A comparison of DNA sequencing and gene expression profiling to assist tissue of origin diagnosis in cancer of unknown primary

Cancer of unknown primary (CUP) is a syndrome defined by clinical absence of a primary cancer after standardised investigations. Gene expression profiling (GEP) and DNA sequencing have been used to predict primary tissue of origin (TOO) in CUP and find molecularly guided treatments; however, a detailed comparison of the diagnostic yield from these two tests has not been described. Here, we compared the diagnostic utility of RNA and DNA tests in 215 CUP patients (82% received both tests) in a prospective Australian study. Based on retrospective assessment of clinicopathological data, 77% (166/215) of CUPs had insufficient evidence to support TOO diagnosis (clinicopathology unresolved). The remainder had either a latent primary diagnosis (10%) or clinicopathological evidence to support a likely TOO diagnosis (13%) (clinicopathology resolved). We applied a microarray (CUPGuide) or custom NanoString 18-class GEP test to 191 CUPs with an accuracy of 91.5% in known metastatic cancers for high–medium confidence predictions. Classification performance was similar in clinicopathology-resolved CUPs – 80% had high–medium predictions and 94% were concordant with pathology. Notably, only 56% of the clinicopathology-unresolved CUPs had high–medium confidence GEP predictions. Diagnostic DNA features were interrogated in 201 CUP tumours guided by the cancer type specificity of mutations observed across 22 cancer types from the AACR Project GENIE database (77,058 tumours) as well as mutational signatures (e.g. smoking). Among the clinicopathology-unresolved CUPs, mutations and mutational signatures provided additional diagnostic evidence in 31% of cases. GEP classification was useful in only 13% of cases and oncoviral detection in 4%. Among CUPs where genomics informed TOO, lung and biliary cancers were the most frequently identified types, while kidney tumours were another identifiable subset. In conclusion, DNA and RNA profiling supported an unconfirmed TOO diagnosis in one-third of CUPs otherwise unresolved by clinicopathology assessment alone. DNA mutation profiling was the more diagnostically informative assay. © 2022 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.     

Meta-analysis uncovers genome-wide significant variants for rapid kidney function decline

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大鼠小肠循环液中酚红的双波长分光光度法的测定

目的：建立大鼠小肠循环液中酚红的测定方法。方法：采用双波长分光光度法,以0.1mol/L NaOH为溶剂,558nm为测定波长,570nm为参比波长。结果：线性范围为1-8μg/ml,回收率为99．88％－99．99％(n=5),日内RSD为0．51－1．27％（n=4),日间RSD为0．58－2．29％（n=4)。结论：该法可用于大鼠小肠液中酚红的测定。     

大鼠脂肪和骨髓来源间充质干细胞基本生物学特征的比较

目的:分离大鼠脂肪和骨髓来源的间充质干细胞,比较两种间充质干细胞的生物学特征。方法:实验于2003-09/2006-11在广州市第一人民医院、湘雅医院中心实验室完成。取SD大鼠的股骨、胫骨、肱骨及腹股沟处脂肪垫进行骨髓间充质干细胞与脂肪间充质干细胞的分离。将骨髓间充质干细胞和脂肪间充质干细胞在含10%血清,1%双抗的低糖DMEM培养基,37℃、体积分数为0.05的CO2条件下进行培养。在细胞达到80%～90%融合时,使用0.25%胰酶消化传代。传代至第3代使用倒置显微镜观察骨髓和脂肪两种不同来源细胞的传代后的形态、贴壁、生长增殖、集落等情况。取消化传3代的两种细胞分别制成单细胞悬液进行细胞贴壁率的检测,贴壁率=贴壁细胞总数/接种细胞总数×100%。取第2代和第5代骨髓间充质干细胞和脂肪间充质干细胞以1×107L-1密度培养。每天同一时间,随机抽取5孔细胞,加入5%噻唑兰20μL/孔,培养4～6h,吸出孔内液体,每孔加150μL二甲基亚砜震荡10min,酶联免疫测定仪测定波长490nm处的吸光度,取5孔吸光度的均值,以时间为横坐标,吸光度值为纵坐标,绘制生长曲线。采用流式细胞仪检测细胞表面CD29、CD34、CD44标记,免疫化学检测细胞CD29、CD34、CD44。结果:①在单位质量骨髓和脂肪组织中获得的间充质干细胞数量相当。两种细胞形态均为条索样,呈成纤维细胞形态。②应用直线相关分析,考察骨髓贴壁率与脂肪贴壁率之间的关系,相关系数r=0.999,决定系数r2=0.997(F=5862.949,P<0.001),两贴壁率之间有直线相关关系,不同的时间点两种细胞的贴壁率相似,并且有同向变化的趋势。③脂肪间充质干细胞的增殖能力与骨髓间充质干细胞相当。④脂肪间充质干细胞和骨髓间充质干细胞表面表达CD29、CD44,不表达CD34。结论:自大鼠脂肪中可提取出与骨髓间充质干细胞生物学特征类似的脂肪间充质干细胞。     

特定培养基条件下大鼠脂肪间充质干细胞体外定向软骨细胞的分化

目的:体外诱导大鼠脂肪间充质干细胞向软骨细胞分化,并对分化细胞进行相应鉴定,观察脂肪间充质干细胞作为软骨组织工程种子细胞的可行性。方法:实验于2005-05/2006-05在湘雅医院中心实验室完成。①取大鼠腹股沟脂肪,消化分离脂肪间充质干细胞进行原代培养。②流式细胞仪检测第3代脂肪间充质干细胞表面CD29,CD34,CD44表达。③传3代细胞进行微团培养1d,换用含体积分数为0.01的新生牛血清、10μg/L的转化生长因子β1、6.25mg/L的胰岛素、6.25mg/L的转铁蛋白、1×10-7mol/L的地塞米松、50mg/L的维生素C的高糖DMEM诱导液,为特定培养条件。④在诱导后4,7,14d应用阿尔新兰染色、蕃红O/固绿染色和Ⅱ型胶原免疫细胞化学评价软骨形成情况。⑤反转录-聚合酶链反应在诱导后0和14d检测脂肪间充质干细胞前Ⅱ型胶原蛋白和聚集蛋白聚糖mRNA的表达。结果:①脂肪间充质干细胞的形态特征:原代脂肪间充质干细胞呈短梭形、梭形及多角形,3代后呈均一长梭形。②脂肪间充质干细胞的表面标志鉴定:脂肪间充质干细胞表达CD29,CD44,基本不表达CD34。③脂肪间充质干细胞诱导后的形态特征:脂肪间充质干细胞经诱导后,由长梭形转变为三角形、多角形或短梭形,逐渐聚集成结节。④脂肪间充质干细胞诱导后的细胞化学染色结果:诱导后脂肪间充质干细胞胞外基质阿尔新兰染色、蕃红O/固绿染色、和Ⅱ型胶原免疫细胞化学着色阳性。⑤反转录-聚合酶链反应检测结果:反转录-聚合酶链反应检测未诱导脂肪间充质干细胞不表达前Ⅱ型胶原蛋白和聚集蛋白聚糖mRNA基因,而诱导后的脂肪间充质干细胞表达前Ⅱ型胶原蛋白和聚集蛋白聚糖mRNA基因。结论:脂肪间充质干细胞在由转化生长因子1、胰岛素、转铁蛋白等组成的特定培养基条件诱导下可以定向软骨细胞分化。