Shashirekha Shetty

NEK2 Induces Drug Resistance Mainly through Activation of Efflux Drug Pumps and Is Associated with Poor Prognosis in Myeloma and Other Cancers

Using sequential gene expression profiling (GEP) samples, we defined a major functional group related to drug resistance that contains chromosomal instability (CIN) genes. One CIN gene in particular, NEK2, was highly correlated with drug resistance, rapid relapse, and poor outcome in multiple cancers. Overexpressing NEK2 in cancer cells resulted in enhanced CIN, cell proliferation and drug resistance, while targeting NEK2 by NEK2 shRNA overcame cancer cell drug resistance and induced apoptosis in vitro and in a xenograft myeloma mouse model. High expression of NEK2 induced drug resistance mainly through activation of the efflux pumps. Thus, NEK2 represents a strong predictor for drug resistance and poor prognosis in cancer and could be an important target for cancer therapy.

Integrative genomic and transcriptomic analysis identified candidate genes implicated in the pathogenesis of hepatosplenic T-cell lymphoma

Hepatosplenic T-cell lymphoma (HSTL) is an aggressive lymphoma cytogenetically characterized by isochromosome 7q [i(7)(q10)], of which the molecular consequences remain unknown. We report here results of an integrative genomic and transcriptomic (expression microarray and RNA-sequencing) study of six i(7)(q10)-positive HSTL cases, including HSTL-derived cell line (DERL-2), and three cases with ring 7 [r(7)], the recently identified rare variant aberration. Using high resolution array CGH, we profiled all cases and mapped the common deleted region (CDR) at 7p22.1p14.1 (34.88 Mb; 3506316-38406226 bp) and the common gained region (CGR) at 7q22.11q31.1 (38.77 Mb; 86259620–124892276 bp). Interestingly, CDR spans a smaller region of 13 Mb (86259620–99271246 bp) constantly amplified in cases with r(7). In addition, we found that TCRG (7p14.1) and TCRB (7q32) are involved in formation of r(7), which seems to be a byproduct of illegitimate somatic rearrangement of both loci. Further transcriptomic analysis has not identified any CDR-related candidate tumor suppressor gene. Instead, loss of 7p22.1p14.1 correlated with an enhanced expression of CHN2 (7p14.1) and the encoded β2-chimerin. Gain and amplification of 7q22.11q31.1 are associated with an increased expression of several genes postulated to be implicated in cancer, including RUNDC3B, PPP1R9A and ABCB1, a known multidrug resistance gene. RNA-sequencing did not identify any disease-defining mutation or gene fusion. Thus, chromosome 7 imbalances remain the only driver events detected in this tumor. We hypothesize that the Δ7p22.1p14.1-associated enhanced expression of CHN2/β2-chimerin leads to downmodulation of the NFAT pathway and a proliferative response, while upregulation of the CGR-related genes provides growth advantage for neoplastic δγT-cells and underlies their intrinsic chemoresistance. Finally, our study confirms the previously described gene expression profile of HSTL and identifies a set of 24 genes, including three located on chromosome 7 (CHN2, ABCB1 and PPP1R9A), distinguishing HSTL from other malignancies.

PDGFRB-rearranged T-lymphoblastic leukemia/lymphoma occurring with myeloid neoplasms: the missing link supporting a stem cell origin

The 2008 WHO classification scheme of hematolymphoid neoplasms recognizes a category of myeloid and lymphoid neoplasms (MLNs) with eosinophilia and abnormalities of PDGFRA , PDGFRB , or FGFR1 .[1][1] The postulated cell of origin for PDGFRA or FGFR1 -rearranged diseases is a pluripotent progenitor

Clinicopathologic and molecular characterization of myeloid neoplasms harboring isochromosome 17(q10).

To the Editor: This is the third in a series of short articles concerning iron deficiency and the role of intravenous (IV) iron. Iron deficiency anemia is nearly ubiquitous in this population [1] and it is the opinion of many key opinion leaders in the field that failure to routinely replace iron intravenously represents and unmet clinical need. In those with uncomplicated iron deficiency without underlying inflammatory disorders which lead to iron restricted erythropoiesis due to hepcidin upregulation, oral iron is effective and inexpensive. Unfortunately, estimates that 70% of those to whom it is prescribed report significant gastrointestinal perturbation, results in significant nonadherence to therapy. Evidence suggests oral iron causes severe adverse invents when inflammatory bowel disease is present and worsens the underlying pathology [2–4]. While some gastroenterologists continue to extol the virtues of low doses of oral iron, even if well tolerated in subjects with quiescent disease, a year of therapy is required to replace stores. European and American guidelines differ. European guidelines state that the preferred route of iron supplementation in inflammatory bowel disease (IBD) is IV, even though some patients will respond to oral iron. IV iron is more effective and better tolerated and improves the quality of life to a greater extent than oral iron supplementation (Grade A) [2]. Absolute indications for IV iron include severe anemia (Hgb <10 g/dl), intolerance of or inappropriate response to oral iron, severe intestinal disease acuity, and concomitant therapy with an erythropoiesis agent or patient preference. Oral iron supplements can be used if absolute indications for IV iron therapy are not met. If oral iron is used, the response and tolerance should be monitored and treatment changed to IV as necessary (Grade C). Because side effects of oral iron are dose related and because its absorption and efficacy are no greater when high doses are used, no more than 100 mg of elemental iron daily should be prescribed (Grade C). American guidelines state, “oral formulations are more convenient and less expensive and may be used as a first-line option for patients whose IBD activity and anemia are mild” [5]. The medical literature is rife with prospective comparative evidence demonstrating superiority of IV iron over oral iron in both efficacy and toxicity. Recent publications support this view [6–8]. With the advent of four new formulations which allow safe and rapid complete replacement dosing in 15–60 min, the failure to routinely administer IV iron to anemic patients with inflammatory bowel disease may represent another unmet clinical need. A recent publication demonstrated that not only does a 15 min infusion of ferric carboxymaltose correct anemia but prevents recurrence of anemia in patients with inflammatory bowel disease [9]. Similar evidence of efficacy has been published with low molecular weight iron dextran [10,11] and ferumoxytol [12]. Although it remains reasonable to try oral iron in those without active disease, considering the litany of gastrointestinal perturbations present in inflammatory bowel disease, even in remission, perhaps it is time for American gastroenterologists to become more congruent with their European colleagues.

CCMCL1: a new model of aggressive mantle cell lymphoma.

To the editor: Mantle cell lymphoma (MCL) is incurable using current standard therapeutic regimens.[1][1] There are relatively few relevant cell lines and mouse models. To evaluate new drugs and develop rational combination therapies, we have established and thoroughly characterized a new MCL cell

Impact of an alternative chromosome 17 probe and the 2013 American Society of Clinical Oncology and College of American Pathologists guidelines on fluorescence in situ hybridization for the determination of HER2 gene amplification in breast cancer.

The dual‐probe fluorescence in situ hybridization (FISH) assay for human epidermal growth factor receptor 2 (HER2) gene amplification in breast cancer provides an HER2:CEP17 (centromere enumeration probe for chromosome 17) ratio. Copy number alteration (CNA) in CEP17 may skew this ratio. The authors analyzed the impact of the 2013 American Society of Oncology/College of American Pathologists (ASCO/CAP) guidelines and an alternative chromosome 17 probe on HER2 status in tumor specimens with CEP17 CNA.

Transient abnormal myelopoiesis of a newborn not associated with chromosome 21 abnormalities or GATA1 mutations

Transient abnormal myelopoiesis (TAM) is a disorder of Down syndrome newborns characterized by megakaryocytic blasts indistinguishable from acute myeloid leukemia (AML), which undergoes spontaneous remission. Acquired GATA1 mutations are present in blasts of both TAM and the subsequent AML which sometimes develops. We present a unique case of a newborn with leukemic megakaryoblasts indistinguishable from those of TAM who had neither extra material from chromosome 21 in the germline or blasts, nor evidence of GATA1 mutations. These findings suggest there are other genetic abnormalities that can lead to TAM besides GATA1 mutation in the setting of trisomy 21. Pediatr Blood Cancer 2015;62:353–355.

Non-t(6;9) and Non-Inv(3) Balanced Chromosomal Rearrangements Are Associated With Poor Survival Outcomes in Myelodysplastic Syndromes

BACKGROUND Cytogenetics is an important predictor of survival in patients with myeloid malignancies including myelodysplastic syndromes (MDS). The roles of balanced chromosomal rearrangements (BCR) specifically balanced translocations and inversions in MDS are less established. We hypothesized that BCR are commonly found in MDS and might confer important prognostic and therapeutic effect. PATIENTS AND METHODS Cytogenetic, hematologic, clinical, and survival data from a total of 302 MDS patients seen at the Cleveland Clinic between the years 2002 and 2011 were collected. Direct sequencing for genes relevant in MDS pathophysiology was performed on patients with BCR. Categorical data were analyzed using the χ2 test and survival outcomes were analyzed using the Kaplan-Meier method. RESULTS Twenty-three patients (8%) carried non-t(6;9) and non-inv(3) BCR. These patients had short overall survival (OS) similar to patients with poor risk cytogenetics, defined according to the International Prognostic Scoring System, which was not altered by new single-nucleotide polymorphism arrays or acquired somatic uniparental disomy lesions. Among the detected somatic mutations, only patients harboring mutations in the RNA splicing gene serine/arginine-rich splicing factor 2 (SRSF2) conferred worse outcomes in this group of patients. Therapeutically, patients who received allogeneic hematopoietic cell transplantations had better OS compared with patients treated with pharmacologic therapies or best supportive care only. CONCLUSION BCR are not common in MDS and are associated with poor survival, which might be influenced by the presence of SRSF2 mutation.

Subjectivity in chromosome band-level estimation: a multicenter study

Purpose:Chromosome band level is the primary quality indicator for G-banded metaphase chromosome analysis. Although current professional guidelines address the minimum necessary band level for constitutional studies, there is no study documenting the comparative performance of different band-level estimation methods.Methods:This study compared 5 band-level estimation methods (Stallard, Vancouver, Welborn, United Kingdom External Quality Assurance Scheme, and Ford) in a multicenter study in which 82 readers from 7 different clinical cytogenetics laboratories evaluated the same 10 karyotypes (5 from amniotic fluid and 5 from peripheral blood) by each method.Results:There was a 94% correlation between the five band-level estimation methods. The Welborn method yielded significantly lower scores for amniotic fluid karyotypes (P < 0.01) but not for peripheral blood karyotypes (P = 0.75). The distribution of scores obtained from different readers suggests a high level of subjectivity in chromosome band–level assessment. The variation in band-level estimation did not correlate with reader experience or study center, except for readers from one laboratory, for which the distribution of scores was significantly lower (P < 0.01).Conclusion:The results from this study suggest that the consistent use of one method is more important than the actual method employed for monitoring karyotype quality.Genet Med 16 2, 170–175.

Novel molecular aberrations and pathologic findings in a tubulocystic variant of renal cell carcinoma

Tubulocystic renal cell carcinoma (TRCC) is an indolent type of renal cell carcinoma with a good prognosis based on the limited number of published cases. Herein, we describe the unusual clinical, pathologic and molecular findings in a case of TRCC. Our patient with TRCC had two local recurrences and a brain metastasis following radical nephrectomy. Unusual histologic findings included focal solid growth pattern and cytologic atypia. A genome-wide molecular inversion probe assay identified copy number (CN) loss in three chromosome regions and one region with copy-neutral loss of heterozygosity (copy-neutral LOH). Copy number variations (CNVs) were observed (chromosomes 4p16.1 and 17q21.31-q21.32) in both the tumor and the normal tissue, and most likely represents benign variations. The loss of entire chromosomes 9, 18 and 15 and copy-neutral LOH involving 6p22.1 was observed only in the tumor. The presence of these clinical, pathologic and molecular findings could be related to an increased risk for tumor recurrence and poor prognosis. The novel molecular findings described in TRCC might represent new targets for novel therapies.