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Clemo, F. A. S., D. B. DeNicola, W. W. Carlton, W. B. Morrison, and E. Walker. "Flow Cytometric DNA Ploidy Analysis in Canine Transitional Cell Carcinoma of Urinary Bladders." Veterinary Pathology 31, no. 2 (March 1994): 207–15. http://dx.doi.org/10.1177/030098589403100208.
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Flow cytometric analysis of DNA ploidy was performed on 51 formalin-fixed, paraffin-embedded samples of canine transitional cell carcinoma of the urinary bladder. The DNA ploidy data obtained were compared to several clinicopathologic features. In addition, the DNA ploidy of 15 hyperplastic/inflamed and 8 normal canine urinary bladders was measured. Forty-three of the 51 neoplastic samples had interpretable DNA histograms. DNA aneuploidy was found in 34/43 (79%) of the transitional cell carcinoma samples. Of the 34 aneuploid neoplasms, 16 (47%) were hyperdiploid, 17 (50%) were tetraploid, and 1 (3%) was hypertetra-ploid. No significant correlation was found between the presence of DNA aneuploidy and the growth pattern. histologic grade, clinical stage, or individual morphologic features of this neoplasm. Additionally, the DNA ploidy was not related to the sex, age, or survival time of dogs with transitional cell carcinoma. All of the normal and all but one of the hyperplastic/inflamed urinary bladders were diploid. The results from this study demonstrated that DNA ploidy can be measured from paraffin-embedded canine samples by flow cytometry, a majority of the canine transitional cell carcinomas were aneuploid, and a significant correlation did not exist between the DNA ploidy and specific clinicopathologic features of this neoplasm.
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Van Treeck, Benjamin J., Mira Lotfalla, Thomas W. Czeczok, Taofic Mounajjed, Roger K. Moreira, Daniela S. Allende, Michelle D. Reid, et al. "Molecular and Immunohistochemical Analysis of Mucinous Cystic Neoplasm of the Liver." American Journal of Clinical Pathology 154, no. 6 (September 3, 2020): 837–47. http://dx.doi.org/10.1093/ajcp/aqaa115.
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Abstract Objectives Mucinous cystic neoplasm of the liver is characterized by neoplastic mucinous and/or biliary epithelium surrounded by ovarian-type stroma. Immunohistochemical studies have shown that the ovarian-type stroma expresses estrogen receptor, suggesting potential hormonal responsiveness. The molecular biology of mucinous cystic neoplasm of the liver remains poorly studied. Methods Transcriptome sequencing and immunohistochemistry were performed on a series of mucinous cystic neoplasms. Results Mucinous cystic neoplasm of the liver exhibited significantly increased RNA expression of ovarian stromal markers WT1, PR, and ER2 and sex cord stromal markers SF-1, inhibin-α, and calretinin compared with nonneoplastic liver. Immunohistochemistry confirmed the RNA-level data. Evidence for sex hormone biosynthesis was identified by significant overexpression of multiple estrogen biosynthetic enzymes. Expression of 17β-hydroxysteroid dehydrogenase 1 was confirmed immunohistochemically. Pathway analysis also identified significant upregulation of the hedgehog and Wnt pathways and significant downregulation of T-helper 1 and T-helper 2 pathways. Conclusions Mucinous cystic neoplasm of the liver recapitulates ovarian stroma at the morphologic, DNA, RNA, and protein levels. These data support the concept that this tumor likely arises from ectopic primitive gonadal tissue and/or stromal cells with capacity to transdifferentiate to ovarian cortical cells.
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Chen, Tsai-Yun, Jiann-Shiuh Chen, Wu-Chou Su, Ming-Shiuan Wu, and Chao-Jung Tsao. "Expression of DNA repair gene Ku80 in lymphoid neoplasm." European Journal of Haematology 74, no. 6 (June 2005): 481–88. http://dx.doi.org/10.1111/j.1600-0609.2005.00428.x.
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Curti, P., P. Beltrami, C. Tallarigo, G. Malossini, A. D'Amico, and D. Schiavone. "Flow Cytometry Role of DNA Analysis." Urologia Journal 61, no. 3 (June 1994): 226–28. http://dx.doi.org/10.1177/039156039406100313.
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We analyzed the results obtained by flow cytometry DNA analysis in prostatic cancer. We considered the diagnostic role of this investigation and the prognostic value observed from correlating the DNA analysis with usual diagnostic and prognostic factors such as staging, grading, PSA, size, etc. Results in literature suggest that further studies are necessary to explain both the biological and cytometrical heterogeneous aspects of this neoplasm.
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Pronier, Elodie, Carole Almire, Hayat Mokrani, Aparna Vasanthakumar, Audrey Simon, Barbara da Costa Reis Monte Mor, Aline Massé, et al. "Inhibition of TET2-mediated conversion of 5-methylcytosine to 5-hydroxymethylcytosine disturbs erythroid and granulomonocytic differentiation of human hematopoietic progenitors." Blood 118, no. 9 (September 1, 2011): 2551–55. http://dx.doi.org/10.1182/blood-2010-12-324707.
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Abstract TET2 converts 5-methylcytosine to 5-hydroxymethylcytosine (5-hmC) in DNA and is frequently mutated in myeloid malignancies, including myeloproliferative neoplasms. Here we show that the level of 5-hmC is decreased in granulocyte DNA from myeloproliferative neoplasm patients with TET2 mutations compared with granulocyte DNA from healthy patients. Inhibition of TET2 by RNA interference decreases 5-hmC levels in both human leukemia cell lines and cord blood CD34+ cells. These results confirm the enzymatic function of TET2 in human hematopoietic cells. Knockdown of TET2 in cord blood CD34+ cells skews progenitor differentiation toward the granulomonocytic lineage at the expense of lymphoid and erythroid lineages. In addition, by monitoring in vitro granulomonocytic development we found a decreased granulocytic differentiation and an increase in monocytic cells. Our results indicate that TET2 disruption affects 5-hmC levels in human myeloid cells and participates in the pathogenesis of myeloid malignancies through the disturbance of myeloid differentiation.
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Grady, W. M. "Epigenetic events in the colorectum and in colon cancer." Biochemical Society Transactions 33, no. 4 (August 1, 2005): 684–88. http://dx.doi.org/10.1042/bst0330684.
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Colon cancers arise from benign neoplasms and evolve into adenocarcinomas through a stepwise histological progression sequence, proceeding from either adenomas or hyperplastic polyps/serrated adenomas. Genetic alterations have been associated with specific steps in this polyp–adenocarcinoma sequence and are believed to drive the histological progression of colon cancer. Recently, epigenetic alterations, which include CGI (CpG island) DNA methylation, have been shown to occur in colon polyps and colon cancer. The aberrant methylation of genes appears to co-operate with the genetic alterations to drive the initiation and progression of colon polyps to colon cancer. CGI DNA methylation is an epigenetic mechanism that represses gene transcription in normal cellular processes, but it becomes excessive and aberrant in many neoplasms. The aberrant DNA methylation affects CpG-rich regions, called CGIs, in the 5′ region of genes and results in transcriptional silencing through effects on transcription factor binding and associated changes in chromatin structure. These hypermethylated genes are not only probable pathogenic events affecting colon-cancer formation, but also neoplasm-specific molecular events that may be useful as molecular markers for colon tumours. Furthermore, aberrant DNA methylation of tumour-suppressor genes may occur secondary to a genetic predisposition or to a field-cancerization effect in the colon and may be useful as molecular markers for the risk of developing colon cancer.
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Shepro, David, and Michael Miller. "Gemcitabine in Blastic Plasmacytoid Dendritic Cell Neoplasm (CD4+CD56+ hematodermic neoplasm)." Blood 124, no. 21 (December 6, 2014): 5457. http://dx.doi.org/10.1182/blood.v124.21.5457.5457.
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Abstract Once thought to be a natural killer cell lymphoma, blastic plasmacytoid dendritic cell neoplasm, also termed CD4+CD56+ hematodermic neoplasm, is a rare clinical entity which derives from plasmacytoid dendritic cells. Cutaneous predominant (with better prognosis) and non-cutaneous subtypes (often accompanied by mediastinal involvement and a poorer prognosis) have been described. Many patients are treated with CHOP-like regimens, but the prognosis remains poor. Patients presenting with only skin lesions (median survival 21 months) had a better prognosis than patients presenting with both cutaneous and extra-cutaneous disease. We describe an 86 yo female with a distant history of breast cancer. She noted rapid development of mildly itchy round pink cutaneous nodlues on the arms, buttock, and legs. She was treated with topical steroids without improvement. The CBC, calcium, and LDH were normal. ECOG 0. There was no adenopathy or organomegaly. Skin biopsy demonstrated a dense lymphoid infiltrate involving the upper and mid dermis, as well as adnexal structures, without epidermotropism. The infiltrate was composed predominantly of large to intermediate sized lymphoid cells having moderate amounts of cytoplasm and oval to cleaved nuclei having open chromatin and one or more small nucleoli. Mitotic figures were present. The neoplastic cells expressed CD4, CD56. Ki-67 was expressed by many of the cells. The cells were negative for CD1a, CD3, CD5, CD7, CD8, PAX-5, CD20, CD79a, CD10, CD23, CD30, CD163, bcl-2, bcl-6, myeloperoxidase, kappa/lambda light chains, p63, Tdt, tryptase, chromogranin, MART-1, mammoglobin, CAM 5.2, and AE1/3. The morphology and immunophenotype was consistent with a CD4+/CD56+ hematodermic neoplasm. The patient preferred no additional staging studies or therapy. Based on the available data, cutaneous-only disease was suggested. The disease was observed without intervention for a few weeks, but progressed on her skin. She then requested a gentle therapy that might provide palliative improvement and prevent progression. Gemcitabine (2′,2′-difluorodeoxycytidine) is a well tolerated pyrimidine antimetabolite that impairs DNA synthesis and promotes induction of apoptosis. In patients with relapsed or refractory aggressive non-Hodgkin lymphoma, gemcitabine led to a 20% response rate with median survival of 6 months. Therapy with Gemcitabine was administered at 1000 mg/M2 on days 1, 8, 15 every 28 days. There was rapid and marked improvement of the skin nodules. Treatment was very well tolerated with minimal bilateral leg edema. A 4 week chemotherapy holiday was associated with regrowth. Photographs document the disease progression before therapy and response of disease with ongoing therapy. Gemcitabine may provide palliative benefit in some patients with blastic plasmacytoid dendritic cell neoplasm. Table Pre Therapy May 15 2014 Day 1 Chemotherapy May 23 2014 Day 22 Chemotherapy June 6 2014 Figure 1 Figure 1. Figure 2 Figure 2. Figure 3 Figure 3. Disclosures Off Label Use: Gemcitabine in blastic plasmacytoid dendritic cell neoplasm (CD4+CD56+ hematodermic neoplasm).
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Weinerman, David J., Rashid Z. Syed, Isaac Galandauer, and Shireen A. Pais. "Mo1217 Does Fluid DNA Analysis Change the Management of Pancreatic Cystic Neoplasm?" Gastrointestinal Endoscopy 75, no. 4 (April 2012): AB354. http://dx.doi.org/10.1016/j.gie.2012.03.923.
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Haferlach, Claudia, Constance Baer, Stephan Hutter, Anna Stengel, Niroshan Nadarajah, Wencke Walter, Manja Meggendorfer, Wolfgang Kern, and Torsten Haferlach. "Primary and Secondary Hematological Neoplasms - Are They Related?" Blood 134, Supplement_1 (November 13, 2019): 1702. http://dx.doi.org/10.1182/blood-2019-126585.
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Background: The pathogenesis of secondary hematological neoplasms occurring after a primary hematological neoplasm and the relationship between both is still unclear. We set up this study in order to evaluate whether both diseases share genomic alterations. Patients and Methods: We selected 25 patients who were diagnosed with a first hematological neoplasm (FHN) (CLL: n=14, other mature B cell neoplasm: n=6, AML: n=4, CML: n=1) and in median 48 months later (range: 16-119) with a second hematological neoplasm (SHN) (t-MDS: n= 21; t-AML: n=1, CMML: n=1; t-MPN: n=1, t-MDS/MPN: n=1). In 9 cases bone marrow was available that had been drawn in complete cytomorphological remission (CR) between FHN and SHN. Whole genome sequencing was performed for all 59 samples: 150 bp paired-end sequences where generated on Illumina HiseqX and NovaSeq 6000 machines (Illumina, San Diego, CA, USA) (median coverage 106x). A mixture of genomic DNA from multiple anonymous donors was used as normal controls. The overlap of genomic alterations present at the different points in time was evaluated. For the assessment of mutations as germline the following parameters were considered: a) variant allele frequency (VAF) 0.4-0.6; b) gnomAD frequency <0.005%; c) CLINVAR entry; d) high pathogenicity rating in the HePPy predictor (Hutter et al. ASH 2019) based on the most common in silico predictors included in dbNSFP. Results: 1) Relation of FHN and SHN by germline variants: In 8 cases 10 variants with a high pathogenicity in silico MLL predictor score in cancer predisposition genes were found (TP53,RUNX1, GATA2, BRCA2, MLH1, FAM175A, TMEM127, PALB2, ANKRD26, and PMS2). However, in CLINVAR only variants in GATA2 and PMS2 were scored as pathogenic/likely pathogenic, while for all other variants either no or conflicting data were available. 2) Relation of FHN and SHN by acquired mutations: A NOTCH2 mutation was detected at the time of CLL diagnosis (VAF 0.42) as well as at the time of t-MDS diagnosis (VAF 0.44) 16 months later, which might be either germline or somatic relating both diseases. In none of the remaining 19 pairs of a primary lymphatic neoplasm and a secondary myeloid neoplasm, there was evidence for shared acquired mutations. Regarding primary myeloid neoplasms, in one NPM1 mutated AML case an IDH1 mutation was present at AML and at t-MDS stage (VAF 0.45; 0.14), while it was not detectable in CR (2 months after diagnosis of AML and 43 months prior to diagnosis of t-MDS). In this case one DNMT3A mutation was present at all 3 points in time (VAF: 0.47, 0.44; 0.37), while a second one was gained at MDS stage (figure 1). No shared acquired mutations were identified between primary and secondary myeloid neoplasm in the remaining cases. 3) Independent/parallel development of FHN and SHN: In 5/9 cases with an available CR sample, mutations, structural variants and/or copy number variations present in the secondary malignancy were already detectable in CR. These included mutations in TP53 (n=3), AHR (n=1), CSNK1A1 (n=1), ASXL2 (n=1), t(2;3)(p16;q26) (n=1), del(2q), del(5q) and del(7p) (n=1). In 3/16 cases without remission sample a clone of the later emerging second neoplasm could be identified in the sample drawn at the time point of diagnosis of the primary disease. These clones harbored mutations in SRSF2 (n=2), PTPN11 (n=1), U2AF1 (n=1), WNK1 (n=1), MLH1 (n=1), TET2 (n=1). These secondary neoplasms were diagnosed 24, 24, and 76 months after the primary neoplasm, respectively. Summary: In more than half of the cases no genetic relation between the first and second hematological neoplasm was identified. Remarkably, in several cases a parallel development of FHN and SHN was observed suggesting that therapy for FNH allowed the outgrowth of SHN. Disclosures Haferlach: MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Baer:MLL Munich Leukemia Laboratory: Employment. Hutter:MLL Munich Leukemia Laboratory: Employment. Stengel:MLL Munich Leukemia Laboratory: Employment. Nadarajah:MLL Munich Leukemia Laboratory: Employment. Walter:MLL Munich Leukemia Laboratory: Employment. Meggendorfer:MLL Munich Leukemia Laboratory: Employment. Kern:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership.
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Gulley, Margaret L., and Weihua Tang. "Using Epstein-Barr Viral Load Assays To Diagnose, Monitor, and Prevent Posttransplant Lymphoproliferative Disorder." Clinical Microbiology Reviews 23, no. 2 (April 2010): 350–66. http://dx.doi.org/10.1128/cmr.00006-09.
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SUMMARYEpstein-Barr virus (EBV) DNA measurement is being incorporated into routine medical practice to help diagnose, monitor, and predict posttransplant lymphoproliferative disorder (PTLD) in immunocompromised graft recipients. PTLD is an aggressive neoplasm that almost always harbors EBV DNA within the neoplastic lymphocytes, and it is often fatal if not recognized and treated promptly. Validated protocols, commercial reagents, and automated instruments facilitate implementation of EBV load assays by real-time PCR. When applied to either whole blood or plasma, EBV DNA levels reflect clinical status with respect to EBV-related neoplasia. While many healthy transplant recipients have low viral loads, high EBV loads are strongly associated with current or impending PTLD. Complementary laboratory assays as well as histopathologic examination of lesional tissue help in interpreting modest elevations in viral load. Circulating EBV levels in serial samples reflect changes in tumor burden and represent an effective, noninvasive tool for monitoring the efficacy of therapy. In high-risk patients, serial testing permits early clinical intervention to prevent progression toward frank PTLD. Restoring T cell immunity against EBV is a major strategy for overcoming PTLD, and novel EBV-directed therapies are being explored to thwart virus-driven neoplasia.
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Real, Mark, Walid M. Chalhoub, and Nadim G. Haddad. "Itʼs in Her DNA: A Case Highlighting the Role of DNA Molecular Analysis in Intraductal Papillary Mucinous Neoplasm." American Journal of Gastroenterology 112 (October 2017): S714—S715. http://dx.doi.org/10.14309/00000434-201710001-01314.
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Wu, Ming-Tsang, Shu-Yi Chen, Trong-Neng Wu, Hsing-Yu Hwang, Chi-Kung Ho, Li-Hung Lee, and Su-Chu Wu. "No association between polymorphisms of the DNA repair geneXRCC1 and cervical neoplasm risk." Environmental Health and Preventive Medicine 8, no. 3 (July 2003): 100–103. http://dx.doi.org/10.1007/bf02897923.
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Karasaki, Hidenori, Yusuke Ono, Kazuya Koizumi, Kiyohiro Andoh, Shingo Asahara, Tomoki Yokochi, Kuniyuki Takahashi, et al. "Cell-free DNA genotyping using digital PCR for early detection of pancreatic neoplasm." Journal of Clinical Oncology 34, no. 4_suppl (February 1, 2016): TPS464. http://dx.doi.org/10.1200/jco.2016.34.4_suppl.tps464.
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TPS464 Background: Pancreatic ductal adenocarcinoma (PDA) is still a dismal disease, and there is an urgent need to establish novel tool for early diagnosis of the tumor. There are two main types of pathologically and genetically distinct precursors for PDA — pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous neoplasia (IPMN). Non-invasive markers for these precursor lesions have the potential to predict subsequent invasive tumor. Methods: Circulating cell-free DNA (cfDNA) released from tumor cells into the blood has been intensively studied as a novel way to monitor the genetic changes. To detect the cfDNA representing for the initiation and progression of PDA could be of the candidate for them. The role of cfDNA genotyping targeting the major driver mutations in these precursors, such as KRAS and GNAS, are currently under investigation in Japanese patients who have pancreatic tumors (UMIN000012810). The major technical challenge is to specifically detect the small fraction of tumor-derived DNA in patient plasma and urine. Since sequencing of target mutant alleles in cfDNA has a limitation to detect very low frequency variants, we sought to establish protocols for super-sensitive and absolute quantification of the “key drivers” for pancreatic tumor using a droplet digital PCR platform (Bio-Rad; QX200). The primary endpoint of this multi-center prospective analysis is to evaluate whether such an approach can appropriately monitor the risk of IPMN progression and detect localized early-stage PDA. Thirty cases of PDA and 90 cases of IPMN have been enrolled thus far. Detailed protocol for the study and improved technical points to quantify low-frequency variants will be discussed.
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Kutyna, Monika M., Li Yan A. Wee, Sharon Paton, Dimitrios Cakouros, Agnieszka Arthur, Rakchha Chhetri, Andreas W. Schreiber, et al. "Therapy-Related Myeloid Neoplasm Has a Distinct Pro-Inflammatory Bone Marrow Microenvironment and Delayed DNA Damage Repair." Blood 136, Supplement 1 (November 5, 2020): 37–38. http://dx.doi.org/10.1182/blood-2020-137277.
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Introduction: Therapy-related myeloid neoplasms (t-MN) are associated with extremely poor clinical outcomes in otherwise long-term cancer survivors. t-MN accounts for ~20% of cases of myeloid neoplasms and is expected to rise due to the increased use of chemotherapy/radiotherapy (CT/RT) and improved cancer survivorship. Historically, t-MN was considered a direct consequence of DNA damage induced in normal hematopoietic stem cells (HSC) by DNA damaging cytotoxics. However, these studies have largely ignored the bone marrow (BM) microenvironment and the effects of age and concurrent/previous cancers. Aim: We performed an exhaustive functional study of mesenchymal stromal cells (MSC) obtained from a comparatively large cohort of t-MN patients and carefully selected control populations to evaluate the long-term damage induced by cytotoxic therapy to BM microenvironment and its impact on malignant and normal haematopoiesis. Methods: Four different cohorts were used: (1) t-MN, in which myeloid malignancy occurred after CT/RT for a previous cancer (n=18); (2) patients with multiple cancer and in which a myeloid neoplasm developed following an independent cancer which was not treated with CT/RT (MC-MN; n=10); (3) primary MN (p-MN; n=7) untreated and without any prior cancer or CT/RT; (4) age-matched controls (HC; n=17). Morphology, proliferation, cellular senescence, differentiation potential and γH2AX DNA damage response was performed. Stem/progenitor supportive capacity was assessed by co-culturing haematopoietic stem cells on MSC feeder-layer in long-term culture initiating assay (LTC-IC). Cytokine measurements were performed using 38-plex magnetic bead panel (Millipore) and RNA sequencing libraries were prepared with Illumina TruSeq Total RNA protocol for 150bp paired-end sequencing on a NextSeq500 instrument. Functional enrichment analysis was performed using EnrichR software. Results: MSC cultured from t-MN patients were significantly different from HC, p-MN and MC-MN MSC according to multiple parameters. They exhibited aberrant morphology consisting of large, rounded and less adhesive cells compared to typical spindle-shaped morphology observed with controls. MSC from myeloid neoplasm also showed impaired proliferation, senescence, osteo- and adipogenic differentiation with t-MN MSC showing the greatest differences. DNA repair was dramatically impaired compared to p-MN and HC (Fig.1A). Importantly, these aberrant t-MN MSC were not able to support normal or autologous in vitro long-term haematopoiesis (Fig.1B). The biological characteristic and poor haematopoietic supportive capacity of MSC could be "cell-intrinsic" or driven by an altered paracrine inflammatory microenvironment. Interestingly, several inflammatory cytokines were higher in t-MN compared with marrow interstitial fluid obtained from p-MN patients (Fig.1Ci) and many of these including Fractalkine, IFNα2, IL-7 and G-CSF were also significantly higher in t-MN MSC conditional media (Fig.1Cii). Together, this data suggest that t-MN microenvironment is distinct from p-MN with paracrine production of pro-inflammatory milieu that may contribute to poor HSC supportive capacity. Preliminary whole transcriptome analysis revealed differential gene expression between t-MN and HC (Fig.1Di) and p-MN MSC. Importantly, the deregulated genes play critical role in cell cycle, DNA damage repair, and cellular senescence pathways explaining phenotypical characteristic of t-MN MSC (Fig.1Dii). Moreover CXCL12 expression, a key regulator of haematopoiesis, was significantly lower in t-MN compared to HC (p=0.002) and p-MN MSC (p=0.009), thus explaining poor HSC supportive capacity. The key difference between the p-MN, MC-MN and t-MN is prior exposure to CT/RT. To study this we obtained MSC from two t-MN patients for whom we had samples at the time of their primary cancer, post high-dose chemotherapy and at the time of t-MN. MSC displayed aberrant proliferation and differentiation capacity after high-dose cytotoxic therapy (2 to 4 years prior to developing t-MN) and remained aberrant at t-MN diagnosis (Fig.1E). Conclusions: BM-MSC from t-MN patients are significantly abnormal compared with age-matched controls and typical myeloid neoplasm. Importantly, prior CT/RT leads to long-term irreversible damage to the BM microenvironment which potentially contributes to t-MN pathogenesis. Disclosures Hughes: Novartis: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding; BMS: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Hiwase:Novartis Australia: Research Funding.
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Dharajiya, Nilesh G., Daniel S. Grosu, Daniel H. Farkas, Ron M. McCullough, Eyad Almasri, Youting Sun, Sung K. Kim, et al. "Incidental Detection of Maternal Neoplasia in Noninvasive Prenatal Testing." Clinical Chemistry 64, no. 2 (February 1, 2018): 329–35. http://dx.doi.org/10.1373/clinchem.2017.277517.
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Abstract BACKGROUND Noninvasive prenatal testing (NIPT) uses cell-free DNA (cfDNA) as an analyte to detect copy-number alterations in the fetal genome. Because maternal and fetal cfDNA contributions are comingled, changes in the maternal genome can manifest as abnormal NIPT results. Circulating tumor DNA (ctDNA) present in cases of maternal neoplasia has the potential to distort the NIPT readout to a degree that prevents interpretation, resulting in a nonreportable test result for fetal aneuploidy. METHODS NIPT cases that showed a distortion from normal euploid genomic representation were communicated to the caregiving physician as nonreportable for fetal aneuploidy. Follow-up information was subsequently collected for these cases. More than 450000 pregnant patients who submitted samples for clinical laboratory testing >3 years are summarized. Additionally, in-depth analysis was performed for >79000 research-consented samples. RESULTS In total, 55 nonreportable NIPT cases with altered genomic profiles were cataloged. Of these, 43 had additional information available to enable follow-up. A maternal neoplasm was confirmed in 40 of these cases: 18 malignant, 20 benign uterine fibroids, and 2 with radiological confirmation but without pathological classification. CONCLUSIONS In a population of pregnant women who submitted a blood sample for cfDNA testing, an abnormal genomic profile not consistent with fetal abnormalities was detected in about 10 out of 100000 cases. A subset of these observations (18 of 43; 41.9%) was attributed to maternal malignant neoplasms. These observational results suggest the need for a controlled trial to evaluate the potential of using cfDNA as an early biomarker of cancer.
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Wang, Yongbao, Justin Windham, Shere Billouin-Frazier, and Dan Jones. "Myeloid Lineage-Associated Mutations Are Detected in Blastic Plasmacytoid Dendritic Cell Neoplasm." Blood 120, no. 21 (November 16, 2012): 5123. http://dx.doi.org/10.1182/blood.v120.21.5123.5123.
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Abstract Abstract 5123 Background/Purpose: Blastic plasmacytoid dendritic cell neoplasm (BPDCN) is a rare but highly aggressive hematologic malignancy that frequently presents with skin, lymph node, and leukemic disease. Since BPDCN can evolve into acute myelomonocytic leukemia (AMML) with other cases associated with monocytosis, a close relationship of BPDCN to the myelomonocytic lineage is suspected. Here we investigate the frequency of myeloid-associated DNA mutations in BPDCN using a targeted exon sequencing panel. Methods: Nine cases of BPDCN (5 skin, 1 lymph node, 3 bone marrow clot sections) were studied. All showed blastic cytomorphology; characteristic expression of CD56 and CD123; CD4 and/or TCL1 expression; and absence of definitive lymphoid, myeloid, and monocytic marker expression. AMML recurrence at 18 months, seen in 1 patient, was also assessed. Genomic DNA was extracted from formalin-fixed paraffin-embedded sections and subjected to a 161-amplicon PCR-based DNA sequencing assay that includes the commonly mutated areas of KRAS, NRAS, IDH1, IDH2, TET2, EZH2, JAK2, and ASXL1. Limited multiplex PCR and product harvesting was performed on an Access Array chip (Fluidigm). Ion adaptors were added and DNA sequencing was performed on a PGM sequencer using the 316 chip with 200 base-pair sequencing chemistry (Life Technologies). Sensitivity of mutation detection varied between 5–10%. Sequencing data were analyzed by SeqNext software (JSI MedSystems). Detected mutations were confirmed using conventional Sanger sequencing, with an approximate sensitivity of 15%, or pyrosequencing (5%). Results: Mutations in one or more of the tested genes were found in 6 of 9 patients, with unconfirmed mutations in 2 additional cases due to low-level mutations in samples with poor quality DNA. One patient with a typical BPDCN showed an IDH2 mutation (R140Q) with recurrence as AMML showing this mutation as well as a double mutation in KRAS (G12R, Q61R). Other mutations identified included 3 in ASXL1 including W608C, NRAS G12D, EZH2 C-terminal truncation, and 2 TET2indels. Conclusions: The presence of myeloid-associated mutations particularly in IDH2, TET2 and ASXL1 in cases of BPDCN is support for a relationship to the myelomonocytic lineage. The presence of shared and new mutations in the AMML recurrence in 1 patient with BPDCN further indicates a pathogenetic relationship between the two entities. Disclosures: Wang: Quest Diagnostics: Employment. Windham:Quest Diagnostics: Employment. Billouin-Frazier:Quest Diagnostics: Employment. Jones:Quest Diagnostics: Employment.
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Stonesifer, KJ, NA Benson, SE Ryden, DF Pawliger, and RC Braylan. "The malignant cells in a Lennert's lymphoma are T lymphocytes with a mature helper surface phenotype. A multiparameter flow cytometric analysis." Blood 68, no. 2 (August 1, 1986): 426–29. http://dx.doi.org/10.1182/blood.v68.2.426.426.
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Abstract The flow cytometric analysis of DNA content in cells obtained from a case of Lennert's lymphoma demonstrated the presence of a discrete hypotetraploid cell population. Correlated multiparameter analysis of DNA, light scatter, and surface antigens by flow cytometry showed that the hypotetraploid cells were intermediate to large cells expressing T11, T3, and T4 antigens and lacking B1 and T8 antigens. These findings suggest that Lennert's lymphoma represents a malignant neoplasm of T- helper lymphocytes.
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Stonesifer, KJ, NA Benson, SE Ryden, DF Pawliger, and RC Braylan. "The malignant cells in a Lennert's lymphoma are T lymphocytes with a mature helper surface phenotype. A multiparameter flow cytometric analysis." Blood 68, no. 2 (August 1, 1986): 426–29. http://dx.doi.org/10.1182/blood.v68.2.426.bloodjournal682426.
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The flow cytometric analysis of DNA content in cells obtained from a case of Lennert's lymphoma demonstrated the presence of a discrete hypotetraploid cell population. Correlated multiparameter analysis of DNA, light scatter, and surface antigens by flow cytometry showed that the hypotetraploid cells were intermediate to large cells expressing T11, T3, and T4 antigens and lacking B1 and T8 antigens. These findings suggest that Lennert's lymphoma represents a malignant neoplasm of T- helper lymphocytes.
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Alkan, Serhan, Ediz Cosar, Melek Ergin, and Eric Hsi. "Detection of T-Cell Receptor-γ Gene Rearrangement in Lymphoproliferative Disorders by Temperature Gradient Gel Electrophoresis." Archives of Pathology & Laboratory Medicine 125, no. 2 (February 1, 2001): 202–7. http://dx.doi.org/10.5858/2001-125-0202-dotcrg.
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Abstract Objective.—Polymerase chain reaction amplification of DNA for T-cell receptor (TCR) gene rearrangement analysis is helpful in the evaluation of T-cell lymphoproliferative disorders. Detection of polymerase chain reaction products is limited by the poor resolution of bands analyzed by agarose or polyacrylamide gel electrophoresis. To improve the detection of a clonal T-cell population, we used temperature gradient gel electrophoresis (TGGE) as an alternative method for analysis of TCR gene rearrangement. Design.—One hundred eighteen archival DNA samples were randomly selected based on previous Southern blot analysis results. Samples included 58 T-cell neoplasms with positivity for TCRβ gene rearrangement, 22 cases of reactive hyperplasia with germline pattern for both TCRβ and JH, and 38 patients with B-cell lymphoma. MOLT-16, a T-cell lymphoblastic cell line, was used for the sensitivity assay. Polymerase chain reaction was performed using GC;chclamped multiplex primers to amplify the TCRγ locus and was analyzed by TGGE. The range of temperature gradients was empirically determined for optimal resolution of bands. Results.—The sensitivity of TGGE was 0.1% when DNA from the MOLT-16 cell line was serially diluted with DNA from reactive lymphoid tissue. Fifty-four (93%) of 58 T-cell neoplasms with TCRβ gene rearrangements showed rearrangement patterns by TCRγ TGGE, and only 1 of 60 samples (reactive or B-cell lymphomas) showed evidence of gene rearrangement by TGGE. Patients with T-cell neoplasm and involvement of multiple sites showed an identical migration pattern by TGGE analysis. Conclusion.—We demonstrate that TGGE is an effective method for analysis of TCR gene rearrangement in the evaluation of nodal and extranodal lymphoid lesions.
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Kutyna, Monika M., Amilia Wee, Sharon Paton, Dimitrios Cakouros, Agnes Arthur, Rakchha Chhetri, Deepak Singhal, Stan Gronthos, and Devendra K. Hiwase. "Aberrant Bone Marrow Microenvironment in Therapy Related Myeloid Neoplasm (t-MN)." Blood 134, Supplement_1 (November 13, 2019): 1694. http://dx.doi.org/10.1182/blood-2019-126457.
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Introduction: Therapy-related myeloid neoplasm (t-MN) is a lethal second hematological malignancy following chemotherapy (CT) and radiotherapy (RT) for primary cancers. It accounts for 15-20% of myelodysplastic syndromes (MDS) and acute myeloid leukemia (AML). AML and MDS are considered to be hematopoietic stem cell (HSC)-autonomous disorders, in which initiation and progression are mainly driven by HSC-intrinsic genetic events. However, emerging data suggest that bone marrow (BM) microenvironment plays critical role in initiation and evolution of MDS and AML (Raaijmakers et al., 2010). Malignant clones can also shape the BM-microenvironment conducive for its survival and proliferation (Medyouf et al., Cell Stem Cell 2014). Although CT/RT can damage BM-microenvironment, very limited studies assessed role of BM-microenvironment in t-MN pathogenesis. Aim: To assess BM-microenvironment changes induced by malignant HSC and changes induced by previous genotoxic stress on BM-microenvironment, we compared BM-mesenchymal stromal cells (MSC) from t-MN patients, with BM-MSC from 1) patients with two unrelated cancers, one of the cancer being MDS/AML, without prior exposure to CT/RT (Double cancers, DC), 2) primary MDS patients (pMDS) and 3) age matched healthy controls (HC). Methods: We characterized BM-MSC from t-MN (n=10), DC (n=8), pMDS (n=6) and age-matched healthy controls (n=10). Morphology (Fei et al., 2014), clonogenic potential (Geyh et al., 2013), proliferation (Prata et al., 2010) and cellular senescence was assessed using previously described methodology. Differentiation potential was assessed by the respective lineage cytochemical staining and quantification of positive cells (mineral quantification for osteogenic cells, and Nile red for adipocytes). DNA damage response was determined by assessing H2AX phosphorylation in the MSC. Results: Only 70% of BM-MSC from t-MN cohort could be expanded to passage 6 compared to 100% of MSC cultures from pMDS, DC and HC. Proliferation rate, assessed by population doubling time, and clonogenic potential was significantly reduced in t-MN patients compared to p-MDS, DC and HC (Fig 1Ai-ii). This was further substantiated by higher senescence rates, assessed by β-galactosidase positive cells at passage 3 (HC 7%±1.9%; pMDS 39%±6%; DC 27%±1%; t-MN 68%±4%) (Fig 1B). Together, it demonstrates that MSC from t-MN have significantly impaired proliferation capacity and higher senescence rate compared to HC, pMDS and DC patients. Interestingly, proliferation capacity and senescence rate was not significantly different between MSC from DC and pMDS patients. We also compared DNA damage repair, following sub-lethal dose of RT, in MSC from t-MN, pMDS and HC. DNA damage repair in t-MN MSC was significantly impaired compared to pMDS and HC (Fig. 1F). Impaired DNA repair could be due to pathogenic germline mutation in DNA repair pathways in some t-MN patients (Singhal et al., ASH 2018). Although MSC from pMDS and DC appeared disorganized, they maintain fibroblast-like morphology similar to HC-MSC. Whereas, most of the MSCs from t-MN cases lost spindle shape morphology and were significantly larger than DC, pMDS and HC (p<0.0001; Fig 1C). Further characterization of the MSC's phenotype revealed that ability to form a mineralized matrix was significantly increased in t-MN MSC compared to HC, pMDS and DC (p=0.04; Fig 1Di-ii). In contrast, quantification of lipid-laden Nile-red-stained adipocytes in t-MN MSCs showed a 5-fold decrease in adipocytes formation compared to HC and ~2-fold compare to pMDS and DC (Fig 1Ei-ii). Conclusions: Our data demonstrate that BM-MSCs from patients with myeloid malignancies are significantly abnormal as compared to age-matched healthy controls. BM-MSCs from T-MN patients have significantly reduced proliferative, clonogenic and DNA repair capacity and have higher senescence rate as compared to BM-MSCs from patients with double cancers. The critical difference between t-MN and DC is previous exposure to CT/RT, providing evidence that prior CT/RT leads to long-term damage to BM-microenvironment, which could be contributing t-MN pathogenesis. Disclosures No relevant conflicts of interest to declare.
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Carretta, Chiara, Selene Mallia, Elena Genovese, Sandra Parenti, Sebastiano Rontauroli, Elisa Bianchi, Sebastian Fantini, et al. "Genomic Analysis of Hematopoietic Stem Cell at the Single-Cell Level: Optimization of Cell Fixation and Whole Genome Amplification (WGA) Protocol." International Journal of Molecular Sciences 21, no. 19 (October 6, 2020): 7366. http://dx.doi.org/10.3390/ijms21197366.
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Single-cell genomics has become the method of choice for the study of heterogeneous cell populations and represents an elective application in defining the architecture and clonal evolution in hematological neoplasms. Reconstructing the clonal evolution of a neoplastic population therefore represents the main way to understand more deeply the pathogenesis of the neoplasm, but it is also a potential tool to understand the evolution of the tumor population with respect to its response to therapy. Pre-analytical phase for single-cell genomics analysis is crucial to obtain a cell population suitable for single-cell sorting, and whole genome amplification is required to obtain the necessary amount of DNA from a single cell in order to proceed with sequencing. Here, we evaluated the impact of different methods of cellular immunostaining, fixation and whole genome amplification on the efficiency and yield of single-cell sequencing.
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Seibel, NL, and IR Kirsch. "Tumor detection through the use of immunoglobulin gene rearrangements combined with tissue in situ hybridization." Blood 74, no. 5 (October 1, 1989): 1791–95. http://dx.doi.org/10.1182/blood.v74.5.1791.1791.
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Abstract Leukemias and lymphomas can now be classified according to the particular immunoglobulin, T-cell receptor, or growth-affecting genes they are expressing. Recognition of the structural alterations of lymphoid DNA has been used to identify neoplasms of previously uncertain lineage, to aid in diagnosis, and to define the state of differentiation of the neoplasm. We have developed a procedurally simple, rapid turnaround technique for using tumor-specific gene alterations as tumor-specific markers. Probes can be constructed that will recognize only the gene expressed in the tumor and not those in any of the normal cells when used with tissue in situ hybridization. We demonstrate the application of direct sequencing of a specific gene of interest from total RNA from a patient with multiple myeloma. A probe is then generated from this sequence and applied directly to patient material.
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Seibel, NL, and IR Kirsch. "Tumor detection through the use of immunoglobulin gene rearrangements combined with tissue in situ hybridization." Blood 74, no. 5 (October 1, 1989): 1791–95. http://dx.doi.org/10.1182/blood.v74.5.1791.bloodjournal7451791.
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Leukemias and lymphomas can now be classified according to the particular immunoglobulin, T-cell receptor, or growth-affecting genes they are expressing. Recognition of the structural alterations of lymphoid DNA has been used to identify neoplasms of previously uncertain lineage, to aid in diagnosis, and to define the state of differentiation of the neoplasm. We have developed a procedurally simple, rapid turnaround technique for using tumor-specific gene alterations as tumor-specific markers. Probes can be constructed that will recognize only the gene expressed in the tumor and not those in any of the normal cells when used with tissue in situ hybridization. We demonstrate the application of direct sequencing of a specific gene of interest from total RNA from a patient with multiple myeloma. A probe is then generated from this sequence and applied directly to patient material.
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Roa López, Gustavo A., Jhon Jairo Suárez, Paola Barato, and Noel Verján García. "Lack of association between Epstein–Barr virus and mammary tumours in dogs." Journal of Veterinary Research 62, no. 3 (October 23, 2018): 309–15. http://dx.doi.org/10.2478/jvetres-2018-0045.
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AbstractIntroductionEpstein–Barr virus (EBV) is a γ-herpesvirus associated with various neoplasms in humans and is a probable aetiological agent in breast cancer; however, a causal relationship has not yet been established. Because of the epidemiological and clinicopathological similarities between breast cancer and canine mammary tumours, dogs have been proposed as a valid model for breast cancer.Material and MethodsA total of 47 canine mammary gland tumour tissues were processed by routine histopathological technique with haematoxylin-eosin staining and classified according to the type of neoplasm. DNA was extracted from paraffin-embedded tissues and the EBNA-1 gene and the BamHI-W region specific for EBV were evaluated by nested PCR.ResultsThe histopathological evaluation revealed 2 benign neoplasms, and many carcinomas: 2 in situ, 9 simple, 3 solid, 10 complex, and 21 mixed. One sample was positive for the EBNA-1 gene, while all were negative for the BamHI-W region.ConclusionNo association was found between EBV and mammary tumours in dogs. However, here we report for the first time the presence of an EBV gene sequence in a canine mammary tumour. It is likely that detection of EBV might be affected by the quality and quantity of DNA extracted from paraffin-embedded tissues. Additional studies are necessary to establish any association of EBV with mammary gland cancer in humans and in dogs, which could eventually lead to better public health prevention and control.
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Tsai, H. T. "Association between Quantitative High-Risk Human Papillomavirus DNA Load and Cervical Intraepithelial Neoplasm Risk." Cancer Epidemiology Biomarkers & Prevention 14, no. 11 (November 1, 2005): 2544–49. http://dx.doi.org/10.1158/1055-9965.epi-05-0240.
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Salta, Sofia, Sandra P. Nunes, Mário Fontes-Sousa, Paula Lopes, Micaela Freitas, Margarida Caldas, Luís Antunes, et al. "A DNA Methylation-Based Test for Breast Cancer Detection in Circulating Cell-Free DNA." Journal of Clinical Medicine 7, no. 11 (November 7, 2018): 420. http://dx.doi.org/10.3390/jcm7110420.
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Background: Breast cancer (BrC) is the most frequent neoplasm in women. New biomarkers, including aberrant DNA methylation, may improve BrC management. Herein, we evaluated the detection and prognostic performance of seven genes’ promoter methylation (APC, BRCA1, CCND2, FOXA1, PSAT1, RASSF1A and SCGB3A1). Methods: Methylation levels were assessed in primary BrC tissues by quantitative methylation-specific polymerase chain reaction (QMSP) and in circulating cell-free DNA (ccfDNA) by multiplex QMSP from two independent cohorts of patients (Cohort #1, n = 137; and Cohort #2, n = 44). Receiver operating characteristic (ROC) curves were constructed, and log-rank test and Cox regression were performed to assess the prognostic value of genes’ methylation levels. Results: The gene-panel APC, FOXA1, RASSF1A, SCGB3A1 discriminated normal from cancerous tissue with high accuracy (95.55%). In multivariable analysis, high PSAT1-methylation levels [>percentile 75 (P75)] associated with longer disease-free survival, whereas higher FOXA1-methylation levels (>P75) associated with shorter disease-specific survival. The best performing panel in ccfDNA (APC, FOXA1 and RASSF1A) disclosed a sensitivity, specificity and accuracy over 70%. Conclusions: This approach enables BrC accurate diagnosis and prognostic stratification in tissue samples, and allows for early detection in liquid biopsies, thus suggesting a putative value for patient management.
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De Luise, Monica, Vito Guarnieri, Claudio Ceccarelli, Leonardo D’Agruma, Anna Maria Porcelli, and Giuseppe Gasparre. "A Nonsense Mitochondrial DNA Mutation Associates with Dysfunction of HIF1α in a Von Hippel-Lindau Renal Oncocytoma." Oxidative Medicine and Cellular Longevity 2019 (January 9, 2019): 1–5. http://dx.doi.org/10.1155/2019/8069583.
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The Von Hippel-Lindau (VHL) syndrome has been rarely associated with renal oncocytomas, and tumors usually show HIF1α chronic stabilization. By contrast, oncocytomas mainly associated with respiratory chain (RC) defects due to severe mitochondrial DNA (mtDNA) mutations are incapable of stabilizing HIF1α, since oxygen consumption by the RC is dramatically diminished and prolylhydroxylase activity is increased by α-ketoglutarate accumulation following Krebs cycle slowdown. Here, we investigate the cooccurrence of a pseudohypoxic condition with oncocytic transformation in a case of VHL-associated renal oncocytoma. While HIF1α was abundant in nuclei concordantly with defects in VHL, negative staining of its targets carbonic anhydrase IX (CAIX) and glucose transporter GLUT1, usually overexpressed in VHL-associated neoplasms, suggested HIF1α to be present in its inactive (hydroxylated) form. MtDNA sequencing and immunohistochemistry analyses revealed a MT-CO1 stop-gain mutation and cytochrome c oxidase loss. We suggest that a mitochondrial respiration impairment may lead to hyperhydroxylation of the transcription factor, which we confirmed by specific staining of hydroxylated HIF1α. Such inactive form hence accumulated in the VHL-deficient tumor, where it may contribute to the benign nature of the neoplasm. We propose that the protumorigenic role of HIF1α in VHL cancers may be blunted through drugs inhibiting mitochondrial respiratory complexes, such as metformin.
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Kutler, David I., Bhuvanesh Singh, Jaya Satagopan, Sat Dev Batish, Marianne Berwick, Philip F. Giampietro, Helmut Hanenberg, and Arleen D. Auerbach. "A 20-year perspective on the International Fanconi Anemia Registry (IFAR)." Blood 101, no. 4 (February 15, 2003): 1249–56. http://dx.doi.org/10.1182/blood-2002-07-2170.
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Fanconi anemia (FA) is an autosomal recessive disorder characterized by cellular hypersensitivity to DNA cross-linking agents and cancer predisposition. Recent evidence for the interactions of ataxia-telangiectasia mutated protein ATM and breast cancer susceptibility proteins BRCA1 and BRCA2 (identified as FANCD1) with other known FA proteins suggests that FA proteins have a significant role in DNA repair/recombination and cell cycle control. The International Fanconi Anemia Registry (IFAR), a prospectively collected database of FA patients, allows us the unique opportunity to analyze the natural history of this rare, clinically heterogeneous disorder in a large number of patients. Of the 754 subjects in this study, 601 (80%) experienced the onset of bone marrow failure (BMF), and 173 (23%) had a total of 199 neoplasms. Of these neoplasms, 120 (60%) were hematologic and 79 (40%) were nonhematologic. The risk of developing BMF and hematologic and nonhematologic neoplasms increased with advancing age with a 90%, 33%, and 28% cumulative incidence, respectively, by 40 years of age. Univariate analysis revealed a significantly earlier onset of BMF and poorer survival for complementation group C compared with groups A and G; however, there was no significant difference in the time to hematologic or nonhematologic neoplasm development between these groups. Multivariate analysis of overall survival time shows that FANCCmutations (P = .007) and hematopoietic stem cell transplantation (P = < .0001) define a poor-risk subgroup. The results of this study of patients registered in the IFAR over a 20-year period provide information that will enable better prediction of outcome and aid clinicians with decisions regarding major therapeutic modalities.
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Al Alwan, N. A. S. "DNA proliferative index as a marker in Iraqi aneuploid mammary carcinoma." Eastern Mediterranean Health Journal 6, no. 5-6 (December 15, 2000): 1062–72. http://dx.doi.org/10.26719/2000.6.5-6.1062.
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This study estimated nuclear DNA ploidy and DNA proliferative indices [PI]in mammary ductal carcinomas from 120 Iraqi female patients. Of the examined specimens, 82.7% were aneuploid. DNA ploidy correlated significantly with histological grade and estrogen receptor content of the primary neoplasm. In aneuploid carcinomas, high PI showed a clearer association than aneuploidy with menopausal status and progesterone receptor content of the tumour. PI and percentage aneuploidy were higher in larger tumours; nodal status showed no association with these cytometric findings. Using PI, patients classified as having Auer aneuploid carcinomas can be divided into subsets with different tumour characteristics, thus improving the selection of those whose high risk, node-negative presentation makes them candidates for adjuvant systemic therapy.
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Di Francia, Raffaele, Stefania Crisci, Tommaso Muto, Concetta Giancola, Luigi Petriccone, Oriana Catapano, Annunziata Cummarro, Antonio Pinto, and Ferdinando Frigeri. "Optimization of a Low-Cost, Sensitive PNA Clamping PCR Method for JAK2 V617F Variant Detection." Journal of Applied Laboratory Medicine 5, no. 4 (March 20, 2020): 643–55. http://dx.doi.org/10.1093/jalm/jfaa041.
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Abstract Background The JAK2 V617F variant is diagnostic for myeloproliferative neoplasms, a group of clonal disorders of hematopoietic stem and progenitor cells. Although several approaches have been developed to detect the variant, a gold standard diagnostic method has not yet been defined. We describe a simple, fast, and cost-effective PCR-based approach that enhances test specificity and sensitivity by blocking the amplification of the large excess of wild-type DNA. Methods The method involves using an oligo peptide nucleic acid (PNA) perfectly matching its corresponding DNA sequence. The PCR protocol was optimized by collecting a detailed thermodynamic data set on PNA-DNA wild-type duplexes by circular dichroism melting experiments. The specificity and sensitivity of PNA clamping PCR were assessed by genotyping 50 patients with myeloproliferative neoplasm who carried the JAK2 V617F variant and 50 healthy donors. Results The optimized protocol enabled selective amplification of the variant alleles, achieving maximum sensitivity (100%) and specificity (100%). Analytical sensitivity was 0.05% of variant alleles as assessed by serial dilutions of DNA from the HEL cell line (which carries the JAK2 V617F variant) mixed to wild-type DNA from healthy donors. The JAK2 V617F variant test performed according to this method has better diagnostic performance than its 2 main PCR-based competitors, at much lower cost. Conclusions High sensitivity and specificity and cost-effectiveness make PNA clamping PCR a useful testing platform for the detection of minor allele variants in small-scale diagnostic laboratories. It promises to improve patient care while enabling significant healthcare savings.
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Gale, Robert, John M. Bennett, and F. Owen Hoffman. "WHO HAS THERAPY-RELATED AML?" Mediterranean Journal of Hematology and Infectious Diseases 9, no. 1 (March 1, 2017): e2017025. http://dx.doi.org/10.4084/mjhid.2017.025.
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Therapy-related leukemia or therapy-related myeloid neoplasm are widely-used terms to designate leukemia developing in persons who previously received anti-cancer therapy (for example, see references 1, 2), especially if the prior anti-cancer therapy included drugs such as alkylators, DNA-intercalators, topoisomerase-2-inhibitors, purines and/or ionizing radiations. Sometimes specific genes such as AML1, EVI1, NRAS or MLL are mutated by therapy or gene variants are produced which activate mutagens or interfere with DNA repair, such FANC, NQ01 or AML2. 3-5 But how can we know if AML in someone is a therapy-related?Keywords: Therapy-related leukemia; alkylators; ionizing radiations; Topoisomerase Inhibitors; DNA Repair
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Wuriningtyas, Lenny Buana, Dwi Reno Pawarti, and Achmad Chusnu Romdhoni. "Filogenetik Human papillomavirus (HPV) tipe 6 dan tipe 11 pada penderita recurrent respiratory papillomatosis." Oto Rhino Laryngologica Indonesiana 44, no. 1 (October 8, 2014): 52. http://dx.doi.org/10.32637/orli.v44i1.83.
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Latar belakang: Papiloma saluran pernapasan berulang (recurrent respiratory papillomatosis/RRP) merupakan neoplasma jinak laring terbanyak akibat infeksi HPV tipe 6 dan tipe 11. RRP merupakan masalah terkait agresivitas dan terapi. Analisis genetik digunakan untuk membedakan varian HPV tipe 6 dan tipe 11. Filogenetik mengevaluasi evolusi sequen DNA virus. Tujuan: Penelitian bertujuan mengidentifikasi sequen DNA dan menganalisis pohon filogenetik HPV tipe 6 dan tipe 11 pada papiloma saluran pernapasan berulang. Metode: Penelitian merupakan observasional deskriptif cross sectional. Analisis menggunakan data pembanding dari GenBank. Filogenetik disusun menggunakan metodeUPGMA (Unweighted Pair Group Method with Arithmetic Mean). Didapatkan 15 sampel jaringan papiloma. Dilakukan pemeriksaan PCR dan analisis sequen DNA. Hasil: Dari 15 sampel penelitian (12 laki-laki, 3 perempuan) didapatkan 9 isolat HPV tipe 6 (8 varian dan 1 subtipe) dan 4 isolat HPV tipe 11 (3 varian dan 1 subtipe). Terdapat mutasi titik yang mengakibatkan munculnya varian dan subtipe HPV tipe 6 maupun tipe 11. Kesimpulan: sequen DNA sampel berasal dari L1 ORF (Late 1 Open Reading Frame) yang merupakan kapsid mayor virus. Proses mutasi level gen berupa substitusi, insersi, dan delesi.Subtipe HPV tipe 6 dan tipe 11 yang ditemukan diperkirakan sebagai subtipe baru dan belum pernah dilaporkan sebelumnya. Lima varian HPV tipe 6 membentuk satu cabang tersendiri pada nomenklatur filogenetik yang sudah ada sehingga diajukan sebagai sublineage baru (sublineage C). Seluruh isolat HPV tipe 11 membentuk cabang pohon tersendiri dan diajukan sebagai sublineage baru (sublineage B).Kata kunci: HPV tipe 6 dan 11, variasi sequen DNA, pohon filogenetik HPV tipe 6 and 11. ABSTRACTBackground: Recurrent respiratory papillomatosis (RRP) is the most common laryngeal benign neoplasm caused by infection of HPV type 6 and 11. RRP is still a serious problem related to agresivity and therapy. Genetic analysis used to determine the variant of HPV type 6 or 11. Phylogenetic tree used to evaluate the evolution of viral DNA squence. Purpose: This study aimed to identify DNA squences and analyse the phylogenetic tree of HPV type 6 and 11 in RRP. Methods: this was a descriptive observational cross sectional study. Data analysis used GenBank database and phylogenetic tree was constructed usedUPGMA (Unweighted Pair Group Method with Arithmetic Mean). 15 papillomas biopsies from RRP patients subjected HPV typing using PCR dan DNA sequensing analysis. Result: From 15 patients with RRP (12 male, 3 female), there were 9 isolates HPV type 6 (8 variants, 1 subtype) and 4 isolates HPV type 11 (3 variants, 1 subtype). There was a point mutation in HPV type 6 and 11. Conclusion: L1 ORF (Late 1 Open Reading Frame) sequensials DNA samples was virus major capsid. There were mutational process at gene level (substitution, insertion, deletion). Subtype of HPV-6 and 11, might be new ones, and had not been reported yet. Five variants of HPV type 6 constructed a different lineage in phylogenetic and it is proposed to be C sublineage. All samples HPV type 11 proposed as B sublineage. Keywords: HPV type 6 and 11, DNA sequences variations, phylogenetic trees HPV type 6 and 11.
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Taylor, Justin, Mark Donoghue, Raajit K. Rampal, Roni Tamari, Martin S. Tallman, Darren R. Feldman, Barry S. Taylor, and Omar I. Abdel-Wahab. "Hematologic Malignancies Arising in Patients with Germ Cell Tumors: Secondary Somatic Differentiation of Hematopoietic Malignancies from Germ Cell Precursors." Blood 132, Supplement 1 (November 29, 2018): 87. http://dx.doi.org/10.1182/blood-2018-99-111976.
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Abstract Genomic analyses have recently illuminated our understanding of therapy-associated myeloid neoplasms in patients receiving therapy for other cancers. One of the most intriguing relationships between solid tumors and myeloid neoplasms involves a unique clinical entity of patients with germ cell tumors (GCT) and myeloid neoplasms. One in 17 patients with primary mediastinal germ cell tumor (PMGCT) develops a hematologic malignancy (most commonly AML, MDS, or histiocytosis) and the median survival in such patients is poor at only 5 months. Intriguingly, the presence of isochromosome 12p [i(12p)], a clonal marker common to GCTs but absent in de novo myeloid neoplasms, has been demonstrated as shared across GCTs and myeloid neoplasms in such individuals. While these data suggest a clonal relationship between the two, the exact nature of the shared origin is unknown. There are two competing hypotheses to explain this: (1) an embryonic progenitor with the capacity to differentiate into germ cell and hematopoietic lineages harbors the initiating genetic alterations and drives development of both malignancies or (2) the leukemia is derived directly from GCTs with the capacity to differentiate into hematopoietic lineages. To trace the clonal evolution of these seemingly unrelated cancer types and identify recurrent genomic lesions in leukemias present in GCT patients, we applied whole exome sequencing (WES), targeted genomic analyses, and/or RNA-seq to leukemias, GCTs, and germline DNA in a series of patients with myeloid neoplasms and concurrent GCTs. We collected 12 patients with GCT and synchronously or metachronously occurring myeloid neoplasms (8 AML, 5 MDS/CMML, 2 histiocytic sarcoma (some had >1 hematologic malignancy)) with an average of 4 months between the two diagnoses. Consistent with prior reports, all were young men (median age 26) with PMGCT and nonseminomatous histology and a 3-month median survival from leukemia diagnosis (Fig. A). In each case, at least one copy number alteration or coding mutation was shared across the GCT and hematopoietic neoplasm, demonstrating the shared origin of both lesions. For example, half of the patients (6/12) carried i(12p) in both the GCT and hematopoietic neoplasm. In the i(12p) negative cases, somatic genetic alterations identified in the GCT were also found in the leukemia. The most common genomic alterations in leukemias beyond i(12p) included mutations activating RAS-PI3K-AKT signaling (including PTEN, RAS and PI3K isoform mutations) or inactivating TP53 (Fig. B). The only exception was a testicular-only GCT patient who developed clonally distinct acute promyelocytic leukemia; however, further analysis identified this as a chemotherapy-induced neoplasm with the PML-RARa breakpoint mapped to an etoposide sensitive area and this patient was not counted amongst the 12 cases. We next traced the evolutionary history of clonally related GCTs and leukemias based on cancer cell fraction of all coding mutations and copy number alterations using WES of DNA from each tumor type and finger nails. In each instance, we identified clonal evolution of the hematopoietic malignancies from antecedent precursors within the GCT. To illustrate this, a 19-year-old male developed successive diagnoses of histiocytic sarcoma, CMML, and AML within 18 months of GCT diagnosis. Lineage tracing by WES of each of these four individual cancers revealed that all four were clonally related, and the histiocytic sarcoma, CMML, and AML were all derived from the GCT with a common precursor giving rise to the three hematopoietic malignancies (Fig. C-D). Moreover, the histiocytic sarcoma evolved separately from CMML/AML in this patient, where the AML represented leukemic transformation from the CMML. These data conclusively demonstrate that myeloid neoplasms developing in patients with PMGCT represent secondary somatic differentiation of a hematologic progenitor from totipotent aberrant cells that are present in the GCT. Thus, GCT-associated leukemias have a unique ontogeny from de novo and/or secondary myeloid neoplasms, which originate from progenitors within the bone marrow. As such, GCT-associated leukemias have characteristic genomic alterations hallmarked by frequent i(12p) in combination with mutations activating RAS-PI3K-AKT signaling and inactivating TP53, and these patients do poorly even when treated with aggressive contemporary chemotherapy. Figure Figure. Disclosures Rampal: Jazz: Consultancy, Honoraria; Celgene: Honoraria; Constellation: Research Funding; Incyte: Honoraria, Research Funding; Stemline: Research Funding. Tallman:ADC Therapeutics: Research Funding; Orsenix: Other: Advisory board; AROG: Research Funding; Cellerant: Research Funding; AbbVie: Research Funding; Daiichi-Sankyo: Other: Advisory board; BioSight: Other: Advisory board.
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Knowles, DM, G. Inghirami, A. Ubriaco, and R. Dalla-Favera. "Molecular genetic analysis of three AIDS-associated neoplasms of uncertain lineage demonstrates their B-cell derivation and the possible pathogenetic role of the Epstein-Barr virus." Blood 73, no. 3 (February 15, 1989): 792–99. http://dx.doi.org/10.1182/blood.v73.3.792.792.
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Abstract Each of three individuals with acquired immunodeficiency syndrome (AIDS) developed a pleomorphic malignant neoplasm in which a precise histopathologic diagnosis could not be rendered. In each case, the tumor cells expressed leukocyte common antigen and a variable constellation of antigens associated with B- and T-cell activation (HLA- DR, T9, T10, BL2, BL3, Ki-24, BLAST-2). They lacked all B cell, T cell, myeloid, and monocyte lineage-restricted antigens, resulting in their classification as hematopoietic neoplasms of uncertain lineage. However, antigen receptor gene rearrangement analysis demonstrated that each of these three neoplasms exhibited clonal immunoglobulin heavy chain and kappa light chain gene rearrangements and lacked T-cell receptor beta chain gene rearrangements and therefore were B cell- derived non-Hodgkin's lymphomas (NHL) representative of an equivalent, relatively mature stage of B-cell differentiation. In contrast with most AIDS-associated NHLs, each of these three neoplasms lacked c-myc gene rearrangements and contained Epstein-Barr virus (EBV) proteins and/or sequences. These studies demonstrate that these three AIDS- associated neoplasms of uncertain lineage exhibit a strikingly similar constellation of distinctly uncommon morphologic, immunophenotypic, and molecular genetic characteristics that distinguishes them substantially from the vast majority of NHLs that have been reported to occur in association with AIDS. The consistent presence of EBV proteins and/or DNA sequences suggests that the Epstein-Barr virus played a pathogenetic role in the development of these three AIDS-associated neoplasms. Finally, these studies further illustrate the utility of antigen receptor gene rearrangement analysis in the diagnosis and classification of hematopoietic neoplasms of uncertain lineage.
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Knowles, DM, G. Inghirami, A. Ubriaco, and R. Dalla-Favera. "Molecular genetic analysis of three AIDS-associated neoplasms of uncertain lineage demonstrates their B-cell derivation and the possible pathogenetic role of the Epstein-Barr virus." Blood 73, no. 3 (February 15, 1989): 792–99. http://dx.doi.org/10.1182/blood.v73.3.792.bloodjournal733792.
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Each of three individuals with acquired immunodeficiency syndrome (AIDS) developed a pleomorphic malignant neoplasm in which a precise histopathologic diagnosis could not be rendered. In each case, the tumor cells expressed leukocyte common antigen and a variable constellation of antigens associated with B- and T-cell activation (HLA- DR, T9, T10, BL2, BL3, Ki-24, BLAST-2). They lacked all B cell, T cell, myeloid, and monocyte lineage-restricted antigens, resulting in their classification as hematopoietic neoplasms of uncertain lineage. However, antigen receptor gene rearrangement analysis demonstrated that each of these three neoplasms exhibited clonal immunoglobulin heavy chain and kappa light chain gene rearrangements and lacked T-cell receptor beta chain gene rearrangements and therefore were B cell- derived non-Hodgkin's lymphomas (NHL) representative of an equivalent, relatively mature stage of B-cell differentiation. In contrast with most AIDS-associated NHLs, each of these three neoplasms lacked c-myc gene rearrangements and contained Epstein-Barr virus (EBV) proteins and/or sequences. These studies demonstrate that these three AIDS- associated neoplasms of uncertain lineage exhibit a strikingly similar constellation of distinctly uncommon morphologic, immunophenotypic, and molecular genetic characteristics that distinguishes them substantially from the vast majority of NHLs that have been reported to occur in association with AIDS. The consistent presence of EBV proteins and/or DNA sequences suggests that the Epstein-Barr virus played a pathogenetic role in the development of these three AIDS-associated neoplasms. Finally, these studies further illustrate the utility of antigen receptor gene rearrangement analysis in the diagnosis and classification of hematopoietic neoplasms of uncertain lineage.
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Pasic, I., A. Shlien, A. Novokmet, C. Zhang, U. Tabori, D. Pinto, S. W. Scherer, and D. Malkin. "CONTRIBUTION OF DNA COPY-NUMBER VARIATION (CNV) TO CANCER SUSCEPTIBILITY AND LARGE-SCALE GENOME ALTERATIONS IN OSTEOSARCOMA (OS)." Clinical & Investigative Medicine 31, no. 4 (August 1, 2008): 19. http://dx.doi.org/10.25011/cim.v31i4.4821.
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Introduction: OS, a common Li-Fraumeni syndrome (LFS)-associated neoplasm, is a common bone malignancy of children and adolescents. Sporadic OS is also characterized by young age of onset and high genomic instability, suggesting a genetic contribution to disease. This study examined the contribution of novel DNA structural variation elements, CNVs, to OS susceptibility. Given our finding of excessive constitutional DNA CNV in LFS patients, which often coincide with cancer-related genes, we hypothesized that constitutional CNV may also provide clues about the aetiology of LFS-related sporadic neoplasms like OS. Methods: CNV in blood DNA of 26 patients with sporadic OS was compared to that of 263 normal control samples from the International HapMap project, as well as 62 local controls. Analysis was performed on DNA hybridized to Affymetrix genome-wide human SNP array 6.0 by Partek Genomic Suite. Results: There was no detectable difference in average number of CNVs, CNV length, and total structural variation (product of average CNV number and length) between individuals with OS and controls. While this data is preliminary (small sample size), it argues against the presence of constitutional genomic instability in individuals with sporadic OS. Conclusion: We found that the majority of tumours from patients with sporadic OS show CN loss at chr3q13.31, raising the possibility that chr3q13.31 may represent a “driver” region in OS aetiology. In at least one OS tumour, which displays CN loss at chr3q13.31, we demonstrate decreased expression of a known tumour suppressor gene located at chr3q13.31. We are investigating the role ofchr3q13.31 in development of OS.
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Kachko, Vera A., Andrew R. Zaretsky, Vladimir E. Vanushko, Nadezhda M. Platonova, Aleksandr Yu Abrosimov, and Galina V. Semkina. "Somatic mutation testing: the role in differential diagnosis of thyroid neoplasms." Endocrine Surgery 13, no. 1 (August 7, 2019): 26–41. http://dx.doi.org/10.14341/serg10181.
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Background: In the preoperative diagnosis of thyroid tumors the cytological examination of the material of fine needle aspiration biopsy is the gold standard and serves as the basis for planning of treatment strategy. However, in 10–30% of cases, it cannot be clearly established by cytology whether the nature of thyroid neoplasm benign or malignant, which leads to the inability to choose the optimal treatment strategy in advance. For such cases, it is extremely important to search for methods of clarifying differential diagnosis, among which mutation testing is currently considered the most promising.
Aims: To evaluate the possibility of using mutation tests for clarifying differential diagnosis of thyroid neoplasms at the preoperative stage.
Materials and methods: We performed the prospective single center study, which included patients with the thyroid neoplasms, who had been treated in the Endocrinology Research Center, Moscow, Russia from 2012 to 2014. Samples of histological material, cytological material and blood plasma of these patients were tested for the presence of somatic mutations in hot spots of the genes BRAF, KRAS, NRAS, TERT, and EIF1AX.
Results: The study included 75 patients, 29 of them with low-risk papillary thyroid cancer, 29 with follicular neoplasm NA of the thyroid gland and 17 with colloid nodular goiter. Mutations in the “hot spots” of the BRAF gene (exon 15, codon area 600–601) were found in 29 patients, mutations in the “hot spots” of the NRAS gene (exon 3, codon 61) – in 8 patients; mutations in the hot spots of the KRAS, TERT and EIF1AX genes were not detected. Correlation of the results of mutational testing of cytological and histological material was 91.7%. Mutations of tumor origin in circulating blood plasma DNA were found in only 1 cases. The prognostic value of the positive result (PPV) of the mutation test on cytological material in relation to the malignant nature of the thyroid tumor was 100% for the BRAF gene and 0% for the NRAS gene.
Conclusions: The mutation test in the “hot spots” of the BRAF gene on cytological material can be used as an additional marker to clarify the nature of thyroid tumors, when the result of cytological examination are uncertain. Either in similar situations for mutation tests in the “hot spots” of genes KRAS, NRAS, EIF1AX and TERT on cytological material, or mutation testing of circulating DNA of blood plasma can’t be used as an additional marker.
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Gaiser, Rogier Aäron, Asif Halimi, Hassan Alkharaan, Liyan Lu, Haleh Davanian, Katie Healy, Luisa W. Hugerth, et al. "Enrichment of oral microbiota in early cystic precursors to invasive pancreatic cancer." Gut 68, no. 12 (March 14, 2019): 2186–94. http://dx.doi.org/10.1136/gutjnl-2018-317458.
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ObjectivesIntraductal papillary mucinous neoplasms (IPMNs) are pancreatic cysts that can progress to invasive pancreatic cancer. Associations between oncogenesis and oral microbiome alterations have been reported. This study aims to investigate a potential intracystic pancreatic microbiome in a pancreatic cystic neoplasm (PCN) surgery patient cohort.DesignPaired cyst fluid and plasma were collected at pancreatic surgery from patients with suspected PCN (n=105). Quantitative and qualitative assessment of bacterial DNA by qPCR, PacBio sequencing (n=35), and interleukin (IL)-1β quantification was performed. The data were correlated to diagnosis, lesion severity and clinical and laboratory profile, including proton-pump inhibitor (PPI) usage and history of invasive endoscopy procedures.ResultsIntracystic bacterial 16S DNA copy number and IL-1β protein quantity were significantly higher in IPMN with high-grade dysplasia and IPMN with cancer compared with non-IPMN PCNs. Despite high interpersonal variation of intracystic microbiota composition, bacterial network and linear discriminant analysis effect size analyses demonstrated co-occurrence and enrichment of oral bacterial taxa including Fusobacterium nucleatum and Granulicatella adiacens in cyst fluid from IPMN with high-grade dysplasia. The elevated intracystic bacterial DNA is associated with, but not limited to, prior exposure to invasive endoscopic procedures, and is independent from use of PPI and antibiotics.ConclusionsCollectively, these findings warrant further investigation into the role of oral bacteria in cystic precursors to pancreatic cancer and have added values on the aetiopathology as well as the management of pancreatic cysts.
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Elzagheid, A., and Y. Collan. "Dependence of DNA-Histograms on The Sampling Techniques in Fine Needle Aspirates of the Breast." Analytical Cellular Pathology 24, no. 4-5 (2002): 159–65. http://dx.doi.org/10.1155/2002/393686.
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48 fine needle aspiration biopsy (FNAB) samples from 25 breast cancer cases, originally used for cytodiagnosis were subjected to DNA cytometry. There were air dried smears stained with the MGG method, and samples stained with HE or PAP stain after 50% ethanol fixation and cytocentrifugation. Different sampling strategies were applied. Four methods were tested: method 1: cell groups measured, method 2: all cells measured, method 3: free cells measured, and method 4: atypical free cells measured. Method 4 showed most often DNA aneuploid histogram patterns, sampling method 1 had the highest number of DNA diploid histogram patterns. Diagnostic approaches may benefit from a sampling method detecting the hiding aneuploid cell population. Grading of neoplasm could potentially benefit from other approaches.
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Zhao, Ye, Zi-xing Chen, Shao-yan Hu, and Jian-nong Cen. "Study on DNA Methylation Status of WT1 Gene in Its Promoter Region in Hematologic Neoplasm Cell Lines." Blood 106, no. 11 (November 16, 2005): 4386. http://dx.doi.org/10.1182/blood.v106.11.4386.4386.
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Abstract The methylation at CpG island in the promoter region of a gene is one of the important epigenetic mechanism which regulates the gene activity. To study the DNA methylation pattern of WT1 gene promoter region within hematologic neoplastic cell lines and its correlation with WT1 gene expression by using the PCR-based methods. RT-PCR and Methylation-specific PCR were performed to study the WT1 gene expression in 8226, HL-60, Jurkat, K562, KG-1, NB4, Raji, SHI-1, U266 and U937 cell lines and the DNA methylation status in promoter region of WT1 gene. After treatment of U937 cell line by 5-aza-CdR, a demethylation inducing agent, the changes of WT1 gene expression level and the methylation status in its promter region in U937 cells was determined. Our Results showed that HL-60, K562, KG-1, NB4, SHI-1 cell lines demonstrated higher level of WT1 expression, while extremely low level was found in 8226, Jurkat, Raji, U266 and U937. The DNA hypermethylation in WT1 gene promoter region was identified in 8226, Jurkat, Raji, U266 and U937 cell lines. The WT1 gene expression in U937 was markedly enhanced after treatment with 5-aza-CdR in company with the decrease of methylated level and the increase of unmethylated level in its promoter region. These results indicate that modulation of the DNA methylation in WT1 promoter region is one of the epigenetic mechanisms to regulate its expression.
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Yang, Bo, Hang Sun, Wei Lin, Wugang Hou, Hang Li, Liying Zhang, Fanfan Li, et al. "Evaluation of global DNA hypomethylation in human prostate cancer and prostatic intraepithelial neoplasm tissues by immunohistochemistry." Urologic Oncology: Seminars and Original Investigations 31, no. 5 (July 2013): 628–34. http://dx.doi.org/10.1016/j.urolonc.2011.05.009.
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Fujiyama, Yoshiki, Yusuke Kumamoto, Nobuyuki Nishizawa, Shuji Nakamoto, Hiroki Harada, Kazuko Yokota, Yoko Tanaka, et al. "Promoter DNA Hypermethylation of the Cysteine Dioxygenase 1 (CDO1) Gene in Intraductal Papillary Mucinous Neoplasm (IPMN)." Annals of Surgical Oncology 27, no. 10 (March 6, 2020): 4007–16. http://dx.doi.org/10.1245/s10434-020-08291-2.
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Ahlquist, David A., Hongzhi Zou, Mike Domanico, Douglas W. Mahoney, Malinda L. Butz, Stephen N. Thibodeau, Barry M. Berger, and Graham P. Lidgard. "A Next Generation Stool DNA Test (NG-Sdna) for Colorectal Cancer Screening: Factors Affecting Neoplasm Detection." Gastroenterology 140, no. 5 (May 2011): S—105. http://dx.doi.org/10.1016/s0016-5085(11)60427-7.
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Lavoie, Jean-Michel, Miguel Alcaide, Rosemary A. Fisher, Michael J. Seckl, Ryan Morin, and Anna V. Tinker. "Targeted Error-Suppressed Detection of Circulating Paternal DNA to Establish a Diagnosis of Gestational Trophoblastic Neoplasm." JCO Precision Oncology, no. 1 (November 2017): 1–6. http://dx.doi.org/10.1200/po.17.00154.
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Mateos, Raúl N., Hidewaki Nakagawa, Seiko Hirono, Shinichi Takano, Mitsuharu Fukasawa, Akio Yanagisawa, Satoru Yasukawa, et al. "Genomic analysis of pancreatic juice DNA assesses malignant risk of intraductal papillary mucinous neoplasm of pancreas." Cancer Medicine 8, no. 10 (June 21, 2019): 4565–73. http://dx.doi.org/10.1002/cam4.2340.
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Downey, Charlene M., and Frank R. Jirik. "DNA mismatch repair deficiency accelerates lung neoplasm development in K‐ras LA1/+ mice: a brief report." Cancer Medicine 4, no. 6 (March 14, 2015): 897–902. http://dx.doi.org/10.1002/cam4.420.
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Erčulj, Nina, Barbara Faganel Kotnik, Maruša Debeljak, Janez Jazbec, and Vita Dolžan. "DNA repair polymorphisms influence the risk of second neoplasm after treatment of childhood acute lymphoblastic leukemia." Journal of Cancer Research and Clinical Oncology 138, no. 11 (July 1, 2012): 1919–30. http://dx.doi.org/10.1007/s00432-012-1265-4.
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Yoo, J., and D. Park. "Detection of Colorectal Neoplasm Using Promoter Methylation of Stool Dna in Stool Samples in Korean Patients." Annals of Oncology 25 (September 2014): iv192. http://dx.doi.org/10.1093/annonc/mdu333.64.
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Alkeswani, Amena, Allen Oak, and Peter Pavlidakey. "A Case of Kaposi Sarcoma Co-infected with Cytomegalovirus." SKIN The Journal of Cutaneous Medicine 4, no. 1 (January 28, 2020): 76–78. http://dx.doi.org/10.25251/skin.4.1.12.
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Background: Kaposi sarcoma (KS) is the most common AIDS-associated neoplasm. It is a vascular neoplasm that occurs as a result of infection with a human herpesvirus (HHV-8). Cytomegalovirus (CMV) and HHV-8 both belong to Herpesviridae, a family of DNA viruses. CMV is highly prevalent in the general population and can cause localized or disseminated disease in AIDS patients.Case: A 42-year-old male with an HIV infection presented with a painful ulcerated growing white nodule with overlying telangiectatic vessels on the right third toe that he noticed 4 weeks ago. A tangential biopsy revealed a vascular proliferation which was diffusely positive for HHV-8. In addition, scattered inclusion bodies were observed, indicating co-infection with CMV.Conclusion: This case reinforces the importance of considering KS as a potential diagnosis in all AIDS patients with unusual exophytic growths to avoid potential misdiagnosis and improper management.
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Curti, P., D. Schiavone, L. S. Azzolina, M. Tontodonati, F. Migliorini, M. Rahmati, and L. Comunale. "Flow-cytometry DNA analysis (FCM) in multiple tissue samples of 69 patients with prostatic cancer treated by radical prostatectomy." Urologia Journal 63, no. 1_suppl (January 1996): 13–16. http://dx.doi.org/10.1177/039156039606301s02.
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We subjected 322 tissue samples of 69 patients with prostatic cancer treated by radical prostatectomy to flow-cytometry DNA analysis. From 1 to 8 tissue samples were analysed for all patients: results showed diploidy in 272 cases and aneuploidy in 50 cases. 45 tumours were classified as diploid, and 24 aneuploid. Aneuploid tumours had one or more aneuploid samples, but in no one case were all specimens of the same neoplasm aneuploid. Aneuploidy status could also change in the same tumour. In conclusion, the study shows that prostatic cancer is often heterogeneous with regard to DNA content and that just one specimen cannot be considered representative of the tumour.