Targetable treatment resistance in thyroid cancer with clonal hematopoiesis.

Anaplastic thyroid cancer (ATC) is a clinically aggressive malignancy with a dismal prognosis. Combined BRAF/MEK inhibition offers significant therapeutic benefit in patients with BRAF V600E -mutant ATCs. However, relapses are common and overall survival remains poor. Compared with differentiated thyroid cancer, a hallmark of ATCs is significant infiltration with myeloid cells, particularly macrophages. ATCs are most common in the aging population, which also has an increased incidence of TET2 -mutant clonal hematopoiesis (CH). CH-mutant macrophages have been shown to accelerate CH-associated pathophysiology including atherosclerosis. However, the clinical and mechanistic contribution of CH-mutant clones to solid tumour biology, prognosis and therapeutic response has not been elucidated. Here we show that TET2 -mutant CH is enriched in the tumour microenvironment of patients with solid tumours and associated with adverse prognosis in ATC patients. We find that Tet2 -mutant macrophages selectively infiltrate mouse Braf V600E -mutant ATC and that their overexpression of Tgfß-family ligands mediates resistance to BRAF/MEK inhibition. Importantly, inhibition of Tgfß signaling restores sensitivity to MAPK pathway inhibition, opening a path for synergistic strategies to improve outcomes of patients with ATCs and concurrent CH.

TAD hierarchy restricts poised LTR activation and loss of TAD hierarchy promotes LTR co-option in cancer.

Transposable elements (TEs) are abundant in the human genome, and they provide the sources for genetic and functional diversity. The regulation of TEs expression and their functional consequences in physiological conditions and cancer development remain to be fully elucidated. Previous studies suggested TEs are repressed by DNA methylation and chromatin modifications. The effect of 3D chromatin topology on TE regulation remains elusive. Here, by integrating transcriptome and 3D genome architecture studies, we showed that haploinsufficient loss of NIPBL selectively activates alternative promoters at the long terminal repeats (LTRs) of the TE subclasses. This activation occurs through the reorganization of topologically associating domain (TAD) hierarchical structures and recruitment of proximal enhancers. These observations indicate that TAD hierarchy restricts transcriptional activation of LTRs that already possess open chromatin features. In cancer, perturbation of the hierarchical chromatin topology can lead to co-option of LTRs as functional alternative promoters in a context-dependent manner and drive aberrant transcriptional activation of novel oncogenes and other divergent transcripts. These data uncovered a new layer of regulatory mechanism of TE expression beyond DNA and chromatin modification in human genome. They also posit the TAD hierarchy dysregulation as a novel mechanism for alternative promoter-mediated oncogene activation and transcriptional diversity in cancer, which may be exploited therapeutically.

Evaluation of neurocognitive and social developments after craniosynostosis surgery.

OBJECTIVE: The study focused on assessing the potential neurocognitive and social developmental issues in children with non-syndromic craniosynostosis (NSC) who received optimal surgical treatment. The primary objective was to determine whether NSC, even after optimal surgical treatment, could have negative effects on brain development. METHODS: The study included a total of 73 pediatric patients aged between 2 and 6 years who had previously undergone surgery for NSC at the Gazi University Faculty of Medicine, Department of Neurosurgery. These patients were carefully matched with 107 healthy children who visited the outpatient clinic of the same department in terms of sociodemographic characteristics such as age, gender, and social status. To assess the neurocognitive and social development of the participants, the child psychologist administered a developmental scale to the child and his/her family via video conference. This scale was adapted from the Bayley-III Infant and Child Development Scale by the Gazi University Faculty of Medicine, Division of Pediatric Neurology. RESULTS: The study found no social or gross motor developmental issues in patients who had undergone optimal surgical treatment for NSC. However, the risk of fine motor developmental deficiencies was 4.79 times higher than that of the normal population, and the risk of language developmental deficiencies was 5.75 times higher than that of the normal population. CONCLUSIONS: Despite timely treatment of NSC, long-term neurocognitive and social development issues may arise in affected children. Therefore, it is crucial to monitor these patients after completing surgical treatment and thoroughly examine their development using a multidisciplinary approach.

Radiotherapy for benign diseases in Turkey: a patterns of care survey of the Turkish Society for Radiation Oncology (TROD 05-002).

PURPOSE: We aimed to investigate the patterns of radiotherapy (RT) care in cases of benign diseases in Turkey. METHODS: A questionnaire survey was sent to all radiation oncology (RO) departments in Turkey. The number of patients treated for benign disease between 2015 and 2020 was requested. A list of benign conditions was given, and information on the number of patients per disease, single and total doses prescribed, weekly fractions, radiation type, energy, and device was requested. RESULTS: Of the 138 RO departments, 29 (21%) responded. The data received concerned 15 (52%) university, 10 (34%) public, and four (14%) private hospitals. A total of 130,846 patients were treated with RT in these departments. Of these patients, 6346 (4.85%) were treated for benign conditions. The most common benign diseases treated with RT were meningioma (35%), plantar fasciitis (19%), schwannoma (16%), arteriovenous malformation (11%), and pituitary adenoma (7%). Most centers performed RT for paraganglioma, heterotopic ossification, vertebral hemangioma, and Graves' ophthalmopathy, but none treated arthrosis. Wide variations were observed across the departments. Radiosurgery for intracranial pathologies was performed intensively in four centers. By contrast, RT for plantar fasciitis was predominantly treated in five centers, one of which had more than 1000 patients. CONCLUSION: The ratio of patients who underwent RT for benign diseases in Turkey among all patients who underwent RT was 4.85%. The common pattern of RT in 72% of patients was radiosurgery for intracranial benign diseases, followed by low-dose RT for plantar fasciitis in 19%.

In vitro 5-fluorouracil release properties investigation from pH sensitive sodium alginate coated and uncoated methyl cellulose/chitosan microspheres.

5-Fluorouracil (5-FU) has been in clinical practice for decades one of the oldest chemotherapy agents. However, intravenous administration of 5-FU requires the development of an oral controlled delivery system for improved patient compliances. For this purpose, 5-FU loaded and sodium alginate (NaAlg) coated and uncoated methyl cellulose (MC)/chitosan (CS) microspheres were prepared by emulsion crosslinking method using a mixture of water and oil. Firstly, MC/CS microspheres were prepared and then coated with NaAlg. The prepared microspheres were characterized by optical microscopy, Fourier transform infrared spectroscopy (FTIR), and differential scanning calorimetry (DSC). Microspheres were also characterized by equilibrium swelling values and drug release profiles. The in vitro drug release studies were carried out with three pH values 1.2, 6.8, and 7.4, respectively, each for 2 h. It was determined that coating the microspheres with NaAlg provides more controlled drug release, especially at pH 1.2. The effects of the preparation conditions, such as coating time, MC/CS ratio, NaAlg concentration, and crosslinker concentration on the 5-FU release were investigated.

Increased skin reactions with hydroxychloroquine during breast radiotherapy.

With the advances in radiation technology, skin reaction due to postoperative radiotherapy (RT) in breast cancer patients is generally mild and tolerable. However, certain drugs may increase the radiation effect. In literature, only few cases of adverse reactions in the radiation field have been reported with the use of Chloroquine. This report describes the case of a 30-year-old young female who had enhanced skin reactions with hydroxychloroquine (HCQ) treatment during breast RT. HCQ should be used with caution in patients undergoing RT due to its potential radiosensitizer effect.

SETD2 regulates chromatin accessibility and transcription to suppress lung tumorigenesis.

SETD2, a H3K36 trimethyltransferase, is the most frequently mutated epigenetic modifier in lung adenocarcinoma, with a mutation frequency of approximately 9%. However, how SETD2 loss of function promotes tumorigenesis remains unclear. Using conditional Setd2-KO mice, we demonstrated that Setd2 deficiency accelerated the initiation of KrasG12D-driven lung tumorigenesis, increased tumor burden, and significantly reduced mouse survival. An integrated chromatin accessibility and transcriptome analysis revealed a potentially novel tumor suppressor model of SETD2 in which SETD2 loss activates intronic enhancers to drive oncogenic transcriptional output, including the KRAS transcriptional signature and PRC2-repressed targets, through regulation of chromatin accessibility and histone chaperone recruitment. Importantly, SETD2 loss sensitized KRAS-mutant lung cancer to inhibition of histone chaperones, the FACT complex, or transcriptional elongation both in vitro and in vivo. Overall, our studies not only provide insight into how SETD2 loss shapes the epigenetic and transcriptional landscape to promote tumorigenesis, but they also identify potential therapeutic strategies for SETD2 mutant cancers.

Recurrence patterns of pancreatic cancer treated with adjuvant intensity modulated radiotherapy.

Background: The aim of this study was to investigate the recurrence patterns in pancreatic cancer patients treated with adjuvant intensity modulated radiotherapy (IMRT) and to correlate the sites of locoregional recurrence with radiotherapy target volumes. Materials and methods: Thirty-eight patients who had undergone resection and adjuvant chemoradiation for pancreatic cancer were evaluated. Radiotherapy (RT) was started after 1-3 cycles of adjuvant chemotherapy (CHT). Clinical target volume (CTV) was contoured according to the RTOG guideline. All patients were treated with IMRT with a dose of 45-50.4 Gy. Computerized tomography (CT) images at the time of recurrence were correlated with radiotherapy plans. Locoregional recurrences were classified as in-field, out-field and marginal. Results: Median overall survival (OS) was 19 months. One- and 2-year OS rates were 73.6% and 37.1%, respectively. Locoregional recurrence and distant metastases were observed in 11 (28.9%) and 23 (60.5%) patients, respectively. For the 11 locoregional recurrences, 7 were in-field, 1 was marginal, and 3 were out-of-field. One patient had isolated local, 2 patients had isolated regional and 15 (57.6%) patients had only distant failures. The first presentations of failures were mostly distant (58%). On multivariate analysis, tumor size ≥ 3 cm (p = 0.011) and positive vascular invasion (p = 0.014) predicted for worse OS rate. Conclusions: The majority of locoregional recurrences were in the radiation field among pancreatic cancer patients treated with postoperative IMRT. However, failures were predominantly distant, and improvement of systemic control may be of particular interest.

Selective local postoperative radiotherapy for T3-T4 N0 laryngeal cancer.

PURPOSE: We aimed to investigate the appropriate postoperative radiotherapy dose and selective volume in T3-4 N0 laryngeal cancer patients treated with either total or partial laryngectomy. METHODS: Patients who received radiotherapy for locally advanced (T3-T4) and pathologic node-negative (N0) squamous cell laryngeal cancer were retrospectively evaluated. Radiotherapy was applied to median 60 Gy (range 54-60 Gy) as selective local radiotherapy (±stoma). The local treatment areas included postoperative bed + laryngeal area for patients with a partial laryngectomy, and the postoperative bed only for patients with total laryngectomy. RESULTS: The median follow-up time was 59 months and 52 patients were included. The 2­year, 5­year, and 8­year locoregional recurrence controls (LRC) were 95.6%. The 2­year and 5­year OS rates were 93.8% and 78.9%, respectively. The 5­year OS for age < 60 years was 95.8%, for above 60 years 56.5%. CONCLUSION: Our data suggest that local selective irradiation to the postoperative bed + stoma is enough in patients with T3-4 N0 laryngeal cancer without applying elective nodal irradiation.

Is there any additional benefit of 68Ga-PSMA PET on radiotherapy target volume definition in patients with glioblastoma?

OBJECTIVE: To investigate the contribution of 68Gallium (68Ga)-PSMA (prostate-specific membrane antigen) positron emission tomography (PET) in defining radiotherapy (RT) target volume for glioblastoma and to compare the target volumes defined by Magnetic Resonance Imaging (MRI). METHODS: RT planning Computed Tomography (CT) images were fused separately with pre-operative MRI and PET/MRI images of 10 glioblastoma patients, retrospectively. The contrast-enhanced area in T1 weighted MRI was contoured as gross tumor volume (GTV) and clinical target volume (CTV1) was obtained by including the cavity and T2/FLAIR hyperintense areas after giving a margin of 2 cm to the GTV. 68Ga-PSMA uptake area was contoured as biological tumor volume (BTV) and CTV2 was obtained with a margin of 2 cm to BTV. Planning target volumes (PTVs) were created with the 3 mm added to the CTVs. Conformity index (CI), dice similarity coefficient (DSC) and overlap volume (OV) were calculated by obtaining the intersection and union volumes. Volumetric comparison, similarity and overlap analyzes were performed statistically by Wilcoxon signed rank and One sample t-test. RESULTS: The median GTV was 21,96 cc (1,04 - 82,04) and BTV was 25,58 cc (2,43 - 99,47). BTV was on average 47% larger than GTV which was statistically significant (p = 0.03). For GTV-BTV, CTV1-CTV2 and PTV1-PTV2; mean values of CI were 0,56, 0,76 and 0,76; DSC were 0,70, 0,86 and 0,86; OV were 0,88, 0,94 and 0,94, respectively. There was no significant difference on size and spatial similarity between CTV1 and CTV2, PTV1 and PTV2. CONCLUSION: Altough BTV was larger than GTV, this significance was lost while we gave the same CTV margin including the peripheral edema. It seems that it may help to improve defining non-enhancing tumor part and also recurrent tumor volume. ADVANCES IN KNOWLEDGE: Recent studies have focused on the role of 68Ga-PSMA PET in imaging of glial tumors. It has been observed that 68Ga-PSMA PET can clearly define the tumor borders and it can be beneficial in target volume delineation, especially in reirradiation of recurrent tumors.

SETD2 loss perturbs the kidney cancer epigenetic landscape to promote metastasis and engenders actionable dependencies on histone chaperone complexes.

SETD2 is a histone H3 lysine 36 (H3K36) trimethyltransferase that is mutated with high prevalence (13%) in clear cell renal cell carcinoma (ccRCC). Genomic profiling of primary ccRCC tumors reveals a positive correlation between SETD2 mutations and metastasis. However, whether and how SETD2 loss promotes metastasis remains unclear. In this study, we used a SETD2-mutant (SETD2MT) metastatic ccRCC human-derived cell line and xenograft models and showed that H3K36me3 restoration greatly reduced distant metastases of ccRCC in mice in a matrix metalloproteinase 1 (MMP1)-dependent manner. An integrated multiomics analysis using assay for transposase-accessible chromatin using sequencing (ATAC-seq), chromatin immunoprecipitation-sequencing (ChIP-seq) and RNA sequencing (RNA-seq) established a tumor suppressor model in which loss of SETD2-mediated H3K36me3 activates enhancers to drive oncogenic transcriptional output through regulation of chromatin accessibility. Furthermore, we uncovered mechanism-based therapeutic strategies for SETD2-deficient cancer through the targeting of specific histone chaperone complexes, including ASF1A/ASF1B and SPT16. Overall, SETD2 loss creates a permissive epigenetic landscape for cooperating oncogenic drivers to amplify transcriptional output, providing unique therapeutic opportunities.

Application potential of three-dimensional silk fibroin scaffold using mesenchymal stem cells for cardiac regeneration.

Cardiac tissue engineering focusing on biomaterial scaffolds incorporating cells from different sources has been explored to regenerate or repair damaged area as a lifesaving approach.The aim of this study was to evaluate the cardiomyocyte differentiation potential of human adipose mesenchymal stem cells (hAD-MSCs) as an alternative cell source on silk fibroin (SF) scaffolds for cardiac tissue engineering. The change in surface morphology of SF scaffolds depending on SF concentration (1-6%, w/v) and increase in their porosity upon application of unidirectional freezing were visualized by scanning electron microscopy (SEM). Swelling ratio was found to increase 2.4 fold when SF amount was decreased from 4% to 2%. To avoid excessive swelling, 4% SF scaffold with swelling ratio of 10% (w/w) was chosen for further studies.Biodegradation rate of SF scaffolds depended on enzymatic activity was found to be 75% weight loss of SF scaffolds at the day 14. The phenotype of hAD-MSCs and their multi-linage potential into chondrocytes, osteocytes, and adipocytes were shown by flow cytometry and immunohistochemical staining, respectively.The viability of hAD-MSCs on 3D SF scaffolds was determined as 90%, 118%, and 138% after 1, 7, and 14 days, respectively. The use of 3D SF scaffolds was associated with increased production of cardiomyogenic biomarkers: α-actinin, troponin I, connexin 43, and myosin heavy chain. The fabricated 3D SF scaffolds were proved to sustain hAD-MSCs proliferation and cardiomyogenic differentiation therefore, hAD-MSCs on 3D SF scaffolds may useful tool to regenerate or repair damaged area using cardiac tissue engineering techniques.

A unified atlas of CD8 T cell dysfunctional states in cancer and infection.

CD8 T cells play an essential role in defense against viral and bacterial infections and in tumor immunity. Deciphering T cell loss of functionality is complicated by the conspicuous heterogeneity of CD8 T cell states described across experimental and clinical settings. By carrying out a unified analysis of over 300 assay for transposase-accessible chromatin sequencing (ATAC-seq) and RNA sequencing (RNA-seq) experiments from 12 studies of CD8 T cells in cancer and infection, we defined a shared differentiation trajectory toward dysfunction and its underlying transcriptional drivers and revealed a universal early bifurcation of functional and dysfunctional T cell states across models. Experimental dissection of acute and chronic viral infection using single-cell ATAC (scATAC)-seq and allele-specific single-cell RNA (scRNA)-seq identified state-specific drivers and captured the emergence of similar TCF1+ progenitor-like populations at an early branch point, at which functional and dysfunctional T cells diverge. Our atlas of CD8 T cell states will facilitate mechanistic studies of T cell immunity and translational efforts.

Different Aspects on Clinical Presentation of Developmental Venous Anomalies: Are They as Benign as Known? A Single Center Experience.

BACKGROUND: Cerebral developmental venous anomalies (DVAs) are frequently diagnosed incidentally owing to the advances in neuroimaging. They are regarded as clinically insignificant due to their supposed quiescent existence which the authors aimed to contradict in this paper. AIM: In the aim of constituting a better understanding of clinical presentation of DVAs and making an estimation regarding the probability of resulting in a hemorrhage, the authors presented their experiences with a case series of DVAs. METHODS: A retrospective analysis was carried out among patients who underwent brain MRI in a radiology department of a university between January of 2019 and January of 2020. RESULTS: A total of 101 patients with DVA were extracted. 38 patients had isolated DVAs, while 63 patients had various accompanying cerebral pathologies, mostly cavernomas (39 patients) and AVMs (11 patients). The main complaints leading investigation were headache, dizziness, ataxia, nausea\vomiting, seizures and focal neurological deficits. 41 patients were truly symptomatic with indicative findings of seizures, neurological deficits or intracranial hemorrhages, and 12 of them had solitary DVAs. 22 patients presented with hemorrhages, and of them, 10 had only DVA, while the rest had some associated lesions, most often cavernoma. Of 22 patients with hemorrhage, 5 were operated, 5 were applied radiosurgery; while the rest were followed without any intervention. CONCLUSION: Although the symptoms in patients with DVA are generally charged on other associated pathologies, the fact that isolated DVAs may occasionally be problematic in the range of minor symptoms and severe hemorrhage should not be underestimated.

Erectile dysfunction in prostate cancer patients treated with intensity-modulated radiation therapy.

BACKGROUND: Sexual dysfunction is an important side-effect after radiotherapy (RT) for prostate cancer (PCa). The aim of this study was to compare sexual functions of PCa patients before and after intensity-modulated RT and to analyze their correlation with penile bulb (PB) doses and patient characteristics. MATERIALS AND METHODS: Forty-two patients who underwent RT ± hormone therapy for PCa between 2010 and 2013 were analyzed. Sexual functions assessed by patient-reported questionnaire and physician reported scale before and 3 years after treatment. The effect of patients' age, prostate volume, testosterone levels, comorbidity, smoking status, tumor stage, RT technique, hormone therapy, and PB doses to sexual functions were investigated. RESULTS: After 3 years of RT, 64.3% of all patients had a lower erectile score; and 75% of patients who were previously potent (n = 24) had become impotent after treatment. However sexual desire still remained in 75.8% of patients who had desire before treatment (n = 33). Statistical analysis showed that two parameters were correlated with postradiotherapy impotency outcome; PB mean radiation dose (P = 0.033) and testosterone levels (P = 0.032). CONCLUSIONS: RT, despite modern techniques, affects the sexual function of PCa patients in varying degrees. Reducing radiation doses to penile structures may play a role in preventing erectile dysfunction.

Primary Immunodeficiency and Cancer in Children; A Review of the Literature.

The life span of patients with primary and secondary immunodeficiencies has increased due to recent advances in diagnostic and therapeutic strategies. Primary immune deficiencies (PIDs) are genetic disorders that predispose patients to frequent infections, autoimmunity and malignancies. Genomic instability due to defective DNA repair processes and other unknown mechanisms in patients with PID leads to an enhanced risk of cancer. PIDs were originally described as rare diseases occurring only in infants and young children, which are associated with severe clinical symptoms. However, advances in gene sequencing technologies, have revealed that they are much more common than originally appreciated and are present in older children, adolescents, and adults. After infection, malignancy is the most prevalent cause of death in both children and adults with PIDs. The overall risk of developing cancer in patients with PID is estimated to range from 4.7 to 5.7 percent. A 1.4 to 1.6-fold excess relative risk of cancer has been reported for PIDs. Increasing awareness among physicians regarding PID and cancer may lead to earlier diagnosis which may decrease morbidity and mortality. In this paper, we review the various categories of PIDs in children and highlight their association with various malignancies. MEDLINE was searched to identify articles for inclusion. Three authors have independently screened literature search results from MEDLINE and abstracted data from studies dealing with cancers of children among primary immune deficiencies.

First report of Nitzschia navis-varingica in the Mediterranean Sea and growth stimulatory effects of Nitzschia navis-varingica, Chrysochromulina alifera and Heterocapsa pygmaea on different mammalian cell types.

A benthic diatom, Nitzschia navis-varingica was found for the first time in the Mediterranean Sea. Effects of this diatom species together with the haptophyte Chrysochromulina alifera and the dinoflagellate Heterocapsa pygmaea isolated from the northeastern Mediterranean Sea coast on prostate, breast cancer and fibroblast cell lines were investigated. Algal extracts did not exert any toxic effect on these cell lines and it had growth stimulatory impact on the cells without discrimination of cell type. Our results suggest potential use of these algal extracts in tissue repair and cell growth boosting additive in the diet of humans as well as animals. Moreover, these algal extracts have potential to be used as natural resource in the skin vitalizing creams of cosmetics industry and as wound healing agents in the atopic drugs.

An integrated model for detecting significant chromatin interactions from high-resolution Hi-C data.

Here we present HiC-DC, a principled method to estimate the statistical significance (P values) of chromatin interactions from Hi-C experiments. HiC-DC uses hurdle negative binomial regression account for systematic sources of variation in Hi-C read counts-for example, distance-dependent random polymer ligation and GC content and mappability bias-and model zero inflation and overdispersion. Applied to high-resolution Hi-C data in a lymphoblastoid cell line, HiC-DC detects significant interactions at the sub-topologically associating domain level, identifying potential structural and regulatory interactions supported by CTCF binding sites, DNase accessibility, and/or active histone marks. CTCF-associated interactions are most strongly enriched in the middle genomic distance range (∼700 kb-1.5 Mb), while interactions involving actively marked DNase accessible elements are enriched both at short (<500 kb) and longer (>1.5 Mb) genomic distances. There is a striking enrichment of longer-range interactions connecting replication-dependent histone genes on chromosome 6, potentially representing the chromatin architecture at the histone locus body.