BRAF V600E Mutations and Beyond: A Molecular Perspective of Melanoma from a Tertiary Cancer Referral Center of India

Vaibhavi VengurlekarObjectives  Malignant melanoma demonstrates frequently occurring mutations of genes in the serine/threonine kinase pathway, namely BRAF, NRAS, and neurofibromin 1. There is rare documentation of a detailed analysis of these mutations in cases of melanoma among Indian patients. We present molecular features in cases of malignant melanoma, diagnosed at a tertiary cancer referral center in India, over a period of 8 years (2011-2018). Materials and Methods  This study was performed on formalin fixed paraffin embedded tissues of 88 histologically confirmed cases of malignant melanoma. BRAF gene alterations were studied by both Sanger sequencing and real-time polymerase chain reaction techniques ( n  = 74). Molecular testing for BRAF and NRAS gene alterations was accomplished in 74/88 cases (80%). Molecular test results were correlated with clinicopathological features using IBM SPSS Statistical software 25.0. Results  The age ranged from 13 to 79 years (median = 57), with a M:F ratio of 1.4:1. BRAF mutations were observed in 12/74 (16.21%) patients, including V600E ( n  = 7), A594T ( n  = 1), T599 = ( n  = 2), V600K ( n  = 1), and Q612P ( n  = 1), while NRAS mutations were observed in 6/38 (15.7%) patients. Among various subtypes, nodular melanoma was the most frequent subtype (33%) among cutaneous malignant melanomas. Among non-cutaneous melanomas, mucosal melanomas were observed in 37.5% of cases. Conclusion  This constitutes one of the few reports on comprehensive analysis of molecular alterations underlying melanomas in Indian patients. A larger sample size, with more extensive molecular markers, would yield additional information on the disease manifestation.

Lifestyle Modifications and Nutritional and Therapeutic Interventions in Delaying the Progression of Chronic Kidney Disease: A Review

Chronic kidney disease (CKD) is a debilitating progressive illness that affects more than 10% of the world's population. In this literature review, we discussed the roles of nutritional interventions, lifestyle modifications, hypertension (HTN) and diabetes mellitus (DM) control, and medications in delaying the progression of CKD. Walking, weight loss, low-protein diet (LPD), adherence to the alternate Mediterranean (aMed) diet, and Alternative Healthy Eating Index (AHEI)-2010 slow the progression of CKD. However, smoking and binge alcohol drinking increase the risk of CKD progression. In addition, hyperglycemia, altered lipid metabolism, low-grade inflammation, over-activation of the renin-angiotensin-aldosterone system (RAAS), and overhydration (OH) increase diabetic CKD progression. The Kidney Disease: Improving Global Outcomes (KDIGO) guidelines recommend blood pressure (BP) control of <140/90 mmHg in patients without albuminuria and <130/80 mmHg in patients with albuminuria to prevent CKD progression. Medical therapies aim to target epigenetic alterations, fibrosis, and inflammation. Currently, RAAS blockade, sodium-glucose cotransporter-2 (SGLT2) inhibitors, pentoxifylline, and finerenone are approved for managing CKD. In addition, according to the completed Study of Diabetic Nephropathy with Atrasentan (SONAR), atrasentan, an endothelin receptor antagonist (ERA), decreased the risk of renal events in diabetic CKD patients. However, ongoing trials are studying the role of other agents in slowing the progression of CKD.

BTEX (benzene, toluene, ethylbenzene, and xylene) and risk of cancer - a study from Centers for Disease Control and Prevention's National Health and Nutrition Examination Survey

Introduction/Objective

BTEX (benzene, toluene, ethylbenzene, and xylene) is well know for its toxicity via through environmental, occupational and recreational exposures. However, there is limited literature about the carcinogenic effect of BTEX. Hence, we aim to study the prevalence and association of cancer amongst individuals with exposure of BTEX.

Methods/Case Report

A retrospective cross-sectional study was performed between 2013 and 2018 utilizing the NHANES database. Adult individuals having data on socio-demographic questionnaires and lab findings on exposure to BTEX were included. Prevalence of cancer was identified amongst exposure to BTEX (vs no-BTEX). Univariate (chi-squre test and Mann–Whitney U test) and Multivariate (survey logistic regression) analysis was performed to evaluate the epidemiologic characteristics of individuals exposred to BTEX and association of cancer with BTEX exposure in comparison to no BTEX exposure.The p value of &lt;0.05 considered statistically significant.

Results (if a Case Study enter NA)

124,162 participants were identified with BTEX exposure. Individuals with BTEX exposure were young (40 vs 51 year old), male (91% vs female: 87%), and Mexican American (92% vs Non-Hispanic Black: 89% vs Non-Hispanic White: 89% vs other Hispanic: 87%). Univariate analysis showed higher total prevalence of cancer in BTEX (9.3% vs. 1.3%; p&lt;0.0001) compared to no BTEX. Individuals with BTEX exposure had higher prevalnece of blood cancer (0.47% vs 0.00; p&lt;0.0001), leukemia (0.56% vs 0.00; p&lt;0.001), and lymphoma (1.72% vs 0.39%; p&lt;0.0001) in comparison with no exposure. Multivaritate analysis showed participants with BTEX exposure had 10% higher risk of cancer (aOR: 1.10; 95%CI: 1.10-1.10; p&lt;0.0001) compared to no BTEX exposure. Additionally, exposure to individual components of benzene (aOR: 1.24; 95%CI: 1.24; p&lt;0.0001), ethylbenzene (aOR: 1.08; 95%CI: 1.08-1.08; p&lt;0.0001), and o-xylene (aOR: 1.19; 95%CI: 1.19-1.19; p&lt;0.0001) had higher risk of cancer compared to no exposure participants.

Conclusion

Our study conclude higher risk of cancer among participants with exposure to benzene, ethylbenzene and o-xylene. Future studies are warranted to evaluate the association of various types of cancers in BTEX exposure.

Impact of Molecular Tumor Board on the Clinical Management of Patients With Cancer

PURPOSE

Multidisciplinary molecular tumor boards (MTBs) help in interpreting complex genomic data generated by molecular tumor profiling and improve patients' access to targeted therapies. The purpose of this study was to assess the impact of our institution's MTB on the clinical management of patients with cancer.

METHODS

This study was conducted at a tertiary cancer center in India. Cases to be discussed in the MTB were identified by molecular pathologists, scientists, or oncologists. On the basis of the clinical data and molecular test reports, a course of clinical management was recommended and made available to the treating oncologist. We determined the proportion of patients who were recommended a change in the clinical management. We also assessed compliance of the treating oncologists with MTB recommendations.

RESULTS

There were 339 discussions for 328 unique patients. The median age of the cohort was 54 years (range 17-87), and the majority of the patients were men (65.1%). Of 339 cases, 133 (39.2%) were recommended continuation of ongoing therapy while the remaining 206 (60.7%) were recommended a change in clinical management. Compliance with MTB recommendations for a change in clinical management was 58.5% (79 of 138 evaluable cases). Compliance and implementation for MTB's recommendation to start a new therapy in 104 evaluable cases were 60.5% and 44.2%, respectively. A total of 248 biopsies had at least one actionable mutation. A total of 646 mutations were identified in the cohort, with EGFR being the most frequently altered gene.

CONCLUSION

MTBs help in interpreting results of molecular tests, understanding the significance of molecular abnormalities, and assessing the benefits of available targeted therapies and clinical trials in the management of patients with targetable genetic alterations.

A Rare Case of a Solitary Fibrous Tumor in a Child, Presenting as a Congenital Mass, Displaying NAB2ex4::STAT6ex2 Gene Fusion with an Incidental Ganglioneuroblastoma

A solitary fibrous tumor (SFT) is a ubiquitous tumor that occurs across all ages. It is rarely reported in pediatric patients, especially as a congenital mass. A 1 year 7-month old male child presented with a slow-growing gluteal mass since birth along with a recent episode of bleeding. Magnetic resonance imaging (MRI) showed a well-defined, T1-hypointense and T2-hyperintense mass in the skin and the subcutaneous plane. Subsequently, he underwent a surgical resection that revealed a 5.7 cm-sized fleshy mass. On histopathologic examination, there was a fairly well-circumscribed, cellular spindle cell tumor, with cells arranged in intersecting fascicles and hemangiopericytomatous pattern with areas of hemorrhage and fibrinoid necrosis. Cells revealed mild nuclear atypia. Mitotic figures were up to 8/10 hpf. Immunohistochemically, the tumor cells were diffusely positive for CD34 and STAT6. Furthermore, the tumor revealed NAB2 exon 4:: STAT6 exon 2 fusion by RT-PCR and Sanger sequencing. Post-excision, during follow-up, the patient developed an adrenal mass that was histopathologically proven as a neuroblastic tumor, not further specified on biopsy and finally as ganglioneuroblastoma, intermixed type on excision. This constitutes one of the rare cases of SFT in a pediatric patient, presenting as a congenital mass, confirmed by STAT6 immunostaining and further, molecular testing. A review of literature of similar cases, including treatment-related implications, is presented.

Incidence of SARS-CoV-2 infection among asymptomatic patients undergoing preoperative COVID testing prior to cancer surgery: ASPECT study

BACKGROUND AND OBJECTIVES

The COVID-19 pandemic, with high rate of asymptomatic infections and increased perioperative complications, prompted widespread adoption of screening methods. We analyzed the incidence of asymptomatic infection and perioperative outcomes in patients undergoing cancer surgery. We also studied the impact on subsequent cancer treatment in those with COVID-19.

METHODS

All patients who underwent elective and emergency cancer surgery from April to September 2020 were included. After screening for symptoms, a preoperative test was performed from nasopharyngeal and oropharyngeal swabs before the procedure. Patients were followed up for 30 days postoperatively and complications were noted.

RESULTS

2108 asymptomatic patients were tested, of which 200 (9.5%) tested positive. Of those who tested positive, 140 (70%) underwent the planned surgery at a median of 30 days from testing positive, and 20 (14.3%) had ≥ Grade III complications. Forty (20%) patients did not receive the intended treatment; 110 patients were retested in the Postoperative period, and 41 (37.3%) tested positive and 9(22%) patients died of COVID-related complications.

CONCLUSION

Routine preoperative testing for COVID-19 helps to segregate patients with asymptomatic infection. Higher complications occur in those who develop COVID-19 in postoperative period. Prolonged delay in surgery after COVID infection may influence planned treatment.

A rare case of a solitary fibrous tumor of vulva, displaying NAB2ex6-STAT6ex17 fusion

A solitary fibrous tumor (SFT), although ubiquitous, is rarely documented in the female genital tract, especially confirmed by STAT6 immunostaining and underlying NAB2-STAT6 gene fusion. A 24-year-old female presented with a gradually increasing vulvar swelling in her right labia, which rapidly increased in size over 1-year duration. Radiologically, a subcutaneous, predominantly solid, lobulated mass, measuring 10 cm in the largest dimension was seen involving her right labia majora and perineum. She underwent tumor resection, elsewhere, where it was reported as a pleomorphic sarcoma. Histopathologic review revealed a cellular tumor comprising spindle cells, displaying mild nuclear variation, arranged diffusely and focally, in a hemangiopericytomatous growth pattern, within a collagenous stroma. Interspersed were blood vessels with perivascular hyalinization and few giant cells. By immunohistochemistry, tumor cells showed patchy immunostaining for CD34 and diffuse immunostaining for STAT6. Furthermore, the tumor displayed NAB2ex6-STAT6ex 17 fusion by RT-PCR technique. This case constitutes one of the few reported cases of vulvar SFT, confirmed by STAT6 immunostaining and the second such case, displaying NAB2-STAT6 gene fusion. Diagnostic and treatment implications are discussed herewith.

Moving Next-Generation Sequencing into the Clinic

With an advancement in the field of molecular diagnostics, there has been a profound evolution in the testing modalities, especially in the field of oncology. In the past decade, sequencing technology has evolved drastically with the advent of high-throughput next-generation sequencing (NGS). Subsequently, the single-gene tests have been replaced by multigene panel-based assays, deep sequencing, massively parallel whole genome, whole-exome sequencing, and so on. NGS has provided molecular diagnostics professionals a wonderful tool to explore and unearth the genetic alterations, underpinning the pathophysiology of the disease. However, this development has posed new challenges which consist of the following; understanding the technology, types of platforms available, various sequencing strategies, bioinformatics and data analysis algorithm, reporting of various variants, and validation of assays and overall for developing NGS assay for clinical utility. The challenges involved sometimes impede development of these high-end assays in laboratories. The present article provides a broad overview of our journey in setting up the NGS assay in a molecular pathology laboratory at a tertiary care oncology center. We hereby describe various important points and steps to be followed while working on the NGS setup, right from its inception to final drafting of the reports, with inclusion of various validation steps. We aim at providing a beginner’s guide to set up NGS assays in the laboratory using recommended best practices and various international guidelines.

Recent update on potential cytotoxicity, biocompatibility and preventive measures of biomaterials used in dentistry

Dental treatment is provided for a wide variety of oral health problems like dental caries, periodontal diseases, periapical infections, replacement of missing teeth and orthodontic problems. Various biomaterials, like composite resins, amalgam, glass ionomer cement, acrylic resins, metal alloys, impression materials, bone grafts, membranes, local anaesthetics, etc., are used for dental applications. The physical and chemical characteristics of these materials influence the outcome of dental treatment. It also impacts on the biological, allergic and toxic potential of biomaterials. With innovations in science and their positive results, there is also a need for awareness about the biological risks of these biomaterials. The aim of dental treatment is to have effective, yet safe, and long-lasting results for the benefit of patients. For this, it is important to have a thorough understanding of biomaterials and their effects on local and systemic health. Materials used in dentistry undergo a series of analyses before their oral applications. To the best of our knowledge, this is the first and original review that discusses the reasons for and studies on the toxicity of commonly used biomaterials for applications in dentistry. It will help clinicians to formulate a methodical approach for the selection of dental biomaterials, thus providing an awareness for forecasting their risk of toxic reactions.

COVID 19 pandemic testing time - Crisis or opportunity in disguise for India?

The current SARS-CoV-2 infection or the COVID 19 pandemic has taken the world by storm, where the best health care systems in the world seem to be overwhelmed and still this virus is eluding us as we are compelled to explore the preventive and/or therapeutic interventions to control the disease outbreak as well as to prevent deaths. In parallel to clinical services, laboratories have been overwhelmed with task of keeping up with ever increasing demand for testing. Real time PCR detection of COVID19 is the gold standard method, however, has certain shortcomings in terms of availability of infrastructure, reagents, consumables, and technical expertise. All these have paved the way for the alternative testing algorithms and strategies. Countries like United States and Italy have struggled with these issues. India has been criticized for not testing enough and not adopting the right policy, but has been managing the disease within its resource limited health care system to a fair extent.

The present review provides the Indian perspective of COVID 19 testing, the journey from not testing enough in the past to a vast expanse and depth of testing in present time.

A Case of Inv(1)(q23q31) TPR-NTRK1 Fusion-Positive Spindle Cell Neoplasm in an Infant-Uncovered by Next-Generation Sequencing: Diagnostic Challenge, Review, and Therapeutic Implications

Lately, NTRK-positive mesenchymal tumors are being increasingly identified, mostly in pediatric patients, in view of associated treatment implications, especially in recurrent and unresectable tumors. A 1-year-old male child presented with a rapidly growing tumor mass in his cervical region of 2 months duration. Radiologic imaging disclosed a tumor measuring 11 cm in size, almost filing his right neck spaces. Review of biopsy sections revealed a cellular tumor comprising spindle cells arranged in sheets and fascicles with interspersed collagenous strands and areas of adipocytic, myxoid, and hyaline degeneration. Immunohistochemically, tumor cells were diffusely positive for CD34 and S100 protein. Subsequently, on testing the tumor for a solid tumor gene panel by next-generation sequencing, it was found to be positive for inv(1)(q23q31) TPR-NTRK1 fusion. Furthermore, tumor cells displayed NTRK1 gene rearrangement by fluorescence in situ hybridization technique. The patient was offered chemotherapy; however, he had a rapid local progression, leading to respiratory obstruction; he then succumbed to the disease. The present case underpins the value of next-generation sequencing as a useful technique for uncovering NTRK-fusion-positive mesenchymal tumors. Review of similar cases, diagnostic challenge, and treatment implications in such cases are discussed.

Examining the transplacental passage of apixaban using the dually perfused human placenta

Essentials Apixaban is a novel oral anticoagulant that has not been studied in pregnant patients. Our objective was to determine the rate and extent of the placental transfer of apixaban. Apixaban rapidly crosses the ex vivo term human placenta from maternal to fetal circulation. Fetal apixaban levels in vivo are estimated to be 35-90% of the corresponding maternal levels.

SUMMARY

Background Apixaban is a novel oral anticoagulant that is increasingly being prescribed to women of reproductive age. However, information regarding its placental transfer is non-existent. Objective To determine the rate and extent of placental transfer of apixaban, using the human placenta ex vivo. Methods Placentae collected after Caesarean or vaginal delivery of healthy term infants were perfused in the respective maternal and fetal circulation. At the start of the experiment, apixaban was added to the maternal circulation at a concentration of 150 ng mL(-1) , and samples from maternal and fetal reservoirs were collected over 3 h. Results There was a rapid decline of apixaban in the maternal compartment, followed by emergence in the fetal compartment with a median fetal-to-maternal drug concentration ratio of 0.77 (interquartile range [IQR], 0.76-0.81) and fetal concentration of 39.0 ng mL(-1) (IQR, 36.8-40.6) after 3 h (n = 5). The perfusion results were subsequently adjusted to account for differences in the concentration of plasma proteins in maternal and fetal blood, as apixaban remains highly bound to albumin and alpha-1 acid glycoprotein. After the adjustment, the predicted fetal-to-maternal ratio of total (bound plus unbound) apixaban concentrations in vivo ranged from 0.35 to 0.90. Conclusions We conclude that unbound apixaban rapidly crosses from the maternal to fetal circulation. We further predict that total apixaban concentrations in cord blood in vivo are 35-90% of the corresponding maternal levels, suggesting that apixaban could have a possible adverse effect on fetal and neonatal coagulation.

Comparison of propofol versus thiopentone with midazolam or lidocaine to facilitate laryngeal mask insertion

PURPOSE

To assess the ease of insertion of laryngeal mask airway (LMA) comparing propofol with lidocaine or midazolam followed by thiopentone and compare the costs with each technique.

METHODS

One hundred and fifty ASA 1 or 2 patients equally divided into three groups scheduled for elective surgery were recruited into this prospective, single blind, randomized, parallel groups study. Anaesthetic induction was achieved with 1 microgram.kg-1 fentanyl i.v. followed by either 2.5 mg.kg-1 propofol (group P), or a sequence of 1.5 mg.kg-1 lidocaine and 5 mg.kg-1 thiopentone (group LT), or midazolam 0.1 mg.kg-1 and, three minutes later, 5 mg.kg-1 thiopentone (group MT). The LMA was inserted by the blinded anaesthetist who assessed and graded the conditions for LMA insertion and noted any adverse responses (i.e., inadequate jaw relaxation, gagging, coughing, limb or head movement, hiccough and laryngospasm). Conditions were considered "excellent" if there were no adverse responses, and "satisfactory" if such a response was mild and transient.

RESULTS

Excellent or satisfactory conditions were observed in 48 (96%) patients in the midazolam-thiopentone group, 46 (92%) in the propofol group, and 34 (68%) in the lidocaine-thiopentone group (P = 0.0001). The incidence of gagging (P = 0.042), limb movement (P = 0.031), and laryngospasm (P = 0.0001) was higher in the lidocaine-thiopentone group.

CONCLUSIONS

With the above doses, a fentanyl-midazolam-thiopentone combination which is about 35% less expensive than fentanyl-propofol, provides equally good conditions for the insertion of LMA.