term outcomes for disease control, late toxicity, and quality-of-life are needed to more fully assess the benefits and risks of dose-escalated radiotherapy in this radioresistant tumor. The authors plan to assess the outcomes of osteosarcoma patients treated with dose-escalated radiotherapy for unresectable or gross residual disease in future studies.

Targeting altered glycosylation in secreted tumor glycoproteins for broad cancer detection

There is an urgent need to develop new tumor biomarkers for early cancer detection, but the variability of tumor-derived antigens has been a limitation. Here we demonstrate a novel anti-Tn antibody microarray platform to detect Tn+ glycoproteins, a near universal antigen in carcinoma-derived glycoproteins, for broad detection of cancer. The platform uses a specific recombinant IgG1 to the Tn antigen (CD175) as a capture reagent and a recombinant IgM to the Tn antigen as a detecting reagent. These reagents were validated by immunohistochemistry in recognizing the Tn antigen using hundreds of human tumor specimens. Using this approach, we could detect Tn+ glycoproteins at subnanogram levels using cell lines and culture media, serum, and stool samples from mice engineered to express the Tn antigen in intestinal epithelial cells. The development of a general cancer detection platform using recombinant antibodies for detection of altered tumor glycoproteins expressing a unique antigen could have a significant impact on cancer detection and monitoring.

Climate-driven variability of the Southern Ocean CO2 sink

The Southern Ocean is a major sink of atmospheric CO2, but the nature and magnitude of its variability remains uncertain and debated. Estimates based on observations suggest substantial variability that is not reproduced by process-based ocean models, with increasingly divergent estimates over the past decade. We examine potential constraints on the nature and magnitude of climate-driven variability of the Southern Ocean CO2 sink from observation-based air-sea O2 fluxes. On interannual time scales, the variability in the air-sea fluxes of CO2 and O2 estimated from observations is consistent across the two species and positively correlated with the variability simulated by ocean models. Our analysis suggests that variations in ocean ventilation related to the Southern Annular Mode are responsible for this interannual variability. On decadal time scales, the existence of significant variability in the air-sea CO2 flux estimated from observations also tends to be supported by observation-based estimates of O2 flux variability. However, the large decadal variability in air-sea CO2 flux is absent from ocean models. Our analysis suggests that issues in representing the balance between the thermal and non-thermal components of the CO2 sink and/or insufficient variability in mode water formation might contribute to the lack of decadal variability in the current generation of ocean models. This article is part of a discussion meeting issue 'Heat and carbon uptake in the Southern Ocean: the state of the art and future priorities'.

Patching sulfur vacancies: A versatile approach for achieving ultrasensitive gas sensors based on transition metal dichalcogenides

Transition metal dichalcogenides (TMDCs) garner significant attention for their potential to create high-performance gas sensors. Despite their favorable properties such as tunable bandgap, high carrier mobility, and large surface-to-volume ratio, the performance of TMDCs devices is compromised by sulfur vacancies, which reduce carrier mobility. To mitigate this issue, we propose a simple and universal approach for patching sulfur vacancies, wherein thiol groups are inserted to repair sulfur vacancies. The sulfur vacancy patching (SVP) approach is applied to fabricate a MoS₂-based gas sensor using mechanical exfoliation and all-dry transfer methods, and the resulting 4-nitrothiophenol (4NTP) repaired molybdenum disulfide (4NTP-MoS₂) is prepared via a sample solution process. Our results show that 4NTP-MoS₂ exhibits higher response (increased by 200 %) to ppb-level NO₂ with shorter response/recovery times (61/82 s) and better selectivity at 25 °C compared to pristine MoS₂. Notably, the limit of detection (LOD) toward NO₂ of 4NTP-MoS₂ is 10 ppb. Kelvin probe force microscopy (KPFM) and density functional theory (DFT) reveal that the improved gas sensing performance is mainly attributed to the 4NTP-induced n-doping effect on MoS₂ and the corresponding increment of surface absorption energy to NO₂. Additionally, our 4NTP-induced SVP approach is universal for enhancing gas sensing properties of other TMDCs, such as MoSe₂, WS₂, and WSe₂.

Germline C1GALT1C1 mutation causes a multisystem chaperonopathy

Mutations in genes encoding molecular chaperones can lead to chaperonopathies, but none have so far been identified causing congenital disorders of glycosylation. Here we identified two maternal half-brothers with a novel chaperonopathy, causing impaired protein O-glycosylation. The patients have a decreased activity of T-synthase (C1GALT1), an enzyme that exclusively synthesizes the T-antigen, a ubiquitous O-glycan core structure and precursor for all extended O-glycans. The T-synthase function is dependent on its specific molecular chaperone Cosmc, which is encoded by X-chromosomal C1GALT1C1. Both patients carry the hemizygous variant c.59C>A (p.Ala20Asp; A20D-Cosmc) in C1GALT1C1. They exhibit developmental delay, immunodeficiency, short stature, thrombocytopenia, and acute kidney injury (AKI) resembling atypical hemolytic uremic syndrome. Their heterozygous mother and maternal grandmother show an attenuated phenotype with skewed X-inactivation in blood. AKI in the male patients proved fully responsive to treatment with the complement inhibitor Eculizumab. This germline variant occurs within the transmembrane domain of Cosmc, resulting in dramatically reduced expression of the Cosmc protein. Although A20D-Cosmc is functional, its decreased expression, though in a cell or tissue-specific manner, causes a large reduction of T-synthase protein and activity, which accordingly leads to expression of varied amounts of pathological Tn-antigen (GalNAcα1-O-Ser/Thr/Tyr) on multiple glycoproteins. Transient transfection of patient lymphoblastoid cells with wild-type C1GALT1C1 partially rescued the T-synthase and glycosylation defect. Interestingly, all four affected individuals have high levels of galactose-deficient IgA1 in sera. These results demonstrate that the A20D-Cosmc mutation defines a novel O-glycan chaperonopathy and causes the altered O-glycosylation status in these patients.

Denosumab salvage therapy in an 11-year-old boy with locally recurrent unresectable giant cell tumor of the lumbar spine after surgery

Giant cell tumors (GCTs) of the bone are locally aggressive primary bone tumors with a benign character. Spinal involvement is rare which accounts for approximately 5% of all primary bone tumors and it is quite rare in the lumbar spine. An 11-year-old boy patient presented with pain of low back and bilateral low extremities. Lumbar CT and MRI revealed a lytic lesion of the L4 vertebra corpus. The patient earned remarkable and timely recovery with 2 surgical interventions and the use of denosumab. Surgical resection for GCTs is still preferable as the initial treatment, denosumab should be utilized after tumor resection whether based on the purpose of prevention or treatment of tumor recurrence.