1
|
Yao F, Zhang R, Lin Q, Xu H, Li W, Ou M, Huang Y, Li G, Xu Y, Song J, Zhang G. Plasma immune profiling combined with machine learning contributes to diagnosis and prognosis of active pulmonary tuberculosis. Emerg Microbes Infect 2024; 13:2370399. [PMID: 38888093 PMCID: PMC11225635 DOI: 10.1080/22221751.2024.2370399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 06/16/2024] [Indexed: 06/20/2024]
Abstract
Tuberculosis (TB) remains one of the deadliest chronic infectious diseases globally. Early diagnosis not only prevents the spread of TB but also ensures effective treatment. However, the absence of non-sputum-based diagnostic tests often leads to delayed TB diagnoses. Inflammation is a hallmark of TB, we aimed to identify biomarkers associated with TB based on immune profiling. We collected 222 plasma samples from healthy controls (HCs), disease controls (non-TB pneumonia; PN), patients with TB (TB), and cured TB cases (RxTB). A high-throughput protein detection technology, multiplex proximity extension assays (PEA), was applied to measure the levels of 92 immune proteins. Based on differential analysis and the correlation with TB severity, we selected 9 biomarkers (CXCL9, PDL1, CDCP1, CCL28, CCL23, CCL19, MMP1, IFNγ and TRANCE) and explored their diagnostic capabilities through 7 machine learning methods. We identified combination of these 9 biomarkers that distinguish TB cases from controls with an area under the receiver operating characteristic curve (AUROC) of 0.89-0.99, with a sensitivity of 82-93% at a specificity of 88-92%. Moreover, the model excels in distinguishing severe TB cases, achieving AUROC exceeding 0.95, sensitivities and specificities exceeding 93.3%. In summary, utilizing targeted proteomics and machine learning, we identified a 9 plasma proteins signature that demonstrates significant potential for accurate TB diagnosis and clinical outcome prediction.
Collapse
Affiliation(s)
- Fusheng Yao
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, People’s Republic of China
| | - Ruiqi Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, People’s Republic of China
| | - Qiao Lin
- The Baoan People's Hospital of Shenzhen, The Second Affiliated Hospital of Shenzhen University, Shenzhen, People’s Republic of China
| | - Hui Xu
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, People’s Republic of China
| | - Wei Li
- Zhuhai ICXIVD Biotechnology Co., Ltd, iCarbonX, Zhuhai, People’s Republic of China
| | - Min Ou
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, People’s Republic of China
| | - Yiting Huang
- Zhuhai ICXIVD Biotechnology Co., Ltd, iCarbonX, Zhuhai, People’s Republic of China
| | - Guobao Li
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, People’s Republic of China
| | - Yuzhong Xu
- The Baoan People's Hospital of Shenzhen, The Second Affiliated Hospital of Shenzhen University, Shenzhen, People’s Republic of China
| | - Jiaping Song
- Zhuhai ICXIVD Biotechnology Co., Ltd, iCarbonX, Zhuhai, People’s Republic of China
| | - Guoliang Zhang
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People's Hospital, Southern University of Science and Technology, Shenzhen, People’s Republic of China
| |
Collapse
|
2
|
Han C, Liu Q, Luo X, Zhao J, Zhang Z, He J, Ge F, Ding W, Luo Z, Jia C, Zhang L. Development of a CRISPR/Cas12a-mediated aptasensor for Mpox virus antigen detection. Biosens Bioelectron 2024; 257:116313. [PMID: 38688229 DOI: 10.1016/j.bios.2024.116313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2023] [Revised: 01/23/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024]
Abstract
The emergence and rapid spread of Mpox (formerly monkeypox) have caused significant societal challenges. Adequate and appropriate diagnostics procedures are an urgent necessity. Herein, we discover a pair of aptamers through the systematic evolution of ligands by exponential enrichment (SELEX) that exhibit high affinity and bind to different sites towards the A29 protein of the Mpox virus. Subsequently, we propose a facile, sensitive, convenient CRISPR/Cas12a-mediated aptasensor for detecting the A29 antigen. The procedure employs the bivalent aptamers recognition, which induces the formation of a proximity switch probe and initiates subsequent cascade strand displacement reactions, then triggers CRISPR/Cas12a DNA trans-cleavage to achieve the sensitive detection of Mpox. Our method enables selective and ultrasensitive evaluation of the A29 protein within the range of 1 ng mL-1 to 1 μg mL-1, with a limit of detection (LOD) at 0.28 ng mL-1. Moreover, spiked A29 protein recovery exceeds 96.9%, while the detection activity remains above 91.9% after six months of storage at 4 °C. This aptasensor provides a novel avenue for exploring clinical diagnosis in cases involving Mpox as facilitating development in various analyte sensors.
Collapse
Affiliation(s)
- Cong Han
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Qirui Liu
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Xuantong Luo
- Tianjin Haihe High School, Tianjin, 300202, PR China
| | - Jian Zhao
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China
| | - Zheng Zhang
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Jiaxuan He
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Feng Ge
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, 300071, PR China
| | - Wei Ding
- Department of Gynecological Oncology, Tianjin Central Hospital of Obstetrics and Gynecology, Nankai University, Tianjin, 300071, PR China
| | - Zhaofeng Luo
- The Cancer Hospital of the University of Chinese Academy of Sciences, Aptamer Selection Center, Institute of Basic Medicine and Cancer (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310022, PR China
| | - Chao Jia
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China.
| | - Liyun Zhang
- State Key Laboratory of Medicinal Chemical Biology, College of Life Sciences, Nankai University, Tianjin, 300350, PR China.
| |
Collapse
|
3
|
Nanes BA, Bhatt K, Azarova E, Rajendran D, Munawar S, Isogai T, Dean KM, Danuser G. Shifts in keratin isoform expression activate motility signals during wound healing. Dev Cell 2024:S1534-5807(24)00389-7. [PMID: 39002537 DOI: 10.1016/j.devcel.2024.06.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 04/15/2024] [Accepted: 06/17/2024] [Indexed: 07/15/2024]
Abstract
Keratin intermediate filaments confer structural stability to epithelial tissues, but the reason this simple mechanical function requires a protein family with 54 isoforms is not understood. During skin wound healing, a shift in keratin isoform expression alters the composition of keratin filaments. If and how this change modulates cellular functions that support epidermal remodeling remains unclear. We report an unexpected effect of keratin isoform variation on kinase signal transduction. Increased expression of wound-associated keratin 6A, but not of steady-state keratin 5, potentiated keratinocyte migration and wound closure without compromising mechanical stability by activating myosin motors to increase contractile force generation. These results substantially expand the functional repertoire of intermediate filaments from their canonical role as mechanical scaffolds to include roles as isoform-tuned signaling scaffolds that organize signal transduction cascades in space and time to influence epithelial cell state.
Collapse
Affiliation(s)
- Benjamin A Nanes
- Department of Dermatology, UT Southwestern Medical Center, Dallas, TX 75390, USA; Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| | - Kushal Bhatt
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Evgenia Azarova
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Divya Rajendran
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Sabahat Munawar
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center, Dallas, TX 75390, USA.
| |
Collapse
|
4
|
Wan Z, Lu J, Lu L, Zhao W, Jiang W. A binding-triggered hybridization chain reaction cascade multi-site activated CRISPR/Cas12a signal amplification strategy for sensitive detection of α-synuclein. Analyst 2024; 149:3725-3731. [PMID: 38757739 DOI: 10.1039/d4an00453a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Alpha-synuclein (α-syn) is closely related to the pathological process of Parkinson's disease (PD). Sensitive detection of α-syn is important for the early diagnosis and disease progression monitoring of PD. Herein, we report a binding-triggered hybridization chain reaction (HCR) cascade multi-site activated CRISPR/Cas12a signal amplification strategy for sensitive detection of α-syn. In this method, antibody-DNA capture probes recognized α-syn and bound with it to increase the local effective concentrations of two DNA strands, promoting their hybridization to form a split HCR trigger. Then the trigger initiated an HCR to generate a long double-stranded structure which contained abundant periodically repeated Cas12a/crRNA target sequences. Finally, the Cas12a/crRNA recognized the target sequence in HCR products and then the cleavage activity toward fluorescent reporters was activated, leading to the recovery of appreciable fluorescence signals. Our method provided a detection limit as low as 9.33 pM and exhibited satisfactory applicability in human serum samples. In summary, this study provides a homogeneous strategy for convenient, sensitive, and accurate detection of α-syn, showing great potential in the early diagnosis of PD.
Collapse
Affiliation(s)
- Zhenzhuo Wan
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
| | - Jiahao Lu
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
| | - Lu Lu
- Department of Oncology, Central Hospital Affiliated to Shandong First Medical University, 250013, Jinan, PR China.
| | - Weichong Zhao
- Department of Oncology, Central Hospital Affiliated to Shandong First Medical University, 250013, Jinan, PR China.
| | - Wei Jiang
- School of Chemistry and Chemical Engineering, Shandong University, 250100, Jinan, PR China.
| |
Collapse
|
5
|
Wang T, Zhang Q, Xu Y, Yan R, Pan Y, Xuan Y, Shen M, Chen X, Zhu H, Ke X, Qu Y, Zhang X. TRAF2 associates with cullin neddylation complex assembly. FEBS J 2024. [PMID: 38978293 DOI: 10.1111/febs.17222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 02/27/2024] [Accepted: 06/27/2024] [Indexed: 07/10/2024]
Abstract
Cullin-based RING ligases (CRLs) comprise the largest family of ubiquitin E3 ligases. CRL activity is tightly regulated by cullin neddylation, which has been associated with various diseases. Although inhibitors of CRLs neddylation have been reported, there is a lack of small molecules that can selectively target individual cullins. Here, we identified a natural product, liquidambaric acid (LDA), with relatively selective inhibition properties against cullin (Cul) 2 neddylation, and found that its target, Tumor Necrosis Factor receptor-associated factor 2 (TRAF2) was required for the activity. TRAF2 associates with the Cul2 neddylation complex and regulates the machinery assembly, especially that of E2 (UBC12) and E3 (RBX1) enzymes. In addition, we demonstrated that by intervention of the associations between TRAF2 and the neddylation machinery, LDA disturbed NEDD8 transfer from E1 to E2, therefore blocking Cul2 neddylation. Taken together, we show that TRAF2 plays a positive role in neddylation cascades, and we have identified a small molecule capable of selective modulation of cullin neddylation.
Collapse
Affiliation(s)
- Tiantian Wang
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Qi Zhang
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Yu Xu
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Rong Yan
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Yuting Pan
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Ying Xuan
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Mengzhen Shen
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Xianzhi Chen
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Hongyan Zhu
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Xisong Ke
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Yi Qu
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| | - Xue Zhang
- Center for Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
- Shanghai Frontiers Science Center of TCM Chemical Biology, Institute of Interdisciplinary Integrative Medicine Research, Shanghai University of Traditional Chinese Medicine, China
| |
Collapse
|
6
|
Wang Y, Liu X, Zeng Y, Saka SK, Xie W, Goldaracena I, Kohman RE, Yin P, Church GM. Multiplexed in situ protein imaging using DNA-barcoded antibodies with extended hybridization chain reactions. Nucleic Acids Res 2024:gkae592. [PMID: 38966983 DOI: 10.1093/nar/gkae592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 05/23/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Antibodies have long served as vital tools in biological and clinical laboratories for the specific detection of proteins. Conventional methods employ fluorophore or horseradish peroxidase-conjugated antibodies to detect signals. More recently, DNA-conjugated antibodies have emerged as a promising technology, capitalizing on the programmability and amplification capabilities of DNA to enable highly multiplexed and ultrasensitive protein detection. However, the nonspecific binding of DNA-conjugated antibodies has impeded the widespread adoption of this approach. Here, we present a novel DNA-conjugated antibody staining protocol that addresses these challenges and demonstrates superior performance in suppressing nonspecific signals compared to previously published protocols. We further extend the utility of DNA-conjugated antibodies for signal-amplified in situ protein imaging through the hybridization chain reaction (HCR) and design a novel HCR DNA pair to expand the HCR hairpin pool from the previously published 5 pairs to 13, allowing for flexible hairpin selection and higher multiplexing. Finally, we demonstrate highly multiplexed in situ protein imaging using these techniques in both cultured cells and tissue sections.
Collapse
Affiliation(s)
- Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Xiaoyu Liu
- Key Laboratory of Quantitative Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518055, China
| | - Yitian Zeng
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Wenxin Xie
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Isabel Goldaracena
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Richie E Kohman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of System Biology, Harvard Medical School, Boston, MA 02115, USA
| | - George M Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| |
Collapse
|
7
|
Feng X, Bi X, Feng J, Hu S, Wang Y, Zhao S, Zhang L. Proximity-Induced Bipedal DNA Walker for Accurately Visualizing microRNA in Living Cancer Cell. Anal Chem 2024; 96:10669-10676. [PMID: 38913536 DOI: 10.1021/acs.analchem.4c01483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
DNA walker, a type of dynamic DNA device that is capable of moving progressively along prescribed walking tracks, has emerged as an ideal and powerful tool for biosensing and bioimaging. However, most of the reported three-dimensional (3D) DNA walker were merely designed for the detection of a single target, and they were not capable of achieving universal applicability. Herein, we reported for the first time the development of a proximity-induced 3D bipedal DNA walker for imaging of low abundance biomolecules. As a proof of concept, miRNA-34a, a biomarker of breast cancer, is chosen as the model system to demonstrate this approach. In our design, the 3D bipedal DNA walker can be generated only by the specific recognition of two proximity probes for miRNA-34a. Meanwhile, it stochastically and autonomously traveled on 3D tracks (gold nanoparticles) via catalytic hairpin assembly (CHA), resulting in the amplified fluorescence signal. In comparison with some conventional DNA walkers that were utilized for living cell imaging, the 3D DNA walkers induced by proximity ligation assay can greatly improve and ensure the high selectivity of bioanalysis. By taking advantage of these unique features, the proximity-induced 3D bipedal DNA walker successfully realizes accurate and effective monitoring of target miRNA-34a expression levels in living cells, affording a universal, valuable, and promising platform for low-abundance cancer biomarker detection and accurate identification of cancer.
Collapse
Affiliation(s)
- Xiyuan Feng
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Xiaofeng Bi
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Jinyue Feng
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Shengqiang Hu
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Yumin Wang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Shulin Zhao
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| | - Liangliang Zhang
- State Key Laboratory for the Chemistry and Molecular Engineering of Medicinal Resources, Key Laboratory for Chemistry and Molecular Engineering of Medicinal Resources (Ministry of Education of China), Collaborative Innovation Center for Guangxi Ethnic Medicine, School of Chemistry and Pharmaceutical Sciences, Guangxi Normal University, Guilin 541004, P. R. China
| |
Collapse
|
8
|
Clayworth K, Gilbert M, Auld V. Cell Biology Techniques for Studying Drosophila Peripheral Glial Cells. Cold Spring Harb Protoc 2024; 2024:pdb.top108159. [PMID: 37399179 DOI: 10.1101/pdb.top108159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2023]
Abstract
Glial cells are essential for the proper development and functioning of the peripheral nervous system (PNS). The ability to study the biology of glial cells is therefore critical for our ability to understand PNS biology and address PNS maladies. The genetic and proteomic pathways underlying vertebrate peripheral glial biology are understandably complex, with many layers of redundancy making it sometimes difficult to study certain facets of PNS biology. Fortunately, many aspects of vertebrate peripheral glial biology are conserved with those of the fruit fly, Drosophila melanogaster With simple and powerful genetic tools and fast generation times, Drosophila presents an accessible and versatile model for studying the biology of peripheral glia. We introduce here three techniques for studying the cell biology of peripheral glia of Drosophila third-instar larvae. With fine dissection tools and common laboratory reagents, third-instar larvae can be dissected, with extraneous tissues removed, revealing the central nervous system (CNS) and PNS to be processed using a standard immunolabeling protocol. To improve the resolution of peripheral nerves in the z-plane, we describe a cryosectioning method to achieve 10- to 20-µm thick coronal sections of whole larvae, which can then be immunolabeled using a modified version of standard immunolabeling techniques. Finally, we describe a proximity ligation assay (PLA) for detecting close proximity between two proteins-thus inferring protein interaction-in vivo in third-instar larvae. These methods, further described in our associated protocols, can be used to improve our understanding of Drosophila peripheral glia biology, and thus our understanding of PNS biology.
Collapse
Affiliation(s)
- Katherine Clayworth
- Department of Zoology, Cell and Developmental Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Mary Gilbert
- Department of Zoology, Cell and Developmental Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Vanessa Auld
- Department of Zoology, Cell and Developmental Biology, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| |
Collapse
|
9
|
Jiang T, Ruan N, Luo P, Wang Q, Wei X, Li Y, Dai Y, Lin L, Lv J, Liu Y, Zhang C. Modulation of ER-mitochondria tethering complex VAPB-PTPIP51: Novel therapeutic targets for aging-associated diseases. Ageing Res Rev 2024; 98:102320. [PMID: 38719161 DOI: 10.1016/j.arr.2024.102320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 04/15/2024] [Accepted: 05/01/2024] [Indexed: 05/12/2024]
Abstract
Aging is a gradual and irreversible natural process. With aging, the body experiences a functional decline, and the effects amplify the vulnerability to a range of age-related diseases, including neurodegenerative, cardiovascular, and metabolic diseases. Within the aging process, the morphology and function of mitochondria and the endoplasmic reticulum (ER) undergo alterations, particularly in the structure connecting these organelles known as mitochondria-associated membranes (MAMs). MAMs serve as vital intracellular signaling hubs, facilitating communication between the ER and mitochondria when regulating various cellular events, including calcium homeostasis, lipid metabolism, mitochondrial function, and apoptosis. The formation of MAMs is partly dependent on the interaction between the vesicle-associated membrane protein-associated protein-B (VAPB) and protein tyrosine phosphatase-interacting protein-51 (PTPIP51). Accumulating evidence has begun to elucidate the pivotal role of the VAPB-PTPIP51 tether in the initiation and progression of age-related diseases. In this study, we delineate the intricate structure and multifunctional role of the VAPB-PTPIP51 tether and discuss its profound implications in aging-associated diseases. Moreover, we provide a comprehensive overview of potential therapeutic interventions and pharmacological agents targeting the VAPB-PTPIP51-mediated MAMs, thereby offering a glimmer of hope in mitigating aging processes and treating age-related disorders.
Collapse
Affiliation(s)
- Tao Jiang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Nan Ruan
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Pengcheng Luo
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Qian Wang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiuxian Wei
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yi Li
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yue Dai
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Li Lin
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Division of Cardiology, Department of Internal Medicine, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiagao Lv
- Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Division of Cardiology, Department of Internal Medicine, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yu Liu
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| | - Cuntai Zhang
- Department of Geriatrics, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China; Key Laboratory of Vascular Aging, Ministry of Education, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| |
Collapse
|
10
|
Kageler L, Perr J, Flynn RA. Tools to investigate the cell surface: Proximity as a central concept in glycoRNA biology. Cell Chem Biol 2024; 31:1132-1144. [PMID: 38772372 PMCID: PMC11193615 DOI: 10.1016/j.chembiol.2024.04.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 04/02/2024] [Accepted: 04/25/2024] [Indexed: 05/23/2024]
Abstract
Proximity is a fundamental concept in chemistry and biology, referring to the convergence of molecules to facilitate new molecular interactions or reactions. Hybrid biopolymers like glycosylphosphatidylinositol (GPI)-anchored proteins, ubiquitinated proteins, glycosylated RNAs (glycoRNAs), and RNAylated proteins exemplify this by covalent bonding of moieties that are often orthogonally active. Hybrid molecules like glycoRNAs are localized to new physical spaces, generating new interfaces for biological functions. To fully investigate the compositional and spatial features of molecules like glycoRNAs, flexible genetic and chemical tools that encompass different encoding and targeting biopolymers are required. Here we discuss concepts of molecular proximity and explore newer proximity labeling technologies that facilitate applications in RNA biology, cell surface biology, and the interface therein with a particular focus on glycoRNA biology. We review the advantages and disadvantages of methods pertaining to cell surface RNA identification and provide insights into the vast opportunities for method development in this area.
Collapse
Affiliation(s)
- Lauren Kageler
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan Perr
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
11
|
Liu Y, Sundah NR, Ho NRY, Shen WX, Xu Y, Natalia A, Yu Z, Seet JE, Chan CW, Loh TP, Lim BY, Shao H. Bidirectional linkage of DNA barcodes for the multiplexed mapping of higher-order protein interactions in cells. Nat Biomed Eng 2024:10.1038/s41551-024-01225-3. [PMID: 38898172 DOI: 10.1038/s41551-024-01225-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Accepted: 05/05/2024] [Indexed: 06/21/2024]
Abstract
Capturing the full complexity of the diverse hierarchical interactions in the protein interactome is challenging. Here we report a DNA-barcoding method for the multiplexed mapping of pairwise and higher-order protein interactions and their dynamics within cells. The method leverages antibodies conjugated with barcoded DNA strands that can bidirectionally hybridize and covalently link to linearize closely spaced interactions within individual 3D protein complexes, encoding and decoding the protein constituents and the interactions among them. By mapping protein interactions in cancer cells and normal cells, we found that tumour cells exhibit a larger diversity and abundance of protein complexes with higher-order interactions. In biopsies of human breast-cancer tissue, the method accurately identified the cancer subtype and revealed that higher-order protein interactions are associated with cancer aggressiveness.
Collapse
Affiliation(s)
- Yu Liu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Noah R Sundah
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Nicholas R Y Ho
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
| | - Wan Xiang Shen
- Department of Pharmacy and Pharmaceutical Sciences, Faculty of Science, National University of Singapore, Singapore, Singapore
| | - Yun Xu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Auginia Natalia
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Zhonglang Yu
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore
| | - Ju Ee Seet
- Department of Pathology, National University Hospital, Singapore, Singapore
| | - Ching Wan Chan
- Department of Surgery, National University Hospital, Singapore, Singapore
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Tze Ping Loh
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore
- Department of Laboratory Medicine, National University Hospital, Singapore, Singapore
| | - Brian Y Lim
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
- Department of Computer Science, School of Computing, National University of Singapore, Singapore, Singapore.
| | - Huilin Shao
- Institute for Health Innovation and Technology, National University of Singapore, Singapore, Singapore.
- Department of Biomedical Engineering, College of Design and Engineering, National University of Singapore, Singapore, Singapore.
- Department of Surgery, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore, Singapore.
| |
Collapse
|
12
|
Sojka DR, Gogler A, Kania D, Vydra N, Wiecha K, Adamiec-Organiściok M, Wilk A, Chumak V, Matyśniak D, Scieglinska D. The human testis-enriched HSPA2 interacts with HIF-1α in epidermal keratinocytes, yet HIF-1α stability and HIF-1-dependent gene expression rely on the HSPA (HSP70) activity. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2024; 1871:119735. [PMID: 38641179 DOI: 10.1016/j.bbamcr.2024.119735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/28/2024] [Accepted: 04/09/2024] [Indexed: 04/21/2024]
Abstract
The Hypoxia-Inducible Factor 1 (HIF-1) is essential for cellular adaptation to reduced oxygen levels. It also facilitates the maintenance and re-establishment of skin homeostasis. Among others, it is involved in regulating keratinocyte differentiation. The stability of the oxygen-liable HIF-1α subunit is regulated by various non-canonical oxygen-independent mechanisms, which among others involve Heat Shock Proteins of the A family (HSPA/HSP70). This group of highly homologous chaperones and proteostasis-controlling factors includes HSPA2, a unique member crucial for spermatogenesis and implicated in the regulation of keratinocyte differentiation. HIF-1 can control the HSPA2 gene expression. In this study, we revealed that HIF-1α is the first confirmed client of HSPA2 in human somatic cells. It colocalises and interacts directly with HSPA2 in the epidermis in situ and immortalised keratinocytes in vitro. Using an in vitro model based on HSPA2-overexpressing and HSPA2-deficient variants of immortalised keratinocytes we showed that changes in HSPA2 levels do not affect the levels and intracellular localisation of HIF-1α or influence the ability of HIF-1 to modulate target gene expression. However, HIF-1α stability in keratinocytes appears critically reliant on HSPAs as a group of functionally overlapping chaperones. In addition to HSPA2, HIF-1α colocalises and forms complexes with HSPA8 and HSPA1, representing housekeeping and stress-inducible HSPA family paralogs, respectively. Chemical inhibition of HSPA activity, but not paralog-specific knockdown of HSPA8 or HSPA1 expression reduced HIF-1α levels and HIF-1-dependent gene expression. These observations suggest that pharmacological targeting of HSPAs could prevent excessive HIF-1 signalling in pathological skin conditions.
Collapse
Affiliation(s)
- Damian Robert Sojka
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland
| | - Agnieszka Gogler
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland
| | - Daria Kania
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland
| | - Natalia Vydra
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland
| | - Klaudia Wiecha
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland
| | - Małgorzata Adamiec-Organiściok
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland; Department of Systems Biology and Engineering, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Agata Wilk
- Department of Biostatistics and Bioinformatics, Maria Sklodowska-Curie National Research Institute of Oncology, Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland; Department of Systems Biology and Engineering, Silesian University of Technology, Akademicka 16, 44-100 Gliwice, Poland
| | - Vira Chumak
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland
| | - Damian Matyśniak
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland
| | - Dorota Scieglinska
- Center for Translational Research and Molecular Biology of Cancer, Maria Skłodowska-Curie National Research Institute of Oncology Gliwice Branch, Wybrzeze Armii Krajowej 15, 44-102 Gliwice, Poland.
| |
Collapse
|
13
|
Zhang Y, Xu Z, Shan M, Cao J, Zhou Y, Chen Y, Shi L. Arterial Smooth Muscle Cell AKAP150 Mediates Exercise-Induced Repression of Ca V1.2 Channel Function in Cerebral Arteries of Hypertensive Rats. Arterioscler Thromb Vasc Biol 2024; 44:1202-1221. [PMID: 38602101 DOI: 10.1161/atvbaha.124.319543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/28/2024] [Indexed: 04/12/2024]
Abstract
BACKGROUND Hypertension is a major, prevalent risk factor for the development and progression of cerebrovascular disease. Regular exercise has been recommended as an excellent choice for the large population of individuals with mild-to-moderate elevations in blood pressure, but the mechanisms that underlie its vascular-protective and antihypertensive effects remain unknown. Here, we describe a mechanism by which myocyte AKAP150 (A-kinase anchoring protein 150) inhibition induced by exercise training alleviates voltage-dependent L-type Ca2+ channel (CaV1.2) activity and restores cerebral arterial function in hypertension. METHODS Spontaneously hypertensive rats and newly generated smooth muscle-specific AKAP150 knockin mice were used to assess the role of myocyte AKAP150/CaV1.2 channel in regulating cerebral artery function after exercise intervention. RESULTS Activation of the AKAP150/PKCα (protein kinase Cα) signaling increased CaV1.2 activity and Ca2+ influx of cerebral arterial myocyte, thus enhancing vascular tone in spontaneously hypertensive rats. Smooth muscle-specific AKAP150 knockin mice were hypertensive with higher CaV1.2 channel activity and increased vascular tone. Furthermore, treatment of Ang II (angiotensin II) resulted in a more pronounced increase in blood pressure in smooth muscle-specific AKAP150 knockin mice. Exercise training significantly reduced arterial myocyte AKAP150 expression and alleviated CaV1.2 channel activity, thus restoring cerebral arterial function in spontaneously hypertensive rats and smooth muscle-specific AKAP150 knockin mice. AT1R (AT1 receptor) and AKAP150 were interacted closely in arterial myocytes. Exercise decreased the circulating Ang II and Ang II-involved AT1R-AKAP150 association in myocytes of hypertension. CONCLUSIONS The current study demonstrates that aerobic exercise ameliorates CaV1.2 channel function via inhibiting myocyte AKAP150, which contributes to reduced cerebral arterial tone in hypertension.
Collapse
MESH Headings
- Animals
- A Kinase Anchor Proteins/metabolism
- A Kinase Anchor Proteins/genetics
- Calcium Channels, L-Type/metabolism
- Calcium Channels, L-Type/genetics
- Rats, Inbred SHR
- Hypertension/physiopathology
- Hypertension/metabolism
- Hypertension/genetics
- Cerebral Arteries/metabolism
- Cerebral Arteries/physiopathology
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/physiopathology
- Male
- Myocytes, Smooth Muscle/metabolism
- Disease Models, Animal
- Physical Conditioning, Animal/physiology
- Protein Kinase C-alpha/metabolism
- Protein Kinase C-alpha/genetics
- Calcium Signaling
- Mice, Inbred C57BL
- Mice
- Rats
- Rats, Inbred WKY
- Angiotensin II
- Blood Pressure
- Signal Transduction
Collapse
Affiliation(s)
- Yanyan Zhang
- Department of Exercise Physiology (Y. Zhang, Z.X., M.S., J.C., Y. Zhou, Y.C., L.S.), Beijing Sport University, China
- Laboratory of Sports Stress and Adaptation of General Administration of Sport (Y. Zhang, L.S.), Beijing Sport University, China
- Key Laboratory of Physical Fitness and Exercise, Ministry of Education (Y. Zhang, L.S.), Beijing Sport University, China
| | - Zhaoxia Xu
- Department of Exercise Physiology (Y. Zhang, Z.X., M.S., J.C., Y. Zhou, Y.C., L.S.), Beijing Sport University, China
| | - Meiling Shan
- Department of Exercise Physiology (Y. Zhang, Z.X., M.S., J.C., Y. Zhou, Y.C., L.S.), Beijing Sport University, China
| | - Jiaqi Cao
- Department of Exercise Physiology (Y. Zhang, Z.X., M.S., J.C., Y. Zhou, Y.C., L.S.), Beijing Sport University, China
| | - Yang Zhou
- Department of Exercise Physiology (Y. Zhang, Z.X., M.S., J.C., Y. Zhou, Y.C., L.S.), Beijing Sport University, China
| | - Yu Chen
- Department of Exercise Physiology (Y. Zhang, Z.X., M.S., J.C., Y. Zhou, Y.C., L.S.), Beijing Sport University, China
| | - Lijun Shi
- Department of Exercise Physiology (Y. Zhang, Z.X., M.S., J.C., Y. Zhou, Y.C., L.S.), Beijing Sport University, China
- Laboratory of Sports Stress and Adaptation of General Administration of Sport (Y. Zhang, L.S.), Beijing Sport University, China
- Key Laboratory of Physical Fitness and Exercise, Ministry of Education (Y. Zhang, L.S.), Beijing Sport University, China
| |
Collapse
|
14
|
Li Y, Qian M, Liu Y, Qiu X. APPROACH: Sensitive Detection of Exosomal Biomarkers by Aptamer-Mediated Proximity Ligation Assay and Time-Resolved Förster Resonance Energy Transfer. BIOSENSORS 2024; 14:233. [PMID: 38785707 PMCID: PMC11117858 DOI: 10.3390/bios14050233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 04/29/2024] [Accepted: 05/05/2024] [Indexed: 05/25/2024]
Abstract
Exosomal biomarker detection holds great importance in the field of in vitro diagnostics, offering a non-invasive and highly sensitive approach for early disease detection and personalized treatment. Here, we proposed an "APPROACH" strategy, combining aptamer-mediated proximity ligation assay (PLA) with rolling circle amplification (RCA) and time-resolved Förster resonance energy transfer (TR-FRET) for the sensitive and semi-homogenous detection of exosomal biomarkers. PLA probes consisted of a cholesterol-conjugated oligonucleotide, which anchored to the membrane of an exosome, and a specific aptamer oligonucleotide that recognized a target protein of the exosome; the proximal binding of pairs of PLA probes to the same exosome positioned the oligonucleotides in the vicinity of each other, guiding the hybridization and ligation of two subsequently added backbone and connector oligonucleotides to form a circular DNA molecule. Circular DNA formed from PLA underwent rolling circle amplification (RCA) for signal amplification, and the resulting RCA products were subsequently quantified by TR-FRET. The limits of detection provided by APPROACH for the exosomal biomarkers CD63, PD-L1, and HER2 were 0.46 ng∙μL-1, 0.77 ng∙μL-1, and 1.1 ng∙μL-1, respectively, demonstrating excellent analytical performance with high sensitivity and quantification accuracy. Furthermore, the strategy afforded sensitive detection of exosomal CD63 with a LOD of 1.56 ng∙μL-1 in complex biological matrices, which underscored its anti-interference capability and potential for in vitro detection. The proposed strategy demonstrates wide-ranging applicability in quantifying diverse exosomal biomarkers while exhibiting robust analytical characteristics, including high sensitivity and accuracy.
Collapse
Affiliation(s)
- Ying Li
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
| | - Meiqi Qian
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
| | | | - Xue Qiu
- Laboratory for Marine Drugs and Bioproducts, Qingdao National Laboratory for Marine Science and Technology, Key Laboratory of Marine Drug, Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China; (Y.L.); (M.Q.)
| |
Collapse
|
15
|
Kurgan N, Kjærgaard Larsen J, Deshmukh AS. Harnessing the power of proteomics in precision diabetes medicine. Diabetologia 2024; 67:783-797. [PMID: 38345659 DOI: 10.1007/s00125-024-06097-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 12/20/2023] [Indexed: 03/21/2024]
Abstract
Precision diabetes medicine (PDM) aims to reduce errors in prevention programmes, diagnosis thresholds, prognosis prediction and treatment strategies. However, its advancement and implementation are difficult due to the heterogeneity of complex molecular processes and environmental exposures that influence an individual's disease trajectory. To address this challenge, it is imperative to develop robust screening methods for all areas of PDM. Innovative proteomic technologies, alongside genomics, have proven effective in precision cancer medicine and are showing promise in diabetes research for potential translation. This narrative review highlights how proteomics is well-positioned to help improve PDM. Specifically, a critical assessment of widely adopted affinity-based proteomic technologies in large-scale clinical studies and evidence of the benefits and feasibility of using MS-based plasma proteomics is presented. We also present a case for the use of proteomics to identify predictive protein panels for type 2 diabetes subtyping and the development of clinical prediction models for prevention, diagnosis, prognosis and treatment strategies. Lastly, we discuss the importance of plasma and tissue proteomics and its integration with genomics (proteogenomics) for identifying unique type 2 diabetes intra- and inter-subtype aetiology. We conclude with a call for action formed on advancing proteomics technologies, benchmarking their performance and standardisation across sites, with an emphasis on data sharing and the inclusion of diverse ancestries in large cohort studies. These efforts should foster collaboration with key stakeholders and align with ongoing academic programmes such as the Precision Medicine in Diabetes Initiative consortium.
Collapse
Affiliation(s)
- Nigel Kurgan
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Jeppe Kjærgaard Larsen
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Atul S Deshmukh
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark.
| |
Collapse
|
16
|
Jung O, Baek MJ, Wooldrik C, Johnson KR, Fisher KW, Lou J, Ricks TJ, Wen T, Best MD, Cryns VL, Anderson RA, Choi S. Nuclear phosphoinositide signaling promotes YAP/TAZ-TEAD transcriptional activity in breast cancer. EMBO J 2024; 43:1740-1769. [PMID: 38565949 PMCID: PMC11066040 DOI: 10.1038/s44318-024-00085-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 04/04/2024] Open
Abstract
The Hippo pathway effectors Yes-associated protein 1 (YAP) and its homolog TAZ are transcriptional coactivators that control gene expression by binding to TEA domain (TEAD) family transcription factors. The YAP/TAZ-TEAD complex is a key regulator of cancer-specific transcriptional programs, which promote tumor progression in diverse types of cancer, including breast cancer. Despite intensive efforts, the YAP/TAZ-TEAD complex in cancer has remained largely undruggable due to an incomplete mechanistic understanding. Here, we report that nuclear phosphoinositides function as cofactors that mediate the binding of YAP/TAZ to TEADs. The enzymatic products of phosphoinositide kinases PIPKIα and IPMK, including phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2) and phosphatidylinositol 3,4,5-trisphosphate (P(I3,4,5)P3), bridge the binding of YAP/TAZ to TEAD. Inhibiting these kinases or the association of YAP/TAZ with PI(4,5)P2 and PI(3,4,5)P3 attenuates YAP/TAZ interaction with the TEADs, the expression of YAP/TAZ target genes, and breast cancer cell motility. Although we could not conclusively exclude the possibility that other enzymatic products of IPMK such as inositol phosphates play a role in the mechanism, our results point to a previously unrecognized role of nuclear phosphoinositide signaling in control of YAP/TAZ activity and implicate this pathway as a potential therapeutic target in YAP/TAZ-driven breast cancer.
Collapse
Affiliation(s)
- Oisun Jung
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Min-Jeong Baek
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Interdisciplinary Graduate Program in Biomedical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Colin Wooldrik
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Interdisciplinary Graduate Program in Biomedical Sciences, University of Nebraska Medical Center, Omaha, NE, USA
| | - Keith R Johnson
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Oral Biology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Kurt W Fisher
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE, USA
| | - Jinchao Lou
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Tanei J Ricks
- Department of Chemistry, University of Memphis, 3744 Walker Avenue, Memphis, TN, 38152, USA
| | - Tianmu Wen
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Michael D Best
- Department of Chemistry, University of Tennessee, 1420 Circle Drive, Knoxville, TN, 37996, USA
| | - Vincent L Cryns
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Richard A Anderson
- University of Wisconsin Carbone Cancer Center, University of Wisconsin School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Suyong Choi
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE, USA.
- Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
| |
Collapse
|
17
|
Chen Y, Wen Y, Wang L, Huo Y, Tao Q, Song Y, Xu L, Yang X, Guo R, Cao C, Yan J, Li L, Liu G. Triblock PolyA-Mediated Protein Biosensor Based on a Size-Matching Proximity Hybridization Analysis. Anal Chem 2024; 96:6692-6699. [PMID: 38632948 DOI: 10.1021/acs.analchem.4c00210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
The antibodies in the natural biological world utilize bivalency/multivalency to achieve a higher affinity for antigen capture. However, mimicking this mechanism on the electrochemical sensing interface and enhancing biological affinity through precise spatial arrangement of bivalent aptamer probes still pose a challenge. In this study, we have developed a novel self-assembly layer (SAM) incorporating triblock polyA DNA to enable accurate organization of the aptamer probes on the interface, constructing a "lock-and-key-like" proximity hybridization assay (PHA) biosensor. The polyA fragment acts as an anchoring block with a strong affinity for the gold surface. Importantly, it connects the two DNA probes, facilitating one-to-one spatial proximity and enabling a controllable surface arrangement. By precisely adjusting the length of the polyA fragment, we can tailor the distance between the probes to match the molecular dimensions of the target protein. This design effectively enhances the affinity of the aptamers. Notably, our biosensor demonstrates exceptional specificity and sensitivity in detecting PDGF-BB, as confirmed through successful validation using human serum samples. Overall, our biosensor presents a novel and versatile interface for proximity assays, offering a significantly improved surface arrangement and detection performance.
Collapse
Affiliation(s)
- Yuru Chen
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture; Shanghai Engineering Research Center of Aquatic-Product Process & Preservation; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Yanli Wen
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Lele Wang
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Yinbo Huo
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Qing Tao
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Yanan Song
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture; Shanghai Engineering Research Center of Aquatic-Product Process & Preservation; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Li Xu
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Xue Yang
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Ruiyan Guo
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Chengming Cao
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Juan Yan
- Laboratory of Quality and Safety Risk Assessment for Aquatic Products on Storage and Preservation (Shanghai), Ministry of Agriculture; Shanghai Engineering Research Center of Aquatic-Product Process & Preservation; College of Food Science and Technology, Shanghai Ocean University, Shanghai 201306, China
| | - Lanying Li
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| | - Gang Liu
- Key Laboratory of Bioanalysis and Metrology for state market regulation, Shanghai Institute of Measurement and Testing Technology, Shanghai 201203, China
| |
Collapse
|
18
|
Nanes BA, Bhatt K, Boujemaa-Paterski R, Azarova E, Munawar S, Rajendran D, Isogai T, Dean KM, Medalia O, Danuser G. Keratin isoform shifts modulate motility signals during wound healing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.04.538989. [PMID: 37205459 PMCID: PMC10187270 DOI: 10.1101/2023.05.04.538989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Keratin intermediate filaments form strong mechanical scaffolds that confer structural stability to epithelial tissues, but the reason this function requires a protein family with 54 isoforms is not understood. During skin wound healing, a shift in keratin isoform expression alters the composition of keratin filaments. How this change modulates cellular function to support epidermal remodeling remains unclear. We report an unexpected effect of keratin isoform variation on kinase signal transduction. Increased expression of wound-associated keratin 6A, but not of steady-state keratin 5, potentiated keratinocyte migration and wound closure without compromising epidermal stability by activating myosin motors. This pathway depended on isoform-specific interaction between intrinsically disordered keratin head domains and non-filamentous vimentin shuttling myosin-activating kinases. These results substantially expand the functional repertoire of intermediate filaments from their canonical role as mechanical scaffolds to include roles as isoform-tuned signaling scaffolds that organize signal transduction cascades in space and time to influence epithelial cell state.
Collapse
Affiliation(s)
- Benjamin A Nanes
- Department of Dermatology, UT Southwestern Medical Center; Dallas, TX 75390, USA
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Kushal Bhatt
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | | | - Evgenia Azarova
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
- Present address: Department of Materials Science and Engineering, Johns Hopkins University; Baltimore, MD 21218, USA
| | - Sabahat Munawar
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Divya Rajendran
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Tadamoto Isogai
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Kevin M Dean
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| | - Ohad Medalia
- Department of Biochemistry, University of Zurich; Zurich CH-8057, Switzerland
| | - Gaudenz Danuser
- Lyda Hill Department of Bioinformatics and Cecil H and Ida Green Center for Systems Biology, UT Southwestern Medical Center; Dallas, TX 75390, USA
| |
Collapse
|
19
|
Woo S, Saka SK, Xuan F, Yin P. Molecular robotic agents that survey molecular landscapes for information retrieval. Nat Commun 2024; 15:3293. [PMID: 38632239 PMCID: PMC11024175 DOI: 10.1038/s41467-024-46978-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 03/14/2024] [Indexed: 04/19/2024] Open
Abstract
DNA-based artificial motors have allowed the recapitulation of biological functions and the creation of new features. Here, we present a molecular robotic system that surveys molecular environments and reports spatial information in an autonomous and repeated manner. A group of molecular agents, termed 'crawlers', roam around and copy information from DNA-labeled targets, generating records that reflect their trajectories. Based on a mechanism that allows random crawling, we show that our system is capable of counting the number of subunits in example molecular complexes. Our system can also detect multivalent proximities by generating concatenated records from multiple local interactions. We demonstrate this capability by distinguishing colocalization patterns of three proteins inside fixed cells under different conditions. These mechanisms for examining molecular landscapes may serve as a basis towards creating large-scale detailed molecular interaction maps inside the cell with nanoscale resolution.
Collapse
Affiliation(s)
- Sungwook Woo
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
- Department of Materials Science and Engineering, Pohang University of Science and Technology, Pohang, 37673, Korea.
| | - Sinem K Saka
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- European Molecular Biology Laboratory (EMBL), Heidelberg, Genome Biology Unit, 69117, Heidelberg, Germany
| | - Feng Xuan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA
- Spear Bio Inc., Woburn, MA, 01801, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
- Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.
| |
Collapse
|
20
|
Ang YS, Yung LYL. Protein-to-DNA Converter with High Signal Gain. ACS NANO 2024; 18:10454-10463. [PMID: 38572806 DOI: 10.1021/acsnano.3c11435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/05/2024]
Abstract
DNA isothermal amplification techniques have been applied extensively for evaluating nucleic acid inputs but cannot be implemented directly on other types of biomolecules. In this work, we designed a proximity activation mechanism that converts protein input into DNA barcodes for the DNA exponential amplification reaction, which we termed PEAR. Several design parameters were identified and experimentally verified, which included the choice of enzymes, sequences of proximity probes and template strand via the NUPACK design tool, and the implementation of a hairpin lock on the proximity probe structure. Our PEAR system was surprisingly more robust against nonspecific DNA amplification, which is a major challenge faced in existing formats of the DNA-based exponential amplification reaction. The as-designed PEAR exhibited good target responsiveness for three protein models with a dynamic range of 4-5 orders of magnitude down to femtomolar input concentration. Overall, our proposed protein-to-DNA converter module led to the development of a stable and robust configuration of the DNA exponential amplification reaction to achieve high signal gain. We foresee this enabling the use of protein inputs for more complex molecular evaluation as well as ultrasensitive protein detection.
Collapse
Affiliation(s)
- Yan Shan Ang
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Lin-Yue Lanry Yung
- Department of Chemical & Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| |
Collapse
|
21
|
Zhao H, Sheng Y, Zhang T, Zhou S, Zhu Y, Qian F, Liu M, Xu W, Zhang D, Hu J. The CRISPR-Cas13a Gemini System for noncontiguous target RNA activation. Nat Commun 2024; 15:2901. [PMID: 38575571 PMCID: PMC10994916 DOI: 10.1038/s41467-024-47281-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 03/22/2024] [Indexed: 04/06/2024] Open
Abstract
Simultaneous multi-target detection and multi-site gene editing are two key factors restricting the development of disease diagnostic and treatment technologies. Despite numerous explorations on the source, classification, functional features, crystal structure, applications and engineering of CRISPR-Cas13a, all reports use the contiguous target RNA activation paradigm that only enables single-target detection in vitro and one-site gene editing in vivo. Here we propose a noncontiguous target RNA activation paradigm of Cas13a and establish a CRISPR-Cas13a Gemini System composed of two Cas13a:crRNA binary complexes, which can provide rapid, simultaneous, highly specific and sensitive detection of two RNAs in a single readout, as well as parallel dual transgene knockdown. CRISPR-Cas13a Gemini System are demonstrated in the detection of two miRNAs (miR-155 and miR-375) for breast cancer diagnosis and two small RNAs (EBER-1 and EBER-2) for Epstein-Barr virus diagnosis using multiple diagnostic platforms, including fluorescence and colorimetric-based lateral flow systems. We also show that CRISPR-Cas13a Gemini System can knockdown two foreign genes (EGFP and mCherry transcripts) in mammalian cells simultaneously. These findings suggest the potential of highly effective and simultaneous detection of multiple biomarkers and gene editing of multiple sites.
Collapse
Affiliation(s)
- Hongrui Zhao
- International Joint Laboratory of Catalytic Chemistry, State Key Laboratory of Advanced Special Steel, Innovation Institute of Carbon Neutrality, College of Sciences, Shanghai University, Shanghai, China
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yan Sheng
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China.
- Institute of Translational Medicine, Shanghai University, Shanghai, China.
| | - Tenghua Zhang
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Shujun Zhou
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Yuqing Zhu
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Feiyang Qian
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China
| | - Meiru Liu
- International Joint Laboratory of Catalytic Chemistry, State Key Laboratory of Advanced Special Steel, Innovation Institute of Carbon Neutrality, College of Sciences, Shanghai University, Shanghai, China
| | - Weixue Xu
- International Joint Laboratory of Catalytic Chemistry, State Key Laboratory of Advanced Special Steel, Innovation Institute of Carbon Neutrality, College of Sciences, Shanghai University, Shanghai, China
| | - Dengsong Zhang
- International Joint Laboratory of Catalytic Chemistry, State Key Laboratory of Advanced Special Steel, Innovation Institute of Carbon Neutrality, College of Sciences, Shanghai University, Shanghai, China.
| | - Jiaming Hu
- International Joint Laboratory of Catalytic Chemistry, State Key Laboratory of Advanced Special Steel, Innovation Institute of Carbon Neutrality, College of Sciences, Shanghai University, Shanghai, China.
- MOE Key Laboratory of Laser Life Science & Institute of Laser Life Science, Guangdong Provincial Key Laboratory of Laser Life Science, College of Biophotonics, South China Normal University, Guangzhou, China.
| |
Collapse
|
22
|
Liu C, Lin H, Yu H, Mai X, Pan W, Guo J, Liao T, Feng J, Zhang Y, Situ B, Zheng L, Li B. Isolation and Enrichment of Extracellular Vesicles with Double-Positive Membrane Protein for Subsequent Biological Studies. Adv Healthc Mater 2024; 13:e2303430. [PMID: 37942845 DOI: 10.1002/adhm.202303430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Indexed: 11/10/2023]
Abstract
The isolation and enrichment of specific extracellular vesicle (EV) subpopulations are essential in the context of precision medicine. However, the current methods predominantly rely on a single-positive marker and are susceptible to interference from soluble proteins or impurities. This limitation represents a significant obstacle to the widespread application of EVs in biological research. Herein, a novel approach that utilizes proximity ligation assay (PLA) and DNA-RNA hybridization are proposed to facilitate the binding of two proteins on the EV membrane in advance enabling the isolation and enrichment of intact EVs with double-positive membrane proteins followed by using functionalized magnetic beads for capture and enzymatic cleavage for isolated EVs release. The isolated subpopulations of EVs can be further utilized for cellular uptake studies, high-throughput small RNA sequencing, and breast cancer diagnosis. Hence, developing and implementing a specialized system for isolating and enriching a specific subpopulation of EVs can enhance basic and clinical research in this field.
Collapse
Affiliation(s)
- Chunchen Liu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Huixian Lin
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Haiyang Yu
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Xueying Mai
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Weilun Pan
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Jingyun Guo
- Breast Center, Department of General Surgery, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Tong Liao
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Junjie Feng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Ye Zhang
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Bo Situ
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Lei Zheng
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - Bo Li
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
- Guangdong Engineering and Technology Research Center for Rapid Diagnostic Biosensors, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| |
Collapse
|
23
|
Sakai T, Choo YY, Mitsuhashi S, Ikebe R, Jeffers A, Idell S, Tucker TA, Ikebe M. Myocardin regulates fibronectin expression and secretion from human pleural mesothelial cells. Am J Physiol Lung Cell Mol Physiol 2024; 326:L419-L430. [PMID: 38349126 DOI: 10.1152/ajplung.00271.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Revised: 01/18/2024] [Accepted: 01/26/2024] [Indexed: 03/20/2024] Open
Abstract
During the progression of pleural fibrosis, pleural mesothelial cells (PMCs) undergo a phenotype switching process known as mesothelial-mesenchymal transition (MesoMT). During MesoMT, transformed PMCs become myofibroblasts that produce increased extracellular matrix (ECM) proteins, including collagen and fibronectin (FN1) that is critical to develop fibrosis. Here, we studied the mechanism that regulates FN1 expression in myofibroblasts derived from human pleural mesothelial cells (HPMCs). We found that myocardin (Myocd), a transcriptional coactivator of serum response factor (SRF) and a master regulator of smooth muscle and cardiac muscle differentiation, strongly controls FN1 gene expression. Myocd gene silencing markedly inhibited FN1 expression. FN1 promoter analysis revealed that deletion of the Smad3-binding element diminished FN1 promoter activity, whereas deletion of the putative SRF-binding element increased FN1 promoter activity. Smad3 gene silencing decreased FN1 expression, whereas SRF gene silencing increased FN1 expression. Moreover, SRF competes with Smad3 for binding to Myocd. These results indicate that Myocd activates FN1 expression through Smad3, whereas SRF inhibits FN1 expression in HPMCs. In HPMCs, TGF-β induced Smad3 nuclear localization, and the proximity ligation signal between Myocd and Smad3 was markedly increased after TGF-β stimulation at nucleus, suggesting that TGF-β facilitates nuclear translocation of Smad3 and interaction between Smad3 and Myocd. Moreover, Myocd and Smad3 were coimmunoprecipitated and isolated Myocd and Smad3 proteins directly bound each other. Chromatin immunoprecipitation assays revealed that Myocd interacts with the FN1 promoter at the Smad3-binding consensus sequence. The results indicate that Myocd regulates FN1 gene activation through interaction and activation of the Smad3 transcription factor.NEW & NOTEWORTHY During phenotype switching from mesothelial to mesenchymal, pleural mesothelial cells (PMCs) produce extracellular matrix (ECM) proteins, including collagen and fibronectin (FN1), critical components in the development of fibrosis. Here, we found that myocardin, a transcriptional coactivator of serum response factor (SRF), strongly activates FN1 expression through Smad3, whereas SRF inhibits FN1 expression. This study provides insights about the regulation of FN1 that could lead to the development of novel interventional approaches to prevent pleural fibrosis.
Collapse
Affiliation(s)
- Tsuyoshi Sakai
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Young-Yeon Choo
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Shinya Mitsuhashi
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Reiko Ikebe
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Ann Jeffers
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Steven Idell
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Torry A Tucker
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| | - Mitsuo Ikebe
- Department of Cellular and Molecular Biology, University of Texas at Tyler Health Science Center, Tyler, Texas, United States
| |
Collapse
|
24
|
Hristov P, Flynn RA. Imaging glycosylated RNAs at the subcellular scale. Nat Biotechnol 2024; 42:574-575. [PMID: 37872411 DOI: 10.1038/s41587-023-02021-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Affiliation(s)
- Petar Hristov
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA
| | - Ryan A Flynn
- Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Boston, MA, USA.
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
- Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA.
| |
Collapse
|
25
|
Shichijo T, Yasunaga JI, Sato K, Nosaka K, Toyoda K, Watanabe M, Zhang W, Koyanagi Y, Murphy EL, Bruhn RL, Koh KR, Akari H, Ikeda T, Harris RS, Green PL, Matsuoka M. Vulnerability to APOBEC3G linked to the pathogenicity of deltaretroviruses. Proc Natl Acad Sci U S A 2024; 121:e2309925121. [PMID: 38502701 PMCID: PMC10990082 DOI: 10.1073/pnas.2309925121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 01/29/2024] [Indexed: 03/21/2024] Open
Abstract
Human retroviruses are derived from simian ones through cross-species transmission. These retroviruses are associated with little pathogenicity in their natural hosts, but in humans, HIV causes AIDS, and human T-cell leukemia virus type 1 (HTLV-1) induces adult T-cell leukemia-lymphoma (ATL). We analyzed the proviral sequences of HTLV-1, HTLV-2, and simian T-cell leukemia virus type 1 (STLV-1) from Japanese macaques (Macaca fuscata) and found that APOBEC3G (A3G) frequently generates G-to-A mutations in the HTLV-1 provirus, whereas such mutations are rare in the HTLV-2 and STLV-1 proviruses. Therefore, we investigated the mechanism of how HTLV-2 is resistant to human A3G (hA3G). HTLV-1, HTLV-2, and STLV-1 encode the so-called antisense proteins, HTLV-1 bZIP factor (HBZ), Antisense protein of HTLV-2 (APH-2), and STLV-1 bZIP factor (SBZ), respectively. APH-2 efficiently inhibits the deaminase activity of both hA3G and simian A3G (sA3G). HBZ and SBZ strongly suppress sA3G activity but only weakly inhibit hA3G, suggesting that HTLV-1 is incompletely adapted to humans. Unexpectedly, hA3G augments the activation of the transforming growth factor (TGF)-β/Smad pathway by HBZ, and this activation is associated with ATL cell proliferation by up-regulating BATF3/IRF4 and MYC. In contrast, the combination of APH-2 and hA3G, or the combination of SBZ and sA3G, does not enhance the TGF-β/Smad pathway. Thus, HTLV-1 is vulnerable to hA3G but utilizes it to promote the proliferation of infected cells via the activation of the TGF-β/Smad pathway. Antisense factors in each virus, differently adapted to control host cellular functions through A3G, seem to dictate the pathogenesis.
Collapse
Affiliation(s)
- Takafumi Shichijo
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
- Laboratory of Virus Control, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| | - Jun-ichirou Yasunaga
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
- Laboratory of Virus Control, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| | - Kei Sato
- Division of Systems Virology, Institute of Medical Science, The University of Tokyo, Tokyo108-8639, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama332-0012, Japan
| | - Kisato Nosaka
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
| | - Kosuke Toyoda
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
- Laboratory of Virus Control, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| | - Miho Watanabe
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
| | - Wenyi Zhang
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
| | - Yoshio Koyanagi
- Laboratory of Systems Virology, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| | - Edward L. Murphy
- Department of Laboratory Medicine, University of California, San Francisco94158
- Department of Epidemiology/Biostatistics, University of California, San Francisco
- Vitalant Research Institute, San Francisco94105
| | | | - Ki-Ryang Koh
- Department of Hematology, Osaka General Hospital of West Japan Railway Company, Osaka545-0053, Japan
| | - Hirofumi Akari
- Center for the Evolutionary Origins of Human Behavior, Kyoto University, Inuyama, Aichi484-8506, Japan
| | - Terumasa Ikeda
- Division of Molecular Virology and Genetics, Joint Research Center for Human Retrovirus infection, Kumamoto University, Kumamoto860-0811, Japan
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX78229
- HHMI, University of Texas Health San Antonio, San Antonio, TX78229
| | - Reuben S. Harris
- Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, TX78229
- HHMI, University of Texas Health San Antonio, San Antonio, TX78229
| | - Patrick L. Green
- Center for Retrovirus Research, Department of Veterinary Biosciences, The Ohio State University, Columbus, OH43210
- Department of Veterinary Biosciences, The Ohio State University, Columbus, OH
| | - Masao Matsuoka
- Department of Hematology, Rheumatology and Infectious Diseases, Faculty of Life Sciences, Kumamoto University, Kumamoto860-8556, Japan
- Laboratory of Virus Control, Institute for Life and Medical Sciences, Kyoto University, Kyoto606-8507, Japan
| |
Collapse
|
26
|
Todisco M, Ding D, Szostak JW. Transient states during the annealing of mismatched and bulged oligonucleotides. Nucleic Acids Res 2024; 52:2174-2187. [PMID: 38348869 PMCID: PMC10954449 DOI: 10.1093/nar/gkae091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/19/2024] [Accepted: 01/29/2024] [Indexed: 03/22/2024] Open
Abstract
Oligonucleotide hybridization is crucial in various biological, prebiotic and nanotechnological processes, including gene regulation, non-enzymatic primer extension and DNA nanodevice assembly. Although extensive research has focused on the thermodynamics and kinetics of nucleic acid hybridization, the behavior of complex mixtures and the outcome of competition for target binding remain less well understood. In this study, we investigate the impact of mismatches and bulges in a 12 bp DNA or RNA duplex on its association (kon) and dissociation (koff) kinetics. We find that such defects have relatively small effects on the association kinetics, while the dissociation kinetics vary in a position-dependent manner by up to 6 orders of magnitude. Building upon this observation, we explored a competition scenario involving multiple oligonucleotides, and observed a transient low specificity of probe hybridization to fully versus partially complementary targets in solution. We characterize these long-lived metastable states and their evolution toward equilibrium, and show that sufficiently long-lived mis-paired duplexes can serve as substrates for prebiotically relevant chemical copying reactions. Our results suggest that transient low accuracy states may spontaneously emerge within all complex nucleic acid systems comprising a large enough number of competing strands, with potential repercussions for gene regulation in the realm of modern biology and the prebiotic preservation of genetic information.
Collapse
Affiliation(s)
- Marco Todisco
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| | - Dian Ding
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, 185 Cambridge Street, Boston, MA 02114, USA
| | - Jack W Szostak
- Howard Hughes Medical Institute, Department of Chemistry, The University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
27
|
Uozumi R, Mori K, Gotoh S, Miyamoto T, Kondo S, Yamashita T, Kawabe Y, Tagami S, Akamine S, Ikeda M. PABPC1 mediates degradation of C9orf72-FTLD/ALS GGGGCC repeat RNA. iScience 2024; 27:109303. [PMID: 38444607 PMCID: PMC10914486 DOI: 10.1016/j.isci.2024.109303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 12/21/2023] [Accepted: 02/16/2024] [Indexed: 03/07/2024] Open
Abstract
GGGGCC hexanucleotide repeat expansion in C9orf72 causes frontotemporal lobar degeneration and amyotrophic lateral sclerosis. Expanded GGGGCC repeat RNA accumulates within RNA foci and is translated into toxic dipeptide repeat proteins; thus, efficient repeat RNA degradation may alleviate diseases. hnRNPA3, one of the repeat RNA-binding proteins, has been implicated in the destabilization of repeat RNA. Using APEX2-mediated proximity biotinylation, here, we demonstrate PABPC1, a cytoplasmic poly (A)-binding protein, interacts with hnRNPA3. Knockdown of PABPC1 increased the accumulation of repeat RNA and RNA foci to the same extent as the knockdown of hnRNPA3. Proximity ligation assays indicated PABPC1-hnRNPA3 and PABPC1-RNA exosomes, a complex that degrades repeat RNA, preferentially co-localized when repeat RNA was present. Our results suggest that PABPC1 functions as a mediator of polyadenylated GGGGCC repeat RNA degradation through interactions with hnRNPA3 and RNA exosome complex.
Collapse
Affiliation(s)
- Ryota Uozumi
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kohji Mori
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shiho Gotoh
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tesshin Miyamoto
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Shizuko Kondo
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Tomoko Yamashita
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Yuya Kawabe
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
- Psychiatry, Minoh Neuropsychiatric Hospital, Minoh, Osaka 562-0004, Japan
| | - Shinji Tagami
- Psychiatry, Minoh Neuropsychiatric Hospital, Minoh, Osaka 562-0004, Japan
- Health and Counseling Center, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shoshin Akamine
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Manabu Ikeda
- Department of Psychiatry, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| |
Collapse
|
28
|
Xia J, Phan HV, Vistain L, Chen M, Khan AA, Tay S. Computational prediction of protein interactions in single cells by proximity sequencing. PLoS Comput Biol 2024; 20:e1011915. [PMID: 38483861 PMCID: PMC10939233 DOI: 10.1371/journal.pcbi.1011915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/13/2024] [Indexed: 03/17/2024] Open
Abstract
Proximity sequencing (Prox-seq) simultaneously measures gene expression, protein expression and protein complexes on single cells. Using information from dual-antibody binding events, Prox-seq infers surface protein dimers at the single-cell level. Prox-seq provides multi-dimensional phenotyping of single cells in high throughput, and was recently used to track the formation of receptor complexes during cell signaling and discovered a novel interaction between CD9 and CD8 in naïve T cells. The distribution of protein abundance can affect identification of protein complexes in a complicated manner in dual-binding assays like Prox-seq. These effects are difficult to explore with experiments, yet important for accurate quantification of protein complexes. Here, we introduce a physical model of Prox-seq and computationally evaluate several different methods for reducing background noise when quantifying protein complexes. Furthermore, we developed an improved method for analysis of Prox-seq data, which resulted in more accurate and robust quantification of protein complexes. Finally, our Prox-seq model offers a simple way to investigate the behavior of Prox-seq data under various biological conditions and guide users toward selecting the best analysis method for their data.
Collapse
Affiliation(s)
- Junjie Xia
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Luke Vistain
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| | - Mengjie Chen
- Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, Illinois, United States of America
- Department Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Aly A. Khan
- Department of Pathology, The University of Chicago, Chicago, Illinois, United States of America
| | - Savaş Tay
- Pritzker School of Molecular Engineering, The University of Chicago, Chicago, Illinois, United States of America
| |
Collapse
|
29
|
Yokoi A, Murayama A, Hashimura M, Oguri Y, Harada Y, Fukagawa N, Hayashi M, Ono M, Ohhigata K, Saegusa M. A Complex Interplay between Notch Effectors and β-Catenin Signaling in Morular Differentiation of Endometrial Carcinoma Cells. THE AMERICAN JOURNAL OF PATHOLOGY 2024; 194:459-470. [PMID: 38096983 DOI: 10.1016/j.ajpath.2023.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/02/2023] [Accepted: 11/28/2023] [Indexed: 12/24/2023]
Abstract
Notch signaling contributes to tissue development and homeostasis, but little is known about its role in morular differentiation of endometrial carcinoma (Em Ca) cells. The current study focused on crosstalk between Notch and β-catenin signaling in Em Ca with morules. Promoters of hairy and enhancer of split 1 (Hes1) and mastermind-like 2 (MAML2) were activated by Notch intracellular domain 1 but not β-catenin, and a positive feedback loop between Hes1 and MAML2 was observed. Immunoreactivities for nuclear β-catenin, Hes1, and MAML2, as well as the interaction between β-catenin and Hes1 or MAML2, were significantly higher in morular lesions compared with surrounding carcinoma in Em Ca. Inhibition of glycogen synthase kinase-3β (GSK-3β) increased expression of total nuclear and cytoplasmic GSK-3β and its phosphorylated forms, as well as Notch intracellular domain 1, Hes1, and active β-catenin. GSK-3β inhibition also decreased proliferation and migration, consistent with the response of cells stably overexpressing Hes1. Finally, the nuclear/cytoplasmic GSK-3β score was significantly higher in morules compared with surrounding carcinoma in Em Ca, and it was positively correlated with nuclear β-catenin, Hes1, and MAML2 scores. This complex interplay between Notch effectors and β-catenin signaling through GSK-3β inhibition contributes to the establishment and maintenance of β-catenin-mediated morular differentiation, which is, in turn, associated with reduced proliferation and inhibition of migration in Em Ca.
Collapse
Affiliation(s)
- Ako Yokoi
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Akari Murayama
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Miki Hashimura
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yasuko Oguri
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Yohei Harada
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Naomi Fukagawa
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Misato Hayashi
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Mototsugu Ono
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Kensuke Ohhigata
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan
| | - Makoto Saegusa
- Department of Pathology, Kitasato University School of Medicine, Sagamihara, Japan.
| |
Collapse
|
30
|
Pumar OYT, Zanotelli MR, Lin MCJ, Schmitt RR, Green KS, Rojas KS, Hwang IY, Cerione RA, Wilson KF. A multiprotein signaling complex sustains AKT and mTOR/S6K activity necessary for the survival of cancer cells undergoing stress. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.03.522657. [PMID: 36711811 PMCID: PMC9881951 DOI: 10.1101/2023.01.03.522657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Cancer cells encounter stresses during tumor progression and metastatic spread, however, how they survive these challenges is not fully understood. We now identify a mechanism for cancer cell survival through the discovery of a multiprotein signaling complex that includes the GTPase Cdc42, the Cdc42 GEF/effector protein Dock7, AKT, mTOR and the mTORC1 regulatory partners TSC1, TSC2, and Rheb. This pro-survival signaling complex sustains the activated state of AKT by preventing its dephosphorylation at Ser473 during serum starvation, resulting in a low but critical activation of a Raptor-independent mTOR/S6K activity. We demonstrate that the Dock7 DHR1 domain, previously of unknown function, is responsible for preserving AKT phosphorylation through an interaction requiring its C2-like motif. Collectively, these findings help address long-standing questions of how Cdc42 signals mTOR activation by elucidating the unique functions of its signaling partner Dock7 as an AKT regulator necessary for resistance to anoikis and apoptosis in cancer cells.
Collapse
Affiliation(s)
| | | | - Miao-chong Joy Lin
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Rebecca R. Schmitt
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Kai Su Green
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Katherine S. Rojas
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Irene Y. Hwang
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| | - Richard A. Cerione
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
- Department of Chemistry, Cornell University, Ithaca, NY 14853, USA
| | - Kristin F. Wilson
- Department of Molecular Medicine, Cornell University, Ithaca, NY 14853, USA
| |
Collapse
|
31
|
Wong E, Malviya M, Jain T, Liao GP, Kehs Z, Chang JC, Studer L, Scheinberg DA, Li YM. HuM195 and its single-chain variable fragment increase Aβ phagocytosis in microglia via elimination of CD33 inhibitory signaling. Mol Psychiatry 2024:10.1038/s41380-024-02474-z. [PMID: 38383769 DOI: 10.1038/s41380-024-02474-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/18/2024] [Accepted: 01/31/2024] [Indexed: 02/23/2024]
Abstract
CD33 is a transmembrane receptor expressed on cells of myeloid lineage and regulates innate immunity. CD33 is a risk factor for Alzheimer's disease (AD) and targeting CD33 has been a promising strategy drug development. However, the mechanism of CD33's action is poorly understood. Here we investigate the mechanism of anti-CD33 antibody HuM195 (Lintuzumab) and its single-chain variable fragment (scFv) and examine their therapeutic potential. Treatment with HuM195 full-length antibody or its scFv increased phagocytosis of β-amyloid 42 (Aβ42) in human microglia and monocytes. This activation of phagocytosis was driven by internalization and degradation of CD33, thereby downregulating its inhibitory signal. HumM195 transiently induced CD33 phosphorylation and its signaling via receptor dimerization. However, this signaling decayed with degradation of CD33. scFv binding to CD33 leads to a degradation of CD33 without detection of the CD33 dimerization and signaling. Moreover, we found that treatments with either HuM195 or scFv promotes the secretion of IL33, a cytokine implicated in microglia reprogramming. Importantly, recombinant IL33 potentiates the uptake of Aβ42 in monocytes. Collectively, our findings provide unanticipated mechanistic insight into the role of CD33 signaling in both monocytes and microglia and define a molecular basis for the development of CD33-based therapy of AD.
Collapse
Affiliation(s)
- Eitan Wong
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Manish Malviya
- Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
| | - Tanya Jain
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
- Program of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, 10021, USA
| | - George P Liao
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
- Program of Pharmacology Weill Graduate School of Medical Sciences of Cornell University, New York, NY, 10021, USA
| | - Zoe Kehs
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA
- Program of Pharmacology Weill Graduate School of Medical Sciences of Cornell University, New York, NY, 10021, USA
| | - Jerry C Chang
- Laboratory of Molecular and Cellular Neuroscience, The Rockefeller University, New York, NY, 10021, USA
| | - Lorenz Studer
- Developmental biology program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10021, USA
| | - David A Scheinberg
- Molecular Pharmacology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
- Program of Pharmacology Weill Graduate School of Medical Sciences of Cornell University, New York, NY, 10021, USA.
| | - Yue-Ming Li
- Chemical Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, 10065, USA.
- Program of Neurosciences, Weill Graduate School of Medical Sciences of Cornell University, New York, NY, 10021, USA.
- Program of Pharmacology Weill Graduate School of Medical Sciences of Cornell University, New York, NY, 10021, USA.
| |
Collapse
|
32
|
Shim T, Kim JY, Kim W, Lee YI, Cho B, Moon C. Cullin-RING E3 ubiquitin ligase 4 regulates neurite morphogenesis during neurodevelopment. iScience 2024; 27:108933. [PMID: 38318354 PMCID: PMC10839267 DOI: 10.1016/j.isci.2024.108933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Revised: 10/30/2023] [Accepted: 01/12/2024] [Indexed: 02/07/2024] Open
Abstract
Neuritogenesis is crucial for establishing proper neuronal connections during brain development; its failure causes neurodevelopmental defects. Cullin-RING E3 ubiquitin ligase complexes participate in various neurodevelopmental processes by regulating protein stability. We demonstrated the regulatory function of Cullin-RING E3 ubiquitin ligase 4 (CRL4) in neurite morphogenesis during early neurodevelopment. Cul4a and Cul4b, the core scaffold proteins of CRL4, exhibit high expression and activation within the cytosol of developing neurons, regulated by neuronal stimulation through N-methyl D-aspartate (NMDA) receptor signaling. CRL4 also interacts with cytoskeleton-regulating proteins involved in neurite morphogenesis. Notably, genetic depletion and inhibition of cytosolic CRL4 enhance neurite extension and branching in developing neurons. Conversely, Cul4a overexpression suppresses basal and NMDA-enhanced neuritogenesis. Furthermore, CRL4 and its substrate adaptor regulate the polyubiquitination and proteasomal degradation of doublecortin protein. Collectively, our findings suggest that CRL4 ensures proper neurite morphogenesis in developing neurons by regulating cytoskeleton-regulating proteins.
Collapse
Affiliation(s)
- Tammy Shim
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
| | - Jae Yeon Kim
- Department of Neurology, University of California, San Francisco, CA 94143, USA
| | - WonCheol Kim
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
| | - Yun-Il Lee
- Division of Biotechnology, DGIST, Daegu 42988, Republic of Korea
| | - Bongki Cho
- Division of Biotechnology, DGIST, Daegu 42988, Republic of Korea
| | - Cheil Moon
- Department of Brain Sciences, DGIST, Daegu 42988, Republic of Korea
- Convergence Research Advanced Centre for Olfaction, DGIST, Daegu 42988, Republic of Korea
| |
Collapse
|
33
|
Chen Z, Sun Q, Yang Y, Nie X, Xiang W, Ren Y, Le T. Aptamer-based diagnostic and therapeutic approaches for animal viruses: A review. Int J Biol Macromol 2024; 257:128677. [PMID: 38072350 DOI: 10.1016/j.ijbiomac.2023.128677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Revised: 11/28/2023] [Accepted: 12/06/2023] [Indexed: 01/27/2024]
Abstract
Animal diseases often have significant consequences due to the unclear and time-consuming diagnosis process. Furthermore, the emergence of new viral infections and drug-resistant pathogens has further complicated the diagnosis and treatment of viral diseases. Aptamers, which are obtained through systematic evolution of ligands by exponential enrichment (SELEX) technology, provide a promising solution as they enable specific identification and binding to targets, facilitating pathogen detection and the development of novel therapeutics. This review presented an overview of aptasensors for animal virus detection, discussed the antiviral activity and mechanisms of aptamers, and highlighted advancements in aptamer-based antiviral research following the COVID-19 pandemic. Additionally, the challenges and prospects of aptamer-based virus diagnosis and treatment research were explored. Although this review was not exhaustive, it offered valuable insights into the progress of aptamer-based antiviral drug research, target mechanisms, as well as the development of novel antiviral drugs and biosensors.
Collapse
Affiliation(s)
- Zhuoer Chen
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Qi Sun
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Ying Yang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Xunqing Nie
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Wenyu Xiang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Yueyang Ren
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China
| | - Tao Le
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, PR China.
| |
Collapse
|
34
|
Zhuo C, Yu D, Cui J, Song Z, Tang Q, Liao X, Liu Z, Xin N, Lou L, Gao F. Proximity hybridization induced bipedal DNA walker and rolling circle amplification for label-free electrochemical detection of apolipoprotein A4. Bioelectrochemistry 2024; 155:108596. [PMID: 37939432 DOI: 10.1016/j.bioelechem.2023.108596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 10/30/2023] [Accepted: 10/31/2023] [Indexed: 11/10/2023]
Abstract
Apolipoprotein A4 (Apo-A4) is considered as a prospective molecular biomarker for diagnosis of depression due to its neurosynaptic toxicity. We develop a proximity hybridization-induced DNAzyme-driven bipedal DNA walker strategy for Apo-A4 quantification based on rolling circle amplification (RCA) triggered by poly adenine binding to Ag nanoparticles (AgNPs). With the help of DNAzyme, the free-running bipedal DNA walker can quickly and sequentially shear a molecular beacon that acts as a primer to initiate the RCA process, producing a large number of long DNA strands containing numerous adenines. The long repetitive adenine strands then absorb large amounts of AgNPs on the electrode interface, which is then electrochemically stripped of the AgNPs. The method has a linear detection range of 0.001 ∼ 100 ng mL-1 and a detection limit of 0.46 pg mL-1. The presented detection strategy is label-free, which allows high sensitivity and selectivity for detection of a wide range of protein targets by corresponding DNA-based affinity probes, which have potential applications in bioanalysis.
Collapse
Affiliation(s)
- Chenyi Zhuo
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Dehong Yu
- The Affiliated Pizhou Hospital of Xuzhou Medical University, Jiangsu 221399, China
| | - Jiuying Cui
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China; West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Zichun Song
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China; West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Qianli Tang
- The Affiliated Hospital of Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China; West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China
| | - Xianjiu Liao
- West Guangxi Key Laboratory for Prevention and Treatment of High-incidence Diseases, Youjiang Medical University for Nationalities, Baise, Guangxi 533000, China.
| | - Zhao Liu
- School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Ning Xin
- School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China
| | - Lu Lou
- Department of Urology, The Affiliated Xuzhou Municipal Hospital of Xuzhou Medical University, Xuzhou First People's Hospital, Xuzhou, China.
| | - Fenglei Gao
- School of Pharmacy, Xuzhou Medical University, 221004 Xuzhou, China.
| |
Collapse
|
35
|
Zafar S, Fatima SI, Schmitz M, Zerr I. Current Technologies Unraveling the Significance of Post-Translational Modifications (PTMs) as Crucial Players in Neurodegeneration. Biomolecules 2024; 14:118. [PMID: 38254718 PMCID: PMC10813409 DOI: 10.3390/biom14010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/09/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Neurodegenerative disorders, such as Parkinson's disease, Alzheimer's disease, and Huntington's disease, are identified and characterized by the progressive loss of neurons and neuronal dysfunction, resulting in cognitive and motor impairment. Recent research has shown the importance of PTMs, such as phosphorylation, acetylation, methylation, ubiquitination, sumoylation, nitration, truncation, O-GlcNAcylation, and hydroxylation, in the progression of neurodegenerative disorders. PTMs can alter protein structure and function, affecting protein stability, localization, interactions, and enzymatic activity. Aberrant PTMs can lead to protein misfolding and aggregation, impaired degradation, and clearance, and ultimately, to neuronal dysfunction and death. The main objective of this review is to provide an overview of the PTMs involved in neurodegeneration, their underlying mechanisms, methods to isolate PTMs, and the potential therapeutic targets for these disorders. The PTMs discussed in this article include tau phosphorylation, α-synuclein and Huntingtin ubiquitination, histone acetylation and methylation, and RNA modifications. Understanding the role of PTMs in neurodegenerative diseases may provide new therapeutic strategies for these devastating disorders.
Collapse
Affiliation(s)
- Saima Zafar
- Department of Neurology, Clinical Dementia Center and DZNE, University Medical Center Goettingen (UMG), Georg-August University, Robert-Koch-Str. 40, 37075 Goettingen, Germany
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Bolan Road, H-12, Islamabad 44000, Pakistan
| | - Shehzadi Irum Fatima
- Department of Neurology, Clinical Dementia Center and DZNE, University Medical Center Goettingen (UMG), Georg-August University, Robert-Koch-Str. 40, 37075 Goettingen, Germany
| | - Matthias Schmitz
- Department of Neurology, Clinical Dementia Center and DZNE, University Medical Center Goettingen (UMG), Georg-August University, Robert-Koch-Str. 40, 37075 Goettingen, Germany
| | - Inga Zerr
- Department of Neurology, Clinical Dementia Center and DZNE, University Medical Center Goettingen (UMG), Georg-August University, Robert-Koch-Str. 40, 37075 Goettingen, Germany
| |
Collapse
|
36
|
Bellanti R, Keddie S, Lunn MP, Rinaldi S. Ultrasensitive assay technology and fluid biomarkers for the evaluation of peripheral nerve disease. J Neurol Neurosurg Psychiatry 2024; 95:114-124. [PMID: 37821222 DOI: 10.1136/jnnp-2023-332031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/22/2023] [Indexed: 10/13/2023]
Abstract
The field of biomarker discovery is rapidly expanding. The introduction of ultrasensitive immunoassays and the growing precision of genetic technologies are poised to revolutionise the assessment and monitoring of many diseases. Given the difficulties in imaging and tissue diagnosis, there is mounting interest in serum and cerebrospinal fluid biomarkers of peripheral neuropathy. Realised and potential fluid biomarkers of peripheral nerve disease include neuronal biomarkers of axonal degeneration, glial biomarkers for peripheral demyelinating disorders, immunopathogenic biomarkers (such as the presence and titre of antibodies or the levels of cytokines) and genetic biomarkers. Several are already starting to inform clinical practice, whereas others remain under evaluation as potential indicators of disease activity and treatment response. As more biomarkers become available for clinical use, it has become increasingly difficult for clinicians and researchers to keep up-to-date with the most recent discovery and interpretation. In this review, we aim to inform practising neurologists, neuroscientists and other clinicians about recent advances in fluid biomarker technology, with a focus on single molecule arrays (Simoa), chemiluminescent enzyme immunoassays (CLEIA), electrochemiluminescence (ECL), proximity extension assays (PEA), and microfluidic technology. We discuss established and emerging fluid biomarkers of peripheral neuropathy, their clinical applications, limitations and potential future developments.
Collapse
Affiliation(s)
- Roberto Bellanti
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
| | - Stephen Keddie
- Department of Neuromuscular Diseases, The Royal London Hospital, London, UK
| | - Michael P Lunn
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, UK
- Department of Neuroinflammation, National Hospital for Neurology and Neurosurgery, London, UK
| | - Simon Rinaldi
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| |
Collapse
|
37
|
Wei SH, Hu J, Sheng Z, Zhang Q, Zhang J, Zhang B, Liu M, Zhang CY. Construction of Fluorescent G-Quadruplex Nanowires for Label-Free and Accurate Monitoring of Circular RNAs in Breast Cancer Cells and Tissues with Low Background. Anal Chem 2024; 96:599-605. [PMID: 38156620 DOI: 10.1021/acs.analchem.3c05116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Abstract
Circular RNAs (circRNAs) represent an emerging category of endogenous transcripts characterized by long half-life time, covalently closed structures, and cell-/tissue-specific expression patterns, making them potential disease biomarkers. Herein, we demonstrate the construction of fluorescent G-quadruplex nanowires for label-free and accurate monitoring of circular RNAs in breast cancer cells and tissues by integrating proximity ligation-rolling circle amplification cascade with lighting up G-quadruplex. The presence of target circRNA facilitates the SplintR ligase-mediated ligation of the padlock probe. Upon the addition of primers, the ligated padlock probe can serve as a template to initiate subsequent rolling circle amplification (RCA), generating numerous long G-quadruplex nanowires that can incorporate with thioflavin T (ThT) to generate a remarkably improved fluorescence signal. Benefiting from good specificity of SplintR ligase-mediated ligation reaction and exponential amplification efficiency of RCA, this strategy can sensitively detect target circRNA with a limit of detection of 4.65 × 10-18 M. Furthermore, this method can accurately measure cellular circRNA expression with single-cell sensitivity and discriminate the circRNA expression between healthy para-carcinoma tissues and breast cancer tissues, holding great potential in studying the pathological roles of circRNA and clinic diagnostics.
Collapse
Affiliation(s)
- Shu-Hua Wei
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Jinping Hu
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Zhimei Sheng
- Department of Pathology, Weifang Medical University, Weifang 261053, China
| | - Qian Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Jie Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Baogang Zhang
- Department of Pathology, Weifang Medical University, Weifang 261053, China
| | - Meng Liu
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Chun-Yang Zhang
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| |
Collapse
|
38
|
He S, Lundberg B, Hallberg J, Klevebro S, Pershagen G, Eneroth K, Melén E, Bottai M, Gruzieva O. Joint association of air pollution exposure and inflammation-related proteins in relation to infant lung function. Int J Hyg Environ Health 2024; 255:114294. [PMID: 37952388 DOI: 10.1016/j.ijheh.2023.114294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 09/21/2023] [Accepted: 11/06/2023] [Indexed: 11/14/2023]
Abstract
BACKGROUND AND AIM Systemic inflammation is one potential mechanism underlying negative impact of air pollution on lung function. Levels of inflammation-related proteins have the potential to characterize infants' susceptibility to air pollution induced lung function impairment. This study aimed to examine the interplay between air pollution exposure and inflammation-related proteins on lung function in 6-months-old infants. METHODS In the EMIL birth cohort from Stockholm (n = 82), dynamic spirometry, along with measurement of plasma levels of 92 systemic inflammation-related proteins (Olink Proseek Multiplex Inflammation panel) have been carried out in infants aged six months. Time-weighted average exposure to particles with an aerodynamic diameter of <10 μm (PM10), <2.5 μm (PM2.5), and nitrogen dioxide (NO2) at residential addresses from birth and onwards was estimated via validated dispersion models. To characterize the abnormality of inflammation-related protein profile, for each protein in each infant, we calculated the relative deviance of the protein level from age- and sex-specific median in terms of its age- and sex-specific interquartile range (IQR), followed by computing the absolute value of the smallest relative deviance, "minimum absolute deviance". Using linear regression models, interaction of air pollution and the abnormal inflammatory profile on lung function was estimated on the additive scale. RESULTS We found joint association of PM exposure and an abnormal inflammatory protein profile in relation to FEV0.5 and FVC. For 0.1 unit increase in minimum absolute deviance, one IQR increase in PM10 was associated with 85.9 ml (95% CI: -122.9, -48.9) additional decrease in FEV0.5, and 72.3 ml (95% CI: -121.5, -23.2) additional decrease in FVC. Similar results were obtained with PM2.5 exposure, while less apparent for NO2. CONCLUSIONS Early life air pollution exposure and abnormal inflammation-related protein profiles may interact synergistically towards lower lung function in infants.
Collapse
Affiliation(s)
- Shizhen He
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.
| | - Björn Lundberg
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Jenny Hallberg
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Susanna Klevebro
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristina Eneroth
- Environment and Health Administration, SLB-analys, Stockholm, Sweden
| | - Erik Melén
- Department of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden; Sachs' Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Matteo Bottai
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Olena Gruzieva
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden; Centre for Occupational and Environmental Medicine, Region Stockholm, Stockholm, Sweden
| |
Collapse
|
39
|
Wenson L, Leino M, Jarvius M, Heldin J, Koos B, Söderberg O. The method developer's guide to oligonucleotide design. Expert Rev Proteomics 2024; 21:65-80. [PMID: 38363709 DOI: 10.1080/14789450.2024.2318565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/22/2024] [Indexed: 02/18/2024]
Abstract
INTRODUCTION Development of new methods is essential to make great leaps in science, opening up new avenues for research, but the process behind method development is seldom described. AREAS COVERED Over the last twenty years we have been developing several new methods, such as in situ PLA, proxHCR, and MolBoolean, using oligonucleotide-conjugated antibodies to visualize protein-protein interactions. Herein, we describe the rationale behind the oligonucleotide systems of these methods. The main objective of this paper is to provide researchers with a description on how we thought when we designed those methods. We also describe in detail how the methods work and how one should interpret results. EXPERT OPINION Understanding how the methods work is important in selecting an appropriate method for your experiments. We also hope that this paper may be an inspiration for young researchers to enter the field of method development. Seeing a problem is a motivation to develop a solution.
Collapse
Affiliation(s)
- Leonie Wenson
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Mattias Leino
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Malin Jarvius
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Johan Heldin
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| | - Björn Koos
- Klinik für Anästhesiologie, Intensivmedizin und Schmerztherapie, Universitätsklinikum Knappschaftskrankenhaus Bochum-Langendreer, Ruhr-Universität Bochum, Bochum, Germany
| | - Ola Söderberg
- Department of Pharmaceutical Biosciences, Uppsala University, Biomedical center, Uppsala, Sweden
| |
Collapse
|
40
|
Du J, He JS, Wang R, Wu J, Yu X. Ultrasensitive reporter DNA sensors built on nucleic acid amplification techniques: Application in the detection of trace amount of protein. Biosens Bioelectron 2024; 243:115761. [PMID: 37864901 DOI: 10.1016/j.bios.2023.115761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 10/23/2023]
Abstract
The detection of protein is of great significance for the study of biological physiological function, early diagnosis of diseases and drug research. However, the sensitivity of traditional protein detection methods for detecting trace amount of proteins was relatively low. By integrating sensitive nucleic acid amplification techniques (NAAT) with protein detection methods, the detection limit of protein detection methods can be substantially improved. The DNA that can specifically bind to protein targets and convert protein signals into DNA signals is collectively referred to reporter DNA. Various NAATs have been used to establish NAAT-based reporter DNA sensors. And according to whether enzymes are involved in the amplification process, the NAAT-based reporter DNA sensors can be divided into two types: enzyme-assisted NAAT-based reporter DNA sensors and enzyme-free NAAT-based reporter DNA sensors. In this review, we will introduce the principles and applications of two types of NAAT-based reporter DNA sensors for detecting protein targets. Finally, the main challenges and application prospects of NAAT-based reporter DNA sensors are discussed.
Collapse
Affiliation(s)
- Jungang Du
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China
| | - Jin-Song He
- College of Food Science and Technology, Yunnan Agricultural University, Kunming, 650201, China
| | - Rui Wang
- Human Phenome Institute, State Key Laboratory of Genetic Engineering, Fudan University, Shanghai, 200438, China.
| | - Jian Wu
- College of Biosystems Engineering and Food Science, Zhejiang University, 866 Yuhangtang Road, Hangzhou, 310058, China; ZJU-Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University, Hangzhou, 311215, China.
| | - Xiaoping Yu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
| |
Collapse
|
41
|
Xia X, Jiang M, Lin C, Ke R. Visualization of Individual RNA Molecules by Proximity Ligation-Based Chromogenic In Situ Hybridization Assay. Methods Mol Biol 2024; 2822:143-156. [PMID: 38907917 DOI: 10.1007/978-1-0716-3918-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2024]
Abstract
RNA in situ hybridization reveals the abundance and location of gene expression in cells or tissues, providing a technical basis for the clinical diagnosis of diseases. In this chapter, we show a "V" shape probe-mediated single-molecule chromogenic in situ hybridization (vsmCISH) technique for bright-field visualization of individual RNA molecules. In our method, several pairs of target hybridization probes are hybridized to RNA molecules and each probe pair forms a "V" shape overhang. The overhang oligonucleotides then mediated the proximity ligation to form DNA circles, followed by rolling circle amplification for signal enhancement and enzyme-catalyzed chromogenic reaction-based readout. The colorimetric assay avoids problems such as photobleaching and autofluorescence of current fluorescent in situ hybridization-based single-molecule RNA detection techniques. Furthermore, the relatively straightforward protocol makes the method useful for biological research and clinical diagnosis applications.
Collapse
Affiliation(s)
- Xueqian Xia
- School of Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Meng Jiang
- School of Medicine, Huaqiao University, Xiamen, Fujian, China
- College of Materials Science and Engineering, Huaqiao University, Xiamen, Fujian, China
| | - Chen Lin
- School of Medicine, Huaqiao University, Xiamen, Fujian, China
| | - Rongqin Ke
- School of Medicine, Huaqiao University, Xiamen, Fujian, China.
| |
Collapse
|
42
|
Novoa-Aponte L, Philpott CC. Proximity Ligation Assay for the Analysis of Iron-Mediated Protein-Protein Interactions in the Nucleus. Methods Mol Biol 2024; 2839:53-75. [PMID: 39008248 DOI: 10.1007/978-1-0716-4043-2_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Iron forms essential cofactors used by many nuclear enzymes involved in genome maintenance. However, unchaperoned nuclear iron may represent a threat to the surrounding genetic material as it promotes redox toxicity that may affect DNA integrity. Safely handling intracellular iron implies metal transfer and cofactor assembly processes based on protein-protein interactions. Identifying those interactions commonly occurs via high-throughput approaches using affinity purification or proximity labeling coupled with mass spectrometry analysis. However, these methods do not identify the subcellular location of the interactions. The one-on-one confirmation of proposed nuclear interactions is also challenging. Many approaches used to look at protein interactions are not tailored for looking at the nucleus because the methods used to solubilize nuclear content are harsh enough to disrupt those transient interactions. Here, we describe step-by-step the use of Proximity Ligation Assay (PLA) to analyze iron-mediated protein-protein interactions in the nucleus of cultured human cells. PLA allows the subcellular visualization of the interactions via the in situ detection of the two interacting proteins using fluorescence confocal microscopy. Briefly, cells are fixed, blocked, permeabilized, and incubated with primary antibodies directed to target proteins. Primary antibodies are recognized using PLA probes consisting of one PLUS and one MINUS oligonucleotide-labeled secondary antibody. If the two proteins are close enough (<40 nm), the PLA probes are ligated and used as the template for rolling circle amplification (RCA) with fluorescently labeled oligonucleotides that yield a signal detectable using fluorescence confocal microscopy. A fluorescently labeled membrane-specific stain (WGA) and the DNA-specific probe DAPI are used to identify cellular and nuclear boundaries, respectively. Confocal images are then analyzed using the CellProfiler software to confirm the abundance and localization of the studied protein-protein interactions.
Collapse
Affiliation(s)
- Lorena Novoa-Aponte
- Genetics and Metabolism Section, Liver Diseases Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Caroline C Philpott
- Genetics and Metabolism Section, Liver Diseases Branch, National Institutes of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
43
|
Torres HM, Fang F, May DG, Bosshardt P, Hinojosa L, Roux KJ, Tao J. Comprehensive analysis of the proximity-dependent nuclear interactome for the oncoprotein NOTCH1 in live cells. J Biol Chem 2024; 300:105522. [PMID: 38043798 PMCID: PMC10788534 DOI: 10.1016/j.jbc.2023.105522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 10/25/2023] [Accepted: 11/21/2023] [Indexed: 12/05/2023] Open
Abstract
Notch signaling plays a critical role in cell fate decisions in all cell types. Furthermore, gain-of-function mutations in NOTCH1 have been uncovered in many human cancers. Disruption of Notch signaling has recently emerged as an attractive disease treatment strategy. However, the nuclear interaction landscape of the oncoprotein NOTCH1 remains largely unexplored. We therefore employed here a proximity-dependent biotin identification approach to identify in vivo protein associations with the nuclear Notch1 intracellular domain in live cells. We identified a large set of previously reported and unreported proteins that associate with NOTCH1, including general transcription and elongation factors, DNA repair and replication factors, coactivators, corepressors, and components of the NuRD and SWI/SNF chromatin remodeling complexes. We also found that Notch1 intracellular domain associates with protein modifiers and components of other signaling pathways that may influence Notch signal transduction and protein stability such as USP7. We further validated the interaction of NOTCH1 with histone deacetylase 1 or GATAD2B using protein network analysis, proximity-based ligation, in vivo cross-linking and coimmunoprecipitation assays in several Notch-addicted cancer cell lines. Through data mining, we also revealed potential drug targets for the inhibition of Notch signaling. Collectively, these results provide a valuable resource to uncover the mechanisms that fine-tune Notch signaling in tumorigenesis and inform therapeutic targets for Notch-addicted tumors.
Collapse
Affiliation(s)
- Haydee M Torres
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA
| | - Fang Fang
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Danielle G May
- Enabling Technologies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Paige Bosshardt
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Leetoria Hinojosa
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA
| | - Kyle J Roux
- Enabling Technologies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA
| | - Jianning Tao
- Cancer Biology & Immunotherapies Group, Sanford Research, Sioux Falls, South Dakota, USA; Department of Chemistry and Biochemistry, South Dakota State University, Brookings, South Dakota, USA; Department of Pediatrics, Sanford School of Medicine, University of South Dakota, Sioux Falls, South Dakota, USA.
| |
Collapse
|
44
|
Kara S, Nimmerjahn F. Analyzing Fcγ-Receptor Interactions on Monocytes with the Proximity Ligation Assay (PLA). Methods Mol Biol 2024; 2713:377-388. [PMID: 37639137 DOI: 10.1007/978-1-0716-3437-0_26] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/29/2023]
Abstract
Proximity ligation assays (PLA) enable the detection and characterization of protein interactions independent of protein abundance or genetic modifications. This technique exploits both antibody and DNA-binding features, providing high selectivity and sensitivity for protein recognition and visualization of single-protein molecules with high spatial accuracy. Here, we describe the general procedure for a direct PLA on splenic monocytes to analyze FcγRIIb homodimerization. However, this method can be applied to other cells and receptors of interest.
Collapse
Affiliation(s)
- Sibel Kara
- Division of Genetics, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany
| | - Falk Nimmerjahn
- Division of Genetics, Department of Biology, University of Erlangen-Nürnberg, Erlangen, Germany.
| |
Collapse
|
45
|
Duckworth AD, Slupsky JR, Kalakonda N. Highly Multiplexed and Simultaneous Characterization of Protein and RNA in Single Cells by Flow or Mass Cytometry Platforms Using Proximity Ligation Assay for RNA. Methods Mol Biol 2024; 2752:143-165. [PMID: 38194033 DOI: 10.1007/978-1-0716-3621-3_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
In situ hybridization of oligonucleotide probes to intracellular RNA allows quantification of predefined gene transcripts within millions of single cells using cytometry platforms. Previous methods have been hindered by the number of RNA that can be analyzed simultaneously. Here we describe a method called proximity ligation assay for RNA (PLAYR) that permits highly multiplexed RNA analysis that can be combined with antibody staining. Potentially any number of RNA combined with antigen can be analyzed together, being limited only by the number of analytes that can be measured simultaneously.
Collapse
Affiliation(s)
- Andrew D Duckworth
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Joseph R Slupsky
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Nagesh Kalakonda
- Department of Molecular and Clinical Cancer Medicine, Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK.
| |
Collapse
|
46
|
Chang YL, Yang CC, Huang YY, Chen YA, Yang CW, Liao CY, Li H, Wu CS, Lin CH, Teng SC. The HSP40 family chaperone isoform DNAJB6b prevents neuronal cells from tau aggregation. BMC Biol 2023; 21:293. [PMID: 38110916 PMCID: PMC10729500 DOI: 10.1186/s12915-023-01798-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 12/05/2023] [Indexed: 12/20/2023] Open
Abstract
BACKGROUND Alzheimer's disease (AD) is the most common neurodegenerative disorder with clinical presentations of progressive cognitive and memory deterioration. The pathologic hallmarks of AD include tau neurofibrillary tangles and amyloid plaque depositions in the hippocampus and associated neocortex. The neuronal aggregated tau observed in AD cells suggests that the protein folding problem is a major cause of AD. J-domain-containing proteins (JDPs) are the largest family of cochaperones, which play a vital role in specifying and directing HSP70 chaperone functions. JDPs bind substrates and deliver them to HSP70. The association of JDP and HSP70 opens the substrate-binding domain of HSP70 to help the loading of the clients. However, in the initial HSP70 cycle, which JDP delivers tau to the HSP70 system in neuronal cells remains unclear. RESULTS We screened the requirement of a diverse panel of JDPs for preventing tau aggregation in the human neuroblastoma cell line SH-SY5Y by a filter retardation method. Interestingly, knockdown of DNAJB6, one of the JDPs, displayed tau aggregation and overexpression of DNAJB6b, one of the isoforms generated from the DNAJB6 gene by alternative splicing, reduced tau aggregation. Further, the tau bimolecular fluorescence complementation assay confirmed the DNAJB6b-dependent tau clearance. The co-immunoprecipitation and the proximity ligation assay demonstrated the protein-protein interaction between tau and the chaperone-cochaperone complex. The J-domain of DNAJB6b was critical for preventing tau aggregation. Moreover, reduced DNAJB6 expression and increased tau aggregation were detected in an age-dependent manner in immunohistochemical analysis of the hippocampus tissues of a mouse model of tau pathology. CONCLUSIONS In summary, downregulation of DNAJB6b increases the insoluble form of tau, while overexpression of DNAJB6b reduces tau aggregation. Moreover, DNAJB6b associates with tau. Therefore, this study reveals that DNAJB6b is a direct sensor for its client tau in the HSP70 folding system in neuronal cells, thus helping to prevent AD.
Collapse
Affiliation(s)
- Ya-Lan Chang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Chan-Chih Yang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Yun-Yu Huang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Yi-An Chen
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Chia-Wei Yang
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Chia-Yu Liao
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan
| | - Hsun Li
- Department of Neurology, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 10051, Taiwan
| | - Ching-Shyi Wu
- Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan
| | - Chin-Hsien Lin
- Department of Neurology, National Taiwan University Hospital, No. 7, Chung-Shan South Road, Taipei, 10051, Taiwan.
| | - Shu-Chun Teng
- Department of Microbiology, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 10051, Taiwan.
- Center of Precision Medicine, National Taiwan University, Taipei, 10051, Taiwan.
| |
Collapse
|
47
|
Zhang L, He M, Wang P, Yu J, Li D. A protocol to investigate the effects of lncRNAs on in vivo protein-protein interactions using proximity ligation assay. STAR Protoc 2023; 4:102757. [PMID: 38043056 PMCID: PMC10701416 DOI: 10.1016/j.xpro.2023.102757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Revised: 11/01/2023] [Accepted: 11/16/2023] [Indexed: 12/05/2023] Open
Abstract
A large variety of cellular signals are triggered and transmitted by protein-protein interactions (PPIs). Long noncoding RNAs regulate PPIs by enhancing or destabilizing these interactions. Here, we use the proximity ligation assay technique to determine PPIs between p53 and SET regulated by long intergenic noncoding RNA 324 (LINC00324). We detail procedures for establishing LINC00324 knockdown and overexpression U2OS and HepG2 cells followed by in situ PLA protocol. This approach has many potential applications for the study of cellular factors that regulate PPIs. For complete details on the use and execution of this protocol, please refer to Zhang et al. (2023).1.
Collapse
Affiliation(s)
- Ling Zhang
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China
| | - Mengfan He
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China
| | - Peizhen Wang
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China
| | - Jianfeng Yu
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China; Department of Life Science and Technology, Changshu Institute of Technology, 99 South Third Ring Road, Suzhou 215500, China
| | - Dawei Li
- Center for Translational Medicine, The Affiliated Zhangjiagang Hospital of Soochow University, Suzhou Medical College of Soochow University, 68 Jiyang West Road, Suzhou 215600, China.
| |
Collapse
|
48
|
Santos R, Lokmane L, Ozdemir D, Traoré C, Agesilas A, Hakibilen C, Lenkei Z, Zala D. Local glycolysis fuels actomyosin contraction during axonal retraction. J Cell Biol 2023; 222:e202206133. [PMID: 37902728 PMCID: PMC10616508 DOI: 10.1083/jcb.202206133] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 04/04/2023] [Accepted: 10/02/2023] [Indexed: 10/31/2023] Open
Abstract
In response to repulsive cues, axonal growth cones can quickly retract. This requires the prompt activity of contractile actomyosin, which is formed by the non-muscle myosin II (NMII) bound to actin filaments. NMII is a molecular motor that provides the necessary mechanical force at the expense of ATP. Here, we report that this process is energetically coupled to glycolysis and is independent of cellular ATP levels. Induction of axonal retraction requires simultaneous generation of ATP by glycolysis, as shown by chemical inhibition and genetic knock-down of GAPDH. Co-immunoprecipitation and proximal-ligation assay showed that actomyosin associates with ATP-generating glycolytic enzymes and that this association is strongly enhanced during retraction. Using microfluidics, we confirmed that the energetic coupling between glycolysis and actomyosin necessary for axonal retraction is localized to the growth cone and near axonal shaft. These results indicate a tight coupling between on-demand energy production by glycolysis and energy consumption by actomyosin contraction suggesting a function of glycolysis in axonal guidance.
Collapse
Affiliation(s)
- Renata Santos
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Laboratory of Dynamics of Neuronal Structure in Health and Disease, Paris, France
- Institut des Sciences Biologiques, Centre national de la recherche scientifique, Paris, France
| | - Ludmilla Lokmane
- Institut de Biologie de l’Ecole Normale Supérieure, École Normale Supérieure, Centre national de la recherche scientifique, Paris Sciences et Lettres Research University, Paris, France
| | - Dersu Ozdemir
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Laboratory of Dynamics of Neuronal Structure in Health and Disease, Paris, France
| | - Clément Traoré
- Brain Plasticity Unit, École Supérieure de Physique et de Chimie Industrielles–ParisTech, Paris, France
| | - Annabelle Agesilas
- Brain Plasticity Unit, École Supérieure de Physique et de Chimie Industrielles–ParisTech, Paris, France
| | - Coralie Hakibilen
- Brain Plasticity Unit, École Supérieure de Physique et de Chimie Industrielles–ParisTech, Paris, France
| | - Zsolt Lenkei
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Laboratory of Dynamics of Neuronal Structure in Health and Disease, Paris, France
- Brain Plasticity Unit, École Supérieure de Physique et de Chimie Industrielles–ParisTech, Paris, France
- GHU-Paris Psychiatrie et Neurosciences, Hôpital Sainte Anne, Paris, France
| | - Diana Zala
- Université Paris Cité, Institute of Psychiatry and Neuroscience of Paris, INSERM U1266, Laboratory of Dynamics of Neuronal Structure in Health and Disease, Paris, France
- Brain Plasticity Unit, École Supérieure de Physique et de Chimie Industrielles–ParisTech, Paris, France
| |
Collapse
|
49
|
Ciganda M, Sotelo-Silveira J, Dubey AP, Pandey P, Smith JT, Shen S, Qu J, Smircich P, Read LK. Translational control by Trypanosoma brucei DRBD18 contributes to the maintenance of the procyclic state. RNA (NEW YORK, N.Y.) 2023; 29:1881-1895. [PMID: 37730435 PMCID: PMC10653379 DOI: 10.1261/rna.079625.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 08/24/2023] [Indexed: 09/22/2023]
Abstract
Trypanosoma brucei occupies distinct niches throughout its life cycle, within both the mammalian and tsetse fly hosts. The immunological and biochemical complexity and variability of each of these environments require a reshaping of the protein landscape of the parasite both to evade surveillance and face changing metabolic demands. In kinetoplastid protozoa, including T. brucei, posttranscriptional control mechanisms are the primary means of gene regulation, and these are often mediated by RNA-binding proteins. DRBD18 is a T. brucei RNA-binding protein that reportedly interacts with ribosomal proteins and translation factors. Here, we tested a role for DRBD18 in translational control. We validate the DRBD18 interaction with translating ribosomes and the translation initiation factor, eIF3a. We further show that DRBD18 depletion by RNA interference leads to altered polysomal profiles with a specific depletion of heavy polysomes. Ribosome profiling analysis reveals that 101 transcripts change in translational efficiency (TE) upon DRBD18 depletion: 41 exhibit decreased TE and 60 exhibit increased TE. A further 66 transcripts are buffered, that is, changes in transcript abundance are compensated by changes in TE such that the total translational output is expected not to change. In DRBD18-depleted cells, a set of transcripts that codes for procyclic form-specific proteins is translationally repressed while, conversely, transcripts that code for bloodstream form- and metacyclic form-specific proteins are translationally enhanced. RNA immunoprecipitation/qRT-PCR indicates that DRBD18 associates with members of both repressed and enhanced cohorts. These data suggest that DRBD18 contributes to the maintenance of the procyclic state through both positive and negative translational control of specific mRNAs.
Collapse
Affiliation(s)
- Martin Ciganda
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - José Sotelo-Silveira
- Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay
| | - Ashutosh P Dubey
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Parul Pandey
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Joseph T Smith
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| | - Shichen Shen
- Department of Pharmaceutical Sciences, University at Buffalo and NYS Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo and NYS Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, USA
| | - Pablo Smircich
- Laboratorio de Bioinformática, Departamento de Genómica, Instituto de Investigaciones Biológicas Clemente Estable, Montevideo 11600, Uruguay
- Sección Genómica Funcional, Facultad de Ciencias, Universidad de la República, Montevideo 11400, Uruguay
| | - Laurie K Read
- Department of Microbiology, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, New York 14203, USA
| |
Collapse
|
50
|
Zhang B, Li Y, Zhang J, Wang Y, Liang C, Lu T, Zhang C, Liu L, Qin Y, He J, Zhao X, Yu J, Hao J, Yang J, Li MJ, Yao Z, Ma S, Cheng H, Cheng T, Shi L. ADAR1 links R-loop homeostasis to ATR activation in replication stress response. Nucleic Acids Res 2023; 51:11668-11687. [PMID: 37831098 PMCID: PMC10681745 DOI: 10.1093/nar/gkad839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 09/12/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Unscheduled R-loops are a major source of replication stress and DNA damage. R-loop-induced replication defects are sensed and suppressed by ATR kinase, whereas it is not known whether R-loop itself is actively involved in ATR activation and, if so, how this is achieved. Here, we report that the nuclear form of RNA-editing enzyme ADAR1 promotes ATR activation and resolves genome-wide R-loops, a process that requires its double-stranded RNA-binding domains. Mechanistically, ADAR1 interacts with TOPBP1 and facilitates its loading on perturbed replication forks by enhancing the association of TOPBP1 with RAD9 of the 9-1-1 complex. When replication is inhibited, DNA-RNA hybrid competes with TOPBP1 for ADAR1 binding to promote the translocation of ADAR1 from damaged fork to accumulate at R-loop region. There, ADAR1 recruits RNA helicases DHX9 and DDX21 to unwind R-loops, simultaneously allowing TOPBP1 to stimulate ATR more efficiently. Collectively, we propose that the tempo-spatially regulated assembly of ADAR1-nucleated protein complexes link R-loop clearance and ATR activation, while R-loops crosstalk with blocked replication forks by transposing ADAR1 to finetune ATR activity and safeguard the genome.
Collapse
Affiliation(s)
- Biao Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Yi Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jieyou Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Yuejiao Wang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Can Liang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ting Lu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Chunyong Zhang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Ling Liu
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Yan Qin
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jiahuan He
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 100006, Beijing, China
| | - Xiangnan Zhao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Jia Yu
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
- State Key Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & School of Basic Medicine, Peking Union Medical College, 100006, Beijing, China
| | - Jihui Hao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Jie Yang
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Mulin Jun Li
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Zhi Yao
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Shuai Ma
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| | - Hui Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Tao Cheng
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
- Tianjin Institutes of Health Science, National Clinical Research Center for Blood Diseases, Institute of Hematology and Blood Diseases Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Tianjin 300020, China
| | - Lei Shi
- State Key Laboratory of Experimental Hematology, Haihe Laboratory of Cell Ecosystem, Key Laboratory of Breast Cancer Prevention and Therapy (Ministry of Education), Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China
| |
Collapse
|