Biopharmaceutical Analysis (Clinical Pharmaceutical Analysis, pharmacogenomics, molecular diagnosis)

1. Research Projects

(1)The National Natural Science Foundation of China (Grant No. 21005088)

(2)The National Natural Science Foundation of China (Grant No. 81673390)

(3)The National Natural Science Foundation of China (Grant No. 82173780)

(4)Jiangsu province social development project of scientific and technical supporting programs (Grant No.BE2012744)

(5)Jiangsu province social development project of scientific and technical supporting programs (Grant No.BE2016745)

(6)The Natural Science Foundation of Jiangsu Province (Grant No. BK2008067)

(7)The Natural Science Foundation of Jiangsu Province (Grant No. BK20151445)

(8)The Natural Science Foundation of Jiangsu Province (Grant No. BK20191322)

(9)General Financial Grant from the China Postdoctoral Science Foundation (Grant No. 2012M512179)

(10)Special Financial Grant from the China Postdoctoral Science Foundation (Grant No.2013T60962)

 2. Academic Awards

2009, third Prize for Science & Technology Development of Jiangsu Province of China, 4/5

2010, first Prize for Science & Technology Development of Yunnan Province of China, 7/10

2011, 9th natural science award for outstanding dissertation of Nanjing, 1/1

2014, first Prize for Science & technology Development/Achievement of the Ministry of Education, 3/9

2016, second Prize for Education scientific research achievement of Jiangsu Province of China, 1/6

3. Representative Research Achievements

(1)DNA walkers have shown superior performance in biosensing due to their programmability to design molecular walking behaviors with specific responses to different biological targets. However, it is still challenging to make DNA walkers capable of distinguishing DNA targets with single-base differences, so that DNA walkers that can be used for circulating tumor DNA sensing are rarely reported. Herein, a flap endonuclease 1 (FEN 1)-assisted DNA walker has been proposed to achieve mutant biosensing. The target DNA is captured on a gold nanoparticle (AuNP) as a walking strand to walk by hybridizing to the track strands on the surface of the AuNP. FEN 1 is employed to report the walking events by cleaving the track strands that must form a three-base overlapping structure recognized by FEN 1 after hybridizing with the captured target DNA. Owing to the high specificity of FEN 1 for structure recognition, the one-base mutant DNA target can be discriminated from wild-type DNA. By constructing a sensitivity-enhanced DNA walker system, as low as 1 fM DNA targets and 0.1% mutation abundance can be sensed, and the theoretical detection limits for detecting the DNA target and mutation abundance achieve 0.22 fM and 0.01%, respectively. The results of epidermal growth factor receptor (EGFR) L858R mutation detection on cell-free DNA samples from 15 patients with non-small cell lung cancer were completely consistent with that of next-generation sequencing, indicating that our DNA walker has potential for liquid biopsy.

(2)Cervical cancer is the fourth leading cause of death in women, especially in developing countries. Specific and economic methodologies for HPV typing are crucial in cancer diagnosis and further disease control. However, routine assays based on real-time polymerase chain reaction (qPCR) or DNA-chip hybridization are either incapable of offering detailed subtype information or involve tedious open-tube operations with the risk of cross-contamination from PCR amplicons. Herein, we proposed a multiplex visualized closed-tube PCR (Multi-Vision) for HPV typing. Using gold nanoparticle probes (AuNPs) as a color change indicator combined with a Hamming distance 2 coding scheme, 13 high-risk HPVs and two subtypes associated with high-incidence benign lesions were successfully typed by performing six closed-tube PCRs. The assay demonstrates high specificity with no cross-reaction among different subtypes under several artificial sample concentrations (from 100 to 103 copies per reaction) and enables highly sensitive detection of as low as 0.5 copies/μL. Further, 105 clinical samples were successfully analyzed using our method with a high concordance rate of 99.05% (104/105) compared to HPV typing kit. The inconsistent sample was confirmed by sequencing to be consistent with the typing results determined by our method, indicating that Multi-Vision could be a useful tool for HPV detection, especially in resource-limited regions.

(3)Digital PCR (dPCR) is one of the most accurate and reliable tools for the examination of genetic alterations in liquid biopsy. The sensitivity of dPCR relies on the partition numbers for dPCR. The challenge is to achieve an ultra-sensitive dPCR without increasing the reaction units. Herein, we proposed the use of invasive reaction to pick up amplified mutants co-existing with many wild-type amplicons at each dPCR reaction unit (termed as Invader-dPCR). As invasive reaction is highly specific in one-base recognition, a 1000-fold sensitivity improvement for mutation detection was achieved in a conventional dPCR platform. As a result, the sample loading could be greatly increased without the increase of the number of dPCR reaction units. For cost-effective detection, we extended the Invader-dPCR to a “multiplex” detection model by using different signal-intensity groups to replace different dyes for identifying multiple targets, allowing the construction of a logic sensor to detect multiple mutants related to personalized medicine. The logic sensor was successfully used to guide the precise use of gefitinib by detecting 17 kinds of drug-sensitive and drug-resistant mutations simultaneously. Invader-dPCR was well validated for both the ultra-sensitive and multiplexed detection, and successfully applied to the detection of clinical samples.

1．Xianyi Cheng, Yaofei Bao, Shuo Liang, Bo Li, Yunlong Liu, Haiping Wu, Xueping Ma, Yanan Chu, Yang Shao, Qi Meng, Guohua Zhou*, Qinxin Song*, Bingjie Zou*. Flap Endonuclease 1‑Assisted DNA Walkers for Sensitively and Specifically Sensing ctDNAs. Anal. Chem. 2021, 93, 9593-9601.（IF= 8.008）

2．Jixue Weng, Nan Sheng, Runyuan Wang, Shuo Liang, Chen Wang, Xue Bai, Guohua Zhou*, Bingjie Zou*, Qinxin Song*. Multiplex Visualized Closed-Tube PCR with Hamming Distance 2 Code for 15 HPV Subtype Typing. Anal. Chem. 2021, 93, 5529-5536.（IF= 8.008）

3．Zheng Xiang, Bingjie Zou, Lixian Zhang, Xueping Ma, Xiemin Qi, Wei Wei*, Qinxin Song*, Guohua Zhou*. Ultra-sensitive and multiplex digital-PCR for quantifying the mutants in cell free DNA by employing invasive reaction as identifier. Sensors & Actuators: B. Chemical 2020, 320, 128362.（IF= 7.460）

4．Nan Sheng, Bingjie Zou, Huan Tong, Yan Lu, Sixi Xing, Qinxin Song*, Guohua Zhou*. Sequence-encoded quantitative invader assay enables highly sensitive hepatitis B virus DNA quantification in a single tube without the use of a calibration curve. Analyst, 2019, 144, 5775-5784.  （IF= 4.019）

5．Zheng Xiang, Ruixuan Wan, Bingjie Zou, Xiemin Qi, Qing Huang, Shalen Kumar, Janet L. Pitman, Guohua Zhou*, Qinxin Song*. Highly sensitive and specific real-time PCR by employing serial invasive reaction as a sequence identifier for quantifying EGFR mutation abundance in cfDNA. Analytical and Bioanalytical Chemistry. 2018, 410, 6751-6759.（IF= 3.286）

6．Huning Jia, Ying Bu, Bingjie Zou, Jianping Wang, Shalen Kumar, Janet L. Pitman, Guohua Zhou* and Qinxin Song*. Signal Amplification of microRNAs with Modified Strand Displacement-based Cycling Probe Technology. Analyst 2016, 141, 6297-6302. （IF= 4.033）

7．Qinxin Song, Xiemin Qi, Huning Jia, Liang He, Shalen Kumar, Janet L. Pitman, Bingjie Zou* and Guohua Zhou*. Invader Assisted ELISA Assay for Colorimetric Detection of Disease Biomarkers Using Oligonucleotide Probe-Modified Gold Nanoparticles. Journal of Biomedical Nanotechnology, 2016, 12, 831-839.（IF= 5.068）

8．Bingjie Zou ‡, Qinxin Song ‡, Jianping Wang, Yunlong Liua and Guohua Zhou*. Invasive Reaction Assisted Strand-displacement Signal Amplification for Sensitive DNA Detection. Chem. Commun., 2014, 50, 13722-13724.（IF= 6.834）

9．Qinxin Song, Danhui Li, Yongzhi Zhou, Jie Yang, Wanqi Yang, Guohua Zhou, Jingyuan Wen*. Enhanced uptake and transport of (+)-Catechin and (-)-Epigallocatechin gallate in niosomal formulation by human intestinal Caco-2 cells. International Journal of Nanomedicine. 2014, 9, 2157-2165.（IF= 4.383）

10．Qinxin Song, Haiping Wu, Fang Feng, Guohua Zhou, Tomoharu Kajiyama, and Hideki Kambara. Pyrosequencing on nicked dsDNA generated by nicking endonucleases. Anal. Chem. 2010, 82, 2074-2081.（IF= 5.712）

Prof. Bingjie Zou

Lecturer Chen Wang