Our Technophile
Soumeya J
Past Master’s student & Postdoc
Soumeya Jaballah (2007-2010/2023-2025): Defended her master’s thesis entitled, “Delineation of MPMV RNA packaging determinants: Structure-function correlation of the 5′ end of MPMV RNA genome”. Her MS thesis work involved investigating the nature of the intervening sequences located between the two disconnected packaging determinants of MPMV. Furthermore, she addressed the question whether the in situ presence of these intervening sequences on the RNA to be packaged is essential for RNA packaging or not. She has published her findings in a leading journal of the field (Jaballah et al., J. Mol. Biol., 2010). In addition, she also contributed to other published work (Al Dhaheri et al., Retrovirology, 2009). After obtaining her PhD degree from the School of Biological Sciences, University of Auckland, New Zealand, she rejoined the Rizvi laboratory as a postdoctoral fellow and worked on testing the next generation of MMTV-based retroviral vectors in tissue culture and animals. Part of her work has recently been published in a leading journal (Jaballah et al., J. Mol. Biol., 2025). Soumeya is currently working as a postdoctoral fellow at Mohammed Bin Rashid University of Medicine and Health Sciences (MBRU), Dubai.
Publications
2025
Jaballah, Soumeya Ali; Ali, Lizna M; Jehad, Mohammad Abdullah; Akhlaq, Shaima; Rizvi, Tahir A.; Mustafa, Farah
Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects Journal Article
In: Journal of Molecular Biology, vol. 437, no. 24, 2025, ISSN: 0022-2836.
@article{Jaballah2025,
title = {Retroviral Vector Technology for Gene Therapy: History, Current Landscape, and Future Prospects},
author = {Soumeya Ali Jaballah and Lizna M Ali and Mohammad Abdullah Jehad and Shaima Akhlaq and Tahir A. Rizvi and Farah Mustafa},
doi = {10.1016/j.jmb.2025.169473},
issn = {0022-2836},
year = {2025},
date = {2025-12-00},
urldate = {2025-12-00},
journal = {Journal of Molecular Biology},
volume = {437},
number = {24},
publisher = {Elsevier BV},
abstract = {The concept of gene therapy and its practice has been prevalent for over five decades. The first successful retroviral vector-based gene therapy trial took place ∼35 years ago, followed by several setbacks. However, recent years have seen a surge in successes, offering new hope to patients with genetic and other disorders once deemed untreatable. Over the past decade, rapid advancements in molecular biology have led to the development of safer and more effective gene therapy strategies with various gene delivery systems now in use. Among these, viral vectors such as retroviruses, adenoviruses, and adeno-associated viruses are the most widely employed in both research and clinical settings. This is due to their natural efficiency in delivering genetic material into target cells. Among these viral vectors, retroviruses stand out for their unique ability to reverse-transcribe and integrate their genetic material into the host genome, ensuring stable and long-term gene expression. This review highlights advances in retroviral vector development, examining both their therapeutic potential and associated challenges. It also explores strategies for vector production, including transient and stable systems tailored to meet clinical and regulatory demands. Significant progress is discussed in mitigating insertional mutagenesis and vector silencing. As a result, next-generation retroviral vectors with improved safety and efficacy have made it past regulatory approval and are commercially available. Current innovations include replication-competent, non-integrating, integration-retargeted, and hybrid CRISPR/Cas-expressing retroviral vectors undergoing pre-clinical and clinical investigations. This reflects a new era in gene therapy, with retroviral vectors reimagined for greater precision, control, and therapeutic impact.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
The concept of gene therapy and its practice has been prevalent for over five decades. The first successful retroviral vector-based gene therapy trial took place ∼35 years ago, followed by several setbacks. However, recent years have seen a surge in successes, offering new hope to patients with genetic and other disorders once deemed untreatable. Over the past decade, rapid advancements in molecular biology have led to the development of safer and more effective gene therapy strategies with various gene delivery systems now in use. Among these, viral vectors such as retroviruses, adenoviruses, and adeno-associated viruses are the most widely employed in both research and clinical settings. This is due to their natural efficiency in delivering genetic material into target cells. Among these viral vectors, retroviruses stand out for their unique ability to reverse-transcribe and integrate their genetic material into the host genome, ensuring stable and long-term gene expression. This review highlights advances in retroviral vector development, examining both their therapeutic potential and associated challenges. It also explores strategies for vector production, including transient and stable systems tailored to meet clinical and regulatory demands. Significant progress is discussed in mitigating insertional mutagenesis and vector silencing. As a result, next-generation retroviral vectors with improved safety and efficacy have made it past regulatory approval and are commercially available. Current innovations include replication-competent, non-integrating, integration-retargeted, and hybrid CRISPR/Cas-expressing retroviral vectors undergoing pre-clinical and clinical investigations. This reflects a new era in gene therapy, with retroviral vectors reimagined for greater precision, control, and therapeutic impact.
Mustafa, Farah; Ahmad, Waqar; Gull, Bushra; Baby, Jasmin; Panicker, Neena G.; Khader, Thanumol Abdul; Baki, Hala Abdul; Rehman, Erum; Salim, Asif M.; Ahmed, Rubina L. G.; Khansaheb, Hamda H.; Habous, Maya; AlDabal, Laila M. J. A.; Jaballah, Soumeya; Alqassim, Saif S.; Alsheikh-Ali, Alawi; Rizvi, Tahir A
miRNA biomarkers for prognosis and therapy monitoring in a multi-ethnic cohort with SARS-CoV-2 infection Journal Article
In: Sci Rep, vol. 15, no. 1, 2025, ISSN: 2045-2322.
@article{Mustafa2025,
title = {miRNA biomarkers for prognosis and therapy monitoring in a multi-ethnic cohort with SARS-CoV-2 infection},
author = {Farah Mustafa and Waqar Ahmad and Bushra Gull and Jasmin Baby and Neena G. Panicker and Thanumol Abdul Khader and Hala Abdul Baki and Erum Rehman and Asif M. Salim and Rubina L. G. Ahmed and Hamda H. Khansaheb and Maya Habous and Laila M. J. A. AlDabal and Soumeya Jaballah and Saif S. Alqassim and Alawi Alsheikh-Ali and Tahir A Rizvi},
doi = {10.1038/s41598-025-15248-6},
issn = {2045-2322},
year = {2025},
date = {2025-12-00},
urldate = {2025-12-00},
journal = {Sci Rep},
volume = {15},
number = {1},
publisher = {Springer Science and Business Media LLC},
abstract = {This study aimed to identify miRNA-based biomarkers in a multi-ethnic cohort of SARS-CoV-2-infected individuals to enhance preparedness for future variants of concern. A total of 31 healthy controls and 154 infected patients were enrolled, from which 13 matched controls and 38 infected nasal swab samples were analyzed using miRNA sequencing, followed by qRT-PCR validation. Among the 1788 miRNAs detected, 14 differentially expressed miRNAs and four novel miRNAs were identified, with novel-miR-264-5p showing a ≥ 2-fold change. Correlation with clinical markers highlighted several miRNAs as potential prognostic biomarkers. Seven miRNAs, including miR-146b-3p, miR-154-5p, miR-5010-3p, miR-127-3p, miR-335-3p, miR-30c-5p, and miR-202-5p, showed strong prognostic potential. Combined ROC analysis demonstrated that a panel of top-performing miRNAs significantly enhanced diagnostic accuracy (AUC 0.939–0.972; p < 0.0001). Moreover, integrating miRNA biomarkers with clinical parameters further improved performance (AUC = 0.982; p < 0.0001). miR-146b-3p, detected exclusively in infected patients, emerged as a highly specific biomarker. Several nasal miRNAs mirrored blood profiles, highlighting the utility of nasal swabs for non-invasive monitoring. Collectively, these findings suggest that miRNA-based biomarkers, alone or combined with clinical markers, offer a promising platform for COVID-19 prognosis and diagnosis, and lay groundwork for future miRNA-based antiviral strategies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
This study aimed to identify miRNA-based biomarkers in a multi-ethnic cohort of SARS-CoV-2-infected individuals to enhance preparedness for future variants of concern. A total of 31 healthy controls and 154 infected patients were enrolled, from which 13 matched controls and 38 infected nasal swab samples were analyzed using miRNA sequencing, followed by qRT-PCR validation. Among the 1788 miRNAs detected, 14 differentially expressed miRNAs and four novel miRNAs were identified, with novel-miR-264-5p showing a ≥ 2-fold change. Correlation with clinical markers highlighted several miRNAs as potential prognostic biomarkers. Seven miRNAs, including miR-146b-3p, miR-154-5p, miR-5010-3p, miR-127-3p, miR-335-3p, miR-30c-5p, and miR-202-5p, showed strong prognostic potential. Combined ROC analysis demonstrated that a panel of top-performing miRNAs significantly enhanced diagnostic accuracy (AUC 0.939–0.972; p < 0.0001). Moreover, integrating miRNA biomarkers with clinical parameters further improved performance (AUC = 0.982; p < 0.0001). miR-146b-3p, detected exclusively in infected patients, emerged as a highly specific biomarker. Several nasal miRNAs mirrored blood profiles, highlighting the utility of nasal swabs for non-invasive monitoring. Collectively, these findings suggest that miRNA-based biomarkers, alone or combined with clinical markers, offer a promising platform for COVID-19 prognosis and diagnosis, and lay groundwork for future miRNA-based antiviral strategies.
2010
Jaballah, S. A.; Aktar, S. J.; Ali, J.; Phillip, P. S.; Dhaheri, N. S. Al; Jabeen, A.; Rizvi, T. A.
In: J Mol Biol, vol. 401, no. 5, pp. 996-1014, 2010, ISSN: 0022-2836.
@article{RN42,
title = {A G-C-rich palindromic structural motif and a stretch of single-stranded purines are required for optimal packaging of Mason-Pfizer monkey virus (MPMV) genomic RNA},
author = {S. A. Jaballah and S. J. Aktar and J. Ali and P. S. Phillip and N. S. Al Dhaheri and A. Jabeen and T. A. Rizvi},
doi = {10.1016/j.jmb.2010.06.043},
issn = {0022-2836},
year = {2010},
date = {2010-01-01},
urldate = {2010-01-01},
journal = {J Mol Biol},
volume = {401},
number = {5},
pages = {996-1014},
abstract = {During retroviral RNA packaging, two copies of genomic RNA are preferentially packaged into the budding virus particles whereas the spliced viral RNAs and the cellular RNAs are excluded during this process. Specificity towards retroviral RNA packaging is dependent upon sequences at the 5' end of the viral genome, which at times extend into Gag sequences. It has earlier been suggested that the Mason-Pfizer monkey virus (MPMV) contains packaging sequences within the 5' untranslated region (UTR) and Gag. These studies have also suggested that the packaging determinants of MPMV that lie in the UTR are bipartite and are divided into two regions both upstream and downstream of the major splice donor. However, the precise boundaries of these discontinuous regions within the UTR and the role of the intervening sequences between these dipartite sequences towards MPMV packaging have not been investigated. Employing a combination of genetic and structural prediction analyses, we have shown that region "A", immediately downstream of the primer binding site, is composed of 50 nt, whereas region "B" is composed of the last 23 nt of UTR, and the intervening 55 nt between these two discontinuous regions do not contribute towards MPMV RNA packaging. In addition, we have identified a 14-nt G-C-rich palindromic sequence (with 100% autocomplementarity) within region A that has been predicted to fold into a structural motif and is essential for optimal MPMV RNA packaging. Furthermore, we have also identified a stretch of single-stranded purines (ssPurines) within the UTR and 8 nt of these ssPurines are duplicated in region B. The native ssPurines or its repeat in region B when predicted to refold as ssPurines has been shown to be essential for RNA packaging, possibly functioning as a potential nucleocapsid binding site. Findings from this study should enhance our understanding of the steps involved in MPMV replication including RNA encapsidation process.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
During retroviral RNA packaging, two copies of genomic RNA are preferentially packaged into the budding virus particles whereas the spliced viral RNAs and the cellular RNAs are excluded during this process. Specificity towards retroviral RNA packaging is dependent upon sequences at the 5' end of the viral genome, which at times extend into Gag sequences. It has earlier been suggested that the Mason-Pfizer monkey virus (MPMV) contains packaging sequences within the 5' untranslated region (UTR) and Gag. These studies have also suggested that the packaging determinants of MPMV that lie in the UTR are bipartite and are divided into two regions both upstream and downstream of the major splice donor. However, the precise boundaries of these discontinuous regions within the UTR and the role of the intervening sequences between these dipartite sequences towards MPMV packaging have not been investigated. Employing a combination of genetic and structural prediction analyses, we have shown that region "A", immediately downstream of the primer binding site, is composed of 50 nt, whereas region "B" is composed of the last 23 nt of UTR, and the intervening 55 nt between these two discontinuous regions do not contribute towards MPMV RNA packaging. In addition, we have identified a 14-nt G-C-rich palindromic sequence (with 100% autocomplementarity) within region A that has been predicted to fold into a structural motif and is essential for optimal MPMV RNA packaging. Furthermore, we have also identified a stretch of single-stranded purines (ssPurines) within the UTR and 8 nt of these ssPurines are duplicated in region B. The native ssPurines or its repeat in region B when predicted to refold as ssPurines has been shown to be essential for RNA packaging, possibly functioning as a potential nucleocapsid binding site. Findings from this study should enhance our understanding of the steps involved in MPMV replication including RNA encapsidation process.
2009
Dhaheri, N. S. Al; Phillip, P. S.; Ghazawi, A.; Ali, J.; Beebi, E.; Jaballah, S. A.; Rizvi, T. A.
Cross-packaging of genetically distinct mouse and primate retroviral RNAs Journal Article
In: Retrovirology, vol. 6, pp. 66, 2009, ISSN: 1742-4690.
@article{RN66,
title = {Cross-packaging of genetically distinct mouse and primate retroviral RNAs},
author = {N. S. Al Dhaheri and P. S. Phillip and A. Ghazawi and J. Ali and E. Beebi and S. A. Jaballah and T. A. Rizvi},
doi = {10.1186/1742-4690-6-66},
issn = {1742-4690},
year = {2009},
date = {2009-01-01},
urldate = {2009-01-01},
journal = {Retrovirology},
volume = {6},
pages = {66},
abstract = {BACKGROUND: The mouse mammary tumor virus (MMTV) is unique from other retroviruses in having multiple viral promoters, which can be regulated by hormones in a tissue specific manner. This unique property has lead to increased interest in studying MMTV replication with the hope of developing MMTV based vectors for human gene therapy. However, it has recently been reported that related as well as unrelated retroviruses can cross-package each other's genome raising safety concerns towards the use of candidate retroviral vectors for human gene therapy. Therefore, using a trans complementation assay, we looked at the ability of MMTV RNA to be cross-packaged and propagated by an unrelated primate Mason-Pfizer monkey virus (MPMV) that has intracellular assembly process similar to that of MMTV. RESULTS: Our results revealed that MMTV and MPMV RNAs could be cross-packaged by the heterologous virus particles reciprocally suggesting that pseudotyping between two genetically distinct retroviruses can take place at the RNA level. However, the cross-packaged RNAs could not be propagated further indicating a block at post-packaging events in the retroviral life cycle. To further confirm that the specificity of cross-packaging was conferred by the packaging sequences (psi), we cloned the packaging sequences of these viruses on expression plasmids that generated non-viral RNAs. Test of these non-viral RNAs confirmed that the reciprocal cross-packaging was primarily due to the recognition of psi by the heterologous virus proteins. CONCLUSION: The results presented in this study strongly argue that MPMV and MMTV are promiscuous in their ability to cross-package each other's genome suggesting potential RNA-protein interactions among divergent retroviral RNAs proposing that these interactions are more complicated than originally thought. Furthermore, these observations raise the possibility that MMTV and MPMV genomes could also co-package providing substrates for exchanging genetic information.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
BACKGROUND: The mouse mammary tumor virus (MMTV) is unique from other retroviruses in having multiple viral promoters, which can be regulated by hormones in a tissue specific manner. This unique property has lead to increased interest in studying MMTV replication with the hope of developing MMTV based vectors for human gene therapy. However, it has recently been reported that related as well as unrelated retroviruses can cross-package each other's genome raising safety concerns towards the use of candidate retroviral vectors for human gene therapy. Therefore, using a trans complementation assay, we looked at the ability of MMTV RNA to be cross-packaged and propagated by an unrelated primate Mason-Pfizer monkey virus (MPMV) that has intracellular assembly process similar to that of MMTV. RESULTS: Our results revealed that MMTV and MPMV RNAs could be cross-packaged by the heterologous virus particles reciprocally suggesting that pseudotyping between two genetically distinct retroviruses can take place at the RNA level. However, the cross-packaged RNAs could not be propagated further indicating a block at post-packaging events in the retroviral life cycle. To further confirm that the specificity of cross-packaging was conferred by the packaging sequences (psi), we cloned the packaging sequences of these viruses on expression plasmids that generated non-viral RNAs. Test of these non-viral RNAs confirmed that the reciprocal cross-packaging was primarily due to the recognition of psi by the heterologous virus proteins. CONCLUSION: The results presented in this study strongly argue that MPMV and MMTV are promiscuous in their ability to cross-package each other's genome suggesting potential RNA-protein interactions among divergent retroviral RNAs proposing that these interactions are more complicated than originally thought. Furthermore, these observations raise the possibility that MMTV and MPMV genomes could also co-package providing substrates for exchanging genetic information.