Transvection mediated by the translocated cyclin D1 locus in mantle cell lymphoma

In mantle cell lymphoma (MCL) and some cases of multiple myeloma (MM), cyclin D1 expression is deregulated by chromosome translocations involving the immunoglobulin heavy chain (IgH) locus. To evaluate the mechanisms responsible, gene targeting was used to study long-distance gene regulation. Remarkably, these targeted cell lines lost the translocated chromosome (t(11;14)). In these MCL and MM cells, the nonrearranged cyclin D1 (CCND1) locus reverts from CpG hypomethylated to hypermethylated. Reintroduction of the translocated chromosome induced a loss of methylation at the unrearranged CCND1 locus, providing evidence of a transallelic regulatory effect. In these cell lines and primary MCL patient samples, the CCND1 loci are packaged in chromatin-containing CCCTC binding factor (CTCF) and nucleophosmin (NPM) at the nucleolus. We show that CTCF and NPM are bound at the IgH 3′ regulatory elements only in the t(11;14) MCL cell lines. Furthermore, NPM short hairpin RNA produces a specific growth arrest in these cells. Our data demonstrate transvection in human cancer and suggest a functional role for CTCF and NPM.     

Quantitative real-time PCR for cancer detection: the lymphoma case

Advances in the biologic sciences and technology are providing molecular targets for diagnosis and treatment of cancer. Lymphoma is a group of cancers with diverse clinical courses. Gene profiling opens new possibilities to classify the disease into subtypes and guide a differentiated treatment. Real-time PCR is characterized by high sensitivity, excellent precision and large dynamic range, and has become the method of choice for quantitative gene expression measurements. For accurate gene expression profiling by real-time PCR, several parameters must be considered and carefully validated. These include the use of reference genes and compensation for PCR inhibition in data normalization. Quantification by real-time PCR may be performed as either absolute measurements using an external standard, or as relative measurements, comparing the expression of a reporter gene with that of a presumed constantly expressed reference gene. Sometimes it is possible to compare expression of reporter genes only, which improves the accuracy of prediction. The amount of biologic material required for real-time PCR analysis is much lower than that required for analysis by traditional methods due to the very high sensitivity of PCR. Fine-needle aspirates and even single cells contain enough material for accurate real-time PCR analysis.     

Rapid detection of eight causative pathogens for the diagnosis of bacterial meningitis by real-time PCR

We aimed to detect causative pathogens in cerebrospinal fluid (CSF) collected from patients diagnosed with bacterial meningitis by real-time polymerase chain reaction (PCR). In addition to Streptococcus pneumoniae, Haemophilus influenzae, and Mycoplasma pneumoniae described previously, five other pathogens, Neisseria meningitidis, Escherichia coli, Streptococcus agalactiae, Staphylococcus aureus, and Listeria monocytogenes, were targeted, based on a large-scale surveillance in Japan. Results in CSF from neonates and children (n = 150), and from adults (n = 18) analyzed by real-time PCR with molecular beacon probes were compared with those of conventional culturing. The total time from DNA extraction from CSF to PCR analysis was 1.5 h. The limit of detection for these pathogens ranged from 5 copies to 28 copies per tube. Nonspecific positive reactions were not recognized for 37 microorganisms in clinical isolates as a negative control. The pathogens were detected in 72.0% of the samples by real-time PCR, but in only 48.2% by culture, although the microorganisms were completely concordant. With the real-time PCR, the detection rate of H. influenzae from CSF was high, at 45.2%, followed by S. pneumoniae (21.4%), S. agalactiae (2.4%), E. coli (1.8%), L. monocytogenes (0.6%), and M. pneumoniae (0.6%). The detection rate with PCR was significantly better than that with cultures in patients with antibiotic administration (χ² = 18.3182; P = 0.0000). In conclusion, detection with real-time PCR is useful for rapidly identifying the causative pathogens of meningitis and for examining the clinical course of chemotherapy.     

CD5-negative blastoid variant mantle cell lymphoma with complex CCND1/IGH and MYC aberrations

The coexistence of CCND1/IGH and MYC rearrangements in mantle cell lymphoma (MCL) is a rare finding associated with a very poor prognosis. In this study, a patient with blastoid variant (MCL) is reported. The disease was clinically aggressive and refractory to chemotherapy, and the patient only survived for 1 month following diagnosis. Conventional cytogenetic study, FISH, and multicolor FISH (mFISH) demonstrated the involvement of the BCL1/CCND1 locus in a complex translocation, t(3;11)(q25;p15)t(11;14)(q13;q32). In addition, subclonal abnormalities in the 8q24 region, manifested as a t(8;14)(q24;q32)/MYC rearrangement, were identified. To the best of our knowledge, this is the first MCL case in Korea bearing these complex genomic aberrations.     

Detection of Leishmania infantum in 4 different dog samples by real-time PCR and ITS-1 nested PCR

The canine visceral leishmaniasis (CVL) diagnosis is an important step of visceral leishmaniasis control program in Brazil, which involves the elimination of infected dogs, the main animal reservoir host of the disease. The aim of the present study was to evaluate a sensitive real-time PCR method for Leishmania infantum detection in 4 different clinical samples of dogs, including the noninvasive conjunctival swab (CS) sample. The results of real-time PCR were compared with those obtained using internal transcribed spacer 1 nested PCR. Animals were divided into 2 groups based on the absence or presence of CVL clinical sings. The CS associated with real-time PCR, using primers addressed to kinetoplast DNA minicircles, was able to detect L. infantum infection in 96.7% of dogs without clinical signs and in 100% of the symptomatic animals, demonstrating the importance of these procedures for diagnosing CVL.     

实时荧光定量PCR技术的优化及其在恙虫病东方体诊断中的应用

目的建立一种优化的实时荧光定量PCR技术,并用于诊断粤北山区恙虫病东方体(Ot)基因型。方法采用优化实时荧光定量PCR技术对感染Ot的患者和鼠类的血液和组织标本检测Ot DNA载量并分析其基因型,并与未优化实时荧光定量PCR和巢式PCR的检测结果进行比较。结果采用优化实时荧光定量PCR技术检测660例发热患者,有224例检测到Ot,其中108例是发热5d内的早期患恙虫病患者,以及在55份鼠类的标本中有12份能检测到感染Ot,均为Gilliam型;未优化实时荧光定量PCR在患病7d以上才能检测到Ot。同时,在鼠类基因扩增片段还显示出与Gilliam、Karp、Kato3株国际参考株不同,经巢式PCR分型证实为Kawasaki型,与巢式PCR基因分型的结果相符。结论优化实时荧光定量PCR技术可作为早期诊断恙虫病的实验方法,用于快速分析Ot基因型,适合在基层医院推广应用。     

Sensitivity and specificity of nested and real-time PCR for the detection of Pneumocystis jiroveci in clinical specimens

A polymerase chain reaction (PCR)-based test for Pneumocystis jiroveci (formerly Pneumocystis carinii f. sp. hominis) might be an alternative to histologic diagnoses of P. jiroveci pneumonia (PCP). However, previously developed nested PCR methods tend to have low specificities (high false-positive rates). In this study, nested and quantitative real-time PCR methods for the amplification of the P. jiroveci DHPS (dihydropteroate synthase) gene were evaluated in a variety of stored clinical samples from Spain, South Africa, and Brazil. The sensitivities of both assays were high, ranging from 62.5% to 100% depending on the type of specimen. In a subset of 71 microscopically confirmed PCP cases and 70 negative cases, the sensitivities and specificities were 94% and 81% for nested PCR and 94% and 96% for real-time PCR, respectively. Real-time PCR has a statistically significantly better specificity than nested PCR (P = .015) and is likely to generate fewer false positives.     

Cotargeting of BTK and MALT1 overcomes resistance to BTK inhibitors in mantle cell lymphoma

Bruton’s tyrosine kinase (BTK) is a proven target in mantle cell lymphoma (MCL), an aggressive subtype of non-Hodgkin lymphoma. However, resistance to BTK inhibitors is a major clinical challenge. We here report that MALT1 is one of the top overexpressed genes in ibrutinib-resistant MCL cells, while expression of CARD11, which is upstream of MALT1, is decreased. MALT1 genetic knockout or inhibition produced dramatic defects in MCL cell growth regardless of ibrutinib sensitivity. Conversely, CARD11-knockout cells showed antitumor effects only in ibrutinib-sensitive cells, suggesting that MALT1 overexpression could drive ibrutinib resistance via bypassing BTK/CARD11 signaling. Additionally, BTK knockdown and MALT1 knockout markedly impaired MCL tumor migration and dissemination, and MALT1 pharmacological inhibition decreased MCL cell viability, adhesion, and migration by suppressing NF-κB, PI3K/AKT/mTOR, and integrin signaling. Importantly, cotargeting MALT1 with safimaltib and BTK with pirtobrutinib induced potent anti-MCL activity in ibrutinib-resistant MCL cell lines and patient-derived xenografts. Therefore, we conclude that MALT1 overexpression associates with resistance to BTK inhibitors in MCL, targeting abnormal MALT1 activity could be a promising therapeutic strategy to overcome BTK inhibitor resistance, and cotargeting of MALT1 and BTK should improve MCL treatment efficacy and durability as well as patient outcomes.     

A one-step real-time PCR assay for rapid prenatal diagnosis of sickle cell disease and detection of maternal contamination.

INTRODUCTION: Mutations at the codon 6 of the beta-globin gene (hemoglobin [Hb] S and HbC) can be routinely identified by various methods and prenatal diagnosis has been available to affected families for several years. However, the presence of maternal cells in fetal samples constitutes a serious potential source of prenatal misdiagnosis and most methods currently used to detect maternal contamination are based on the analysis of highly polymorphic loci. In addition, these methods are labor intensive and time consuming and risk carry-over contamination. METHOD: We describe here a one-step method for mutation detection that uses fluorescent hybridization probes with melting curve analysis for both simultaneously prenatal diagnosis of sickle cell disease and potential maternal contamination. RESULTS: Retrospective and prospective prenatal diagnosis studies (conducted in 20 and 50 cases, respectively), using both the regular procedure and real-time PCR assay show perfect concordant results. We show in addition, that as little as 5% maternal contamination can be detected and that genotype determinations are unambiguous.     

靶向药物联合治疗复发难治套细胞淋巴瘤的方案探讨

目的探讨套细胞淋巴瘤(MCL)复发难治患者不宜化疗时的有效治疗方案。方法针对1名复发难治MCL老年患者在服用伊布替尼治疗过程中,由于合并感染及全身情况不佳而无法耐受治(化)疗的情况,采用靶向药物bcl-2抑制剂(100 mg/d)联合BTK抑制剂(伊布替尼560 mg/d)予以治疗,治疗结束后评估该治疗方案的有效性。结果患者接受BTK抑制剂伊布替尼联合靶向药物bcl-2抑制剂治疗后,病情得到控制:脱离输血依赖,肿瘤缩小,血象恢复、临床症状及影像学达到部分缓解。结论靶向药物bcl-2抑制剂联合BTK抑制剂治疗方案对于无法接受化疗的复发难治MCL患者,是1种安全有效,耐受良好的治疗选择。     

Development and validation of a quantitative real-time PCR assay for the early diagnosis of coccidioidomycosis

A new real-time polymerase chain reaction (RT-PCR) assay based on a Coccidioides genus–specific molecular beacon probe was developed for the detection of coccidioidomycosis and validated with tissues from animal models and clinical samples. The assay showed high analytic reproducibility (r² > 0.99) and specificity for cultured strains (100%); the lower limit of detection was 1 fg of genomic DNA/μL of reaction. Fungal burdens in the organs of mice infected with Coccidioides posadasii strain Silveira were more accurately quantified by RT-PCR compared to colony-forming unit for all tissues. The RT-PCR assay was positive for 97.7% of spleen and 100% of liver or lung. Progression of infection in all organs was similar by both methods (P > 0.05). The sensitivity of the assay also was 100% for paraffin-embedded samples and samples from patients with positive cultures. Our RT-PCR assay is effective for the diagnosis and monitoring of Coccidioides infection, and its use also avoids the biohazard and time delay of identifying cultures in the clinical setting.     

Rapid real-time fluorescent PCR gene dosage test for the diagnosis of DNA duplications and deletions

BACKGROUND: Current methods to determine gene dosage are time-consuming and labor-intensive. We describe a new and rapid method to assess gene copy number for identification of DNA duplications or deletions occurring in Charcot-Marie-Tooth disease type 1A (CMT1A) and hereditary neuropathy with liability to pressure palsies (HNPP), respectively. METHODS: We studied 16 patients with HNPP, 4 with CMT1A, and 49 control subjects. We used real-time PCR on the LightCycler system with use of a single capillary tube and no post-PCR handling. A polymorphic fragment of the PMP22 gene was amplified to determine gene dosage for heterozygous samples. The presence of two alleles was used to indicate that no deletion was present in HNPP samples. The ratio obtained between the areas under each allele melting curve of heterozygous CMT1A samples was used to determine whether the sequence was duplicated or normal. Homozygous samples required a competitive gene dosage test, where the ratio between the areas under the melting curves of the target DNA of samples and of the competitor molecule was used to determine whether the target sequence was duplicated, deleted, or normal. Samples from HNPP, CMT1A, and controls were analyzed. RESULTS: Area ratios were approximately 0.6, 1.0, and 2.0 for HNPP, control, and CMT1A samples, respectively. The results agreed with those obtained by Southern blotting and microsatellite analysis in the same samples. CONCLUSIONS: Direct and competitive real-time fluorescent PCR can differentiate one, two, or three copies of the target DNA. The method described is sensitive and accurate for detection of CMT1A duplications and HNPP deletions and is faster and easier than current methods.     

半巢式聚合酶链反应方法检测弥漫性大B细胞淋巴瘤bcl-2/IgH基因重排

目的寻找一种敏感、特异的方法检测弥漫性大B细胞淋巴瘤（DLBCL）bcl-2／IgH基因重排，并通过测定产物的序列，以了解所建方法的可靠性、方法运用专业引物设计软件设计bcl-2／IgH基因重排半巢式PCR引物，对52例经临床病理确诊的DLBCL石蜡包埋组织及10例慢性扁桃体炎患者的新鲜扁桃体组织通过半巢式递降温度梯度PCR（touch down PCR）扩增，检测bcl-2／IgH基因重排，并对其产物进行克隆和序列分析。结果 通过一步法检测到bcl-2／IgH基因重排8例，其中DLBCL6例，新鲜扁桃体组织2例；进行第2次半巢式PCR时仅在DLBCL中发现5例阳性，新鲜扁桃体组织均阴性。将阳性产物在网上序列分析显示：一步法检测到的8例中有3例为假阳性，而半巢式PCR扩增出的5例均为bcl-2／IgH基因重排片段。3例假阳性的片段分别与人类第19号染色体BAC331191，LLNLR-245D11基因片段及1号染色体RP11-498P10基因片段同源。结论常用的检测bcl-2／IgH基因重排引物扩增结果存在一定假阳性，其机制可能是因为人类基因组中存在与常用引物同源性较高的序列。为研究设计的引物与传统的引物结合，进行半巢式PCR可以排除这种假阳性扩增，提高诊断的准确性。     

PCR for the diagnosis of toxoplasmosis after hematopoietic stem cell transplantation

Toxoplasma gondii is a ubiquitous pathogen that causes significant morbidity and mortality in immunocompromised patients. Although relatively uncommon, toxoplasmosis is increasingly recognized as a severe complication of hematopoietic stem cell transplantation. Timely and accurate diagnosis of this treatable infection is critical. PCR-based testing has become the preferred method for diagnosis, occasionally replacing tissue biopsy. This article reviews the clinical, diagnostic and therapeutic aspects of toxoplasmosis in the setting of hematopoietic stem cell transplantation and the current and future role of PCR-based testing for early detection and diagnosis.     

实时荧光PCR检测宫颈组织TSLC1基因表达

目的建立检测肺癌肿瘤抑制因子1(TSLC1)基因mRNA表达的实时荧光聚合酶链反应(PCR)方法。方法设计特异性引物和TaqM an探针,以3-磷酸甘油醛脱氢酶(GAPDH)基因作为对照,建立检测TSLC1基因表达的实时荧光PCR方法,并采用细胞株和宫颈组织样本进行验证。结果该方法检测TSLC1基因mRNA的检测下限为每反应10个细胞或2拷贝cDNA,总不精密度为3.1%。TSLC1基因mRNA在子宫肌瘤、低度鳞状上皮内病变(LSIL)、高度鳞状上皮内病变(HSIL)与宫颈癌患者宫颈组织中的表达率分别为100%、75%、55%和24%。宫颈癌细胞株中未检出TSLC1基因mRNA表达。所有样本中均有GAPDH基因mRNA表达。结论该实时荧光PCR方法能够有效检测TSLC1基因mRNA表达,是进一步研究TSLC1基因在宫颈癌发生中的作用及宫颈癌早期诊断的重要工具。