RNA sequencing steps toward the first line

• DNA is the sequence that codes for proteins.
• Messenger RNA is transcribed from the DNA sequence of genes and translated into protein.
• It can be difficult to predict how a change in the DNA sequence will affect messenger RNA and protein quantity and quality.
• DNA translocation changes can cause the joining of sequences from two different genes or different parts of the same gene.
• DNA sequencing is often used clinically to predict how DNA changes might affect proteins.
• Alternatively, RNA sequencing can be used as a more direct measure of the effect of DNA changes on the protein products.
• This sequencing is important for identifying changes in cancer that may indicate response to targeted therapy, prognosis, or diagnosis.

     

Prediction and validation of hematopoietic stem and progenitor cell off-target editing in transplanted rhesus macaques

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Neuroblastoma: a master of disguise and a challenge to cure

Neuroblastoma is one of the commonest childhood cancers and typically affects very young children. It is characterized by a very broad spectrum of clinical presentation and outcome, driven by the biology of the tumour. This ranges from ‘low risk’ tumours, most commonly found in infants, which may spontaneously regress and have an excellent prognosis with minimal or no treatment, to ‘high risk’ disease, which carries a poor prognosis despite intensive multi-modal treatment. Although particular presentations may be associated with favourable or unfavourable outcome, the clinical features may mask the underlying biology of the tumour and a full assessment of the clinical and biological features is required to determine appropriate treatment. The International Neuroblastoma Risk Group classification, based on the age of the patient and the stage, grade and genetics of the tumour, is used to stratify treatment according to risk factors. This review provides an overview of current neuroblastoma management, focusing on how classification is applied in practice, and how this is used to determine individual patient treatment. The challenges that remain in treating patients with high-risk disease are discussed.     

染色体微阵列产前诊断8q13.3微缺失一例

目的应用染色体微阵列分析(chromosome microarray analysis,CMA)技术对1例超声结构异常胎儿进行全基因组拷贝数变异(copy number variations,CNVs)检测,探讨CMA在超声结构异常胎儿产前诊断中的意义。方法应用常规G显带染色体核型分析胎儿及其父母的染色体核型,应用CMA技术分析胎儿及其父母的CNVs。结果G显带核型分析显示胎儿核型与母亲一致,为46,XN,t(8;11)(q21.2;q13)mat,父亲核型正常;父母CMA检测结果均未见异常;胎儿的检测结果为arr[GRCh37]8q13.3(71314082-73322915)×1,提示一条8号染色体的8q13.3区域发生2.00 Mb缺失。结论超声结构异常胎儿染色体核型分析检出的平衡易位,需借助CMA等技术进一步确定是否存在微缺失微重复。     

Knockdown of PVT1 inhibits IL-1β-induced injury in chondrocytes by regulating miR-27b-3p/TRAF3 axis

Long noncoding RNA plasmacytoma variant translocation 1 (PVT1) has been identified to implicate in the progression of osteoarthritis (OA). However, the mechanism underlying PVT1 in OA development remains largely unknown. This study aimed to investigate the effect of PVT1 on interleukin-1 beta (IL-1β)-induced injury in chondrocytes and explore potential mechanism. The cartilage tissues from 25 OA patients and normal controls were collected. Human transformed chondrocytes C28/I2 were stimulated by IL-1β. The levels of PVT1, microRNA (miR)-27b-3p, and tumor necrosis factor receptor-associated factor 3 (TRAF3) were detected by quantitative real-time polymerase chain reaction or western blot. IL-1β-induced injury was investigated by cell viability, apoptosis, autophagy and inflammatory response using 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide, flow cytometry, western blot and enzyme linked immunosorbent assay, respectively. The target association between miR-27b-3p and PVT1 or TRAF3 was explored by luciferase reporter, RNA immunoprecipitation and RNA pull-down assays. We found that PVT1 expression was enhanced in OA patients and IL-1β-treated C28/I2 cells. Silence of PVT1 promoted cell viability and autophagy but suppressed apoptosis and inflammatory response in IL-1β-treated C28/I2 cells. miR-27b-3p was confirmed as a target of PVT1 and its deficiency reversed the suppressive effect of PVT1 knockdown on IL-1β-induced injury. TRAF3 was a target of miR-27b-3p and attenuated the effect of miR-27b-3p on IL-1β-induced injury in C28/I2 cells. Moreover, TRAF3 expression was positively regulated by PVT1 via sponging miR-27b-3p. Collectively, knockdown of PVT1 increased cell viability and autophagy but inhibited apoptosis and inflammatory response in chondrocytes treated by IL-1β via up-regulating miR-27b-3p and down-regulating TRAF3.     

Clinicopathologic characteristics of follicular lymphoma in hepatitis C virus-infected patients

Follicular lymphoma (FL) is the most common subtype of indolent non-Hodgkin lymphoma. It has been hypothesized that chronic hepatitis C virus (HCV) infection stimulates IGH-BCL2 clone proliferation, leading to development of FL. Furthermore, regression of FL after antiviral treatment without chemotherapy has been reported in HCV-infected patients. To clarify the relationship between HCV and FL, we compared the prevalence of IGH-BCL2 translocation and other clinicopathologic characteristics between HCV-infected and HCV-uninfected FL patients and determined the impact of HCV eradication on the oncologic outcomes of HCV-infected FL patients. The study included HCV-infected patients (cases) with FL seen at our institution during 2004-2018. Cases were matched with HCV-uninfected FL patients (controls) according to year of lymphoma diagnosis, sex, and hepatitis B serology. We studied 19 cases and 57 controls. More cases than controls had splenic involvement of FL (26% vs 5%, P = 0.02), higher histologic grade (grade 3 in 56% vs 24%, P = 0.01), absent or weak CD10 expression (42% vs 11%, P = 0.005), and absent BCL2 expression (33% vs 4%, P = 0.004). Compared to controls, cases had a lower rate of detection of IGH-BCL2 translocation (31% vs 68%, P = 0.02). Finally, cases with a sustained virologic response (virologic cure of HCV) had a better 10-year overall survival rate than did cases not treated with antivirals or controls (P = 0.001). In conclusion, HCV-infected patients with FL have unique clinicopathologic characteristics including improved overall survival with HCV eradication. The pathogenesis of FL in HCV-infected patients seems unrelated to antiapoptotic effect of IGH-BCL2 rearrangement.     

Wolf-Hirschhorn综合征4例及文献复习

目的　探讨Wolf-Hirschhorn综合征（WHS）临床特征及基因突变。方法　回顾分析2017-11-20—2018-05-26南京医科大学附属儿童医院收治的4例发育延迟及智力低下患儿的临床资料，临床拟诊为WHS。应用染色体微阵列芯片分析技术进行基因检测，并复习相关文献总结疾病特点。结果　2例男性和2例女性患儿因生后特殊面容（希腊头盔样面容）、智力低下、发育延迟、肌张力低下、癫痫，应用染色体微阵列芯片分析技术发现患儿4p16.3区域2.24～3.8 Mb的缺失，确诊WHS，给予抗癫痫及康复治疗并定期随访。结论　尽早完善染色体芯片技术检查有助于早期诊断WHS，且能判断预后。染色体微阵列芯片分析与传统细胞遗传学分析方法相比，具有高分辨和高准确度的优点，可为产前遗传学诊断提供更详细信息。     

基因组时代产前诊断面临的机遇和挑战

        自20世纪70年代开始，染色体核型分析技术作为诊断胎儿染色体异常的金标准已使用多年，但该技术存在分辨率较低（5~10Mb）、培养周期长、检测通量低及有培养失败风险等局限性。随后，靶向诊断技术（FISH、QF-PCR、MLPA）的出现，大大缩短了检测时间，与染色体核型技术联合应用，可早期诊断常见的胎儿染色体异常。此外，Sanger测序作为基因变异检测的金标准，可用于明确致病的单基因疾病的产前诊断。然而，以上技术均无法实现在全基因组范围内进行快速、高分辨率地诊断胎儿致病性变异。 浏览更多请关注微信公众号及当期杂志。     

Frequency and clinical manifestation of prenatal cytogenetic diagnosis of chromosomal polymorphisms in Northeast China

ObjectiveTo retrospectively analyze the incidence of chromosomal polymorphisms in prenatal cytogenetic diagnostic cases and the effect of the clinical manifestation of these fetuses.Materials and methods490 fetuses with chromosomal polymorphisms among 9996 pregnant women who underwent prenatal cytogenetic diagnosis were included in this study and were set as group 1. Other 500 pregnant women, whose fetuses were with normal karyotypes, were randomly selected from the remaining pregnant women and set as group 2. Clinical information and outcomes and maternal serum screening results of group 1 were compared with group 2.ResultsThe frequency of fetal chromosomal polymorphism was 4.90% (490/9996). The most common variants observed were 1/9/16 qh± (2.27%, 227/9996), followed by inv(9) (0.90%, 90/9996). 94.62% (264/279) of fetal chromosomal variants were inherited from parents. No statistical difference was found in clinical information and outcomes and maternal serum screening results between group 1 and group 2.ConclusionThe fetus with chromosomal polymorphism has no impact on serum markers of second trimester screening and does not play an important role for the clinical outcome of the current pregnancy either, whether it is inherited from the parents or a de novo mutation.