Zhigang Zhang

Bio: Zhigang Zhang is an academic researcher from Shanghai Jiao Tong University. The author has contributed to research in topics: Cancer & Medicine. The author has an hindex of 48, co-authored 281 publications receiving 9429 citations. Previous affiliations of Zhigang Zhang include Chongqing University & Chinese Academy of Sciences.

Serum DKK1 as a protein biomarker for the diagnosis of hepatocellular carcinoma: a large-scale, multicentre study

Abstract: Summary Background Hepatocellular carcinoma (HCC) is prevalent worldwide and improvements in timely and effective diagnosis are needed. We assessed whether measurement of Dickkopf-1 (DKK1) in serum could improve diagnostic accuracy for HCC. Methods We analysed data for patients with HCC, chronic hepatitis B virus (HBV) infection, liver cirrhosis, and healthy controls, recruited from two Chinese centres between December, 2008, and July, 2009. A validation cohort matched for age and sex was recruited from another centre in China between February, 2009, and June, 2011. DKK1 was measured in serum by ELISA by independent researchers who had no access to patients' clinical information. We used receiver operating characteristics (ROC) to calculate diagnostic accuracy. Findings We assessed serum DKK1 in 831 participants: 424 with HCC, 98 with chronic HBV infection, 96 with cirrhosis, and 213 healthy controls. The validation cohort comprised 453 participants: 209 with HCC, 73 with chronic HBV infection, 72 with cirrhosis, and 99 healthy controls. Levels of DKK1 in serum were significantly higher in patients with HCC than in all controls. ROC curves showed the optimum diagnostic cutoff was 2·153 ng/mL (area under curve [AUC] 0·848 [95% CI 0·820–0·875], sensitivity 69·1%, and specificity 90·6% in the test cohort; 0·862 [0·825–0·899], 71·3%, and 87·2% in the validation cohort). Similar results were noted for early-stage HCC (0·865 [0·835–0·895], 70·9%, and 90·5% in the test cohort; 0·896 [0·846–0·947], 73·8%, and 87·2% in the validation cohort). Furthermore, DKK1 maintained diagnostic accuracy for patients with HCC who were α-fetoprotein (AFP) negative (0·841 [0·801–0·882], 70·4%, and 90·0% in the test cohort; 0·869 [0·815–0·923], 66·7%, and 87·2% in the validation cohort), including for patients with early-stage HCC (0·870 [0·829–0·911], 73·1%, and 90·0% in the test cohort; 0·893 [0·804–0·983], 72·2%, and 87·2% in the validation cohort), compared with all controls. Raised concentrations of DKK1 in serum could differentiate HCC from chronic HBV infection and cirrhosis (0·834 [0·798–0·871], 69·1%, and 84·7% in the test cohort; 0·873 [0·832–0·913], 71·3%, and 90·6% in the validation cohort). Moreover, measurement of DKK1 and AFP together improved diagnostic accuracy for HCC versus all controls compared with either test alone (0·889 [0·866–0·913], 73·3%, and 93·4% in the test cohort; 0·888 [0·856–0·920], 78·5%, and 87·2% in the validation cohort). Interpretation DKK1 could complement measurement of AFP in the diagnosis of HCC and improve identification of patients with AFP-negative HCC and distinguish HCC from non-malignant chronic liver diseases. Funding National Key Basic Research Programme of China, National Key Sci-Tech Special Projects of Infectious Diseases, National Natural Science Foundation of China, Research Fund for the Doctoral Programme of Higher Education of China.

Phylogenomic reconstruction of lactic acid bacteria: an update.

Abstract: Lactic acid bacteria (LAB) are important in the food industry for the production of fermented food products and in human health as commensals in the gut. However, the phylogenetic relationships among LAB species remain under intensive debate owing to disagreements among different data sets. We performed a phylogenetic analysis of LAB species based on 232 genes from 28 LAB genome sequences. Regardless of the tree-building methods used, combined analyses yielded an identical, well-resolved tree topology with strong supports for all nodes. The LAB species examined were divided into two groups. Group 1 included families Enterococcaceae and Streptococcaceae. Group 2 included families Lactobacillaceae and Leuconostocaceae. Within Group 2, the LAB species were divided into two clades. One clade comprised of the acidophilus complex of genus Lactobacillus and two other species, Lb. sakei and Lb. casei. In the acidophilus complex, Lb. delbrueckii separated first, while Lb. acidophilus/Lb. helveticus and Lb. gasseri/Lb. johnsonii were clustered into a sister group. The other clade within Group 2 consisted of the salivarius subgroup, including five species, Lb. salivarius, Lb. plantarum, Lb. brevis, Lb. reuteri, Lb. fermentum, and the genera Pediococcus, Oenococcus, and Leuconostoc. In this clade, Lb. salivarius was positioned most basally, followed by two clusters, one corresponding to Lb. plantarum/Lb. brevis pair and Pediococcus, and the other including Oenococcus/Leuconostoc pair and Lb. reuteri/Lb. fermentum pair. In addition, phylogenetic utility of the 232 genes was analyzed to identify those that may be more useful than others. The genes identified as useful were related to translation and ribosomal structure and biogenesis (TRSB), and a three-gene set comprising genes encoding ultra-violet resistance protein B (uvrB), DNA polymerase III (polC) and penicillin binding protein 2B (pbpB). Our phylogenomic analyses provide important insights into the evolution and diversification of LAB species, and also revealed the phylogenetic utility of several genes. We infer that the occurrence of multiple, independent adaptation events in LAB species, have resulted in their occupation of various habitats. Further analyses of more genes from additional, representative LAB species are needed to reveal the molecular mechanisms underlying adaptation of LAB species to various environmental niches.

The proximal origin of SARS-CoV-2.

Abstract: SARS-CoV-2 is the seventh coronavirus known to infect humans; SARSCoV, MERS-CoV and SARS-CoV-2 can cause severe disease, whereas HKU1, NL63, OC43 and 229E are associated with mild symptoms6. Here we review what can be deduced about the origin of SARS-CoV-2 from comparative analysis of genomic data. We offer a perspective on the notable features of the SARS-CoV-2 genome and discuss scenarios by which they could have arisen. Our analyses clearly show that SARS-CoV-2 is not a laboratory construct or a purposefully manipulated virus.