Cryo-EM structure of DNA-bound Smc5/6 reveals DNA clamping enabled by multi-subunit conformational changes

Structural maintenance of chromosomes (SMC) complexes are essential for chromatin organization and functions throughout the cell cycle. The cohesin and condensin SMCs fold and tether DNA, while Smc5/6 directly promotes DNA replication and repair. The functions of SMCs rely on their abilities to engage DNA, but how Smc5/6 binds and translocates on DNA remains largely unknown. Here, we present a 3.8 Å cryogenic electron microscopy (cryo-EM) structure of DNA-bound Saccharomyces cerevisiae Smc5/6 complex containing five of its core subunits, including Smc5, Smc6, and the Nse1-3-4 subcomplex. Intricate interactions among these subunits support the formation of a clamp that encircles the DNA double helix. The positively charged inner surface of the clamp contacts DNA in a nonsequence-specific manner involving numerous DNA binding residues from four subunits. The DNA duplex is held up by Smc5 and 6 head regions and positioned between their coiled-coil arm regions, reflecting an engaged-head and open-arm configuration. The Nse3 subunit secures the DNA from above, while the hook-shaped Nse4 kleisin forms a scaffold connecting DNA and all other subunits. The Smc5/6 DNA clamp shares similarities with DNA-clamps formed by other SMCs but also exhibits differences that reflect its unique functions. Mapping cross-linking mass spectrometry data derived from DNA-free Smc5/6 to the DNA-bound Smc5/6 structure identifies multi-subunit conformational changes that enable DNA capture. Finally, mutational data from cells reveal distinct DNA binding contributions from each subunit to Smc5/6 chromatin association and cell fitness. In summary, our integrative study illuminates how a unique SMC complex engages DNA in supporting genome regulation.

Structural maintenance of chromosomes (SMC) complexes are essential genome regulators in both prokaryotes and eukaryotes. In eukaryotes, the cohesin and condensin SMC complexes organize DNA, while the Smc5/6 complex (referred to as Smc5/6) directly regulates DNA replication and repair (1). At the structural level, SMC complexes share similarities while possessing unique attributes (1). Each complex contains a pair of SMC subunits and a set of non-SMC subunits. The SMC subunits define the tripartite filamentous architecture of the complex: their approximal 50-nm long coiled coil arm region connects their dimerized hinge and adenosine triphosphatase (ATPase) head regions (1). A non-SMC kleisin subunit uses its N- and C-terminal domains to link the head of one SMC to the head-proximal arm region (neck) of another SMC, forming a trimeric SMC-kleisin structure. In cohesin and condensin, two large U-shaped HEAT (Huntington, elongation factor 3, PR65/A, TOR) repeat HAWK (HEAT proteins associated with kleisins) subunits attach to the middle region of the kleisin. By contrast, the Smc5/6 kleisin (Nse4) binds to smaller WH (winged helix)-containing KITE (kleisin interacting tandem WH elements) subunits (Nse1 and Nse3) (2).SMC-mediated functions depend on interactions with DNA. Recent cryogenic electron microscopy (cryo-EM) structures of DNA-bound cohesin and condensin revealed that their HAWK subunits and the SMC head-neck regions form a clamp to enclose a single DNA double helix (3–7). DNA clamping can be critical for cohesin and condensin to extrude DNA loops for chromatin folding (5, 7–9). DNA loop extrusion additionally requires arm bending at a region called the elbow, which is found in both cohesin and condensin (5, 7–9). By contrast, a lack of arm bending in Smc5/6 was suggested by negative stain EM and cross-linking mass spectrometry (CLMS) data (10–14). Since Smc5/6 does not contain HAWK proteins nor shows arm-bending, it has remained unclear how Smc5/6 engages DNA to accomplish its multiple functions.Here we address the molecular mechanisms by which this unique SMC complex binds DNA using an integrative approach, coupling a cryo-EM-based structural characterization with CLMS analyses and functional investigation. Our atomic structure of a DNA-bound Saccharomyces cerevisiae Smc5/6 complex reveals that the head-neck Smc5-6 regions and the Nse1-3-4 subcomplex together form a clamp entrapping the DNA helix. The structure further reveals protein subunit folds and association, as well as how the subunits collaborate to entrap DNA. Comparison of CLMS analyses of DNA-free Smc5/6 with the structure of the DNA-bound Smc5/6 unveils large scale, multi-subunit conformational changes that enable Smc5/6 to encircle DNA. Finally, our mutational data suggest distinct contributions from each of the DNA binding regions to Smc5/6 chromatin association and cellular fitness. Comparison of our findings with those of other SMCs reveals that diverse SMC complexes use a similar DNA clamping strategy despite structural differences, and that Smc5/6 possesses unique features distinct from cohesin, condensin, and prokaryotic SMCs. Our work lays the foundation for an in-depth understanding of how Smc5/6 fulfills unique roles in genome protection.     

The impact of geographic unit of analysis on socioeconomic inequalities in cancer survival and distant summary stage – a population‐based study

Objective: When using area‐level disadvantage measures, size of geographic unit can have major effects on recorded socioeconomic cancer disparities. This study examined the extent of changes in recorded socioeconomic inequalities in cancer survival and distant stage when the measure of socioeconomic disadvantage was based on smaller Census Collection Districts (CDs) instead of Statistical Local Areas (SLAs). Methods: Population‐based New South Wales Cancer Registry data were used to identify cases diagnosed with primary invasive cancer in 2000–2008 (n=264,236). Logistic regression and competing risk regression modelling were performed to examine socioeconomic differences in odds of distant stage and hazard of cancer death for all sites combined and separately for breast, prostate, colorectal and lung cancers. Results: For all sites collectively, associations between socioeconomic disadvantage and cancer survival and distant stage were stronger when the CD‐based socioeconomic disadvantage measure was used compared with the SLA‐based measure. The CD‐based measure showed a more consistent socioeconomic gradient with a linear upward trend of risk of cancer death/distant stage with increasing socioeconomic disadvantage. Site‐specific analyses provided similar findings for the risk of death but less consistent results for the likelihood of distant stage. Conclusions: The use of socioeconomic disadvantage measure based on the smallest available spatial unit should be encouraged in the future. Implications for public health: Disadvantage measures based on small spatial units can more accurately identify socioeconomic cancer disparities to inform priority settings in service planning.     

在猪肝-肠联合移植中瓜氨酸是移植肠急性排斥反应的血清学指标

目的:研究在猪肝-小肠联合移植实验中,移植肠的急性排斥反应对血清瓜氨酸浓度的影响.方法:共进行肝-小肠联合移植15次,术后给予免疫抑制剂治疗,存活时间超过7天的受者猪在研究范围之内.术后按计划对肝-小肠联合移植实验后,测定受者猪的血清瓜氨酸浓度.在取血的同时采集移植肠黏膜作移植肠的急性排斥反应的病理评分,并作瓜氨酸浓度-急性排斥反应病理评分的线性回归分析.结果:15头猪中有11头存活时间超过7天.在受者猪肾功能正常的情况下,随着排斥反应逐级增强,血清瓜氨酸水平逐渐减低,而且具有显著性差异(P＜0.05).瓜氨酸浓度-急性排斥反应病理评分的线性回归分析结果为:瓜氨酸浓度=36.02-8.26×病理评分,相关系数为r=0.91.结论:在猪肝-小肠联合移植中瓜氨酸是一种移植肠急性排斥反应的血清学指标.     

从污染的淤积海水及贝类中检出甲型肝炎病毒RNA

目的 了解辽宁省近海海水及贝类甲型肝炎病毒的污染状况。方法 应用聚合酶链反应技术检测辽宁省近海海域淤积海水样品及贝类中的甲型肝炎病毒（HAV）RNA。结果 月牙湾淤积海水样检出HAVRAN,25份贝类样品中检出HAVRNA阳性5份。结论 辽宁省近海海水及贝类已受到HAV的污染,应加强卫生监督。     

Impact of National Centralized Drug Procurement Policy on Antiviral Utilization and Expenditure for Hepatitis B in China

Background and AimsThe National Centralized Drug Procurement (NCDP) policy was launched in mainland China in April 2019, with entecavir (ETV) and tenofovir disoproxil fumarate (TDF) being included in the procurement list. We conducted the current study to investigate the impact of the NCDP policy on the utilization and expenditures of antiviral therapy for chronic hepatitis B (CHB) in China.MethodsProcurement records, including monthly purchase volume, expenditure, and price of nucleos(t)ide analogs (NAs), were derived from the National Healthcare Security Administration from April 2018 to March 2021. The changes in volumes and expenditures of the first-line NAs and bid-winning products were calculated. The effects of price, volume, and structure related to drug expenditure were calculated by the Addis and Magrini (AM) Index System Analysis.ResultsThe purchase volume of NAs significantly increased from 134.3 to 318.3 million DDDs, whereas the expenditure sharply decreased from 1,623.41 to 490.43 million renminbi (RMB) or 241.94 to 73.09 million US dollars (USD). The proportions of first-line NAs rose from 72.51% (ETV: 69.00%, TDF: 3.51%) to 94.97% (ETV: 77.42%, TDF: 17.55%). AM analysis showed that the NCDP policy decreased the expenditure of all NAs (S=0.91) but increased that of the first-line NAs in the bid-winning list (S=1.13). Assuming the population size of CHB patients remains stable and a compliance rate of ≥75%, the proportion of CHB patients receiving first-line antiviral therapy would increase from 6.36–8.48% to 11.56–15.41%.ConclusionsThe implementation of the NCDP policy significantly increased the utilization of first-line NAs for CHB patients at a lower expenditure. The findings provided evidence for optimizing antiviral therapy strategy and allocating medical resources in China.     

儿童多发伤的ICU救治138例

目的总结儿童多发性创伤ICU的救治经验。方法对2005—2010年收治的138例多发伤患儿的伤情、诊断、治疗结果进行回顾性分析,总结多发伤的救治经验。结果本组病例138例患儿115例撤离呼吸机,休克纠正、循环稳定、凝血功能恢复正常、内环境稳定,病情平稳,无明显其它并发症后,转回原科室。死亡23例（16．67％）,死亡原因为脑疝及心脏与大血管损伤,如严重肝、脾、胰损伤、重度失血性休克和MODS等。结论损伤控制策略在ICU成功救治多发伤患儿的生命中起重要作用;严重多发伤患儿经外科处理后应转至ICU综合治疗,在整个抢救过程中,应严密监护,紧急处理休克、创伤、呼吸衰竭等主要问题,同时尽量兼顾全身情况,促进患儿康复。     

缓解期精神分裂症患者抑郁和自尊状况的调查及心理干预

目的了解缓解期精神分裂症患者抑郁/自尊状况及心理干预对其的影响。方法采用抑郁自评量表(self-ratting depression scale,SDS)及自尊量表(self-esteem scale,SES)对56例缓解期精神分裂症患者进行问卷调查,随机抽取其中20名患者进行深入访谈并进行逐步分析。根据调查分析存在的心理问题,有针对的实施为期6周的心理干预,然后再次测评SDS及SES,并与干预前进行比较。结果进行心理干预前后,缓解期精神分裂症患者SDS评分由(48.96±5.95)下降至(41.76±6.72);SES评分由(26.72±7.84)上升至(34.51±8.63);其差异有统计学意义(P<0.01)。结论缓解期精神分裂症患者存在多种内心体验而表现出抑郁或自卑,心理干预可改善缓解期精神分裂症患者的抑郁和自卑。     

Polyphenol Mechanisms against Gastric Cancer and Their Interactions with Gut Microbiota: A Review

The lack of new drugs and resistance to existing drugs are serious problems in gastric cancer(GC) treatment. The research found polyphenols possess anti-Helicobacter pylori(Hp) and antitumor activities and may be used in the research and development of drugs for cancer prevention and treatment. However, polyphenols are affected by their chemical structures and physical properties, which leads to relatively low bioavailability and bioactivity in vivo. The intestinal flora can improve the absorption, utilization, and biological activity of polyphenols, whereas polyphenol compounds can increase the richness of the intestinal flora, reduce the activity of carcinogenic bacteria, stabilize the proportion of core flora, and maintain homeostasis of the intestinal microenvironment. Our review summarizes the gastrointestinal flora-mediated mechanisms of polyphenol against GC.     

心脑血管疾病用药不良反应与药品品种关系的聚类分析

目的寻找心脑血管疾病用药的不良反应与药品品种间聚类关系,促进临床安全合理用药。方法运用数据挖掘技术中的两阶段聚类算法对药品的严重不良反应与药品品种间的关系进行聚类分析。结果由聚类结果可知,在使用心脑血管疾病用药时,出现的严重和新的严重不良反应为肝功能异常、肾功能异常、呼吸困难、横纹肌溶解,导致这些严重不良反应的药物有受体类药物、钙离子拮抗剂、降低胆固醇类药物。结论在选择心脑血管疾病用药时,受体类药物、钙离子拮抗剂、降低胆固醇类药物应慎用、少用,尽量避免严重的不良反应发生。     

Phenotype of Asthma-COPD Overlap in COPD and Severe Asthma Cohorts

BackgroundAsthma and chronic obstructive pulmonary disease (COPD) are airway diseases with similar clinical manifestations, despite differences in pathophysiology. Asthma-COPD overlap (ACO) is a condition characterized by overlapping clinical features of both diseases. There have been few reports regarding the prevalence of ACO in COPD and severe asthma cohorts. ACO is heterogeneous; patients can be classified on the basis of phenotype differences. This study was performed to analyze the prevalence of ACO in COPD and severe asthma cohorts. In addition, this study compared baseline characteristics among ACO patients according to phenotype.MethodsPatients with COPD were prospectively enrolled into the Korean COPD subgroup study (KOCOSS) cohort. Patients with severe asthma were prospectively enrolled into the Korean Severe Asthma Registry (KoSAR). ACO was defined in accordance with the updated Spanish criteria. In the COPD cohort, ACO was defined as bronchodilator response (BDR) ≥ 15% and ≥ 400 mL from baseline or blood eosinophil count (BEC) ≥ 300 cells/μL. In the severe asthma cohort, ACO was defined as age ≥ 35 years, smoking ≥ 10 pack-years, and post-bronchodilator forced expiratory volume in 1 s/forced vital capacity < 0.7. Patients with ACO were divided into four groups according to smoking history (threshold: 20 pack-years) and BEC (threshold: 300 cells/μL).ResultsThe prevalence of ACO significantly differed between the COPD and severe asthma cohorts (19.8% [365/1,839] vs. 12.5% [104/832], respectively; P < 0.001). The percentage of patients in each group was as follows: group A (light smoker with high BEC) – 9.1%; group B (light smoker with low BEC) – 3.7%; group C (moderate to heavy smoker with high BEC) – 73.8%; and group D (moderate to heavy smoker with low BEC) – 13.4%. Moderate to heavy smoker with high BEC group was oldest, and showed weak BDR response. Age, sex, BDR, comorbidities, and medications significantly differed among the four groups.ConclusionThe prevalence of ACO differed between COPD and severe asthma cohorts. ACO patients can be classified into four phenotype groups, such that each phenotype exhibits distinct characteristics.