Human phenomics is defned as the comprehensive collection of observable phenotypes and characteristics infuenced by a complex interplay among factors at multiple scales.These factors include genes,epigenetics at the m...Human phenomics is defned as the comprehensive collection of observable phenotypes and characteristics infuenced by a complex interplay among factors at multiple scales.These factors include genes,epigenetics at the microscopic level,organs,microbiome at the mesoscopic level,and diet and environmental exposures at the macroscopic level.“Phenomic imaging”utilizes various imaging techniques to visualize and measure anatomical structures,biological functions,metabolic processes,and biochemical activities across diferent scales,both in vivo and ex vivo.Unlike conventional medical imaging focused on disease diagnosis,phenomic imaging captures both normal and abnormal traits,facilitating detailed correlations between macro-and micro-phenotypes.This approach plays a crucial role in deciphering phenomes.This review provides an overview of diferent phenomic imaging modalities and their applications in human phenomics.Additionally,it explores the associations between phenomic imaging and other omics disciplines,including genomics,transcriptomics,proteomics,immunomics,and metabolomics.By integrating phenomic imaging with other omics data,such as genomics and metabolomics,a comprehensive understanding of biological systems can be achieved.This integration paves the way for the development of new therapeutic approaches and diagnostic tools.展开更多
Characterization of the colon cancer immunome and its autoantibody signature from differentially-reactive antigens （DIRAGs） could provide insights into aberrant cellular mechanisms or enriched networks associated wi...Characterization of the colon cancer immunome and its autoantibody signature from differentially-reactive antigens （DIRAGs） could provide insights into aberrant cellular mechanisms or enriched networks associated with diseases. The purpose of this study was to characterize the antibody profile of plasma samples from 32 colorectal cancer （CRC） patients and 32 controls using proteins isolated from 15,417 human cDNA expression clones on microarrays. 671 unique DIRAGs were identified and 632 were more highly reactive in CRC samples. Bioinformatics analyses reveal that compared to control samples, the immunoproteomic IgG profiling of CRC samples is mainly associated with cell death, survival, and proliferation pathways, especially proteins involved in EIF2and mTOR signaling. Ribosomal proteins （e.g., RPL7, RPL22, and RPL27A） and CRC-related genes such as APC, AXIN1, E2F4, MSH2, PMS2, and TP53 were highly enriched. In addition, dif- ferential pathways were observed between the CRC and control samples. Furthermore, 103 DIR- AGs were reported in the SEREX antigen database, demonstrating our ability to identify known and new reactive antigens. We also found an overlap of 7 antigens with 48 ＂CRC genes.＂ These data indicate that immunomies profiling on protein mieroarrays is able to reveal the complexity of immune responses in cancerous diseases and faithfully reflects the underlying pathology.展开更多
基金Shanghai Municipal Science and Technology Major Project(2017SHZDZX01).
文摘Human phenomics is defned as the comprehensive collection of observable phenotypes and characteristics infuenced by a complex interplay among factors at multiple scales.These factors include genes,epigenetics at the microscopic level,organs,microbiome at the mesoscopic level,and diet and environmental exposures at the macroscopic level.“Phenomic imaging”utilizes various imaging techniques to visualize and measure anatomical structures,biological functions,metabolic processes,and biochemical activities across diferent scales,both in vivo and ex vivo.Unlike conventional medical imaging focused on disease diagnosis,phenomic imaging captures both normal and abnormal traits,facilitating detailed correlations between macro-and micro-phenotypes.This approach plays a crucial role in deciphering phenomes.This review provides an overview of diferent phenomic imaging modalities and their applications in human phenomics.Additionally,it explores the associations between phenomic imaging and other omics disciplines,including genomics,transcriptomics,proteomics,immunomics,and metabolomics.By integrating phenomic imaging with other omics data,such as genomics and metabolomics,a comprehensive understanding of biological systems can be achieved.This integration paves the way for the development of new therapeutic approaches and diagnostic tools.
基金supported by the Life Science Krems Fund (Project No. 30)Jubilumsfonds of the Austrian National Bank (Project No. 15192)Vienna Science and Technology Fund (Project No LS11-026) of Austria
文摘Characterization of the colon cancer immunome and its autoantibody signature from differentially-reactive antigens （DIRAGs） could provide insights into aberrant cellular mechanisms or enriched networks associated with diseases. The purpose of this study was to characterize the antibody profile of plasma samples from 32 colorectal cancer （CRC） patients and 32 controls using proteins isolated from 15,417 human cDNA expression clones on microarrays. 671 unique DIRAGs were identified and 632 were more highly reactive in CRC samples. Bioinformatics analyses reveal that compared to control samples, the immunoproteomic IgG profiling of CRC samples is mainly associated with cell death, survival, and proliferation pathways, especially proteins involved in EIF2and mTOR signaling. Ribosomal proteins （e.g., RPL7, RPL22, and RPL27A） and CRC-related genes such as APC, AXIN1, E2F4, MSH2, PMS2, and TP53 were highly enriched. In addition, dif- ferential pathways were observed between the CRC and control samples. Furthermore, 103 DIR- AGs were reported in the SEREX antigen database, demonstrating our ability to identify known and new reactive antigens. We also found an overlap of 7 antigens with 48 ＂CRC genes.＂ These data indicate that immunomies profiling on protein mieroarrays is able to reveal the complexity of immune responses in cancerous diseases and faithfully reflects the underlying pathology.
