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Silva JM, Qi W, Pinho AJ, Pratas D. AlcoR: alignment-free simulation, mapping, and visualization of low-complexity regions in biological data. Gigascience 2022; 12:giad101. [PMID: 38091509 PMCID: PMC10716826 DOI: 10.1093/gigascience/giad101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 09/29/2023] [Accepted: 11/07/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Low-complexity data analysis is the area that addresses the search and quantification of regions in sequences of elements that contain low-complexity or repetitive elements. For example, these can be tandem repeats, inverted repeats, homopolymer tails, GC-biased regions, similar genes, and hairpins, among many others. Identifying these regions is crucial because of their association with regulatory and structural characteristics. Moreover, their identification provides positional and quantity information where standard assembly methodologies face significant difficulties because of substantial higher depth coverage (mountains), ambiguous read mapping, or where sequencing or reconstruction defects may occur. However, the capability to distinguish low-complexity regions (LCRs) in genomic and proteomic sequences is a challenge that depends on the model's ability to find them automatically. Low-complexity patterns can be implicit through specific or combined sources, such as algorithmic or probabilistic, and recurring to different spatial distances-namely, local, medium, or distant associations. FINDINGS This article addresses the challenge of automatically modeling and distinguishing LCRs, providing a new method and tool (AlcoR) for efficient and accurate segmentation and visualization of these regions in genomic and proteomic sequences. The method enables the use of models with different memories, providing the ability to distinguish local from distant low-complexity patterns. The method is reference and alignment free, providing additional methodologies for testing, including a highly flexible simulation method for generating biological sequences (DNA or protein) with different complexity levels, sequence masking, and a visualization tool for automatic computation of the LCR maps into an ideogram style. We provide illustrative demonstrations using synthetic, nearly synthetic, and natural sequences showing the high efficiency and accuracy of AlcoR. As large-scale results, we use AlcoR to unprecedentedly provide a whole-chromosome low-complexity map of a recent complete human genome and the haplotype-resolved chromosome pairs of a heterozygous diploid African cassava cultivar. CONCLUSIONS The AlcoR method provides the ability of fast sequence characterization through data complexity analysis, ideally for scenarios entangling the presence of new or unknown sequences. AlcoR is implemented in C language using multithreading to increase the computational speed, is flexible for multiple applications, and does not contain external dependencies. The tool accepts any sequence in FASTA format. The source code is freely provided at https://github.com/cobilab/alcor.
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Affiliation(s)
- Jorge M Silva
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Weihong Qi
- Functional Genomics Center Zurich, ETH Zurich and University of Zurich, Winterthurerstrasse, 190, 8057, Zurich, Switzerland
- SIB, Swiss Institute of Bioinformatics, 1202, Geneva, Switzerland
| | - Armando J Pinho
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
| | - Diogo Pratas
- IEETA, Institute of Electronics and Informatics Engineering of Aveiro, and LASI, Intelligent Systems Associate Laboratory, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
- Department of Electronics Telecommunications and Informatics, University of Aveiro, Campus Universitario de Santiago, 3810-193, Aveiro, Portugal
- Department of Virology, University of Helsinki, Haartmaninkatu, 3, 00014 Helsinki, Finland
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Li GH, Qu Q, Qi TT, Teng XQ, Zhu HH, Wang JJ, Lu Q, Qu J. Super-enhancers: a new frontier for epigenetic modifiers in cancer chemoresistance. J Exp Clin Cancer Res 2021; 40:174. [PMID: 34011395 PMCID: PMC8132395 DOI: 10.1186/s13046-021-01974-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/05/2021] [Indexed: 02/06/2023] Open
Abstract
Although new developments of surgery, chemotherapy, radiotherapy, and immunotherapy treatments for cancer have improved patient survival, the emergence of chemoresistance in cancer has significant impacts on treatment effects. The development of chemoresistance involves several polygenic, progressive mechanisms at the molecular and cellular levels, as well as both genetic and epigenetic heterogeneities. Chemotherapeutics induce epigenetic reprogramming in cancer cells, converting a transient transcriptional state into a stably resistant one. Super-enhancers (SEs) are central to the maintenance of identity of cancer cells and promote SE-driven-oncogenic transcriptions to which cancer cells become highly addicted. This dependence on SE-driven transcription to maintain chemoresistance offers an Achilles' heel for chemoresistance. Indeed, the inhibition of SE components dampens oncogenic transcription and inhibits tumor growth to ultimately achieve combined sensitization and reverse the effects of drug resistance. No reviews have been published on SE-related mechanisms in the cancer chemoresistance. In this review, we investigated the structure, function, and regulation of chemoresistance-related SEs and their contributions to the chemotherapy via regulation of the formation of cancer stem cells, cellular plasticity, the microenvironment, genes associated with chemoresistance, noncoding RNAs, and tumor immunity. The discovery of these mechanisms may aid in the development of new drugs to improve the sensitivity and specificity of cancer cells to chemotherapy drugs.
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Affiliation(s)
- Guo-Hua Li
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiang Qu
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha, 410008, People's Republic of China
| | - Ting-Ting Qi
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Xin-Qi Teng
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Hai-Hong Zhu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Jiao-Jiao Wang
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China
| | - Qiong Lu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
| | - Jian Qu
- Department of Pharmacy, the Second Xiangya Hospital, Central South University; Institute of Clinical Pharmacy, Central South University, 139 Middle Renmin Road, Changsha, Hunan, 410011, People's Republic of China.
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Feng X, Hao X, Shi R, Xia Z, Huang L, Yu Q, Zhou F. Detection and Comparative Analysis of Methylomic Biomarkers of Rheumatoid Arthritis. Front Genet 2020; 11:238. [PMID: 32292416 PMCID: PMC7119472 DOI: 10.3389/fgene.2020.00238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 02/28/2020] [Indexed: 01/05/2023] Open
Abstract
Rheumatoid arthritis (RA) is a common autoimmune disorder influenced by both genetic and environmental factors. To investigate possible contributions of DNA methylation to the etiology of RA with minimum confounding genetic heterogeneity, we investigated genome-wide DNA methylation in disease-discordant monozygotic twin pairs. This study hypothesized that methylomic biomarkers might facilitate accurate RA detection. A comprehensive series of biomarker detection algorithms were utilized to find the best methylomic biomarkers for detecting RA patients using the methylomic data of the peripheral blood samples. The best model achieved 100.00% in accuracy (Acc) with 81 methylomic biomarkers and a 10-fold cross-validation (10FCV) strategy. Some of the methylomic biomarkers were experimentally confirmed to be associated with the onset or development of RA. It is also interesting to observe that many of the detected biomarkers were from chromosome Y, supporting the knowledge that RA has a significant gender discrepancy.
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Affiliation(s)
- Xin Feng
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China.,Jilin Institute of Chemical Technology, Jilin, China.,BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Xubing Hao
- BioKnow Health Informatics Lab, College of Software, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Ruoyao Shi
- BioKnow Health Informatics Lab, College of Life Sciences, Jilin University, Changchun, China
| | - Zhiqiang Xia
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Lan Huang
- College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, China
| | - Fengfeng Zhou
- BioKnow Health Informatics Lab, College of Computer Science and Technology, and Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, Jilin University, Changchun, China
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