The genomic and evolutionary landscapes of anaplastic thyroid carcinoma.

Anaplastic thyroid carcinoma is arguably the most lethal human malignancy. It often co-occurs with differentiated thyroid cancers, yet the molecular origins of its aggressivity are unknown. We sequenced tumor DNA from 329 regions of thyroid cancer, including 213 from patients with primary anaplastic thyroid carcinomas. We also whole genome sequenced 9 patients using multi-region sequencing of both differentiated and anaplastic thyroid cancer components. Using these data, we demonstrate thatanaplastic thyroid carcinomas have a higher burden of mutations than other thyroid cancers, with distinct mutational signatures and molecular subtypes. Further, different cancer driver genes are mutated in anaplastic and differentiated thyroid carcinomas, even those arising in a single patient. Finally, we unambiguously demonstrate that anaplastic thyroid carcinomas share a genomic origin with co-occurring differentiated carcinomas and emerge from a common malignant field through acquisition of characteristic clonal driver mutations.

The nature and timing of coagulation dysfunction in a cohort of trauma patients in the Australian pre-hospital setting.

BACKGROUND: Acute Traumatic Coagulopathy (ATC) is a complex pathological process that is associated with patient mortality and increased blood transfusion requirements. It is evident on hospital arrival, but there is a paucity of information about the nature of ATC and the characteristics of patients that develop ATC in the pre-hospital setting. The objective of this study was to describe the nature and timing of coagulation dysfunction in a cohort of injured patients and to report on patient and pre-hospital factors associated with the development of ATC in the field. METHODS: This was a prospective observational study of a convenience sample of trauma patients. Patients had blood taken during the pre-hospital phase of care and evaluated for derangements in Conventional Coagulation Assays (CCA) and Rotational Thromboelastometry (ROTEM). Associations between coagulation derangement and pre-hospital factors and patient outcomes were evaluated. RESULTS: A total of 216 patients who had either a complete CCA or ROTEM were included in the analysis. One hundred and eighty (83 %) of patients were male, with a median injury severity score of 17 [interquartile range (IQR) 10-27] and median age of 34 years [IQR = 25.0-52.0]. Hypofibrinogenemia was the predominant abnormality seen, (CCA Hypofibrinogenemia: 51/193, 26 %; ROTEM hypofibrinogenemia: 65/204, 32 %). Increased CCA derangement, the presence of ROTEM coagulopathy, worsening INR, worsening FibTEM and decreasing fibrinogen concentration, were all associated with both mortality and early massive transfusion. CONCLUSION: Clinically significant, multifaceted coagulopathy develops early in the clinical course, with hypofibrinogenemia being the predominant coagulopathy. In keeping with the ED literature, pre-hospital coagulation dysfunction was associated with mortality and early massive transfusion. Further work is required to identify strategies to identify and guide the pre-hospital management of the coagulation dysfunction seen in trauma.

Correlation between KRAS Mutation and CTLA-4 mRNA Expression in Circulating Tumour Cells: Clinical Implications in Colorectal Cancer.

Combination strategies of KRAS inhibition with immunotherapy in treating advanced or recurrent colorectal carcinoma (CRC) may need to be assessed in circulating tumour cells (CTCs) to achieve better clinical outcomes. This study aimed to investigate the genomic variations of KRAS in CTCs and matched CRC tissues and compared mRNA expression of KRAS and CTLA-4 between wild-type and KRAS-mutated CTCs and CRC tissues. Clinicopathological correlations were also compared. Six known mutations of KRAS were identified at both codon 12 and codon 13 (c.35G>T/G12V, c.35G>A7/G12D, c.35G>C/G12A, c.34G>A/G12S, c.38G>C/G13A, and c.38G>A/G13D). Three CTC samples harboured the identified mutations (16.7%; 3/18), while fifteen matched primary tumour tissues (65.2%, 15/23) showed the mutations. CTCs harbouring the KRAS variant were different from matched CRC tissue. All the mutations were heterozygous. Though insignificant, CTLA-4 mRNA expression was higher in patients carrying KRAS mutations. Patients harbouring KRAS mutations in CTCs were more likely to have poorly differentiated tumours (p = 0.039) and with lymph node metastasis (p = 0.027) and perineural invasion (p = 0.014). KRAS mutations in CTCs were also significantly correlated with overall pathological stages (p = 0.027). These findings imply the genetic basis of KRAS with immunotherapeutic target molecules based on a real-time platform. This study also suggests the highly heterogeneous nature of cancer cells, which may facilitate the assessment of clonal dynamics across a single patient's disease.

Current advances in detecting genetic and epigenetic biomarkers of colorectal cancer.

Colorectal carcinoma (CRC) is the third most common cancer in terms of diagnosis and the second in terms of mortality. Recent studies have shown that various proteins, extracellular vesicles (i.e., exosomes), specific genetic variants, gene transcripts, cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and altered epigenetic patterns, can be used to detect, and assess the prognosis of CRC. Over the last decade, a plethora of conventional methodologies (e.g., polymerase chain reaction [PCR], direct sequencing, enzyme-linked immunosorbent assay [ELISA], microarray, in situ hybridization) as well as advanced analytical methodologies (e.g., microfluidics, electrochemical biosensors, surface-enhanced Raman spectroscopy [SERS]) have been developed for analyzing genetic and epigenetic biomarkers using both optical and non-optical tools. Despite these methodologies, no gold standard detection method has yet been implemented that can analyze CRC with high specificity and sensitivity in an inexpensive, simple, and time-efficient manner. Moreover, until now, no study has critically reviewed the advantages and limitations of these methodologies. Here, an overview of the most used genetic and epigenetic biomarkers for CRC and their detection methods are discussed. Furthermore, a summary of the major biological, technical, and clinical challenges and advantages/limitations of existing techniques is also presented.

Reducing inappropriate polypharmacy for older patients at specialist outpatient clinics: a systematic review.

OBJECTIVE: Polypharmacy is associated with negative clinical consequences. The efficacy of deprescribing interventions within medical specialist outpatient clinics remains unclear. Here, we reviewed the research on the effectiveness of deprescribing interventions implemented within specialist outpatient clinics for patients ≥ 60 years. METHODS: Systematic searches of key databases were undertaken for studies published between January 1990 and October 2021. The diverse nature of the study designs made it unsuitable for pooling for meta-analysis, thus, a narrative review was conducted and presented in both text and tabular formats. The primary outcome for review was that intervention resulted in a change in medication load (either total number of medications or appropriateness of medication). Secondary outcomes were the maintenance of deprescription and clinical benefits. Methodological quality of the publications was assessed using the revised Cochrane risk-of-bias tools. RESULTS: Nineteen studies with a total of 10,914 participants were included for review. These included geriatric outpatient clinics, oncology/hematology clinics, hemodialysis clinics, and designated polypharmacy/multimorbidity clinics. Four randomized controlled trials (RCTs) reported statistically significant reductions in medication load with intervention; however, all studies had a high risk of bias. The inclusion of a pharmacist in outpatient clinics aims to increase deprescribing, however, the current evidence is mainly restricted to prospective and pilot studies. The data on secondary outcomes were very limited and highly variable. CONCLUSIONS: Specialist outpatient clinics may provide valuable settings for implementing deprescribing interventions. The addition of a multidisciplinary team including a pharmacist and the use of validated medication assessment tools appear to be enablers. Further research is warranted.

Clinical and economic burden of benign and malignant skin lesions in renal transplant recipients.

BACKGROUND: Studies evaluating the economic burden of dermatological care in the transplant setting are currently not available in Australia. AIMS: To evaluate the clinical and economic burden of benign and malignant skin lesions in renal transplant recipients in Central Queensland. METHODS: A bottom-up approach was used to determine the clinical burden and direct costs from patient-level Medicare data obtained from Service Australia for skin lesions. RESULTS: Seventy-six percent of the renal transplant population in Central Queensland participated in this study. The median age was 57.0 years (standard deviation ± 13.6) and the majority (61.8%) of participants were men. The mean duration after transplant surgery was 99.9 months (interquartile range, 73.2-126.6 months). During a 2-year follow-up, 22 (40%) patients were diagnosed with benign skin lesions, 21 (38%) with nonmelanoma skin carcinoma (NMSC) and one (2%) with melanoma. There was a total of 231 visits to clinicians for diagnostic and therapeutic skin procedures and the direct costs to Medicare was $48 806 Australian Dollars (AUD) or $30 427 US Dollars (USD). Approximately 86% of the total direct costs was spent for nonNMSC and mean direct costs for NMSC was $763 AUD (or $476 USD). CONCLUSION: This Medicare data-based study provides further insight into the burgeoning clinical and economic burden of the care for benign and malignant skin lesions in the renal transplantation setting in Australia.

Implications of estrogen and its receptors in colorectal carcinoma.

Estrogens have been implicated in the pathogenesis of various cancer types, including colorectal carcinoma (CRC). Estrogen receptors such as ERα and ERß activate intracellular signaling cascades followed by binding to estrogen, resulting in important changes in cellular behaviors. The nuclear estrogen receptors, i.e. ERß and ERα are responsible for the genomic actions of estrogens, whereas the other receptor, such as G protein-coupled estrogen receptor (GPER) regulates rapid non-genomic actions, which lead to secondary gene expression changes in cells. ERß, the predominant estrogen receptor expressed in both normal and non-malignant colonic epithelium, has protective roles in colon carcinogenesis. ERß may exert the anti-tumor effect through selective activation of pro-apoptotic signaling, increasing DNA repair, inhibiting expression of oncogenes, regulating cell cycle progression, and also by changing the micro-RNA pool and DNA-methylation. Thus, a better understanding of the underlying mechanisms of estrogen and its receptors in CRC pathogenesis could provide a new horizon for effective therapeutic development. Furthermore, using synthetic or natural compounds as ER agonists may induce estrogen-mediated anti-cancer activities against colon cancer. In this study, we report the most recent pre-clinical and experimental evidences related to ERs in CRC development. Also, we reviewed the actions of naturally occurring and synthetic compounds, which have a protective role against CRC development by acting as ER agonist.

Assessment of Papillary Thyroid Carcinoma with Ultrasound Examination.

Ultrasound examination of the thyroid is useful for preoperative assessment of thyroid nodules including papillary thyroid carcinoma. The examination mainly is to determine the malignant potential of thyroid nodule(s). There are different systems to predict malignant potential in the thyroid nodules and cervical lymph nodes by ultrasound. Ultrasound is used in conjunction with fine-needle aspiration to diagnosis papillary thyroid carcinoma. It is used as guidance to locate the sites to obtain the samples for diagnosis and research in papillary thyroid carcinoma.

Papillary Thyroid Carcinoma: Current Position in Epidemiology, Genomics, and Classification.

Papillary thyroid carcinoma is the most common type of thyroid malignancy both in adults and pediatric population. Since the 1980s, there are changes in criteria in labelling thyroid lesions as "papillary thyroid carcinomas." Radiation exposure is a well-established risk factor for papillary thyroid carcinoma. Other environmental risk factors include dietary iodine, obesity, hormones, and environmental pollutants. Papillary thyroid carcinomas could occur in familial settings, and 5% of these familial cases have well-studied driver germline mutations. In sporadic papillary thyroid carcinoma, BRAF mutation is common and is associated with clinicopathologic and prognostic markers. The mutation could aid in the clinical diagnosis of papillary thyroid carcinoma. Globally, thyroid cancer is among the top ten commonest cancer in females. In both adult and pediatric populations, there are variations of prevalence of thyroid cancer and rising incidence rates of thyroid cancer worldwide. The increase of thyroid cancer incidence was almost entirely due to the increase of papillary thyroid carcinoma. The reasons behind the increase are complex, multifactorial, and incompletely understood. The most obvious reasons are increased use of diagnostic entities, change in classification of thyroid neoplasms, as well as factors such as obesity, environmental risk factors, and radiation. The prognosis of the patients with papillary thyroid carcinoma is generally good after treatment. Nevertheless, cancer recurrence and comorbidity of second primary cancer may occur, and it is important to have awareness of the clinical, pathological, and molecular parameters of papillary thyroid carcinoma.

Fine-Needle Aspiration Under Guidance of Ultrasound Examination of Thyroid Lesions.

Fine-needle aspiration biopsy is the most common method for preoperative diagnosis of thyroid carcinomas including papillary carcinoma. The procedure is best performed with ultrasound by operator with professional skill and knowledge. Several guidelines recommend the indication of fine-needle aspiration concerning the pattern of ultrasound and size of nodules. Besides, fine-needle aspiration biopsy of lymph nodes should be performed if malignancies are suspected. Fine-needle aspiration biopsy of thyroid gland is mostly safe, but complications such as blood extravasation-related complications, acute thyroid enlargement, infection in thyroid gland, and pneumothorax could occur. The most frequent complications are blood extravasation-related complications, which could be fatal. Similarly, acute thyroid enlargement could also be severe. To conclude, fine-needle aspiration biopsy is useful and should be performed under the precise indication and the updated knowledge of complications including the way of handling if they occur.

Macroscopic Examination of Surgical Specimen of Papillary Thyroid Carcinoma.

Standardized pathology reporting of thyroid cancer is important for quality clinical management, research as well as education purposes. International Collaboration on Cancer Reporting (ICCR) has produced a Dataset for reporting carcinoma of thyroid. Of the 19 core elements to report, six (operative procedure, operative findings, specimen submitted, tumor focality, tumor site, tumor dimensions) depend on the proper macroscopic examination of the surgical specimen with thyroid carcinoma. The other core elements to report depend on proper and adequate sampling on macroscopic examination. Thus, proper handling, examination, dissection, and sampling of different types, the surgical specimen(s) are needed in different situations for patients with thyroid carcinomas.

Histopathological Assessment for Papillary Thyroid Carcinoma.

Histologic assessments of papillary thyroid carcinoma are crucial for management of patients with the cancer as well as research on the cancer as papillary thyroid carcinoma has different histologic subtypes and many parameters which are essential in predicting the biological aggressiveness of the cancer. The histologic assessments should be guided by universally adopted protocols including World Health Organization (WHO) classification of endocrine tumors, International Collaboration on Cancer Reporting (ICCR) dataset, American Thyroid Association initial risk stratification for differentiated thyroid carcinomas and TNM stage groupings. The essential steps in histologic assessment involve the identification of characteristic features of papillary thyroid carcinoma, correct histologic subtyping, noting the number of carcinomas, measuring the size of the carcinoma, documenting the different aggressive histological parameters (mitotic activity, presence of tumor encapsulation/circumscription, lymphatic vessel invasion, blood vessel invasion, necrosis, extrathyroidal extension), resection margin status, associated pathology, presence of parathyroid gland, lymph node and distant metastases as well as synthesis of pathological stage based on the various clinical, macroscopic, and histological features.

Liposomal siRNA Delivery in Papillary Thyroid Carcinoma Cells.

The discovery of RNA interference (RNAi) has opened a new strategy in cancer therapy, especially by silencing target genes. Pharmacologically it can be achieved by introducing of small (19-21 base pairs) dsRNA molecules known as small interfering RNA (siRNA) targeting interested genes. siRNA mediated gene has been widely investigated for its utility in treating various diseases including cancer. However, the systemic delivery of interested siRNA via non-viral methods remains a major challenge with large numbers of polymeric and liposomal systems being tested. The most effective methods involving cationic liposomes delivery to cells. Nonetheless, systemic delivery of siRNA via cationic lipid particles is often poor due to rapid uptake by reticuloendothelial organs, resulting in decreased delivery of these particles to the site of interest. Polyethylene glycol (PEG) has been used in siRNA-liposomes formulation to minimize reticuloendothelial uptake. Also, PEGylation permits the accumulation of the liposomes-loaded siRNA at the tumor sites with defective vasculatures such as enhanced permeability and retention phenomena. Thus, a simple method to prepare stable PEGylated siRNA-loaded lipid particles could provide better systemic delivery system in treating various cancers, including papillary thyroid carcinoma. Here we illustrate a simple protocol for the formulation of siRNA-loaded lipid particles by hydration of freeze-dried matrix (HFDM) method for effective delivery of target specific siRNA to papillary thyroid carcinoma cells.

Concepts of Pathological Staging and Prognosis in Papillary Thyroid Carcinoma.

American Joint Committee on Cancer (AJCC)/Union for International Cancer Control (AJCC/UICC) staging and American Thyroid Association (ATA) risk predication system are the best predicators of mortality and cancer recurrence, respectively, in patients with differentiated thyroid carcinoma, including papillary thyroid carcinoma. In ATA risk stratification of differentiated thyroid carcinomas, clinical features, nodal features, and pathological features are assessed. Many of the features are also assessed in pathological staging. The prognostic stage grouping of papillary thyroid carcinoma in AJCC/UICC depends on the age of the patients as well as the standard parameters-extent of tumor (T), lymph node status (N), and presence of distant metastasis (M). Major changes noted in the current pathological staging protocol include the cut-off age from 45-year to 55-year in grouping of patients, use of gross invasion of strap muscles instead of minimal microscopic extrathyroidal extensions as T3b and downstage of many prognostic groups such as those with lymph node metastases (without distant metastases) from Stage III to Stage II. The staging protocol have moved many patients with papillary thyroid carcinoma into good prognostic groups for better predication of patients' survival rates and to avoid unnecessary treatment. This new approach has been verified by different groups globally, although modifications could be expected in the future for better prognostic assessment in patients with papillary thyroid carcinoma.

Single Nucleotide Polymorphisms in Papillary Thyroid Carcinoma: Clinical Significance and Detection by High-Resolution Melting.

Single nucleotide polymorphisms (SNPs) can have a variety of implications for the progression and development of papillary thyroid carcinomas (PTCs). Identification of SNPs, either as germline variants or mutations occurring in tumor tissue, can thus have useful implications for patient management. There are many potential methods that can be used to identify a specific SNP or other genetic variant, and among these is high-resolution melting (HRM). HRM can be used to detect the presence of a genetic variant in a single sealed tube, involving undertaking a polymerase chain reaction (PCR) in the presence of a saturating intercalating dye. Once PCR is complete, the amplicons produced can be melted through incremental raising of the temperature and the genotype of individual samples determined by changes in the change in fluorescence as the fluorescent dye is released by the melting DNA. In this chapter, we detail a method for the genotyping of DNA samples using HRM.

Long Non-Coding RNAs Profiling Using Microarray in Papillary Thyroid Carcinoma.

Long non-coding RNAs (lncRNAs) have been implicated in various cancers, including papillary thyroid carcinomas (PTCs). Genome-wide analysis (GWAS) of lncRNAs expression in PTC samples exhibited up and down regulation of lncRNAs, thus, acting as tumor promoting oncogenes or tumor suppressors in the pathogenesis of PTC by interacting with target genes. For example, lncRNAs such as HOTAIR, NEAT1, MALAT1, FAL1, HOXD-AS1, etc. are overexpressed in PTC in comparison to that of non-cancerous thyroid tissues, which stimulate the pathogenesis of PTC. On the other hand, lncRNAs such as MEG3, CASC2, PANDAR, LINC00271, NAMA, PTCSC3, etc. are down regulated in PTC tissues when compared to that of non-cancerous thyroid samples, suppressing formation of PTC. Also, several lncRNAs such as BANCR acts as oncogenic or tumor suppressor in PTC formation depending on which they are interacting with. In addition, lncRNAs expression in patients with PTC associated with clinicopathological parameters such as distance metastasis, lymph node metastasis, tumor size, pathological stage, and response to therapy. Thus, lncRNAs profiles could have the potential to be used as prognostic or predictive biomarker in patients with PTC. Therefore, we describe the microarray method to examine lncRNAs expression in PTC tissue samples, which could facilitate better management of patients with PTC. Furthermore, this method could be fabricated to examine lncRNAs expression in other biological and/or clinical samples.

BRAF Mutations in Papillary Thyroid Carcinoma: A Genomic Approach Using Probe-Based DNA Capture for Next-Generation Sequencing.

The BRAF V600E mutation in papillary thyroid carcinoma is the major mutation in classical subtype of papillary thyroid carcinoma and other cancers. It is the most studied predictor of clinical and pathological characteristics as well as molecular targets for cancer therapy. On the other hand, there is potential for many more forms of activating mutation in BRAF that are not detectable by simple assays to detect V600E, or even simple polymerase chain reaction (PCR)-based sequencing for full-length BRAF. Such activating mutations could arise from larger-scale rearrangements which may apparently leave no sequence change to BRAF while causing increased expression or activation by unusual means, such as gene fusion. Detection of these kinds of changes can take place using a variety of methods, though capture-based sequencing can identify the existence of such forms of mutant BRAF without needing foreknowledge of the loci involved in these kinds of mutation. In this chapter, we detail a method for capture of specific DNA sequences and their amplification to prepare for massively parallel sequencing.

Application of Immunohistochemistry in Papillary Thyroid Carcinoma.

Immunohistochemistry (IHC) is an economic and precise method to localize the presence of specific protein at cellular level in tissue. Although many papillary thyroid carcinomas do not require IHC to render a diagnosis, there are certain scenarios in which IHC are important. The major diagnostic applications of IHC include confirmation of papillary thyroid carcinoma in sites other than the thyroid, distinguish papillary thyroid carcinoma from other primary thyroid neoplasms in thyroid, and identify papillary thyroid carcinoma from secondary tumors to the thyroid. At research level, IHC could help identify prognostic information, identify underlying genetic alterations, and predict response to treatment in papillary thyroid carcinoma. The understanding of principle and recent advances in IHC will improve the diagnosis and management of patients with thyroid lesions including papillary thyroid carcinoma.

Whole-Slide Imaging: Updates and Applications in Papillary Thyroid Carcinoma.

Whole-slide imaging (WSI) has wide spectrum of application in histopathology, especially in the study of cancer including papillary thyroid carcinoma. The main applications of WSI system include research, teaching, and assessment and recently pathology practices. The other major advantages of WSI over histological sections on glass slides are easier storage and sharing of information as well as adaptation of use in artificial intelligence. The applications of WSI depend on factors such as volume of services requiring WSI, physical factors (computer server, bandwidth limitation of networks, storages requirements for data), adaption of the WSI images with the laboratory workflow, personnel (IT expert, pathologist, technicians) adaptation to the WSI workflow, validation studies, ethics, and cost efficiency of the application(s).