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Liu J, Chang X, Qian L, Chen S, Xue Z, Wu J, Luo D, Huang B, Fan J, Guo T, Nie X. Proteomics-Derived Biomarker Panel Facilitates Distinguishing Primary Lung Adenocarcinomas With Intestinal or Mucinous Differentiation From Lung Metastatic Colorectal Cancer. Mol Cell Proteomics 2024; 23:100766. [PMID: 38608841 PMCID: PMC11092395 DOI: 10.1016/j.mcpro.2024.100766] [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: 09/12/2023] [Revised: 03/07/2024] [Accepted: 04/09/2024] [Indexed: 04/14/2024] Open
Abstract
The diagnosis of primary lung adenocarcinomas with intestinal or mucinous differentiation (PAIM) remains challenging due to the overlapping histomorphological, immunohistochemical (IHC), and genetic characteristics with lung metastatic colorectal cancer (lmCRC). This study aimed to explore the protein biomarkers that could distinguish between PAIM and lmCRC. To uncover differences between the two diseases, we used tandem mass tagging-based shotgun proteomics to characterize proteomes of formalin-fixed, paraffin-embedded tumor samples of PAIM (n = 22) and lmCRC (n = 17).Then three machine learning algorithms, namely support vector machine (SVM), random forest, and the Least Absolute Shrinkage and Selection Operator, were utilized to select protein features with diagnostic significance. These candidate proteins were further validated in an independent cohort (PAIM, n = 11; lmCRC, n = 19) by IHC to confirm their diagnostic performance. In total, 105 proteins out of 7871 proteins were significantly dysregulated between PAIM and lmCRC samples and well-separated two groups by Uniform Manifold Approximation and Projection. The upregulated proteins in PAIM were involved in actin cytoskeleton organization, platelet degranulation, and regulation of leukocyte chemotaxis, while downregulated ones were involved in mitochondrial transmembrane transport, vasculature development, and stem cell proliferation. A set of ten candidate proteins (high-level expression in lmCRC: CDH17, ATP1B3, GLB1, OXNAD1, LYST, FABP1; high-level expression in PAIM: CK7 (an established marker), NARR, MLPH, S100A14) was ultimately selected to distinguish PAIM from lmCRC by machine learning algorithms. We further confirmed using IHC that the five protein biomarkers including CDH17, CK7, MLPH, FABP1 and NARR were effective biomarkers for distinguishing PAIM from lmCRC. Our study depicts PAIM-specific proteomic characteristics and demonstrates the potential utility of new protein biomarkers for the differential diagnosis of PAIM and lmCRC. These findings may contribute to improving the diagnostic accuracy and guide appropriate treatments for these patients.
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Affiliation(s)
- Jiaying Liu
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Xiaona Chang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Liujia Qian
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Shuo Chen
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Zhangzhi Xue
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
| | - Junhua Wu
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Danju Luo
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Bo Huang
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Jun Fan
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Tiannan Guo
- Center for ProtTalks, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, Zhejiang, China; Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China.
| | - Xiu Nie
- Department of Pathology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China.
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Kosovsky GY, Glazko VI, Abramov OI, Glazko TT. Melanophilin Polymorphism in Ferrets of Different Color. DOKL BIOCHEM BIOPHYS 2023; 513:S12-S17. [PMID: 38189891 DOI: 10.1134/s1607672923700655] [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: 10/20/2023] [Revised: 11/08/2023] [Accepted: 11/10/2023] [Indexed: 01/09/2024]
Abstract
In mammals, the main contribution to the variability of pigmentation is made by two groups of genes directly related to the metabolic pathways of pigment synthesis and controlling the transport of melanosomes in melanocytes to keratinocytes. In order to identify the genetic basis of pigmentation variants, the nucleotide sequences of the melanophilin gene were compared in two groups of ferrets-silver-colored and wild-type animals-using sequencing of 16 exons. In carriers of silver color, a single nucleotide deletion was detected in the 9th exon, leading to a shift in the reading frame and the formation of a stop codon downstream. The protein encoded by the mutant allele is almost completely devoid of the C terminal domain of the protein responsible for the contact of melanosomes with actin during their moving to the periphery of melanocytes, but it retains the leading domain involved in the formation of melanosomes. The combination of the preservation of the N domain and the defect of the C domain of the mutant protein for the first time makes it possible to explain the incomplete dominance of the wild-type protein in heterozygotes.
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Affiliation(s)
- G Yu Kosovsky
- Afanas'ev Research Institute of Fur-Bearing Animal Breeding and Rabbit Breeding, Rodniki Village, Ramenki district, city, Moscow oblast, Russia.
| | - V I Glazko
- Afanas'ev Research Institute of Fur-Bearing Animal Breeding and Rabbit Breeding, Rodniki Village, Ramenki district, city, Moscow oblast, Russia
| | - O I Abramov
- Afanas'ev Research Institute of Fur-Bearing Animal Breeding and Rabbit Breeding, Rodniki Village, Ramenki district, city, Moscow oblast, Russia
| | - T T Glazko
- Afanas'ev Research Institute of Fur-Bearing Animal Breeding and Rabbit Breeding, Rodniki Village, Ramenki district, city, Moscow oblast, Russia
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Gu L, Xia C, Yang S, Yang G. The adaptive evolution of cancer driver genes. BMC Genomics 2023; 24:215. [PMID: 37098512 PMCID: PMC10131384 DOI: 10.1186/s12864-023-09301-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 04/08/2023] [Indexed: 04/27/2023] Open
Abstract
BACKGROUND Cancer is a life-threatening disease in humans; yet, cancer genes are frequently reported to be under positive selection. This suggests an evolutionary-genetic paradox in which cancer evolves as a secondary product of selection in human beings. However, systematic investigation of the evolution of cancer driver genes is sparse. RESULTS Using comparative genomics analysis, population genetics analysis and computational molecular evolutionary analysis, the evolution of 568 cancer driver genes of 66 cancer types were evaluated at two levels, selection on the early evolution of humans (long timescale selection in the human lineage during primate evolution, i.e., millions of years), and recent selection in modern human populations (~ 100,000 years). Results showed that eight cancer genes covering 11 cancer types were under positive selection in the human lineage (long timescale selection). And 35 cancer genes covering 47 cancer types were under positive selection in modern human populations (recent selection). Moreover, SNPs associated with thyroid cancer in three thyroid cancer driver genes (CUX1, HERC2 and RGPD3) were under positive selection in East Asian and European populations, consistent with the high incidence of thyroid cancer in these populations. CONCLUSIONS These findings suggest that cancer can be evolved, in part, as a by-product of adaptive changes in humans. Different SNPs at the same locus can be under different selection pressures in different populations, and thus should be under consideration during precision medicine, especially for targeted medicine in specific populations.
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Affiliation(s)
- Langyu Gu
- State Key Laboratory for Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong, 510275, China.
| | - Canwei Xia
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Shiyu Yang
- The Affiliated Brain Hospital, Guangzhou Medical University, Guangzhou, 510180, Guangdong, China
| | - Guofen Yang
- Department of Gynecology, First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, 510060, Guangdong, China.
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Frégeau-Proulx L, Lacouture A, Weidmann C, Jobin C, Audet-Walsh É. FACS-Free isolation and purification protocol of mouse prostate epithelial cells for organoid primary culture. MethodsX 2022; 9:101843. [PMID: 36147450 PMCID: PMC9486617 DOI: 10.1016/j.mex.2022.101843] [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: 04/14/2022] [Accepted: 08/29/2022] [Indexed: 11/17/2022] Open
Abstract
This protocol enables the generation of mouse prostate organoids without using flow cytometry, facilitating its implementation in most research laboratories. Usage of prostate organoids allows the study of complex in vivo phenotypes, beyond what can be done with immortalized cell lines.
The prostate is a gland that contributes to men's fertility. It is highly responsive to androgens and is often the site of carcinogenesis, as prostate cancer is the most frequent cancer in men in over a hundred countries. To study the normal prostate, few in vitro models exist, and most of them do not express the androgen receptor (AR). To overcome this issue, prostate epithelial cells can be grown in primary culture ex vivo in 2- and 3-dimensional culture (organoids). However, methods to purify these cells often require flow cytometry, thus necessitating specialized instruments and expertise. Herein, we present a detailed protocol for the harvest, purification, and primary culture of mouse prostate epithelial cells to grow prostate organoids ex vivo. This protocol does not require flow cytometry approaches, facilitating its implementation in most research laboratories, and organoids grown with this protocol are highly responsive to androgens. In summary, we present a new simple method that can be used to grow prostate organoids that recapitulate the androgen response of this gland in vivo.
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Affiliation(s)
- Lilianne Frégeau-Proulx
- Endocrinology - Nephrology Research Axis, CHU de Québec - Université Laval Research Center, Québec, QC, Canada.,Department of molecular medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada.,Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Aurélie Lacouture
- Endocrinology - Nephrology Research Axis, CHU de Québec - Université Laval Research Center, Québec, QC, Canada.,Department of molecular medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada.,Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Cindy Weidmann
- Endocrinology - Nephrology Research Axis, CHU de Québec - Université Laval Research Center, Québec, QC, Canada.,Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Cynthia Jobin
- Endocrinology - Nephrology Research Axis, CHU de Québec - Université Laval Research Center, Québec, QC, Canada.,Department of molecular medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada.,Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
| | - Étienne Audet-Walsh
- Endocrinology - Nephrology Research Axis, CHU de Québec - Université Laval Research Center, Québec, QC, Canada.,Department of molecular medicine, Faculty of Medicine, Université Laval, Québec, QC, Canada.,Centre de recherche sur le cancer de l'Université Laval, Québec, QC, Canada
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