Analysis of patients with endometrial carcinoma using the ProMise classifier: a pilot study from India

BACKGROUND

Molecular subtyping of endometrial carcinomas (EC) has been shown to classify tumors into prognostically relevant groups. Characterizing EC with a limited number of markers viz., POLE mutations, p53 mutations, and MMR status, can provide valuable information.

DESIGN

Paraffin sections of a cohort of 48 EC from a tertiary care center were characterized for the above-mentioned molecular markers and analyzed in the context of survival.

METHODS

Formalin fixed paraffin embedded tissues from 48 EC were characterized for POLE mutations by Sanger sequencing (exons 9-14), for MMR (MLH1, MH2, MSH6) using immunohistochemistry (IHC) and copy number (high/low) using p53 IHC. Mutational status was integrated along with the clinicopathological details and survival analysis performed.

RESULTS

Eleven (22.9%) patients were MMR deficient, 3 (6.3%) had POLE mutation, while 2 (4.1%) had both POLE and P53 mutations (regarded as multiple classifiers). Twelve (25%) patients were found to have P53 mutations, while the remaining 20 (41.7%) had no specific molecular profile (NSMP). Median follow-up duration was 43.5 (2-62) months with 8 recurrences and 9 deaths. Tumors with POLE mutation had the most favorable prognosis followed by the NSMP and the MMR mutated group while the P53 and multiple classifier groups had the worst prognosis in terms of OS (Log-rank p: 0.006) and PFS (Log-rank p: 0.001).

CONCLUSION

The integration of molecular-clinicopathologic data for endometrial cancer classification, through cost-effective, clinically applicable assays appears to be a highly objective tool that can be adopted even in resource-limited settings. It has the potential to cause a shift in the paradigm of EC pathology and management practice.

Comparative analysis of mutational patterns in triple negative breast cancer before and after neoadjuvant chemotherapy in patients with residual disease

Triple-negative breast cancer (TNBC) is a heterogeneous disease with poor survival compared to other subtypes. Patients with residual disease after neoadjuvant chemotherapy (NAC) face an increased risk of relapse and death. We aimed to characterize the mutational landscape of this subset to offer insights into relapse pathogenesis and potential therapeutic targets. We retrospectively analyzed archived paired (pre- and post-NAC) tumor samples from 25 patients with TNBC with residual disease using a targeted 72-gene next-generation sequencing panel. Our findings revealed a stable mutational burden in both pre- and post-NAC samples, with a median count of 12 variants (IQR 7-17.25) per sample. TP53, PMS2, PTEN, ERBB2, and NOTCH1 variants were observed in pre-NAC samples predominantly. Notably, post-NAC samples exhibited a significant increase in AR gene mutations, suggesting potential prognostic and predictive implications. No difference in mutational burden was found between patients who did and did not receive platinum (p = 0.94), or between those with and without recurrence (p = 0.49). We employed K-means clustering to categorize the patients based on their variant profiles, aiding in the prediction of possible patterns associated with recurrence. Our study was limited by its small sample size and retrospective design, suggesting the need for further validation in larger prospective cohorts.

Role of Genetic Testing in the Management of Indeterminate Thyroid Nodules in the Indian Setting

The increased detection of thyroid nodules in the human population has led to an increase in the number of thyroid surgeries without an improvement in survival outcomes. Though the choice for surgery is straightforward in malignant thyroid nodules, the decision is far more complex in those nodules that get categorized into indeterminate thyroid nodules (ITN) by fine needle aspiration. Therefore, there is a pressing need to develop a tool that will aid in decision-making among the ITN. In this context, the development of various molecular testing (MT) panels has helped to confirm or rule out malignancy, reducing unnecessary surgeries and potentially guiding the extent of surgery as well. Currently, such tests are widely used among the Western population but these MT panels are not used by the South Asian population because of non-availability of validated panels and the high cost involved. There is a need to develop a suitable panel which is population-specific and validate the same. In this review, we would focus on current trends in the management of ITN among the South Asian population and how to develop a novel MT panel which is cost-effective, with high diagnostic accuracy obviating the need for expensive panels that already exist.

Droplet digital PCR (ddPCR) using FFPE DNA to assess methylation status of MGMT gene among patients with IDH mutant astrocytoma and IDH wild-type glioblastoma

MGMT promoter methylation analysis in formalin-fixed paraffin-embedded (FFPE) tissues can be challenging since the DNA obtained is often fragmented. Bisulfite conversion, which is essential to determine methylation status, further degrades DNA. While conventional methylation-specific PCR (MSP) and pyrosequencing assays have long been used to determine the methylation status of MGMT, this study was designed to determine the utility of one-tube DNA extraction method coupled with a droplet digital PCR (ddPCR) assay, to study the epigenetic changes in the promoter region of the MGMT gene using DNA obtained from FFPE.The FFPE blocks of 30 (n=30) patients with Central Nervous System (CNS) WHO grade 4 tumours, previously tested by MSP (2011-2021) were retrieved; DNA was extracted using one-tube extraction method and bisulfite converted. All converted samples were analyzed for methylation status of the MGMT promoter region with a laboratory designed Methylation-Specific ddPCR (MS ddPCR) using degenerate primers and probes that were labelled with FAM or HEX flurocein dye.Of the 30 cases, 20 cases were MGMT methylated and 10 cases were unmethylated by MS ddPCR. The results of MS ddPCR were then compared with those obtained by MSP and found to be concordant in 93.3% (28/30) of the cases and discordant in 2 cases. The Cohen's kappa coefficient (κ) was 0.84. The sensitivity, specificity, positive predictive value and negative predictive value of the assay in detecting the methylation status was found to be 95%, 90%, 95% and 90%.The results show that MS ddPCR is a valuable tool to detect the methylation status of MGMT in FFPE with high sensitivity. This method is cost-effective and easy to perform and could be an attractive alternative to the routine method of MSP.

Utility of reverse transcriptase - Multiplex ligation-dependant probe amplification (RT-MLPA) in the molecular classification of Diffuse Large B cell lymphoma (DLBCL) by cell-of-origin (COO)

Classifying diffuse large B cell lymphomas, not otherwise specified (DLBCL, NOS), is based on their cell-of-origin (COO) which is included in the WHO classification (2016), is essential to characterize them better in context of prognostication. While gene expression profiling (GEP) considered the gold standard and more recently, the Nanostring-based approach, classify these tumors accurately, many laboratories with limited resources and instrumentation need an alternate approach that is reliable, inexpensive, and with a reasonable turnaround. The Reverse Transcriptase Multiplex Ligation Dependant Probe Amplification (RT-MLPA) to subtype DLBCL, NOS cases, as designed by CALYM group appears to provide a good alternative but needs to be validated in other centres. Therefore, this study evaluated DLBCL, NOS and compared the results of RT-MLPA to that obtained by immunohistochemistry using the Hans algorithm.

Materials and Methods

Sixty-five DLBCL, NOS cases were included and the RT-MLPA was set up and standardized using probes that were designed by the CALYM study group. Briefly, RNA was extracted converted to cDNA and the 21-gene expression classifier that also included probes to detect MYD88 mutations and EBER mRNA was performed by MLPA. The results were analyzed by the open home grown software designed by the same group and compared to the results obtained by IHC.

Results

Forty-four of the sixty-five cases provided concordant results (k = 0.35) and if the MYD88 results were to be used as a classifier the concordance would have improved from 67.7% to 82%. The 21 discordant cases were divided into five categories to provide a possible explanation for the discordance. Further 26% and 31% of the samples tested were positive for MYD88 mutations and EBER mRNA, respectively. The test had a turnaround of three days.

Conclusion

The test provided moderate (67.7%) concordance when compared with IHC and perhaps would have provided higher concordance if compared with GEP. The test also has the advantage of providing information on the MYD88 and EBV infection status. It was found to be reliable, easy to perform and standardize, requiring only routine instruments available in most molecular laboratories. The RT-MLPA assay therefore provides an alternative for laboratories that would require subtyping of DLBCL, NOS cases in the absence of an access to GEP or other instrument intensive methods.

Editing the core region in HPFH deletions alters fetal and adult globin expression for treatment of β-hemoglobinopathies

Reactivation of fetal hemoglobin (HbF) is a commonly adapted strategy to ameliorate β-hemoglobinopathies. However, the continued production of defective adult hemoglobin (HbA) limits HbF tetramer production affecting the therapeutic benefits. Here, we evaluated deletional hereditary persistence of fetal hemoglobin (HPFH) mutations and identified an 11-kb sequence, encompassing putative repressor region (PRR) to β-globin exon-1 (βE1), as the core deletion that ablates HbA and exhibits superior HbF production compared with HPFH or other well-established targets. PRR-βE1-edited hematopoietic stem and progenitor cells (HSPCs) retained their genome integrity and their engraftment potential to repopulate for long-term hematopoiesis in immunocompromised mice producing HbF positive cells in vivo. Furthermore, PRR-βE1 gene editing is feasible without ex vivo HSPC culture. Importantly, the editing induced therapeutically significant levels of HbF to reverse the phenotypes of both sickle cell disease and β-thalassemia major. These findings imply that PRR-βE1 gene editing of patient HSPCs could lead to improved therapeutic outcomes for β-hemoglobinopathy gene therapy.

Ultrasound-guided dry needling of masticatory muscles in trigeminal neuralgia - A case series of 35 patients

Background

Trigeminal neuralgia (TGN) is considered a sensory neuropathy. However, reports of pain on chewing/speaking suggest a masticatory myofascial involvement.

Objective

To examine the effect of ultrasound-guided dry needling (USGDN), which deactivates myofascial trigger points in masticatory, neck, and facial muscles on TGN symptoms.

Methods

Charts of 35 patients treated for TGN were retrospectively reviewed. Treatment was USGDN alone or combined with trigeminal ganglion/mandibular nerve pulsed radiofrequency (PRF), followed by yoga mudras to stretch masticatory and facial muscles. Patients were followed for 1-8 years. Outcome parameters were reduction of medications with reduction in neuralgic attack frequency and Numeric Rating Scale (NRS) score.

Results

23 patients (65.7%) received USGDN alone, 12 patients (34.3%) received PRF treatment before USGDN. A significant reduction in the mean (SD) NRS (5.7 [1.2] vs 8.8 [1.6]; P < .001) and neuralgic attack frequency (47 [27] vs 118 [70] attacks/day; P < .001) was seen after PRF compared with baseline, respectively. Following USGDN, the mean (SD) NRS further decreased significantly to 1.0 (0.9) (P < .001). USGDN alone produced a similar improvement in the NRS (8.9 [1.5] at baseline reduced to 0.6 [0.7] post-USGDN; P < .001). Patients in both groups reported a cessation in neuralgic attacks after USGDN. Post-USGDN, 18/27 patients completely discontinued medication, with the mean (SD) carbamazepine dose significantly reducing from 716.7 (260.9) mg/day at baseline to 113.0 (250.2) mg/day post-USGDN (P < .001).

Conclusion

Decisive relief of TGN by USGDN suggests neuromyalgia involving masticatory muscles. Prospective, controlled studies could confirm these findings.

Impact of Grade on Survival in Pleomorphic Xanthoastrocytoma and Low Prevalence of BRAF V600E Mutation

BACKGROUND

The prevalence of BRAFV600E mutations in pleomorphic xanthoastrocytoma (PXA) World Health Organization (WHO) Grade 2 and PXA WHO Grade 3 reported varies from 60% to 80%, yet the prognostic implications remain unclear.

METHODS

We reviewed the demographic and clinicoradiologic data of 20 PXAs WHO Grade 2 and 13 PXAs WHO Grade 3, operated between 2007 and 2020, to ascertain extent of excision, recurrence, progression-free survival (PFS), and overall survival (OS). PXAs WHO Grade 3 were defined by the presence of >5 mitoses/high-power field. PXAs WHO Grade 3 received adjuvant radiation therapy and chemotherapy whereas PXAs received radiation therapy if subtotally excised. All samples were analyzed for the presence of BRAFV600E mutation using DNA obtained from paraffin blocks using droplet-digital polymerase chain reaction.

RESULTS

The median patient age at diagnosis was 22 years with a male preponderance. BRAFV600E mutations were noted in 30% of tumors; 8 PXAs WHO Grade 2 and 2 PXAs WHO Grade 3. Recurrence occurred in 6 of 13 PXA WHO Grade 3 (55%) and 1 of 20 PXAs WHO Grade 2 (5%). At median follow-up of 45 months, the OS was 54 months and 33 months in the PXA WHO Grade 2 and PXA WHO Grade 3 groups, respectively (P = 0.02). OS and PFS did not differ between BRAF-mutated and BRAF-negative tumors.

CONCLUSIONS

BRAFV600E mutations are less frequent in our population than reported in the literature. The BRAF mutation does not significantly impact OS and PFS. PXAs WHO Grade 3 are a distinct clinical entity, associated with worse PFS and OS than PXAs WHO Grade 2.

Telomerase Reverse Transcriptase Promoter Mutations in A Cohort Of Adult Gliomas - Clinicopathological Correlates

BACKGROUND

Introduction: Gliomas were previously classified histologically, although now the latest WHO classification incorporates several molecular markers to classify these. Detection of TERT promoter mutations is assuming increased importance due to its relevance to prognostication.

OBJECTIVE

: The aim of this study was to determine the frequency of TERT promoter mutations, association of TERT promoter mutations with other molecular alterations and to assess the role of TERT promoter mutations in overall survival and progression-free survival in relation to histological and molecular glioma subtypes.

MATERIALS AND METHODS

This study analyzed a cohort of 107 adult patients with diffuse gliomas, WHO grades II and III and glioblastoma, by immunohistochemistry for IDH and ATRX mutations, FISH for 1p/19q co-deletions and PCR sequencing for TERT promoter mutation. Further, five glioma molecular sub-groups were derived using three molecular alteration and included the sub-groups with: i) IDH mutations only, ii) IDH and TERT mutations only, iii) IDH and 1p/19q co-deletion only, iv) Triple negative, and v) Triple positive.

RESULTS

IDH mutations and 1p/19q co-deletions were individually and significantly associated with an improved progression free (P = 0.001 and P = 0.002, respectively) and overall survival (P = 0.000 and P = 0.005, respectively) in the present cohort of gliomas. TERT promoter mutations occurred frequently in anaplastic oligodendrogliomas (94%), oligodendrogliomas (87.5%) and glioblastomas (54%). Sub-division into molecular sub-groups showed that the triple-positive tumors carried the best prognosis, followed by IDH only, triple negative and finally the TERT mutation only tumors (P < 0.000).

CONCLUSION

: This indicates that sub-classification using these molecular markers separates tumors into prognostically relevant categories.

ZFTA-fusion in supratentorial ependymomas: low prevalence in South Asians and no correlation with survival

BACKGROUND

- Supratentorial ependymomas (STEs) are an aggressive group of ependymoma, topographically distinct from their posterior fossa and spinal counterparts. ZFTA fusion-positive cases have been reported to account for the majority of STEs, although data on its association with poorer outcomes is inconsistent.

MATERIALS AND METHODS

- We assessed the prevalence of the ZFTA-fusion by RT PCR and FISH in a cohort of 61 patients (68 samples) with STE. Our primary outcome was to determine the role of the ZFTA-fusion on progression-free and overall survival of patients with STE. Our secondary objectives were to assess the impact of ZFTA-fusion on NF-kB pathway signalling via surrogate markers of this pathway, namely COX-2, CCND1 and L1CAM.

RESULTS

- ZFTA-fusion was noted in 21.3% of STEs in our cohort. The presence of this rearrangement did not significantly impact the PFS or OS of patients with STEs and was not associated with upregulation of markers of the NF-kB pathway. Only gross total resection was significantly associated with better progression-free survival.

CONCLUSION

- In contradiction to prior reports from across the world, the ZFTA-fusion is far less prevalent among our population. It does not appear to drive NF-kB signaling or significantly affect outcomes. Gross total resection (GTR) must be attempted in all cases of STE and adjuvant radiation and/or chemotherapy employed when GTR is not achieved.

USP8, USP48, and BRAF mutations differ in their genotype-phenotype correlation in Asian Indian patients with Cushing's disease

PURPOSE

To estimate the prevalence of USP8, USP48, and BRAF mutations in patients with Cushing's disease (CD) from the Indian subcontinent, and determine their genotype-phenotype correlation.

METHODS

We prospectively recruited 46 patients with CD who underwent surgery between September 2015 and July 2019 at our institute. Fresh frozen tumour tissue was obtained in all patients. Using Sanger sequencing, the presence of somatic USP8 mutations was documented and the frequency of USP48 and BRAF mutations in USP8 wild-type corticotroph adenomas was determined. Clinical, hormonal, and surgical data were then compared between USP8-, USP48- and BRAF-variant carriers and patients with wild-type tumours.

RESULTS

Signature USP8 mutations were detected in 17 (37%) patients. Of the 29 USP8 wild-type adenomas, 4 (13.8%) harboured USP48 mutations, one of them being a splice-site mutation that has previously not been described. BRAF mutations were not found in any of the 29 patients. Corticotroph adenomas with USP8 mutations had a higher incidence of Crooke's hyaline change than wild-type tumours (70.6 vs. 37.9%, p = 0.032). Adenomas with USP48 mutations had a higher rate of cavernous sinus invasion than their wild-type counterparts (50 vs. 4%, p = 0.042). No other significant phenotypic difference could be established between mutant and wild-type tumours.

CONCLUSIONS

The prevalence of USP8 mutations in our series of patients with CD was 37%. The prevalence of USP48 mutations in USP8 wild-type adenomas was 13.8%, including a novel splice-site mutation. BRAF mutations were not found in any USP8 wild-type tumour. USP8-mutants showed significantly more Crooke's hyaline change and USP48-mutants were more likely to demonstrate cavernous sinus invasion.

Genes of the month: H3.3 histone genes: H3F3A and H3F3B

Histones constitute the chief protein component of DNA. They help to maintain chromatin structure and regulate gene expression. The long double-stranded DNA molecule winds around histone octamers to form nucleosomes which serve the purpose of compacting DNA within the confines of the nuclear membrane. There are five major types of histones, namely H1/H5, H2, H3 and H4. H3.3 is a subtype of H3 histone and can be encoded either by the H3F3A or H3F3B genes independently. Amino acids such as lysine and arginine found in the histone tails are sites of post-translational modifications (PTMs) such as methylation and acetylation. These PTMs in histones are involved in the regulation of gene expression by chromatin remodelling and by controlling DNA methylation patterns. Mutations in histone genes can affect sites of PTMs causing changes in local and global DNA methylation status. These effects are directly linked to neoplastic transformation by altered gene expression. Recurrent H3.3 histone mutations are increasingly identified in several malignancies and developmental disorders. The following review attempts to shed light on the diseases associated with H3.3 histone mutations.

Clinical Profile and Mutations Associated with Multiple Endocrine Neoplasia-Type1 (MEN1) and Their First-Degree Relatives at Risk of Developing MEN1: A Prospective Study

Multiple Endocrine Neoplasia type-1 (MEN1) is an autosomal dominant disorder with a combined occurrence of tumours of parathyroid glands, pancreatic islets, and anterior pituitary. About 90% of these patients carry mutations in the MEN1 gene, though the spectrum is not well defined in India. Forty clinically suspected cases of MEN1 were enrolled prospectively over six years; 32 patients (23 index-cases and nine affected relatives) with≥2 classical endocrine tumours of MEN1 were considered definite, and eight were categorised as 'MEN1-like'. Details of their clinical presentation, treatment and mutational analysis including MEN1 gene, 3' and 5' untranslated regions (UTR) of MEN1, CDKN1B, and CaSR genes were collated. Asymptomatic first-degree relatives were also screened. Among the 32 definite MEN1 patients, all had primary hyperparathyroidism, 22 (68.7%) had gastroentero-pancreatic neuroendocrine tumours, and 21 (66%) had pituitary adenoma. Of the 23 definite index-cases, 13 (56.5%) carried mutations in the MEN1 gene. Five of nine affected first-degree relatives (55.5%), and four of 10 asymptomatic relatives (40%) also had MEN1 mutations. Seven of 10 MEN1 mutation-negative definite index-cases harboured p.V109G polymorphism in the CDKN1B gene. All eight MEN1-like cases were negative for mutations and large deletions in MEN1, mutations in 3' and 5' UTR of MEN1, CaSR and CDKN1B genes. The study has helped to clearly document the pattern of mutations among Indian MEN1 patients. However, the absence of MEN1 mutation in ~44% of cases and the presence of p.V109G polymorphism in CDKN1B gene raise the question whether such polymorphisms could independently contribute to pathogenesis.

Morphologic and Immunohistochemical Analysis of Mesenteric and Retroperitoneal Mucinous Cystic Neoplasms

Introduction/Objective

Mucinous cystic neoplasms (MCN) are neoplasms with mucinous epithelium surrounded by ovarian-type stroma, occurring in the pancreas and liver. Reports of MCN arising outside the liver and pancreas are rare. We aim to perform a clinicopathologic, morphologic and immunohistochemical analysis of mesenteric and retroperitoneal MCN arising separate from the pancreas and liver.

Methods

Seven mesenteric or retroperitoneal MCN (n=7) were identified and clinical and radiologic information obtained, where available. The following immunostains were performed on each case: keratin 7, keratin 19, estrogen receptor, progesterone receptor, calretinin, inhibin-α, and SF-1.

Results

All seven MCN were from women with a median age of 41 years (range: 28-70 years). The median size of the MCN was 8cm (range: 8-14.5 cm) involving the retroperitoneum (n=5) and mesoappendix (n=2). One patient was diagnosed with a synchronous right ovarian mucinous cystadenoma. Morphologically, all MCN displayed mucinous or mixed non-mucinous-mucinous cuboidal to columnar epithelium without dysplasia. Ovarian-type stroma was identified underlying the epithelium with foci of luteinized stromal cells. The ovarian-type stroma expressed estrogen and progesterone receptors in all seven cases, two cases stained with SF-1 showed diffuse strong stromal positivity, and one case stained with inhibin showed focal strong stromal positivity. Additional immunohistochemical analysis with CK7, CK19, calretinin, inhibin-α, and SF-1 on all cases is pending.

Conclusion

Clinicopathologic, morphologic, and immunohistochemical characteristics of mesenteric/retroperitoneal MCN are similar to their pancreas and liver counterparts. Familiarity with this entity and knowing it can arise in mesenteric/retroperitoneal locations is important for accurate diagnosis and to distinguish it from mucinous carcinoma, teratoma, endometriosis and other differential diagnoses which have different implications. We propose that mesenteric/retroperitoneal MCN may possibly arise from primordial germ cells that underwent aberrant migration during their retroperitoneal descent through the fetal dorsal mesentery which gives rise to the neck and body of the pancreas as well as the mesentery and mesoappendix.

Microsatellite instability in young patients with mucinous colorectal cancers - characterization using molecular testing, immunohistochemistry, and histological features

CONTEXT

The incidence of colorectal cancers (CRCs) in young Indian patients is higher than the international average. CRCs in young patients are commonly of mucinous type and show microsatellite instability (MSI).

AIMS

To ascertain the MSI status of mucinous CRCs in patients ≤40 years of age by molecular testing and to correlate this with immunohistochemical (IHC) analysis and tumor histology.

SUBJECTS AND METHODS

Archived formalin-fixed paraffin embedded tissue blocks of 30 young mucinous CRC patients were retrieved. MSI testing was done using two mononucleotide markers - BAT26 and NR24. IHC analysis was done using MLH1, MSH2, and MSH6. Histological features of all cases were studied. Data were analyzed using the SPSS software and the Pearson's chi-square test and Fisher's exact test.

RESULTS

Eight out of 30 cases (26.7%) showed MSI by molecular testing. IHC identified seven of these cases. Histological features showing a statistically significant association with MSI were the presence of a well-differentiated adenocarcinoma component (P = 0.003), peritumoral lymphocytes (P = 0.002) and tumor budding (P = 0.021).

CONCLUSION

The detection of defective mismatch repair (MMR) proteins using IHC for MLH1, MSH2, and MSH6 and molecular testing using BAT26 and NR24 appears to be a good protocol to detect CRCs with MSI. Histology could be useful in identifying cases that require screening for presence of MMR protein defects.

Presurgical Screening of Fine Needle Aspirates from Thyroid Nodules for BRAF Mutations: A Prospective Single Center Experience

OBJECTIVE

Analysis of BRAF V600E mutation in thyroid fine needle aspirates (FNA) is an important adjunct to cytology, particularly among FNA placed in the "indeterminate category." However, such a prospective evaluation of FNA obtained from patients with thyroid nodules has been lacking from India.

MATERIAL AND METHODS

FNA from 277 patients were prospectively evaluated for BRAF mutations by Sanger's sequencing. A subset of 30 samples was also analyzed by pyrosequencing using the PyroMark BRAF mutation kit.

RESULTS

Overall, 27.2% of FNA samples were positive for mutations including 19 (35.8%) of the 53 histologically confirmed papillary thyroid carcinoma (PTC), 2 of the 25 follicular variants of PTC, and 1 anaplastic thyroid carcinoma. Only 1 (2.7%) of the 37 samples in the atypia of undetermined significance/follicular lesion of unknown significance category was BRAF positive. The sensitivity of cytology improved marginally from 67.1% to 68.3% when evaluated with BRAF. Further, a comparison of the clinicopathological characteristics of BRAF positive and negative PTCs showed a significant association (P = 0.05) between lymph node metastasis and BRAF positivity.

CONCLUSION

BRAF positivity was lower than that reported from East Asia with the test being useful in confirming malignancies among the suspicious of malignancy and malignant categories.

Pyrosequencing: a rapid and effective sequencing method to diagnose drug-resistant tuberculosis

PURPOSE

This study was undertaken to evaluate the efficiency of the pyrosequencing (PSQ) assay for the rapid detection of resistance to rifampicin (RIF), fluoroquinolones (FQs) and second-line injectables (SLIs) such as capreomycin (CAP) and kanamycin (KAN) in Mycobacterium tuberculosis (Mtb) clinical isolates.

METHODOLOGY

Pyrosequencing is a simple and accurate short read DNA sequencing method for genome analysis. DNA extraction from Mtb clinical isolates was performed using Tris-HCl buffer and chloroform. The rpoB (RIF), gyrA (FQs) and rrs (aminoglycosides) genes were amplified, followed by sequencing using the PyroMark Q24 ID system. The PSQ results were compared with the results from the conventional drug susceptibility testing performed in the laboratory.

RESULTS

The sensitivity of the PSQ assay for the detection of resistance to RIF, FQ, CAP and KAN was 100 %, 100 %, 40 % and 50 %, respectively. The specificity of the PSQ assay was 100 %.

CONCLUSION

The PSQ assay is a rapid and effective method for detecting drug resistance mutations from Mtb clinical isolates in a short period of time.

Re-operative Surgery for Pheochromocytoma-Paraganglioma: Analysis of 13 Cases from a Single Institution

Re-operative adrenal surgery for recurrent pheochromocytoma/paraganglioma (PCC/PGL) is a therapeutic situation not commonly encountered. The recurrence rate of pheochromocytoma is estimated to be 6.1-16.5% of patients from published retrospective series; there are no reports from the Asian continent. A retrospective analysis of the departmental database was performed on patients who had undergone surgery for PCC/PGL from January 2004 to December 2014 at the Christian Medical College Hospital, Vellore, India. Among 99 patients identified during the study period, there were 14 recurrent tumours and 13 patients underwent re-operative surgery. We located eight recurrences on the right side, three on the left side and three in the midline. All 14 recurrences were functioning, and the biochemical analysis as well as imaging studies were positive in 13 of them. The mean duration to recurrence from the time of the primary surgery was 76.3 months (range 6-180 months). Of the 89 patients who underwent their first operation at our centre, 67.4% reported for follow-up for a mean period of 25 months (range 4-132 months). Four of these required re-operation with a recurrence rate of 4.5% (4/89). The open approach was used for all but one of the recurrent tumours. Recurrence following surgery for PCC/PGL is a rarely studied though significant problem. Right adrenal tumour recurrences were most common, and all these recurrences were in the retrocaval region; this typical phenomenon may be dubbed the 'right retrocaval trap'. The reason for this was presumably due to difficult access and inadequate exposure of this area in open and laparoscopic surgery, resulting in incomplete dissection.

Outcome of Treatment for Medullary Thyroid Carcinoma-a Single Centre Experience

We conducted this study to evaluate the demography, clinical presentation, management and outcomes of medullary thyroid carcinoma (MTC) from the Indian context. This was a retrospective study of patients with MTC managed between January 2008 and December 2016. All pertinent data was collected and the results were analysed using STATA (v.13.1). MTC accounted for 90/2022 (4.45%) patients managed with thyroid cancer during the study period. The mean age of presentation was 40 years (range 14-70 years) with 47 males and 43 females. The most common presentation included goitre with cervical lymphadenopathy seen in 60 patients (66.7%). There were 11 patients (12.2%) with systemic metastasis at presentation. Rearranged during transfection (RET) testing was performed in 71 patients and was positive in 25 (35.2%). The mutations among these patients were seen in the following codons: 634 (12), 804 (8), 790 (3) and 618 (2). Persistent hypercalcitoninemia (calcitonin > 50 pg/ml) was observed in 62/80 (77.5%) patients. Forty patients underwent a meta-iodo-benzyl-guanidine (MIBG) scan in the postoperative period, 10 were positive. The mean duration of follow-up was 32 months and 10 patients defaulted from follow-up. Sixteen patients developed metastasis during the period of follow-up while eight patients expired. The mean survival was 85.75 months (95% CI 78.7-92.7). MTC accounted for 4.5% of thyroid carcinomas in this cohort among which 35% were hereditary. Persistent hypercalcitoninemia following surgery is seen in more than 70% of patients but this does not affect survival. RET screening should be performed for all patients with MTC as curative surgery can be offered for mutation positive offspring.

Tricky typhus ticks two: A report of two sisters from North India presenting with acute respiratory distress syndrome due to scrub typhus

Scrub typhus is emerging as an important cause of acute febrile illness in Northern India. This is a report of two sisters presenting concurrently with acute respiratory distress syndrome. A diagnosis of scrub typhus was made in both the patients, and they were successfully treated with doxycycline.

V-raf murine sarcoma viral oncogene homolog B (BRAF) mutations in hairy cell leukaemia

INTRODUCTION

Hairy cell leukemia (HCL) is a B-cell non-Hodgkin lymphoma with distinct clinical, morphological and immunophenotypic features; however, there are many other B-cell lymphomas, which closely mimic HCL. Accurate diagnosis of HCL is important as treatment with 2-chloro-2'-deoxyadenosine (cladribine) is associated with >80% chance of complete cure. The recent description of BRAF p.V600E mutations in almost all HCL cases in various studies has not only improved the pathogenetic understanding of this entity but also increased the diagnostic accuracy of this disorder.

AIM

The aim of the study was to standardize a molecular test for diagnosis of HCL and compare with standard established morphological, cytochemical and immunophenotypic parameters for HCL diagnosis.

MATERIALS AND METHODS

The incidence of this mutation was sought in 20 patients with either classical HCL or HCL variant (HCLv) by Sanger sequencing and allele-specific polymerase chain reaction. BRAF p.V600E mutation was present in all HCL cases and absent in the only HCLv case.

RESULTS

A high degree of correlation was noted between the presence of BRAF p.V600E and established diagnostic criteria in 20/20 patients with HCL/HCLv. Our data supports the observation that this mutation is present in all cases of HCL and is absent in HCLv. Hence, detection of the BRAF p. V600E mutation can be a useful adjunct in the diagnostic algorithm.

Mutations seen among patients with pheochromocytoma and paraganglioma at a referral center from India

Determining the mutational status of susceptibility genes including RET, VHL, SDHx (SDHB, SDHC, SDHD) among patients with pheochromocytoma/paraganglioma (PCC/PGL) is gaining importance. These genes have not been systematically characterized among patients with PCC/PGL from India. The aim of the work was to screen the most frequently mutated genes among patients with PCC/PGL to determine the frequency and spectrum of mutations seen in this region. Fifty patients with PCC/PGL treated at our tertiary care hospital between January 2010 and June 2012 were screened for mutations in susceptibility genes using an algorithmic approach. Thirty-two percent (16/50) of patients were found to be positive for mutations including mutations among RET (n=4), VHL (n=6), SDHB (n=3), and SDHD (n=3) genes. None of these patients were positive for SDHC mutations. A significant association was found between young patients with bilateral tumors and VHL mutations (p=0.002). Two of the 3 patients with extra-adrenal SDHB associated tumors, had unique mutations, viz., c.436delT (exon 5) and c.788_857del (exon 8), one of which was malignant. High frequency of mutations seen among patients in this study emphasizes the need to consider mutational analysis among Indian patients with PCC/PGL.

CD103+ γδ T cell large granular lymphocytosis in a patient with refractory celiac disease: a diagnostic enigma

Indolent γδ T cell lymphomas/leukemias are rare and overlap with the morphological spectrum of large granular lymphocyte (LGL) leukemia. We report an extremely rare case of CD103(+) γδ T LGL leukemia in a patient with celiac disease who presented with refractory diarrhea. Whether the refractory diarrhea in our patient was a manifestation of LGL leukemia itself or whether the clonal LGL expansion is a manifestation of refractory celiac disease (RCD) remains an enigma. This report highlights the diagnostic difficulties and the need of consensus in categorizing clonal CD103(+) lymphocytosis in patients with RCD.

RET mutations in a large indian family with medullary thyroid carcinoma

BACKGROUND

Medullary thyroid carcinoma (MTC) is a tumor arising from the para follicular (C) cells of the thyroid gland and can occur either sporadically or as part of an inherited syndrome. A proportion of these cases carry an autosomal dominant mutation in the RET (REarranged during Transfection) proto-oncogene. Screening for these mutations in the affected patients and the carriers "at risk" which includes the first-degree relatives is of utmost importance for early detection and prompt treatment including prophylactic thyroidectomy in cases that harbor these mutations.

RESULTS

This report presents details of screening and subsequent follow-up of a large Indian family, where the index case was found to carry p. Cys634Ser mutation involving exon 11 of the RET gene. These data are of value considering the paucity of information within the region in context of screening large families affected by these mutations.

Lymph node infarction and lymphoma

Non Hodgkin lymphoma with infarction at initial presentation is rare and can be confused with an acute inflammatory process. A 47 year-old-man presented with complaint of swelling in the left parotid region for 2 weeks which increased in size with severe, continuous and throbbing pain in the last 2-3 days. A clinical diagnosis of parotid abscess was made. Incision and drainage did not yield any pus. Fine needle aspiration cytology showed a highly cellular tumor comprising of somewhat uniform round cells with granular nuclear chromatin. Ghost outline of cytoplasm was noted. A diagnosis of infarcted neoplasm of the parotid gland, probably acinic cell carcinoma was suggested. Histopathologically, it was reported as non-Hodgkin lymphoma with infarction which was confirmed by immunohistochemistry. DOI: http://dx.doi.org/10.3126/jpn.v4i7.10319 Journal of Pathology of Nepal (2014) Vol. 4, 591-593 

Usefulness of Succinate dehydrogenase B (SDHB) immunohistochemistry in guiding mutational screening among patients with pheochromocytoma-paraganglioma syndromes

Genetic testing of pheochromocytomas (PCC) and paragangliomas (PGL), although expensive, is gradually becoming a part of the routine laboratory investigation for patients with PCC-PGL syndrome. Recently, Succinate dehydrogenase B (SDHB) immunochemistry has been shown to be an excellent indicator of germline mutations in the SDH genes and could help significantly reduce cost. This study assesses the utility of SDHB immunohistochemical analysis when used to guide genetic analysis, with emphasis on cost benefits it could provide in a resource-limited setting. Forty-four cases of PCC/PGL characterized by genetic analysis were included to determine their SDHB expression pattern by immunohistochemistry. SDHB antibody expression was negative among three cases each, with SDHB and SDHD mutations. Immunohistochemistry results were positive for all three cases of RET, a single case of neurofibromatosis and for two cases with Von Hippel-Lindau (VHL) mutations while the remaining two cases with VHL mutations showed a diffuse 'cytoplasmic blush'. Thirty of the remaining 31 samples demonstrated positive staining and were negative for mutations, while a lone sample that was negative for staining and mutation was not included in the final analysis as the internal control for the sample was not adequately stained. Cost analysis in our settings showed that triaging with SDHB immunohistochemistry could potentially reduce costs by USD 320-500 per patient. SDHB immunohistochemistry, when used as a guide to genetic testing, can significantly reduce the effort, time and costs of testing among patients with PCC-PGL, a huge benefit in resource limited settings.

Lennert's lymphoma: clinicopathological profile of five cases

BACKGROUND AND AIM

Lennert's lymphoma is a rare variant of peripheral T-cell lymphoma (PTCL) not otherwise specified (NOS) rich in epithelioid histiocytes. This study aims to analyze the clinical, morphologic, and immunophenotypic profile of cases of Lennert's lymphoma from our country and determines the utility of T-cell receptor (TCR) gene rearrangement in the diagnosis.

MATERIALS AND METHODS

All cases diagnosed as Lennert's lymphoma during the period of January 2001 to August 2011 were included in this study. Hematoxylin and eosin (H and E) stained slides and immunohistochemistry results were analyzed and TCR gene rearrangement was performed.

RESULTS

There were five cases of Lennert's lymphoma diagnosed in our institution during this period, which included two males and three females. All cases showed effacement of lymph node architecture by diffuse infiltration of small lymphoid T cells [CD3+, CD4+, CD8+, T-cell intracellular antigen 1 (TIA-1+), Granzyme B-] and clusters of epithelioid histiocytes throughout the lymph node and scattered large transformed cells (CD20-, CD30+, CD15-/+). TCR rearrangement was done in three cases by polymerase chain reaction (PCR) and showed the presence of a clonal T-cell population.

CONCLUSIONS

Lennert's lymphoma constituted 0.11% of all non-Hodgkin lymphomas (NHLs) in our institution. Differentiation from classical Hodgkin's lymphoma is sometimes difficult by morphology and immunohistochemistry alone and TCR gene rearrangement was extremely useful in diagnosis.

Molecular characteristics of meningiomas in a cohort of Indian patients: loss of heterozygosity analysis of chromosomes 22, 17, 14 and 10

BACKGROUND

Though, loss of heterozygosity (LOH) at chromosome 22q is considered to be the most likely initiating event in the formation of meningiomas, LOH at other chromosomes (1, 3, 6, 9, 10, 11, 14.17, and 18) have been implicated in its progression. The aim of this study was to analyze microsatellite markers on a select set of chromosomes including, 22q, 10q, 14q, and 17p for LOH in patients with meningiomas.

MATERIALS AND METHODS

Tumor tissue and its corresponding blood sample were collected from 27 patients with meningioma. Four polymorphic microsatellite markers (D10S520, D17S1289, D14S555, and D22S417) were characterized for LOH analysis.

RESULTS

There were 14 World Health Organization (WHO) grade I, 12 WHO grade II and 1 WHO grade III meningiomas. LOH was seen most often at D22S417 with an equal distribution between the grades (33% of informative samples in each grade). Though, LOH at D14S555 was seen in 50% of informative WHO grade II tumors, compared to 11.1% of informative WHO grade I tumors it did not reach statistical significance. However, allelic imbalance (AI) at D14S555 was significantly associated with atypia (P = 0.05). LOH at D17S1289 was seen only in one tumor sample, and none of the informative samples displayed LOH at D10S520.

CONCLUSION

The frequency and equal distribution of LOH at chromosome 22 supports the hypothesis that it is an early event in the tumorigenesis of meningiomas. The association of AI at D14S555 in WHO grade II meningiomas needs to be investigated on a larger set of samples.

P.Arg82Leu von Hippel-Lindau (VHL) gene mutation among three members of a family with familial bilateral pheochromocytoma in India: molecular analysis and in silico characterization

Various missense mutations in the VHL gene have been reported among patients with familial bilateral pheochromocytoma. However, the p.Arg82Leu mutation in the VHL gene described here among patients with familial bilateral pheochromocytoma, has never been reported previously in a germline configuration. Interestingly, long-term follow-up of these patients indicated that the mutation might have had little impact on the normal function of the VHL gene, since all of them have remained asymptomatic. We further attempted to correlate this information with the results obtained by in silico analysis of this mutation using SIFT, PhD-SNP SVM profile, MutPred, PolyPhen2, and SNPs&GO prediction tools. To gain, new mechanistic insight into the structural effect, we mapped the mutation on to 3D structure (PDB ID 1LM8). Further, we analyzed the structural level changes in time scale level with respect to native and mutant protein complexes by using 12 ns molecular dynamics simulation method. Though these methods predict the mutation to have a pathogenic potential, it remains to be seen if these patients will eventually develop symptomatic disease.

Mycobacterium fortuitum skin infection as a complication of anabolic steroids: a rare case report

Mycobacterium fortuitum is a rare cause of recurrent skin abscesses in an immunocompetent person. We report the case of a 37-year-old man presenting with multiple recurrent non-healing skin abscesses. Culture of the abscess wall yielded growth of M fortuitum. In our case, we highlight the association of anabolic steroids with non-tuberculous mycobacterial skin abscesses that fail to resolve despite repeated drainage.

Status of O⁶ -methylguanine-DNA methyltransferase [MGMT] gene promoter methylation among patients with glioblastomas from India

BACKGROUND

O⁶ -methylguanine DNA methyltransferase [MGMT] gene promoter methylation has emerged as a promising marker in determining resistance to temozolomide, used in the treatment of patients with glioblastomas.

AIM

To determine the frequency of MGMT promoter methylation among patients with glioblastomas using methylation-specific polymerase chain reaction (MSP) and compare it to the results obtained by bisulfite sequencing of a subset of samples.

MATERIALS AND METHODS

DNA obtained from the frozen tissue of 27 samples of glioblastomas and three other gliomas, were analyzed for MGMT promoter methylation using a nested MSP assay. Sixteen samples were also subjected to bisulfite sequencing to determine the methylation status of 27 CpG sites within the sequenced region of the MGMT promoter. Data with respect to radiation, chemotherapy and survival outcome was also collected.

RESULTS

MGMT promoter methylation was seen in 67% of the cases included in the study using frozen tissues by MSP analysis, while 62% were methylated among glioblastomas alone. There was a 100% concordance between the results obtained by MSP analysis and bisulfite sequencing. Clinical outcome was known among 67% of cases and methylation was higher among those patients who had no recurrence, though it was not statistically significant [P=0.44].

CONCLUSION

The frequency of methylation seen in this study concurs with that reported earlier from the country. MSP was easy to perform and interpret. However, the utility of this testing system in a routine diagnostic setting is still being debated.

Role of cortical sparing adrenalectomy and novel variant of mutation in patient with von Hippel-Lindau disease

Neurofibromatosis type 1 is the most common phakomatoses and is inherited in autosomal dominant fashion with complete penetrance. Secondary hypertension is common in these patients due to various causes including adrenal tumors. Pheochromocytoma is a rare catecholamine producing tumor seen in 0.5% to 5% of patients with neurofibromatosis. The combination of pheochromocytoma with neurofibromatosis is rarely reported in the literature. We recently encountered an elderly lady with this combination who successfully underwent adrenalectomy. We report the case for the uncommon occurrence and to highlight the relevant literature review about pheochromocytoma in neurofibromatosis.

Chryseobacterium meningosepticum bacteremia in diabetic nephropathy patient on hemodialysis

The Chryseobacterium species are inhabitants of soil and water. In the hospital environment, they exist in water systems and wet surfaces. We report here a case of Chryseobacterium meningosepticum bacteremia in a diabetic nephropathy patient on hemodialysis. He was successfully treated with Vancomycin and ceftazidime for three weeks with good clinical outcome. This is the first case reported in dialysis patients from India.