Namrata Setia

Genomic Heterogeneity as a Barrier to Precision Medicine in Gastroesophageal Adenocarcinoma

Gastroesophageal adenocarcinoma (GEA) is a lethal disease where targeted therapies, even when guided by genomic biomarkers, have had limited efficacy. A potential reason for the failure of such therapies is that genomic profiling results could commonly differ between the primary and metastatic tumors. To evaluate genomic heterogeneity, we sequenced paired primary GEA and synchronous metastatic lesions across multiple cohorts, finding extensive differences in genomic alterations, including discrepancies in potentially clinically relevant alterations. Multiregion sequencing showed significant discrepancy within the primary tumor (PT) and between the PT and disseminated disease, with oncogene amplification profiles commonly discordant. In addition, a pilot analysis of cell-free DNA (cfDNA) sequencing demonstrated the feasibility of detecting genomic amplifications not detected in PT sampling. Lastly, we profiled paired primary tumors, metastatic tumors, and cfDNA from patients enrolled in the personalized antibodies for GEA (PANGEA) trial of targeted therapies in GEA and found that genomic biomarkers were recurrently discrepant between the PT and untreated metastases. Divergent primary and metastatic tissue profiling led to treatment reassignment in 32% (9/28) of patients. In discordant primary and metastatic lesions, we found 87.5% concordance for targetable alterations in metastatic tissue and cfDNA, suggesting the potential for cfDNA profiling to enhance selection of therapy.Significance: We demonstrate frequent baseline heterogeneity in targetable genomic alterations in GEA, indicating that current tissue sampling practices for biomarker testing do not effectively guide precision medicine in this disease and that routine profiling of metastatic lesions and/or cfDNA should be systematically evaluated. Cancer Discov; 8(1); 37-48. ©2017 AACR.See related commentary by Sundar and Tan, p. 14See related article by Janjigian et al., p. 49This article is highlighted in the In This Issue feature, p. 1.

Profiling of ABC transporters ABCB5, ABCF2 and nestin-positive stem cells in nevi, in situ and invasive melanoma

Distinct ABCB5 forms and ABCF2, members of the ATP-binding cassette (ABC) superfamily of transporters, are normally expressed in various tissues and cells, and enhanced expression of both has been demonstrated in select cancers. In melanoma cell lines, gene expression profiling of ABC transporters has revealed enhanced expression of melanocyte-specific ABCB5 and ABCF2 proteins. Given this, our primary aim was to ascertain immunohistochemical expression of the ABC transporters ABCB5 and ABCF2 and, the stem cell marker, nestin in a spectrum of benign and malignant nevomelanocytic proliferations, including nevi (n=30), in situ (n=31) and invasive (n=24) primary cutaneous melanomas to assess their role in the stepwise development of malignancy. In addition, their expression was compared with established melanoma prognosticators to ascertain their utility as independent prognosticators. A semiquantitative scoring system was utilized by deriving a cumulative score (based on percentage positivity cells and intensity of expression) and statistical analyses was carried out using analysis of variance with linear contrasts. Mean cumulative score in nevi, in situ and invasive melanoma were as follows: 3.8, 4.4 and 5.3 for ABCB5, respectively (P<0.005 for all), and 4.6, 4.6 and 5.3 for nestin, respectively (P=not significant for all). No appreciable expression of ABCF2 was noted in any of the groups. While ulcerated lesions of melanoma demonstrated lower levels of expression of ABCB5 and nestin than non-ulcerated lesions, and nestin expression was lower in lesions with mitoses >1, after controlling for the presence of ulceration and mitotic activity, the expression of both proteins did not significantly correlate with known melanoma prognosticators. The gradual increase in the expression of ABCB5 from benign nevus to in situ to invasive melanoma suggests that it plays a role in melanomagenesis. On the basis of our findings, a prospective study with follow-up data is required to ascertain the utility of ABCB5 as a therapeutic target.

A protein and mRNA expression-based classification of gastric cancer

The overall survival of gastric carcinoma patients remains poor despite improved control over known risk factors and surveillance. This highlights the need for new classifications, driven towards identification of potential therapeutic targets. Using sophisticated molecular technologies and analysis, three groups recently provided genetic and epigenetic molecular classifications of gastric cancer (The Cancer Genome Atlas, ‘Singapore-Duke’ study, and Asian Cancer Research Group). Suggested by these classifications, here, we examined the expression of 14 biomarkers in a cohort of 146 gastric adenocarcinomas and performed unsupervised hierarchical clustering analysis using less expensive and widely available immunohistochemistry and in situ hybridization. Ultimately, we identified five groups of gastric cancers based on Epstein–Barr virus (EBV) positivity, microsatellite instability, aberrant E-cadherin, and p53 expression; the remaining cases constituted a group characterized by normal p53 expression. In addition, the five categories correspond to the reported molecular subgroups by virtue of clinicopathologic features. Furthermore, evaluation between these clusters and survival using the Cox proportional hazards model showed a trend for superior survival in the EBV and microsatellite-instable related adenocarcinomas. In conclusion, we offer as a proposal a simplified algorithm that is able to reproduce the recently proposed molecular subgroups of gastric adenocarcinoma, using immunohistochemical and in situ hybridization techniques.

Morphological findings in bone marrow biopsy and aspirate smears of visceral Kala Azar: a review.

CONTEXT Visceral leishmaniasis (VL) is endemic in India and may simulate and cause many hematological disorders like pancytopenia, myelofibrosis, myelodysplasia and hemophagocytosis. AIMS The study aims to investigate the hematological manifestation of Visceral Leishmaniasis and associated changes that may be observed in bone marrow aspirate smears and biopsy which may warn a pathologist of possible infections. SETTINGS AND DESIGN This is a retrospective study of 18 VL cases on B (b) one marrow aspirate and biopsy in the department of Pathology in a tertiary care teaching hospital in New Delhi. METHODS AND MATERIAL Giemsa stained slides of bone marrow aspirates and hematoxylin and Eosin stained biopsy slides were reviewed in detail by two competent pathologists. All the findings were tabulated and discussed and comparisons made with the previous similar studies. RESULTS Hyper cellular marrow, increased lymphocytes and plasma cells, marrow granulomas, hemophagocytosis, myelofibrosis, myelodysplasia and gelatinous transformation of the marrow were notable features the presence of which together or individually should caution a pathologist to search for Leishman Donovan (LD) bodies in patients especially in a non-endemic zone in a tropical country.

Premature Coronary Artery Disease and Familial Hypercholesterolemia: Need for Early Diagnosis and Cascade Screening in the Indian Population

Cardiovascular disease (CVD) is the leading cause of death in India, accounting for 28% of mortality. The average age of onset of CVD is younger (below 55 years) among Indians than in other populations. This may be due to bad lifestyle, genetic factors, or both. Hypertension, smoking, diabetes, and physical inactivity have been identified as modifiable risk factors for heart disease. Hypercholesterolemia is the most common and treatable cause of heart disease. Genetic factors that lead to hypercholesterolemia have not been fully studied in India. Familial Hypercholesterolemia results from mutations in the LDL receptor, ApoB, PCSK9, and ApoE genes. There is an urgent need to screen subjects with premature CAD and their relatives in India for the presence of FH, identify the mutations that lead to high cholesterol, and carry out cascade screening in the at-risk relatives. Those harbouring mutations in the above genes can be treated to lower the cholesterol levels, prevent early CVD, and avoid death. A programme based on these lines has been initiated in Delhi.

Familial Gastric Cancers

Although the majority of gastric carcinomas are sporadic, approximately 10% show familial aggregation, and a hereditary cause is determined in 1%-3% cases. Of these, hereditary diffuse gastric cancer is the most recognized predisposition syndrome. Although rare, the less commonly known syndromes also confer a markedly increased risk for development of gastric cancer. Identification and characterization of these syndromes require a multidisciplinary effort involving oncologists, surgeons, genetic counselors, biologists, and pathologists. This article reviews the molecular genetics, clinical and pathologic features, surveillance guidelines, and preventive measures of common and less common hereditary gastric cancer predisposition syndromes.

Cutaneous neoplasms with prominent Verocay body-like structures: the so-called "rippled pattern".

A striking appearance resulting from alternating areas of epithelial cell cords and stroma seen in some cutaneous adnexal neoplasms has been referred to as the “rippled pattern.” Histologically, this pattern may be indistinguishable from Verocay bodies described in schwannomas. A number of common and clinically diverse cutaneous neoplasms can be linked by the presence of this unusual growth pattern. The heterogeneous group of tumors that have been known to demonstrate this feature includes those with epithelial, adnexal, fibrohistiocytic, mesenchymal, and melanocytic lineage. The objective of this review is to alert the dermatopathologist to the range of neoplasms, which can potentially show this attribute, so that a misdiagnosis can be avoided.

Hematological profile in pyrexia of unknown origin: role of bone marrow trephine biopsy vis-à-vis aspiration.

Abstract Background: Bone marrow examination, by aspiration and/or trephine biopsy, is an important procedure in arriving at a diagnosis for long-duration febrile illness. The role of trephine biopsy in immunocompromised host, especially HIV-positive patients, has been well studied in the literature. However, its utility in immunocompetent patients is still shrouded by controversy. Thus, the authors attempted to evaluate the utility of marrow aspirate vis-à-vis trephine biopsy in establishing a diagnosis in cases of pyrexia of unknown origin in immunocompetent individuals, along with an analysis of haematological alterations in these patients. Materials and methods: Over a period of 8 years, 121 patients with pyrexia of unknown origin underwent both bone marrow aspiration and trephine biopsy as a part of diagnostic work-up. These cases were reviewed for their clinical data and hematological findings, including detailed morphological features in aspiration smears and trephine biopsies. Bone marrow aspiration and biopsy were compared for their diagnostic efficacy in these patients. Results: A wide age range (2–65 years) was noted with a slight male predominance (2 : 1). Anemia was the most common feature in peripheral blood findings, seen in 97·5% of patients. Bone marrow aspiration was diagnostic in only 16·5% of cases, which revealed leishmaniasis or pure red cell aplasia. Granulomas were infrequent in marrow aspiration smears, as only two cases (1·6%) showed ill defined epithelioid cell collections. Compared to this, trephine biopsy offered a diagnosis in 76% of the cases. Granulomas were a frequent finding in the trephine biopsy, being present in 70% of the cases included. Additional cases diagnosed on biopsy (over those diagnosed with aspiration smears) included lymphoma, tuberculosis, fungal infection, sarcoidosis and hypocellular marrow. Conclusion: Bone marrow trephine biopsy is an important adjunct to aspiration in arriving at an aetiological diagnosis of patient with long-duration febrile illness, and should be routinely performed in such cases. The presence of granulomas in trephine biopsy increases the likelihood of an etiologic diagnosis in these patients.

High-throughput Protein and mRNA Expression-based Classification of Gastric Cancers Can Identify Clinically Distinct Subtypes, Concordant With Recent Molecular Classifications.

Gastric cancers have recently been classified into several types on the basis of molecular characterization, and the new taxonomy has shown to have clinical relevance. However, the technology required for thorough molecular classification is complicated and expensive, currently preventing widespread use. We aimed to reproduce the results of molecular classification using only simple techniques, that is, immunohistochemical analysis and in situ hybridization. We classified a cohort of 349 successive gastric adenocarcinomas into 5 subtypes, on the basis of protein or mRNA expression of MLH1, E-cadherin, p53, and Epstein-Barr virus. We observed that the subtypes presented distinct clinicopathologic characteristics and corresponded to the molecular classifications previously reported. Epstein-Barr virus –positive tumors were more common in male individuals and in the body of the stomach. Microsatellite-unstable (MSI) tumors, which showed aberrant MLH1 expression, were correlated with increased age and intestinal histology. Both types showed better overall survival than the other types. Gastric cancers with reduced expression of E-cadherin, corresponding to the epithelial to mesenchymal transition or genome stable subtypes, showed the poorest overall survival, with a high prevalence of poorly cohesive carcinoma (ie, diffuse type, of the Lauren classification system). In conclusion, we were able to reproduce a previously reported molecular classification of gastric cancers using immunohistochemical analysis and in situ hybridization. We verified the effectiveness and applicability of this method, which shows promise for use in a clinical setting in the foreseeable future.

Lymph node extramedullary hematopoiesis in breast cancer patients receiving neoadjuvant therapy: A potential diagnostic pitfall

Extramedullary hematopoiesis (EMH) develops as a compensatory mechanism associated with hematologic processes but it may occur in association with chemotherapy. Three cases of EMH arising in axillary lymph nodes following neoadjuvant therapy for breast carcinoma are reported herein. Three women ranging in age from 41 to 47 years presented with unilateral breast masses measuring 0.6 to 4.0 cm in greatest dimension and were diagnosed with infiltrating ductal carcinoma, grade III by core needle biopsies. Two of the tumors were triple negative and one was estrogen receptor positive. All patients subsequently received neoadjuvant therapy followed by lumpectomies. No residual carcinoma was identified in postchemotherapy breast resection specimens. One patient underwent a sentinel lymph node procedure, the second patient an axillary lymph node dissection, and the third patient had a core biopsy of an enlarged axillary lymph node. The patient that underwent axillary lymph node dissection had metastatic carcinoma in one of her lymph nodes. Foci of EMH consisting of myeloid, erythroid, and megakaryocytic precursors were present within the nodal parenchyma and/or subcapsular sinuses of axillary lymph nodes of all three cases. Megakaryocytes were immunoreactive with factor VIII, erythroid elements with Glycophorin and myeloid precursors with myeloperoxidase. With increasing use of neoadjuvant therapy for breast carcinoma, EMH within lymph nodes is more likely to be encountered. Hematopoietic precursors present in lymph nodes may potentially be misdiagnosed as metastatic tumor cells, particularly as lobular carcinoma or metaplastic carcinoma. Therefore, caution should be exercised when evaluating axillary lymph nodes in the clinical setting of neoadjuvant therapy for breast carcinoma.