Anti-sense, Sense and Epigenetics in Severe Malaria
Ashis Das, Birla Institute of Technology and Science
Project Accession:
IADA-PRj88xd76p
Project Description:
Anti-sense, Sense and Epigenetics in Severe Malaria
Project Mode:
Individual
Access Mode:
Open Access
Grant No.:
PID: 2019-1121
Funding Agency:
Indian Council of Medical Research (ICMR)
Release Date:
Sept. 30, 2026
Organism Category:
Microorganism
Ethical Clearance:
Number of Study:
1
Study(s):
Study Date:
Sept. 22, 2026
Study Type:
Gene Expression Profiling (EFO:0002770)
Study Abstract:
The malaria parasite mitochondria are critical targets for antimalarial drugs, but emerging drug resistance against existing protein targets necessitates novel therapeutic approaches. Using custom-designed, multi-probe microarrays and pooled RNA sequencing experiments in patient samples of Plasmodium falciparum, we identified specific Natural Antisense Transcripts (NATs) encoded by both the mitochondrial genome and the nucleus, which are directed to the parasite mitochondria. These findings span three clinical manifestations of malaria - hepatic dysfunction (HD), cerebral malaria (CM), and thrombocytopenia. Although mitochondrial activity is known to be reduced in blood-stage malaria, a significant number of mitochondrial sense-antisense transcript pairs show correlated gene expression in the CM cluster. The thrombocytopenia cluster shows the most upregulated antisense transcripts. This study provides direct evidence for the origin of NATs from the mitochondrial genome. It further provides a dynamic gene regulation profile of key sense and antisense transcripts responsible for mitochondrial translation and bioenergetics. Our findings suggest that active-post transcriptional gene regulation effectively sustains the metabolic flexibility of the parasite mitochondria. Identifying key genes with differentially regulated NATs specific to the observed disease phenotypes presents novel chemotherapeutic targets, disrupting essential functions of the parasite mitochondria.
Organism:
Plasmodium falciparum (Taxon ID: 5833)
Authors:
- Ashis Das, Birla Institute of Technology and Science (BITS), Pilani campus, adas@pilani.bits-pilani.ac.in
Publications:
doi.org/10.1186/s12864-026-12733-8
Keywords:
malaria parasite, mitochondrial proteins, antisense transcripts, antimalarial targets, Disease Phenotypes
Samples:
28 Download
Experiment(s):
Experiment Description:
Total RNA from 28 clinical isolates of Plasmodium falciparum was isolated from malaria patients with differing clinical conditions (n=28). Each of these samples was hybridized individually on custom-designed 8*60K arrays printed on the Agilent platform for their sense and antisense transcriptional profiling
Experiment Date:
Feb. 21, 2023 - June 21, 2024
Experiment Technology:
RNA Microarray (OBI:0000632)
Experiment Type:
Expression profiling by array
Molecule Name:
total RNA
Instrument Model:
Agilent Custom P falciparum Gene Expression 8x60k Microarray: AMADID: 86486
Experiment Label:
Cy3
Experiment Protocols:
- Array Scanning and Feature Extraction Protocol - Raw data extraction from images was obtained using Agilent Feature Extraction software. The hybridized slides were scanned using the Agilent Microarray Scanner (Agilent Technologies, Part Number G2600D).
- Nucleic Acid Extraction Protocol - RNA from enriched blood was isolated using TRIzol as per manufacturer's protocols.
- Nucleic Acid Hybridization to Array Protocol - Labeled cRNA samples were fragmented at 60°C and hybridized onto an Agilent Custom Plasmodium falciparum Gene Expression Microarray 8X60K using the Gene Expression Hybridization kit (Agilent Technologies, In situ Hybridization kit, Part Number 5190-0404). Hybridization was carried out in Agilent's SureHyb Chambers at 65°C for 16 h.
- Nucleic Acid Labeling Protocol - Samples were labeled using an Agilent Quick-Amp labeling Kit (p/n5190-0442). Total RNA was reverse transcribed at 40°C using an oligo-dT primer tagged to a T7 polymerase promoter and converted to double-stranded cDNA. Synthesized double-stranded cDNA was used as the template for cRNA generation. cRNA was generated by in vitro transcription, and the dye Cy3 CTP(Agilent) was incorporated during this step. The cDNA synthesis and in vitro transcription steps were carried out at 40°C. Labeled cRNA was cleaned using Qiagen RNeasy columns (Qiagen, Cat No: 74106).
- Sample Collection Protocol - Venous blood samples were collected from P. falciparum-infected adult patients admitted to S.P. Medical College, Bikaner, India after informed patient consent. Whole blood was processed on Histopaque-gradient density centrifugation for leucodepletion. Mono-infection by P. falciparum was confirmed by PCR diagnosis. Inclusion required evidence of parasite by slide microscopy and RDT positivity; patients with co-morbidities (dengue, viral infection, other concurrent illness) were excluded.
Experiment Design:
Case Control Design, Disease State Design
Datafiles:
Raw Files: 28
| # | Filename | Size |
|---|---|---|
| 1 | GSM8415647_UNC1.txt.gz | 9975572 |
| 2 | GSM8415648_UNC2.txt.gz | 10062088 |
| 3 | GSM8415649_UNC3.txt.gz | 9864211 |
| 4 | GSM8415650_UNC4.txt.gz | 9982852 |
| 5 | GSM8415651_UNC5.txt.gz | 10121593 |
| 6 | GSM8415652_UNC6.txt.gz | 9561866 |
| 7 | GSM8415653_HD1.txt.gz | 10062241 |
| 8 | GSM8415654_HD2.txt.gz | 10097318 |
| 9 | GSM8415655_HD3.txt.gz | 10126491 |
| 10 | GSM8415656_HD4.txt.gz | 10141254 |
| 11 | GSM8415657_HD5.txt.gz | 10084416 |
| 12 | GSM8415658_HD6.txt.gz | 10059122 |
| 13 | GSM8415659_HD7.txt.gz | 10111327 |
| 14 | GSM8415660_HD8.txt.gz | 10166604 |
| 15 | GSM8415661_HD9.txt.gz | 10022490 |
| 16 | GSM8415662_HD10.txt.gz | 10046246 |
| 17 | GSM8415663_HD11.txt.gz | 9343006 |
| 18 | GSM8415664_HD12.txt.gz | 9923779 |
| 19 | GSM8415665_CM1.txt.gz | 9826089 |
| 20 | GSM8415666_CM2.txt.gz | 10119927 |
| 21 | GSM8415667_CM3.txt.gz | 10121191 |
| 22 | GSM8415668_CM4.txt.gz | 10116091 |
| 23 | GSM8415669_TH1.txt.gz | 9978873 |
| 24 | GSM8415670_TH2.txt.gz | 9915023 |
| 25 | GSM8415671_TH3.txt.gz | 9990261 |
| 26 | GSM8415672_TH4.txt.gz | 9340087 |
| 27 | GSM8415673_TH5.txt.gz | 10067548 |
| 28 | GSM8415674_TH6.txt.gz | 10020407 |