The Bottleneck in Cloning: Can it be Overcome?

 As a kid the topic of cloning always fascinated me, largely due to a number of cartoon characters who possessed the ability. One character in particular would walk into a machine the size of a telephone booth and press a button that activated with an onset of noise, light, and colored smoke. Following the commotion, a perfect clone of the character would emerge, fully clothed and developed. Immediately, my imagination would flicker with notions of all the potential benefits of having a clone at my disposal. Ironically, I did not know that cloning processes had been successfully carried out with complex, sexually reproducing organisms until I was in high school. As I was conducting my research for this topic I would ask peers, friends and/or family if they were familiar with cloning success stories such as Dolly the Sheep and many were completely unaware of the matter. In reality, the primary cloning method, Somatic Cell Nuclear Transfer (SCNT) is not an effortless or high success rate procedure, even decades from its inception in 1958. The high rate of trial and error, and the high defect rates among even viable specimens incurs legitimate ethical debate regarding widespread implementation or avenues into human cloning. However, to classify cloning methods or technologies as “failures” is a misconception as well as being highly reductive. The limitation of SCNT and the efforts to address the technological and procedural flaws led to breakthroughs in the field of epigenetic reprogramming that have been successfully pivoted across a plethora of sectors. Furthermore, these breakthroughs could potentially reinvigorate cloning technologies and resolve these fundamental barriers that constrain overall success. 

In order to understand the current limitations of SCNT, a fundamental breakdown of the cloning method is necessary. The procedure requires a somatic cell from the organism that is to be cloned (primary), which may be selected from a number of differentiated body cells such as a skin cell for example. A secondary, donor organism provides an enucleated oocyte or an egg cell that has had its nucleus removed, leaving behind the remaining cell cytoplasm (contains mRNA and modifying proteins). The primary donor cell nucleus is then transplanted into the enucleated oocyte where the cytoplasm reprograms the somatic nucleus to an embryonic state. Then through a series of chemical and electrical stimulants (electrical impulses, calcium ion activation, etc.) the activated egg cell, which acts like a zygote, divides until it reaches an embryonic stage, which may then be implanted into the surrogate or tertiary organism. However it is during the stages of epigenetic reprogramming and modification that most errors arise as variability in gene expression may alter properties such as cell differentiation drastically. The following statement reinforces this notion as “Cell fate determination is largely achieved by activating some genes while suppressing other genes through epigenetic modification such as DNA methylation, histone modification, genomic imprinting, and X chromosome inactivation… It is thought that the low cloning efficiency, abnormal embryo phenotype, and low viability of animals generated by SCNT are due to incomplete reprogramming of donor nuclei” (Wang et al., 2020). The cytoplasm performs the tasks of reprogramming the donor nucleus to an embryonic state but it does so only partially with complications related to activation, timing or incomplete gene expressions. The donor nucleus also retains some of the gene expressions associated with its former somatic state which may inhibit future developmental stages. The factors discussed makeup only a handful of the parameters that may potentially impact success rates and specimen viability. As a result, “The standard SCNT efficiency is only 1%–5%, which results in a general failure of the technology to be applied in mammals extensively” (Li & Sun, 2022). Abnormal gene expression, developmental defects, embryonic/fetal miscarriage and reduced viability are all conditional outcomes regarded as failures in SCNT processes. 

The era in which SCNT was developed and conceptualized was defined by high stake competitiveness, intense pressure from oversight committees, and geopolitical rivalries where ethics lagged far behind results and achievements. Following the end of the Cold War and the rise of globalization, ethical concerns permeated technological and scientific industries. The growing use of cloning technologies was in particular subject to intense ethical debate on account of the tremendous potential for science research and the deep philosophical questions that these technologies raised about human identity, human autonomy and human dignity. Critics against human cloning and by extension, the cloning of other complex organisms, remarked that “SCNT is not ethically acceptable because it infringes on the dignity and individuality of the individual produced, affects the right of the child produced to ignore, and limits the oocyte donor as a by-product and may have adverse effects on the children born… cloning violates human dignity, takes away uniqueness, threatens humanity and people are considered as instruments in the process” (Blesa et al., 2016). The low success rates and high rate of developmental abnormalities with the use of SCNT procedures exacerbated these concerns. But those who support the use of cloning technologies contended that uses of SCNT could offer revolutionary benefits to medicine and biotechnology. Shafique notes in his article, “Scientific and Ethical Implications of Human and Animal Cloning,” that “Current applications of SCNT in human therapeutic cloning include using the embryonic stem cells (ESCs) research into hereditary diseases, model systems in assessing drug toxicity, and regenerative medicine… hESCs and induced pluripotent stem cells (hiPSCs) offer sources for generation of an unlimited number of differentiated human somatic cells.” Likewise, the authors of “Ethical aspects of nuclear and mitochondrial DNA transfer” note in favor of cloning technologies that, “The main arguments in favor of the procedure maintain that people have a right to reproductive freedom, as opposed to the right of the cloned child to be him- or herself, for his or her genetic identity is what makes him or her a unique individual, and not to be predetermined” (Blesa et al., 2016). However, public opposition and legitimate ethical concerns ultimately weighed considerable governmental and international inhibition on cloning technologies. The United Nations and other organizations declared their opposition to human reproductive cloning, and numerous countries passed  laws prohibiting or strongly restricting SCNT experiments with human embryos. This effectively put an end to the widespread adoption of reproductive cloning technologies and caused a shift in scientific research towards stem cell research and epigenetic reprogramming. 

Due to the technological and procedural flaws highlighted earlier and the inhibitive  policies imposed on cloning procedures, technologies and research, there was a focus shift in biotechnology from organismal cloning to further exploring epigenetic reprogramming. In response to the inefficiency of SCNT, researchers attempted to understand how differentiated somatic cells could be reverted into pluripotent cells and then used to form desired specialized somatic cells (i.e. muscle cells, skin cells). Cerneckis et al notes in their article that “iPSCs have been widely applied to model human development and diseases, perform drug screening, and develop cell therapies… We also consider how iPSC-derived cellular models can be used in high-throughput drug screening and drug toxicity studies… developing autologous and allogeneic iPSC-based cell therapies and their potential to alleviate human diseases” (Cerneckis et al., 2024). These developments demonstrate that the scientific principles originally explored through cloning research could be repurposed into more practical, scalable, and ethically acceptable biomedical technologies. Rowe and Daley also touch on this notion, stating that “The discovery that mature human somatic cells from the skin or blood could be reprogrammed to a pluripotent state and then differentiated along alternative cell lineages offered the theoretical opportunity for personalized cell-based autologous therapies in a wide array of diseases” (Rowe & Daley, 2018). The advent of iPSC technologies enabled researchers to overcome several ethical issues involved with the use of embryonic stem cells and somatic cloning, while also pioneering breakthroughs in producing specialized human tissues. Progress in organoid culture, tissue engineering, and patient-specific disease modeling greatly broadened the application of biotechnology by enabling researchers to model complex biological systems in vitro environments with unprecedented fidelity. The challenges in cloning technologies, therefore, did not hinder faith in scientific progress, but rather inspired new avenues in biotechnology to move away from cloning towards regenerative medicine, tissue engineering, disease modeling, development of organoids and personalized therapeutic applications.  

Although high inefficiency rates in SCNT remain prevalent, continuous improvement of biotechnology offers hope that the cloning “bottleneck” may not be irreversible. Instead of abandoning cloning technologies, researchers have worked to improve the quality of the donor cells, epigenetic stability and developing methods to incorporate modern gene editing tools like CRISPR into the SCNT process. Zhu et al discusses how “The combination of gene editing and somatic cell nuclear transfer (SCNT)…  has proven beneficial in several fields, such as the genetic improvement of animal traits, production of gene-edited animal models, xenotransplantation, and the enhancement and conservation of endangered species resources… amniotic cells are thus better SCNT candidates than fibroblasts because they offer genomic stability, low tumorigenic and teratogenic risks, reduced immunogenicity, high differentiation potential” (Zhu et al., 2025). The results reported here indicate that limitations in donor cells might account for some of the factors impacting the low viability rate reported in cloning, but are not simply a consequence of said procedure. Grzybek et al further reinforces this notion, stating that, “The efficiency of the SCNT method in swine models varies from 0.2% to 7% of newborns per constructed embryo” because “the SCNT method uses somatic cells with low viability and not fully reprogrammed epigenetic memory” (Grzybek et al., 2023). In addition many abnormalities and defects with the placenta, which occur in the development of cloned embryos may be eliminated in the future in attribution to the development of artificial gestation systems and synthetic womb technologies. Thus, the overall perception of SCNT as a highly inefficient procedure is likely to erode over time as it becomes aided by the recent developments in epigenetics, regenerative medicine, gene editing technologies and other bio-related technologies. 

The reality of SCNT, in contrast to its pop culture cloning counterparts, reveals a procedure constrained by severe inefficiencies, developmental abnormalities and complex ethical concerns. Partial epigenetic reprogramming paired with somatic gene expression retention is the main bottleneck impeding success in cloning processes, with low viability and abnormal embryonic development in many specimens. However the value of cloning as a science supersedes the mere application of producing a cloned organism. The desire to overcome the issues and failures of SCNT propagated advances in the areas of epigenetic reprogramming, iPSCs, tissue engineering and disease modeling. New developments and advancements in the field of biotechnology delivers a hopeful outlook into overcoming the limitations identified and addressing the inefficiencies of cloning. Overall, cloning technologies must not be perceived through a lens of failure, but rather as a stepping stone for innovations in biotechnology that widened our understanding of cellular identity and development. 

References

Blesa, J. R., Tudela, J., & Aznar, J. (2016). Ethical aspects of nuclear and mitochondrial DNA transfer. The Linacre quarterly, 83(2), 179–191. https://doi.org/10.1080/00243639.2016.1180773

Cerneckis, J., Cai, H., & Shi, Y. (2024). Induced Pluripotent Stem Cells (iPSCs): Molecular Mechanisms of Induction and Applications. Signal Transduction and Targeted Therapy, 9(1). https://doi.org/10.1038/s41392-024-01809-0 ‌

Grzybek, M., Flisikowski, K., Giles, T., Dyjak, M., Ploski, R., Gasperowicz, P., Emes, R. D., & Lisowski, P. (2023). Methylation Genome-Wide Profiling in Lowly and Highly Efficient Somatic Cell Nuclear Transfer in Pigs. Applied Sciences, 13(8), 4798. https://doi.org/10.3390/app13084798

Li, Y., Sun, S., Xu, Y., Zhang, J., Du, Y., Cao, Y., Liao, Z., Xie, Y., Bian, X., Huang, J., Wang, M., Liu, Z., Sun, Q., & Lu, F. (2025). Efficient Somatic Cell Nuclear Transfer by Overcoming Both Pre- and Post-Implantation Epigenetic Barriers. PubMed, e04669–e04669. https://doi.org/10.1002/advs.202504669 ‌ ‌

Li, Y., & Sun, Q. (2022). Epigenetic manipulation to improve mouse SCNT embryonic development. Frontiers in Genetics, 13. https://doi.org/10.3389/fgene.2022.932867 ‌

Rowe, R. G., & Daley, G. Q. (2019). Induced pluripotent stem cells in disease modelling and drug discovery. Nature reviews. Genetics, 20(7), 377–388. https://doi.org/10.1038/s41576-019-0100-z

Sidra Shafique. (2020). Scientific and Ethical Implications of Human and Animal Cloning. International Journal of Science, Technology and Society, 8(1), 9-17. https://doi.org/10.11648/j.ijsts.20200801.12

Wang, X., Qu, J., Li, J., He, H., Liu, Z., & Huan, Y. (2020). Epigenetic Reprogramming During Somatic Cell Nuclear Transfer: Recent Progress and Future Directions. Frontiers in Genetics, 11. https://doi.org/10.3389/fgene.2020.00205 ‌

Yun, J. H., Kang, H.-G., Choi, E. Y., Jeon, S.-B., Kim, M. J., Jeong, P.-S., Song, B.-S., Kim, S.-U., Min, K.-S., & Sim, B.-W. (2025). Lycopene enhances epigenetic reprogramming and zygotic genome activation in the porcine somatic cell nuclear transfer embryo. Scientific Reports, 15(1). https://doi.org/10.1038/s41598-025-15672-8 ‌

Zhu, C., Liu, Y., Xu, H., Wang, S., Zhou, H., Cao, J., Meng, F., & Zhang, Y. (2025). Production of second-generation sheep clones via somatic cell nuclear transfer using amniotic cells as nuclear donors. Theriogenology, 232, 79–86. https://doi.org/10.1016/j.theriogenology.2024.11.001