Topology,structures, and energy landscapes of human chromosomes

Chromosome conformation capture experiments provide a rich set of data concerning the spatial organization of the genome. We use these data along with a maximum entropy approach to derive a least-biased effective energy landscape for the chromosome. Simulations of the ensemble of chromosome conformations based on the resulting information theoretic landscape not only accurately reproduce experimental contact probabilities, but also provide a picture of chromosome dynamics and topology. The topology of the simulated chromosomes is probed by computing the distribution of their knot invariants. The simulated chromosome structures are largely free of knots. Topologically associating domains are shown to be crucial for establishing these knotless structures. The simulated chromosome conformations exhibit a tendency to form fibril-like structures like those observed via light microscopy. The topologically associating domains of the interphase chromosome exhibit multistability with varying liquid crystalline ordering that may allow discrete unfolding events and the landscape is locally funneled toward “ideal” chromosome structures that represent hierarchical fibrils of fibrils.The genome’s 3D organization is thought to play a crucial role in many biological processes, including gene regulation, DNA replication, and cell differentiation (1). A theoretical framework for picturing the structure and dynamics of chromosomes thus promises significantly to advance our understanding of cell biology. It is a challenge to develop from first principles an energy landscape theory for chromosomes analogous to that for proteins, which has proved rather successful in providing quantitative insights into protein folding thermodynamics, kinetics, and evolution as well as providing protein structure prediction schemes (2–4). The difficulty arises from several factors, the first being the complexity of the team of molecular players that contribute to chromosome organization. Although one chromosome is made of a single DNA molecule, an array of different proteins is involved in its 3D organization (5); of these only a few have been fully characterized. Even at the shortest length scales, the double-stranded DNA is wrapped by core histone proteins into nucleosomes, which can go on to form higher-order structures such as the proposed 30-nm fibers upon stabilization by histone proteins H1 (6). Long-range contacts between genomic loci can also form in the presence of CCCTC-binding factor (CTCF) (7). The second difficulty is that the chromosome is large in molecular terms. It is so large, in fact, that its dynamics can be so slow that the chromosome may be a far from equilibrium structure, unlike most folded proteins (8, 9). To complicate matters further, chromosome organization has been reported to be variable and to depend both on cell type and phase in the cell cycle (10, 11). There are apparently thus many global attractors on any realistic chromosome landscape. An energy landscape theory built at atomistic resolution using physicochemical interactions of known components for chromosome organization seems thus currently out of reach. Here we explore a way to skirt some of the difficulties by using a maximum entropy approach to derive an effective equivalent equilibrium energy landscape for chromosomes by using physical contact frequencies measured in chromosome conformation capture experiments.     

Monosomy of chromosome 17 in breast cancer during interpretation of HER2 gene amplification

Monosomy of chromosome 17 may affect the assessment of HER2 amplification. Notably, the prevalence ranges from 1% up to 49% due to lack of consensus in recognition. We sought to investigate the impact of monosomy of chromosome 17 to interpretation of HER2 gene status. 201 breast carcinoma were reviewed for HER2 gene amplification and chromosome 17 status. FISH analysis was performed by using double probes (LSI/CEP). Absolute gene copy number was also scored per each probe. HER2 FISH test was repeated on serial tissue sections, ranging in thickness from 3 to 20 µm. Ratio was scored and subsequently corrected by monosomy after gold control test using the aCGH method to overcome false interpretation due to artefactual nuclear truncation. HER2 immunotests was performed on all cases. 26/201 cases were amplified (13%). Single signals per CEP17 were revealed in 7/201 (3.5%) cases. Five out of 7 cases appeared monosomic with aCGH (overall, 5/201, 2.5%) and evidenced single signals in >60% of nuclei after second-look on FISH when matching both techniques. Among 5, one case showed amplification with a pattern 7/1 (HER2/CEP17>2) of copies (3+ at immunotest); three cases revealed single signals per both probes (LSI/CEP=1) and one case revealed a 3:1 ratio; all last 4 cases showed 0/1+ immunoscore. We concluded that: 1) monosomy of chromosome 17 may be observed in 2.5% of breast carcinoma; 2) monosomy of chromosome 17 due to biological reasons rather than nuclear truncation was observed when using the cut-off of 60% of nuclei harboring single signals; 3) the skewing of the ratio due to single centromeric 17 probe may lead to false positive evaluation; 4) breast carcinomas showing a 3:1 ratio (HER2/CEP17) usually show negative 0/1+ immunoscore and <6 gene copy number at FISH.     

精索静脉曲张严重少精子症患者Y染色体微缺失分析

目的:探讨精索静脉曲张和Y染色体微缺失对生精障碍的影响。方法:对随机挑选的100例左侧精索静脉曲张严重少精子症患者(精子浓度<5×106/ml,组1),100例左侧精索静脉曲张轻度少精子症患者[精子浓度(10～20)×106/ml,组2],100例特发性严重少精子症患者(组3),100例特发性轻度少精子症患者(组4)和30例正常生育男性对照组(组5)采用聚合酶链反应(PCR)技术进行Y染色体微缺失检测,选取无精子因子(AZF)a、b和c区9个序列标签位点(STS)。结果:组1中有19例患者存在AZF微缺失(19%);组3中有11例患者存在AZF微缺失(11%),其余各组均未发现AZF微缺失;组1比组3有较高的缺失率。结论:在治疗精索静脉曲张严重生精障碍患者前应先进行Y染色体微缺失检测,避免不必要的治疗。     

外源性PTEN对胰腺癌细胞ASPC-1增殖、侵袭及转移的影响

目的 研究第10染色体同源丢失性磷酸酶-张力蛋白基因(PTEN)对胰腺癌细胞系ASPC-1细胞周期、细胞增殖、血管内皮生长因子(VEGF)和表皮生长因子受体(EGFR)蛋白表达、裸鼠成瘤及转移能力的影响.方法 将含PTEN基因的质粒pE-PTEN转染ASPC-1细胞,以空质粒pE转染为对照,分别获得ASPC-1-pE-PTEN (A-pE-P)细胞及ASPC-1-pE (A-pE)细胞.应用RT-PCR检测细胞PTEN mRNA表达;免疫细胞化学法检测PTEN、VEGF、EGFR蛋白表达;克隆形成实验观察克隆形成数;Transwell小室观察细胞侵袭能力;裸鼠皮下注射癌细胞法观察成瘤情况.结果 与ASPC-1细胞比较,A-pE-P细胞的PTEN mRNA表达增加179.3％,PTEN蛋白表达明显增加;VEGF蛋白表达明显减少;EGFR蛋白表达无明显变化;G2/M期细胞数明显增加[(31.5±1.76)％比(26.81±1.03)％,P＜0.05];克隆形成数降低[(24.0±3.9)比(33.3 ±3.4),F=4.283,P＜0.01],克隆形成率降低28％;穿膜细胞数明显减少[每高倍视野(46.3±6.6)比(63.8±7.5)个,F=2.476,P＜0.05];种植瘤体积明显缩小[(142.4±30.9)比(202.7±43.6)mm3,t=4.834,P＜0.01],抑瘤率达42.4％;远处转移灶明显减少[(2.0±0.7)比(5.0±1.3)个,t =0.451,P＜0.01].结论 PTEN基因转染后ASPC-1细胞VEGF表达减少,细胞生长被阻滞在G2/M期,增殖及转移被抑制.     

Prenatal diagnosis and molecular cytogenetic characterization of a small supernumerary marker chromosome derived from chromosome 15 in a pregnancy associated with recurrent Down syndrome

ObjectiveWe present prenatal diagnosis and molecular cytogenetic characterization of a small supernumerary marker chromosome (sSMC) derived from chromosome 15 in a pregnancy associated with recurrent Down syndrome.Case reportA 33-year-old, gravida 4, para 2, woman underwent amniocentesis at 16 weeks of gestation because of a previous child with Down syndrome and a karyotype of 46,XY,der(14;21)(q10; q10),+21. In this pregnancy, amniocentesis revealed a karyotype of 47,XX,+21[12]/48,XX,+21,+mar[3]. The parental karyotypes were normal. The pregnancy was terminated, and a malformed fetus was delivered with characteristic craniofacial appearance of Down syndrome and hypoplastic middle phalanx of the fifth fingers. The placenta had a karyotype of 47,XX,+21[37]/48,XX,+21,+mar[3]. The umbilical cord had a karyotype of 47,XX,+21[38]/48,XX,+21,+mar[2]. In addition to trisomy 21, array comparative genomic hybridization (aCGH) on the DNA extracted from umbilical cord revealed 40～50% mosaicism for a 2.604-Mb duplication of 15q25.2–q25.3, or arr 15q25.2q25.3 (83,229,665–85,834,131) × 2.4 [GRCh37 (hg19)] encompassing 19 Online Mendelian Inheritance in Man (OMIM) genes. Quantitative fluorescent polymerase chain reaction (QF-PCR) using the DNAs extracted from cultured amniocytes and parental bloods revealed maternal origin of the sSMC(15) and the extra chromosome 21.Conclusion: aCGH is useful for identification of the nature of sSMC, and QF-PCR is useful for determination of the parental origin of the aberrant chromosomes.     

FHACT: the FISH-based HPV-associated cancer test that detects nonrandom gain at four genomic loci as biomarkers of disease progression

Despite implementation of screening programs for human papillomavirus (HPV)-associated cancers, in particular cervical, scientific studies continue to uncover viral and host biomarkers that could serve to further optimize the detection of individuals with underlying or at risk for developing precancer or cancer. Nonrandom host somatic chromosomal alterations are frequently shared across HPV-associated cancers, but with varying frequencies, potentially with functional roles. At least for 3q26 gain, there is firm preliminary evidence to support that this genomic alteration can serve as a biomarker of disease progression of cervical cancer. In the current review, the FISH-based HPV-associated cancer test is described that enables detection of genomic imbalance at four loci (3q26, 5p15, 20q13, centromere 7) in a single hybridization on a cell-by-cell basis in cytology specimens. When implemented as a secondary screening assay, the FISH-based HPV-associated cancer test could assist in the detection of clinically relevant HPV-associated disease and help guide patient management decisions.     

淀粉样变性分型的研究进展简

淀粉样变性是由蛋白结构异常造成的一组疾病.淀粉样物质在不同脏器沉积进而影响脏器功能.根据致病蛋白种类可将淀粉样变性分为多种亚型,每种亚型的临床表现、治疗方案和预后都不尽相同.传统的免疫荧光和免疫组织化学分型方法存在抗体种类有限、背景染色干扰等问题,具有一定的误诊率.最近,以蛋白质组学为基础的激光显微切割联合质谱分析技术（LMD/MS）被成功应用于淀粉样变性分型.本文就淀粉样变性分型方法的最新研究进展进行综述.     

耐甲氧西林金黄色葡萄球菌SCCmec基因分型及耐药谱分析

目的 研究耐甲氧西林金黄色葡萄球菌(MRSA) SCCmec基因分型情况,并对其耐药谱进行分析.方法 收集从临床标本分离出的MRSA 91株,应用多重PCR法对MRSA进行SCCmec基因分型,采用MicroScanWalk-Away-40全自动微生物鉴定药敏分析仪进行细菌的鉴定及药敏试验,部分药敏试验采用K-B法.结果 91株MRSA中SCCmecⅡ型72株,占79.1％,SCCmecⅢ型16株,占17.6％,未分型3株,占3.3％,未见SCCmec Ⅰ型及SCCmecⅣ型;ICU中MRSA所占比例最多,为SCCmecⅡ型51.4％、SCCmecⅢ型37.5％,2种SCCmec基因型的MRSA对万古霉素、磺胺甲噁唑/甲氧苄啶、利奈唑胺、喹奴普汀/达福普汀的耐药率为0,对氯霉素的耐药率分别为11.1％和12.5％,对利福平的耐药率分别为8.3％和37.5％,其余均呈高水平耐药,2种SCCmec基因型的MRSA均表现为多药耐药.结论 临床分离的MRSA以SCCmecⅡ型为主,且对抗菌药物呈多药耐药.     

Successive transformation of chronic myelomonocytic leukaemia into acute myeloblastic then lymphoblastic leukaemia, both with minor-bcr rearrangement

We report a case of chronic myelomonocytic leukaemia (CMML), which transformed first into acute myeloblastic leukaemia (AML) and then into acute lymphoblastic leukaemia (ALL). In the AML and ALL phases, chromosome analysis showed a classic Philadelphia chromosome (Ph) t(9;22)(q34;q11). Molecular studies showed breakpoint cluster region rearrangement between exons e1 and a2 compatible with a p190^bcr/abl breakpoint as observed in Ph-positive lymphoblastic acute leukaemia. The minor (m-bcr) rearrangement was also detected during complete remission.
This observation supports a multistep pathogenesis of leukaemias, and that the p190^bcr/abl breakpoint may influence the course of the disease.     

元江县微小按蚊卵巢营养细胞多线性染色体观察

云南省元江县采集的微小按蚊分别单只雌蚊驯养，解剖分离卵巢营养细胞，染色后光镜观察、记录染色体图谱。经观察365个卵巢多线染色体标本。其染色体由5臂共3条染色体组成：Ⅰ号染色体为具端着丝点的性染色体（X染色体），仅见一臂；Ⅱ号为1对具亚中着丝点的常染色体，分右臂（2R）和左臂（2L）；Ⅲ号为1对具中着丝点的常染色体，含右臂（3R）和左臂（3L）。与广西微小按蚊卵巢营养细胞多线染色体比较，发现有12处差异。