Investigating Cryptosporidium spp. Using Genomic, Proteomic and Transcriptomic Techniques: Current Progress and Future Directions
Abstract
:1. Introduction
2. Genomics of Cryptosporidium spp.
2.1. Exploring Cryptosporidium Diversity and Evolutionary History through Whole Genome Sequencing
2.1.1. Early Studies on the Cryptosporidium Genome Preceding the Genomic Era
2.1.2. The Cryptosporidium Genomic Era: Opening Paths for Future Analyses
2.1.3. Draft Genome Sequencing to Enhance Our Understanding of Cryptosporidium Parasites
2.1.4. Utilizing the Latest Genomic Advancements for Cryptosporidium Research
2.2. Unraveling Cryptosporidium’s Secrets through Comparative Genomics
2.3. Overcoming Challenges in Isolating Cryptosporidium DNA from Clinical Samples
3. Proteome
3.1. MALDI-MS/MS-Based Proteomics in Cryptosporidium Studies
3.1.1. MALDI-MS/MS-Based Proteomics Preceding the Genomic Era of Cryptosporidium
3.1.2. Application of MALDI-MS/MS-Based Proteomics for Clinical Samples
3.2. LC-MS/MS-Based Proteomics in Cryptosporidium Studies
3.2.1. LC-MS/MS-Based Proteomics: Unveiling Insights into the Biology of Cryptosporidium
3.2.2. LC-MS/MS-Based Proteomics: Characterizing Specific Cryptosporidium Fractions
3.2.3. LC-MS/MS-Based Proteomics: Host–Parasite Interactions
3.2.4. LC-MS/MS-Based Proteomics: Drug Targets and Diagnosis
4. Transcriptome
4.1. Hybridization-Based Characterization of the Cryptosporidium Transcriptome
4.2. Reverse-Transcription PCR (RT-PCR)-Based Transcriptomics
4.3. Sequenced-Based Characterization Cryptosporidium spp.
4.3.1. Host–Parasite Interaction
4.3.2. Drug and Therapeutic Targets
5. Discussion
6. Future Perspectives
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Species | Genomes ID | Platform | Genome Size (Mbp) | # of Contigs | # of Reads | Contig N50 (bp) | Average Coverage |
---|---|---|---|---|---|---|---|
C. hominis | TU502 237895 | Sanger Dideoxy Sequencing | 8.70 | 1422 | - | 48,000 | 12 |
TU502 2012 | Illumina MiSeq | 9.10 | 119 | 1,810,060 | 238,509 | 96 | |
30976 | Illumina Genome Analyzer IIx 100 bp paired-end | 9.05 | 53 | 35,360,353 | 470,636 | 511 | |
37999 | Illumina Genome Analyzer IIx 100 bp paired-end | 9.05 | 78 | 16,569,87 | 406,678 | 367.4 | |
33537 | 454 GS-FLX Titanium | 9.60 | 1464 | 1,157,140 | 27,749 | 31 | |
30974 | 454 GS-FLX Titanium | 8.84 | 443 | 1,048,412 | 78,110 | 43 | |
SWEH2 | Ion Torrent | 8.81 | 1629 | 1,791,829 | 9465 | 35.2 | |
SWEH5 | Ion Torrent | 8.82 | 1342 | 2,058,197 | 14,514 | 42.4 | |
UdeA01 | Illumina MiSeq | 9.04 | 8 | 1,080,44 | 1,103,974 | 53.4 | |
UKH1 | Illumina MiSeq | 9.14 | 156 | 3,798,205 | 179,408 | 197.3 | |
UKH3 | Illumina MiSeq | 9.07 | 179 | 1,238,762 | 167,737 | 35.8 | |
UKH4 | Illumina HiSeq | 9.39 | 2164 | 11,895,367 | 48,766 | 321.5 | |
UKH5 | Illumina HiSeq | 9.06 | 526 | 12,649,912 | 81,885 | 362.2 | |
C. parvum | Iowa II 5807 | Sanger Dideoxy Sequencing | 9.10 | 18 | - | 1,014,526 | 13 |
UKP1 | Illumina HiSeq | 8.88 | 14 | 26,000,000 | 1,092,230 | 600 | |
31727 | Illumina Genome Analyzer IIx 100 bp paired-end | 9.08 | 337 | 13,074,496 | 76,396 | 116.0 | |
34902 | Illumina Genome Analyzer IIx 100 bp paired-end | 9.11 | 1076 | 18,907,631 | 21,594 | 168.7 | |
35090 | Illumina Genome Analyzer IIx 100 bp paired-end | 9.04 | 3256 | 14,188,762 | 4248 | 3.256 | |
C. baileyi | TAMU-09Q1 | gDNA Illumina library fragment size (bp) 654 | 8.43 | 145 | 6,240,960 | 203,018 | 70.06 |
C. muris | 5808 | 4.5× Sanger and 10× 454 | 9.25 | 97 | 520,347 | 10 | |
C. chipmunk genotype I | 1280935 | Illumina Genome Analyzer IIx 100 bp paired-end | 9.05 | 50 | 9,509,783 | 117,886 | 200 |
C. bovis | 310047 | Illumina HiSeq 250 bp paired-end | 9.11 | 59 | 7,080,000 | 444,382 | 196 |
C. ryanae | 515981 | Illumina HiSeq 250 bp paired-end | 9.06 | 100 | 5,130,000 | 231,122 | 142.5 |
C. meleagridis | UKMEL1 | Illumina MiSeq | 8.9 | 57 | 11,431,022 | 322,908 | 110.4 |
Year | The Greatest Milestone | Genomic Approach | Outcome of Study | Reference |
---|---|---|---|---|
1999 | Initial genomic exploration into C. parvum Iowa strain | Random sequence analysis |
| [13] |
2000 | First cDNA sequence survey of C. parvum Iowa oocysts/sporozoites | Random sequence analysis with GSS approach to gene discovery |
| [6] |
2004 | Complete genome sequencing of C. parvum Iowa type II strain | Whole-genome with shotgun Sanger sequencing |
| [11] |
2004 | Complete genome sequencing C. hominis TU502 | Whole-genome with shotgun Sanger sequencing |
| [19] |
2012 | Comparative genome analysis of two C. parvum isolates (TU114 and C. parvum Iowa) | Whole-genome sequencing |
| [12] |
2015 | Sequencing of genomes C. chipmunk genotype I | Whole genome sequencing |
| [23] |
2015 | Comparative genome analysis of C. hominis and C. parvum | Whole genome sequencing |
| [14] |
2016 | Sequencing of genomes: C. meleagridis UKMEL1, C. baileyi TAMU-09Q1 and C. hominis TU502_2012 and UKH1 | Draft genome sequencing |
| [7] |
2016 | Genome sequencing of Cryptosporidium spp. in clinical samples | Single-cell sequencing |
| [21] |
2017 | Sequencing of the genomes of two specimens of C. parvum form China and Egypt | Whole genome sequencing |
| [15] |
2018 | Analysis of genetic diversity of C. hominis infections in slum-dwelling infants in Bangladesh | Long-read resequencing |
| [22] |
2018 | Analysis of a zoonotic isolate of C. parvum UKP1 isolated from a person with cryptosporidiosis | Draft genome sequencing |
| [8] |
2020 | Comparative analysis of Cryptosporidium species that infect humans | Whole-genome sequencing |
| [16] |
2020 | Sequencing of the genomes of C. bovis and C. ryanae | Whole-genome sequencing |
| [9] |
Year | The Greatest Milestone | Outcome of Study | Reference |
---|---|---|---|
2000 | Initial proteomic study of whole and freeze–thawed C. parvum oocysts and freeze–thawed C. muris |
| [24] |
2007 | Proteomic analysis of C. parvum oocysts |
| [25] |
2007 | Large-scale global proteomic analysis of non-excyted and excyted C. parvum sporozoites |
| [27] |
2008 | In-depth analysis of the expressed protein repertoire of C. parvum |
| [28] |
2010 | Proteome analysis for identifying the key components of the C. parvum oocyst wall |
| [29] |
2013 | Proteome analysis of C. parvum sporozoites |
| [30] |
2015 | Proteomic analysis of rhoptry-enriched fractions from C. parvum |
| [31] |
2021 | Proteomic analysis of C. andersoni oocysts before and after excystation |
| [32] |
2021 | Proteomic analysis of Cryptosporidium spp. from clinical samples |
| [35] |
2021 | Assessing the effectiveness of cow colostrum for treating cryptosporidiosis in calves and its impact on serum proteomes |
| [33] |
2021 | Characterize the changes to the proteome induced by C. parvum infection |
| [34] |
2021 | Investigation of the underlying biochemical interaction in C57BL/6J mice infected with C. parvum |
| [26] |
Specimens | Strain | Technique | Search Engines | Reference Genome | Protein Coding Genes in Reference Genome |
---|---|---|---|---|---|
C. parvum and C.muris oocysts | Iowa and RN66 | MALDI-TOF peptide mass fingerprinting (PMF) | - | - | - |
C. parvum sporozoites | Iowa | MALDI-TOF MS | - | - | - |
C. parvum sporozoites non-excysted and excysted | ISSC162 | Combination of LC-MS/MS and iTRAQ isobaric labeling | ProQUANT software 1.1 (Applied Biosystems, Foster City, CA) | C. parvum Iowa type II | 3941 |
C. parvum excysted oocyst/sporozoite | Iowa | Three independent platforms: 1-DE LC-MS/MS, 2-DE LC-MS/MS, and MudPIT | MASCOT search tool, SEQUEST algorithm version 27 | C. parvum Iowa type II | 3941 |
C. parvum sporozoites | Iowa | SDS-PAGE and LC-MS/MS | MASCOT search tool | C. parvum Iowa type II C. hominis TU502 | 3941 3886 |
C. parvum oocysts | Iowa | LC-MS/MS | SEQUEST search tool, NR database at the NCBI | C. parvum Iowa type II C. hominis TU502 | 3941 3886 |
C. parvum Isolate | Iowa | SDS-PAGE and LC-MS/MS | MASCOT in the NCBI, CryptoDB v5.0, and EupathDB v2.16 databases | C. parvum Iowa type II | 3941 |
C. andersoni oocysts | - 1 | SDS-PAGE and LC-MS/MS | MaxQuant search engine (v.1.5.2.8), UniProt database | C. andersoni 30847 | 3876 |
Cryptosporidium spp. | - | MALDI-TOF MS | flexControl software on a microflex LT/SH MALDI-TOF (Bruker Daltonik GmbH) | C. parvum Iowa type II C. hominis TU502 | 3941 3886 |
Cryptosporidium spp. | - | Label-free proteomic quantification techniques and LC-MS/MS | Maxquant search engine (v.1.5.2.8, Max Planck Institute of Biochemistry, Munich, Germany) | C. parvum Iowa type II C. hominis TU502 | 3941 3886 |
C. parvum | - | Multi-omics approach: GC-MS and LC-HR-MS | The Protein Discoverer 2.2 (Thermo Fisher Scientific, Bremen, Germany) and Sequest HT search engines | C. parvum Iowa type II C. hominis TU502 | 3941 3886 |
Year | The Greatest Milestone | Outcome of Study | Reference |
---|---|---|---|
2011 | Construction and analysis of full-length cDNA library of C. parvum |
| [40] |
2012 | CpArray15K in profiling the gene expressions in the oocysts of C. parvum and their responses to UV irradiation |
| [37] |
2016 | New insights into the intracellular development of C. parvum |
| [41] |
2017 | Discovery of parasite RNA Transcripts delivery to infected epithelial cells during cryptosporidiosis |
| [38] |
2018 | RNA-Seq insights from intestinal proliferating stages to infectious sporozoites |
| [43] |
2019 | Comparison of gene expression in the sporozoite and intracellular stages of C. parvum by RNA-Seq |
| [42] |
2021 | Analysis of Long Non-Coding RNA in C. parvum |
| [44] |
2021 | Transcriptome analysis of the ileocecal tissue infected with C. parvum for exploring its potential to induce digestive adenocarcinoma in a rodent model |
| [39] |
2022 | Whole transcriptome analysis of HCT-8 cells infected by C. parvum |
| [45] |
2022 | Dual transcriptomics to determine IFN-g-independent transcriptomic response to C. parvum infection |
| [47] |
2023 | Transcriptomic analysis of infectivity of C. hominis and C. parvum |
| [46] |
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Dąbrowska, J.; Sroka, J.; Cencek, T. Investigating Cryptosporidium spp. Using Genomic, Proteomic and Transcriptomic Techniques: Current Progress and Future Directions. Int. J. Mol. Sci. 2023, 24, 12867. https://doi.org/10.3390/ijms241612867
Dąbrowska J, Sroka J, Cencek T. Investigating Cryptosporidium spp. Using Genomic, Proteomic and Transcriptomic Techniques: Current Progress and Future Directions. International Journal of Molecular Sciences. 2023; 24(16):12867. https://doi.org/10.3390/ijms241612867
Chicago/Turabian StyleDąbrowska, Joanna, Jacek Sroka, and Tomasz Cencek. 2023. "Investigating Cryptosporidium spp. Using Genomic, Proteomic and Transcriptomic Techniques: Current Progress and Future Directions" International Journal of Molecular Sciences 24, no. 16: 12867. https://doi.org/10.3390/ijms241612867