Search

Characterizing the binding preferences of transcription factors (TFs) in different cell types and conditions is key to understand how they orchestrate gene expression. Here, we develop TFscope, a machine learning approach that identifies sequence features explaining the binding differences observed between two ChIP-seq experiments targeting either the same TF in two conditions or two TFs with similar motifs (paralogous TFs). TFscope systematically investigates differences in the core motif, nucleotide environment and co-factor motifs, and provides the contribution of each key feature in the two experiments. TFscope was applied to > 305 ChIP-seq pairs, and several examples are discussed., (© 2024. The Author(s).)

Stereotactic radiotherapy (SRT ) is a multi-step procedure with each step requiring extreme accuracy. Physician-dependent accuracy includes appropriate disease staging, multi-disciplinary discussion with shared decision-making, choice of morphological and functional imaging methods to identify and delineate the tumor target and organs at risk, an image-guided patient set-up, active or passive management of intra-fraction movement, clinical and instrumental follow-up. Medical physicist-dependent accuracy includes use of advanced software for treatment planning and more advanced Quality Assurance procedures than required for conventional radiotherapy. Consequently, all the professionals require appropriate training in skills for high-quality SRT. Thanks to the technological advances, SRT has moved from a "frame-based" technique, i.e. the use of stereotactic coordinates which are identified by means of rigid localization frames, to the modern "frame-less" SRT which localizes the target volume directly, or by means of anatomical surrogates or fiducial markers that have previously been placed within or near the target. This review describes all the SRT steps in depth, from target simulation and delineation procedures to treatment delivery and image-guided radiation therapy. Target movement assessment and management are also described., Competing Interests: Conflicts of interest The authors have no conflict of interest to declare., (© 2022 Greater Poland Cancer Centre.)

The liver is the first metastatic site in 15-25% of colorectal cancer patients and one of the first metastatic sites for lung and breast cancer patients. A computed tomography (CT ) scan with contrast medium is a standard procedure for assessing liver lesions but magnetic resonance imaging (MRI) characterizes small lesions better thanks to its high soft-tissue contrast. Positron emission tomography with computed tomography (PET-CT ) plays a complementary role in the diagnosis of liver metastases. Triphasic (arterial, venous and time-delayed) acquisition of contrast-medium CT images is the first step in treatment planning. Since the liver exhibits a relatively wide mobility due to respiratory movements and bowel filling, appropriate techniques are needed for target identification and motion management. Contouring requires precise recognition of target lesion edges. Information from contrast MRI and/or PET-CT is crucial as they best visualize metastatic disease in the parenchyma. Even though different fractionation schedules were reported, doses and fractionation schedules for liver stereotactic radiotherapy (SRT ) have not yet been established. The best local control rates were obtained with BED 10 values over 100 Gy. Local control rates from most retrospective studies, which were limited by short follow-ups and included different primary tumors with intrinsic heterogeneity, ranged from 60% to 90% at 1 and 2 years. The most common SRT-related toxicities are increases in liver enzymes, hyperbilirubinemia and hypoalbuminemia. Overall, late toxicity is mild even in long-term follow-ups., Competing Interests: Conflicts of interest The authors have no conflict of interest to declare., (© 2022 Greater Poland Cancer Centre.)

30-60% of cancer patients develop lung metastases, mostly from primary tumors in the colon-rectum, lung, head and neck area, breast and kidney. Nowadays, stereotactic radiotherapy (SRT ) is considered the ideal modality for treating pulmonary metastases. When lung metastases are suspected, complete disease staging includes a total body computed tomography (CT ) and/or positron emission tomography-computed tomography (PET -CT ) scan. PET -CT has higher specificity and sensitivity than a CT scan when investigating mediastinal lymph nodes, diagnosing a solitary lung lesion and detecting distant metastases. For treatment planning, a multi-detector planning CT scan of the entire chest is usually performed, with or without intravenous contrast media or esophageal lumen opacification, especially when central lesions have to be irradiated. Respiratory management is recommended in lung SRT, taking the breath cycle into account in planning and delivery. For contouring, co-registration and/or matching planning CT and diagnostic images (as provided by contrast enhanced CT or PET-CT ) are useful, particularly for central tumors. Doses and fractionation schedules are heterogeneous, ranging from 33 to 60 Gy in 3-6 fractions. Independently of fractionation schedule, a BED 10 > 100 Gy is recommended for high local control rates. Single fraction SRT (ranges 15-30 Gy) is occasionally administered, particularly for small lesions. SRT provides tumor control rates of up to 91% at 3 years, with limited toxicities. The present overview focuses on technical and clinical aspects related to treatment planning, dose constraints, outcome and toxicity of SRT for lung metastases., Competing Interests: Conflicts of interest The authors have no conflict of interest to declare., (© 2022 Greater Poland Cancer Centre.)

Background: Thymomas can benefit of cytoreductive surgery even if a complete resection is not feasible. The pleural cavity is the most common site of progression and the resection of pleural metastases can be performed in selected patients. We evaluated the results of stereotactic body radiation therapy for the treatment of pleural metastases in patients not eligible for surgery., Methods: We retrospectively selected 22 patients treated with stereotactic body radiation therapy for pleural metastases between 2013 and 2019. According to RECIST criteria 1.1 modified for thymic epithelial tumors, time to local failure and progression free survival were calculated using Kaplan-Meier method., Results: The median age was 40 years (range, 29-73 years). There were 1 A, 3 AB, 3 B1, 3 B2, 3 B2/B3 and 9 B3 thymomas. Pleural metastases and primary tumor were synchronous in 8 patients. Five patients had a single pleural metastatic site and 17 presented multiple localizations. Sixteen patients received stereotactic body radiation therapy on multiple sites of pleural metastases. The median dose of radiation was 30 Gy (range, 24-40 Gy). With a median follow-up of 33.2 months (95% CI: 13.1-53.3 months), ten patients experienced disease progression with a median progression free survival was 20.4 months (95% CI: 10.7-30.0 months). The disease control rate was 79% and 41% after 1 and 2 years, respectively. Local disease control rate was 92% and 78% after 1 and 2 years, respectively. There were not significant differences in progression free survival between patients diagnosed with synchronous and metachronous metastases (P=0.477), across those treated or not with chemotherapy (P=0.189) and between those who received or not a previous surgical resection of the pleural metastases (P=0.871). There were not grade 3-4 toxicities related to the treatment., Conclusions: Stereotactic body radiation therapy of pleural metastases is feasible and offers a promising local control of diseases. The impact of this treatment on patients' survival is hardly predictable because of the heterogeneous clinical behavior of thymomas., Competing Interests: Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://dx.doi.org/10.21037/jtd-19-3799). The authors have no conflicts of interest to declare., (2021 Journal of Thoracic Disease. All rights reserved.)

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism.

Long regulatory elements (LREs), such as CpG islands, polydA:dT tracts or AU-rich elements, are thought to play key roles in gene regulation but, as opposed to conventional binding sites of transcription factors, few methods have been proposed to formally and automatically characterize them. We present here a computational approach named DExTER (Domain Exploration To Explain gene Regulation) dedicated to the identification of candidate LREs (cLREs) and apply it to the analysis of the genomes of P. falciparum and other eukaryotes. Our analyses show that all tested genomes contain several cLREs that are somewhat conserved along evolution, and that gene expression can be predicted with surprising accuracy on the basis of these long regions only. Regulation by cLREs exhibits very different behaviours depending on species and conditions. In P. falciparum and other Apicomplexan organisms as well as in Dictyostelium discoideum, the process appears highly dynamic, with different cLREs involved at different phases of the life cycle. For multicellular organisms, the same cLREs are involved in all tissues, but a dynamic behavior is observed along embryonic development stages. In P. falciparum, whose genome is known to be strongly depleted of transcription factors, cLREs are predictive of expression with an accuracy above 70%, and our analyses show that they are associated with both transcriptional and post-transcriptional regulation signals. Moreover, we assessed the biological relevance of one LRE discovered by DExTER in P. falciparum using an in vivo reporter assay. The source code (python) of DExTER is available at https://gite.lirmm.fr/menichelli/DExTER., Competing Interests: The authors have declared that no competing interests exist.

Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss several hits, especially for species that are phylogenetically distant from reference organisms. A solution to this problem is then to integrate additional contextual information to the procedure. Here, we propose to use domain co-occurrence to increase the sensitivity of pairwise sequence comparisons. Domain co-occurrence is a strong feature of proteins, since most protein domains tend to appear with a limited number of other domains on the same protein. We propose a method to take this information into account in a typical BLAST analysis and to construct new domain families on the basis of these results. We used Plasmodium falciparum as a case study to evaluate our method. The experimental findings showed an increase of 14% of the number of significant BLAST hits and an increase of 25% of the proteome area that can be covered with a domain. Our method identified 2240 new domains for which, in most cases, no model of the Pfam database could be linked. Moreover, our study of the quality of the new domains in terms of alignment and physicochemical properties show that they are close to that of standard Pfam domains. Source code of the proposed approach and supplementary data are available at: https://gite.lirmm.fr/menichelli/pairwise-comparison-with-cooccurrence.

Purpose: To evaluate a retrospective single-institution outcome after hypofractionated stereotactic body radiotherapy (SBRT) for adrenal metastases., Methods and Materials: Between February 2002 and December 2009, we treated 48 patients with SBRT for adrenal metastases. The median age of the patient population was 62.7 years (range, 43-77 years). In the majority of patients, the prescription dose was 36 Gy in 3 fractions (70% isodose, 17.14 Gy per fraction at the isocenter). Eight patients were treated with single-fraction stereotactic radiosurgery and forty patients with multi-fraction stereotactic radiotherapy., Results: Overall, the series of patients was followed up for a median of 16.2 months (range, 3-63 months). At the time of analysis, 20 patients were alive and 28 patients were dead. The 1- and 2-year actuarial overall survival rates were 39.7% and 14.5%, respectively. We recorded 48 distant failures and 2 local failures, with a median interval to local failure of 4.9 months. The actuarial 1-year disease control rate was 9%; the actuarial 1- and 2-year local control rate was 90%., Conclusion: Our retrospective study indicated that SBRT for the treatment of adrenal metastases represents a safe and effective option with a control rate of 90% at 2 years., (Copyright © 2012 Elsevier Inc. All rights reserved.)

Aims and Background: Surveys in clinical practice are useful to find how current clinical approaches follow recommendations from evidence-based medicine, to stimulate discussion in a multidisciplinary team, and to hypothesize collaborative multicentric trials. To assess management strategies for the use of radiotherapy in the treatment of lung cancer in Italy, in 2009, the Italian Society of Radiation Oncology Lung Cancer Study Group proposed the survey to all Italian radiation oncology institutions. Results were compared with literature data and international reports., Study Design: Questionnaires on patterns of care of non-small cell lung cancer were sent to radiation oncology centers active at June 2009 and evaluated data recorded in 2008., Results: A total of 65 of 143 Italian centers responded to the questionnaire. The responding centers reflect the distribution of radiotherapy centers throughout the country. Of the treated patients, 55.2% were stage III, and most cases had a good performance status. FDG-PET was routinely used by 51% of centers for diagnostic and contouring phases. Postoperative radiotherapy was prescribed to pN1 and pN2 patients in 42.2% and 98.5%, respectively. The possible use of neo-adjuvant concomitant chemoradiation was declared by 70% of responders. A sequential chemoradiation approach was actually used in 43.6% of cases, induction chemotherapy followed by concomitant radiochemotherapy in 42.4%, and upfront concomitant radiochemotherapy in only 14%. In 53% of the institutions, patients have a clinical examination by a radiation oncologist only after the beginning of chemotherapy and in 82.4% of cases they have already received 2-4 cycles of chemotherapy. Most of the institutions exclude elective nodal irradiation from routine application. Total dose and fractionation in adjuvant, neoadjuvant, curative and palliative settings confirm literature data. There were significant differences in treatment planning constraints applied for lung, esophageal and cardiac tissues. Of the responding centers, 41% had stereotactic therapy for primary inoperable lung cancer and for metastatic lesions., Conclusions: In Italy, daily practice differs in some ways from the evidence supported by the results of meta-analyses/clinical trials as regards concurrent chemoradiation approaches. It could be postulated that there is an urgent need for groups that collaborate with the other societies involved in the treatment of non-small cell lung cancer in order to offer the best therapy to our patients.

Aims and Background: In patients with recurrent prostate cancer, discriminating local or systemic recurrence is critical to decide second-line treatment. We investigated the capability of stereotactic body radiotherapy to treat limited nodal recurrences, detected using choline PET scan., Methods and Study Design: Seventy-one patients with biochemical failure were studied after prostate cancer treatment: prostatectomy (28), radiotherapy (15) or both (28). Following computed tomography and choline PET imaging, stereotactic body radiotherapy was delivered on pathological lymphatic areas by 6 MV Linac, using dynamic micromultileaf collimation and intensity-modulated arc therapy optimization. Sixty days post-treatment, choline PET/CT imaging was carried out., Results: Median follow-up was 29 months (range, 14.4-48). Choline PET detected recurrences in 39 of 71 patients. Median PSA velocity was 0.40 ng/ml/year in PET-negative patients and 2.88 ng/ml/year in PET-positive subjects (P < 0.05). Twenty-five patients with limited nodal recurrences, out of the 71 submitted to choline PET, received eradicative radiotherapy. Persistent regression was recorded in 13; early spread to bone was found in 2 cases; lymph node recurrences in 8, all in sites outside the irradiated areas; 2 patients were lost to follow-up. At the 3-year follow-up, overall survival, disease-free survival and local control rates were 92%, 17% and 90%, respectively. In patients with a complete regression, PSA fell from 5.65 to 1.40 ng/ml (median). PSA nadir value (median 1.06 ng/ml) was maintained for 5.6 months (median)., Conclusions: Stereotactic body radiotherapy was effective in disease eradication of limited nodal recurrences from prostate cancer, saving patients from, or at least postponing, systemic treatments.

Purpose: An analysis is performed of the setup errors measured by a kV cone beam computed tomography (CBCT) for intracranial stereotactic radiotherapy (SRT) patients immobilized by a thermoplastic mask and a bite-block and positioned using stereotactic coordinates. We evaluated the overall positioning precision and accuracy of the immobilizing and localizing systems. The potential of image-guided radiotherapy to replace stereotactic methods is discussed., Methods and Materials: Fifty-seven patients received brain SRT. After a frame-guided setup, before each fraction (131 fractions), a CBCT was acquired and the detected displacements corrected online. Translational and rotational errors were analyzed calculating overall mean and standard deviation. A separate analysis was performed for bite-block (in conjunction with mask) and for simple thermoplastic mask. Interobserver variability for CBCT three-dimensional registration was assessed. The residual error after correction and intrafractional motion were calculated., Results: The mean module of the three-dimensional displacement vector was 3.0 +/- 1.4 mm. Setup errors for bite block and mask were smaller (2.9 +/- 1.3 mm) than those for thermoplastic mask alone (3.2 +/- 1.5 mm), but statistical significance was not reached (p = 0.15). Interobserver variability was negligible. The maximum margin calculated for residual errors and intra fraction motion was small but not negligible (1.57 mm)., Conclusions: Considering the detected setup errors, daily image guidance is essential for the efficacy of SRT treatments when mask immobilization is used, and even when a bite-block is used in conjunction. The frame setup is still used as a starting point for the opportunity of rotational corrections. Residual margins after on-line corrections must be evaluated.

Purpose: Different biologically equivalent dose (BED) values associated with stereotactic radiotherapy (SRT) of patients with primary and metastatic pulmonary nodules were studied. The BED values were calculated for tumoral tissue and low alpha/beta ratio, assuming that better local response could be obtained by using stereotactic high-BED treatment., Methods and Materials: Fifty-eight patients with T1-T3 N0 non-small-cell lung cancer and 46 patients with metastatic lung nodules were treated with SRT. The BED was calculated for alpha/beta ratios of 3 and 10. Overall survival (OS) was assessed according to Kaplan-Meier and appraised as a function of three BED levels: low (30-50 Gy), medium (50-70 Gy), and high (70-98 Gy; alpha/beta = 10)., Results: The OS rates for all 104 patients at 12, 24, and 36 months were 73%, 48.3%, and 35.8%, respectively. Local response greater than 50% for low, medium, and high BED values was observed in 54%, 47%, and 73%, respectively. In the high-BED treated group, OS rates at 12, 24, and 36 months (80.9%, 70%, and 53.6%, respectively) were significantly improved compared with low- (69%, 46.1%, and 30.7%, respectively) and medium-BED (67%, 28%, and 21%, respectively) treated patients. Results are also discussed in terms of BED calculated on alpha/beta 3 Gy characteristic of the microcapillary bed. No acute toxicity higher than Grade 1 was observed., Conclusions: Radioablation of pulmonary neoplastic nodules may be achieved with SRT delivered by using a high-dose fraction with high BED value.

Introduction: Free-breathing stereotactic radiotherapy for lung malignancies requires reliable prediction of respiratory motion and accurate target localization. A protocol was adopted for reproducibility and reduction of respiratory motion and for target localization by CBCT image guidance. Tumor respiratory displacements and tumor positioning errors relative to bony anatomy alignment are analyzed., Materials and Method: Image guided SRT was performed for 99 lung malignancies. Two groups of patients were considered: group A did not perform any breathing control; group B controlled visually their respiratory cycle and volumes on an Active Breathing Coordinator (ABC) monitor during the acquisition of simulation CT and CBCT, and treatment delivery. GTV on end inhale and exhale CT data sets were fused in an ITV and the extent of tumor motion evaluated between these 2 phases. A pre-treatment CBCT was acquired and aligned to the reference CT using bony anatomy; for tumor positioning the ITV contour on the reference CT was matched to the visible tumor on CBCT. Interobserver variability of tumor positioning was evaluated. ITV and CBCT tumor dimensions were compared., Results: 3D tumor breathing displacement (mean+/-SD) was significantly higher for group A (14.7+/-9.9 mm) than for group B (4.7+/-3.1 mm). The detected differences between tumor and bony structure alignment below 3 mm were 68% for group B and 45% for group A, reaching statistical significance. Interobserver variability was 1.7+/-1.1 mm (mean+/-SD). Dimensions of tumor image on CBCT were consistent with ITV dimensions for group B (max difference 14%)., Conclusions: The adopted protocol seems effective in reducing respiratory internal movements and margin. Tumor positioning errors relative to bony anatomy are also reduced. However bony anatomy as a surrogate of the target may still lead to some relevant positioning errors. Target visualization on CBCT is essential for an accurate localization in lung SRT.

Purpose: To analyze the patterns of practice and survival in a series of 1722 adult astrocytoma patients treated in 12 Italian radiotherapy centers., Methods and Materials: A total of 1722 patients were treated with postoperative radiotherapy (90% World Health Organization [WHO] Grade 3-4, 62% male, 44% aged >60 years, 25% with severe neurologic deficits, 44% after gross total resection, 52% with high-dose radiotherapy, and 16% with chemotherapy). Variations in the clinical-therapeutic features in three subsequent periods (1985 through 2001) were evaluated, along with overall survival for the different subgroups., Results: The proportion of women, of older patients, of those with worse neurologic performance status (NPS), with WHO Grade 4, and with smaller tumors increased with time, as did the proportion of those treated with radical surgery, hypofractionated radiotherapy, and more sophisticated radiotherapy techniques, after staging procedures progressively became more accurate. The main prognostic factors for overall survival were age, sex, neurologic performance status, WHO grade, extent of surgery, and radiation dose., Conclusions: Recently, broader selection criteria for radiotherapy were adopted, together with simpler techniques, smaller total doses, and larger fraction sizes for the worse prognostic categories. Younger, fit patients are treated more aggressively, more often in association with chemotherapy. Survival did not change over time. The accurate evaluation of neurologic status is therefore of utmost importance before the best treatment option for the individual patient is chosen.