This pioneering research, conducted by a team led by co-first authors Seong Guk Park, PhD, and Elizabeth Kellogg, PhD, from the Department of Structural Biology at St. Jude, was recently published in the journal Nucleic Acids Research. Their method stands out as it enables the rapid optimization of promising CAST candidates, ultimately uncovering essential mechanistic insights that will inform further engineering endeavors. This advancement marks a significant stride in addressing the limitations that have traditionally encumbered the adaptation of CASTs for human applications.

CASTs, which were discovered in 2017, provide a one-step solution for genome editing by integrating large DNA sequences at designated locations in the genome, guided by RNA sequences. Their specificity has been well-documented within bacterial systems, their original hosts; however, they have been less effective in human cells. Consequently, the research team’s objective concentrated on enhancing these natural systems to increase their applicability in human and other eukaryotic organisms.

Corresponding author Elizabeth Kellogg emphasized the necessity of a scalable method to evaluate engineered CASTs’ strengths and weaknesses. Prior to the development of this high-throughput screening approach, the understanding of CASTs was limited to measuring overall activity, without thoroughly assessing the specificity of their DNA integrations. The researchers aimed to fill this void in knowledge by designing a method that could simultaneously measure both aspects.

Utilizing this new screening technique, the team focused on a specific subtype known as the V-K CAST. This variant is particularly advantageous due to its relatively simpler structure compared to other CASTs, making it ideal for experimentation. By altering the proteins of the V-K CAST, the researchers were able to explore a vast range of mutations, evaluating thousands of variants in a single experiment. This broad approach allowed them to delve deep into the mutational landscape of the CAST system, which was previously unexplored territory.

Co-first author Seong Guk Park elaborated on the motivation behind this study, revealing their intention to test all possible single mutations to identify those that could enhance CAST efficiency. Their comprehensive strategy, which did not target any specific regions of the CAST, was instrumental in uncovering beneficial mutations. The team’s exhaustive exploration yielded insights that could significantly impact future research in genetic editing.

Following the application of the V-K CAST mutational screening, the researchers discovered that certain combinations of the most promising mutations could have additive benefits. Specifically, they observed a fivefold increase in activity attributable to just a few modifications. Remarkably, this increase in activity did not come at the expense of specificity—an achievement that previous engineering strategies had been unable to accomplish. This kind of advancement exemplifies the potential of the team’s high-throughput screening method to revolutionize genetic engineering approaches.

With this pressing need for specificity and efficiency in genetic editing, Kellogg and her team are encouraged by the groundbreaking possibilities brought forth by this research. The intricate nature of the natural CAST systems presents hurdles, but the screening approach enables more aspirations in the design of proteins with enhanced capabilities. The researchers are optimistic about future developments resulting from this work, believing that it could lead to more minimal systems conducive for clinical applications.

The study not only underscores the steps taken by St. Jude’s researchers to optimize CASTs, but it also highlights the collaborative efforts undertaken by a diverse team of experts. The contributions of Jung-Un Park from the University of California, Berkeley, along with colleagues Esteban Dodero-Rojas, John Bryant Jr., and Geetha Sankaranarayanan, add depth to the findings and reflect the integrative nature of modern scientific research.

Funded by prominent organizations such as the National Institutes of Health, the Pew Charitable Trusts, and various other institutions, this study exemplifies a commitment to advancing genetic research. The financial backing underscores the importance of this research in providing innovative solutions to pressing health concerns, emphasizing the collaboration between research institutions and funding bodies in the pursuit of transformative scientific knowledge.

As research continues in this dynamic area, Kellogg and her colleagues will remain steadfast in their endeavors to refine CAST designs further. The high-throughput screen they’ve developed will facilitate ambitious efforts to progress in protein design. While the complexities inherent to natural systems are extensive, the newfound capabilities will undoubtedly catalyze advancements in genetic engineering, potentially revolutionizing therapies for genetic disorders and beyond.

The implications of this research stretch far beyond the laboratory. As these engineered CASTs find greater utility in clinical settings, they could pave the way for new therapeutic approaches, enabling precise modifications that enhance human health. With ongoing research and development, the future of genetic editing appears promising, with potential breakthroughs lying just ahead.

The journey of refining CRISPR-associated transposons is a testament to the synergy of scientific exploration and technological advancement. By tapping into the nuances of genetic editing, researchers are positioned to tackle some of humanity’s most enduring challenges, ultimately contributing to a healthier, more informed world.

In conclusion, this research not only leads to practical applications in genetic engineering but also exemplifies the broader potential of interdisciplinary cooperation in science. By embracing methodologies that enhance specificity and efficiency, researchers are forging new paths in the quest for medical breakthroughs, ensuring that the work at St. Jude Children’s Research Hospital resonates for generations.

Subject of Research: CRISPR-associated transposons (CASTs)
Article Title: Screening Approach Enhances CRISPR Genome-Editing Efficiency
News Publication Date: September 23, 2025
Web References: St. Jude Children’s Research Hospital, Nucleic Acids Research
References: National Institutes of Health, Pew Charitable Trusts, Cystic Fibrosis Foundation, Jane Coffin Childs Memorial Fund, Korea Health Industry Development Institute, National Cancer Institute, American Lebanese Syrian Associated Charities
Image Credits: St. Jude Children’s Research Hospital

Keywords

CRISPR, gene editing, genome engineering, CASTs, biomedical applications, specificity, efficiency, high-throughput screening, protein design, genetic disorders.

Neuroblastoma, a cancer originating in nerve tissue, typically arises from immature neural crest cells that fail to differentiate properly. This failure results in cells locked in a developmental limbo, endowing the tumor with remarkable plasticity — the ability to shift between distinct cellular states. These transitions between an adrenergic state, characterized by differentiated cells more susceptible to treatment, and a mesenchymal state, marked by less differentiated and therapy-resistant cells, have long perplexed oncologists. This dynamic plasticity enables tumor cells to evade therapies targeting a specific cellular identity, contributing to relapse and therapeutic failure. The newly published research exposes a yet underestimated degree of this plasticity, revealing that tumor cells can undergo multidirectional state transitions, exacerbating treatment challenges.

The team, led by Jun Yang, MD, PhD, from the Department of Surgery at St. Jude, focused their efforts on leveraging a unique class of compounds known as molecular glues. These small molecules exert their anti-cancer effects by binding specific target proteins and recruiting them to the cell’s degradation machinery, effectively “gluing” them together for destruction. Indisulam, a molecular glue drug, acts by targeting RBM39, an essential RNA splicing factor critical for neuroblastoma cell survival. By promoting the degradation of RBM39, indisulam disrupts RNA splicing processes, triggering cell death. Despite potent initial anti-tumor activity, prior models consistently encountered tumor relapse, indicating the presence of resistance mechanisms yet to be elucidated.

To dissect the resistive behavior, the researchers employed a triangulated approach, integrating genetic mouse models, patient-derived xenografts, and cell line-based systems. Surprisingly, each model exhibited distinct RNA sequencing profiles and patterns, a reflection of neuroblastoma’s profound heterogeneity. This variability hindered identification of a uniform therapeutic target and underscored the complexity of cellular states within tumors. However, leveraging sophisticated computational analyses projecting tumor profiles onto developmental trajectories, the team uncovered a remarkable phenomenon: neuroblastoma cells not only transit between adrenergic and mesenchymal states but also acquire novel traits during these shifts, suggesting an adaptive plasticity far more elaborate than previously recognized.

This revelation explained why monotherapies targeting single cell populations had limited efficacy. “Because tumors are a mixture of numerous subpopulations that can dynamically interconvert, targeting all of these simultaneously with drugs is not feasible due to toxicity concerns,” Dr. Yang noted. Instead, an alternative strategy was required—one that could neutralize tumor plasticity itself or exploit vulnerabilities shared across cellular states. Indisulam’s unique mode of action opened a new therapeutic window, but how to enhance its durability became the critical question.

Investigations revealed that treatment with indisulam triggered an innate immune response within the tumor microenvironment. Notably, the researchers observed recruitment of natural killer (NK) cells—potent immune effectors capable of direct tumor cell killing independent of prior sensitization. NK cells play a vital role in immune surveillance and are increasingly recognized as formidable adversaries against cancer cells. The induction of NK cell infiltration suggested that indisulam not only inhibits tumor intrinsic pathways but also activates an extrinsic anti-tumor immune mechanism.

Complementing these findings, the study detected upregulation of GD2, a glycosphingolipid abundantly expressed on neuroblastoma cells’ surfaces and a validated target for immunotherapy. GD2-targeted therapies, such as anti-GD2 monoclonal antibodies, have significantly improved outcomes in high-risk neuroblastoma by mediating antibody-dependent cellular cytotoxicity (ADCC). By combining indisulam with anti-GD2 antibodies, the researchers harnessed a dual mechanism: indisulam directly activated NK cells, enhancing their cytotoxic potential, while anti-GD2 antibodies flagged tumor cells for elimination through ADCC. This synergy translated into a “one-two knockout punch,” yielding complete tumor eradication in preclinical models regardless of the tumor’s cellular state.

This therapeutic breakthrough addresses a critical unmet need in neuroblastoma treatment. High-risk patients—who constitute nearly half of all cases—typically face aggressive therapies involving high-dose chemotherapy with substantial toxicity and relapse rates approaching 50%. Traditional treatment paradigms have struggled due to insufficient druggable targets and the tumor’s remarkable ability to evade single-targeted agents. The indisulam-immunotherapy combination circumvents this challenge by exploiting tumor biology and orchestrating an immune response that doesn’t rely solely on the tumor’s inherent molecular features, but rather leverages the immune system’s adaptable and potent cytotoxic arsenal.

The research team undertook extensive validation of this therapeutic approach across various experimental platforms. Beyond observing therapeutic efficacy, they conducted mechanistic studies illuminating the interplay between RNA splicing disruption, immune activation, and tumor plasticity. By uncovering the pleiotropic roles of indisulam—both as a molecular glue affecting key splicing factors and as an immunomodulatory agent—they have provided a conceptual advance that could reshape how molecular glues are perceived and employed in cancer therapy.

Beyond the immediate clinical implications for neuroblastoma, these findings carry broader significance for oncology. Tumor plasticity and heterogeneity represent formidable obstacles across multiple cancer types, undermining precision medicine efforts. This study exemplifies how combining targeted molecular degradation strategies with immune-based interventions can surmount these hurdles, highlighting a paradigm shift towards composite therapeutic regimens that address both intrinsic tumor cell biology and extrinsic tumor-immune system interactions.

Continuing this promising line of inquiry, the St. Jude team plans to further optimize the combination strategy and advance it toward clinical trials. Rigorous safety and efficacy assessments in human subjects will be paramount to translate these preclinical successes into viable treatments for children afflicted with neuroblastoma. Moreover, expanding understanding of molecular glue drugs’ immunomodulatory properties could unlock new avenues for their use across various malignancies characterized by dynamic cellular states and immune evasion.

The collaborative nature of this study, involving researchers from St. Jude, The Institute of Cancer Research in London, Max Planck Institute of Biochemistry, Eisai Inc., Nationwide Children’s Hospital, and The University of Tennessee Health Science Center, underscores the multidisciplinary effort required to unravel such complex biological phenomena. Funded by major grants from the American Cancer Society, the National Cancer Institute, and the American Lebanese Syrian Associated Charities (ALSAC), this comprehensive research initiative embodies a concerted push to confront and conquer childhood cancers.

In summary, this study conclusively demonstrates that tumor plasticity in neuroblastoma is more intricate and multidirectional than previously acknowledged, rendering traditional monotherapies inadequate. However, by harnessing the dual forces of indisulam-induced RNA splicing disruption and immune system activation—amplified through synergy with anti-GD2 immunotherapy—the researchers have devised a potent therapeutic approach able to thwart tumor adaptability and achieve complete responses in preclinical models. This advancement offers renewed hope for children battling neuroblastoma and opens a promising frontier for integrating molecular glue compounds within immune oncology paradigms.

Subject of Research: Neuroblastoma plasticity and therapeutic intervention combining molecular glues and immunotherapy

Article Title: ‘Molecular glue’ harnesses the power of the immune system to treat neuroblastoma

News Publication Date: September 17, 2025

Web References:

• St. Jude Neuroblastoma Information
• Jun Yang Lab at St. Jude
• St. Jude Research Departments
• St. Jude Homepage
• St. Jude Progress Magazine
• St. Jude Twitter

References:
Yang, J., Singh, S., Fang, J., Jin, H., Van de Velde, L.-A., Cortes, A., et al. (2025). Molecular glue-induced degradation of RBM39 combined with immunotherapy achieves complete responses in neuroblastoma. Nature Communications. https://doi.org/10.1038/s41467-025-63979-x

Image Credits: St. Jude Children’s Research Hospital

Keywords: Neuroblastoma, Immunotherapy, Molecular glue, Indisulam, Tumor plasticity, RNA splicing, Natural Killer cells, GD2, Antibody-dependent cellular cytotoxicity (ADCC), Pediatric cancer

Childhood cancer survivors experience cardiomyopathy at rates up to fifteen times higher than their healthy siblings, a disparity primarily attributed to the cardiotoxic side effects of cancer therapies such as anthracycline chemotherapy and radiation. The complex interplay between treatment exposures, age at diagnosis, and traditional cardiovascular risk factors only partially explains this elevated prevalence. Genetic predisposition has long been suspected as a critical factor, but the specifics remained undefined until now. The meticulous work carried out by Dr. Yadav Sapkota and colleagues at St. Jude brings clarity to these genetic factors by focusing on TTN and BAG3—genes that play critical roles in cardiac muscle structure and regulation.

TTN encodes titin, the largest known human protein, fundamental to the structural integrity and elasticity of cardiac sarcomeres. Mutations in TTN have been implicated in various cardiomyopathies due to impaired mechanical stability and signaling within cardiac muscle cells. BAG3, on the other hand, encodes a multifunctional co-chaperone protein involved in protein quality control and autophagy, processes vital for the maintenance of cardiac myocyte health. Disruptions in BAG3 function have been connected to myofibrillar myopathy and dilated cardiomyopathy. Understanding how variations in these genes influence cardiomyopathy risk after cancer therapy could revolutionize risk stratification and patient management.

The team performed their analysis using a cohort drawn from two extensive survivor groups: the St. Jude Lifetime Cohort (SJLIFE) and the Childhood Cancer Survivor Study (CCSS). They analyzed genetic variants found in survivors who developed late-onset cardiomyopathy at least five years post-cancer treatment, contrasting their findings with known data from the general population’s dilated cardiomyopathy cases and adult cancer survivor datasets. This comparative approach allowed them to discern how genetic risks diverge between childhood and adult cancer survivor populations as well as from familial forms of cardiomyopathy.

One of the most striking revelations concerns the dichotomy between early- and late-onset cardiomyopathy genetically. Familial, early-onset cardiomyopathy is often driven by rare pathogenic variants with strong effect sizes found in families with a history of the disease. These variants typically manifest in youth or early adulthood. In contrast, late-onset cardiomyopathy in the general population tends to be sporadic and influenced by common variants that exert more modest, cumulative effects. The study showed common variants in TTN and BAG3 conferred a protective effect against late-onset cardiomyopathy in childhood cancer survivors similar to patterns observed in the general population.

Conversely, rare variants previously associated with a heightened risk of early-onset cardiomyopathy neither predicted nor correlated with late-onset cardiomyopathy in survivors of childhood cancer. This finding challenges the pre-existing assumption that the genetic architecture of cancer therapy-related cardiomyopathy mirrors that of familial dilated cardiomyopathy or that observed in adult cancer survivors. Instead, it highlights that the genetic determinants of cardiotoxicity in pediatric cancer survivors form a distinct spectrum, shaped by unique biological interactions between treatment injury and genetic background.

Dr. Sapkota emphasized these findings in the context of familial versus sporadic disease mechanisms: "Rare variants typically perturb cardiomyocyte function early in life, leading to aggressive disease onset. Our data indicate these rare variants do not contribute substantially to the late-onset cardiomyopathy observed after childhood cancer, underscoring a different genetic etiology for these survivors." He added that common variants appear to modulate risk more subtly but meaningfully over decades, paralleling the sporadic dilated cardiomyopathy trends noted in the broader population.

These nuanced genetic discoveries open the door to more tailored screening strategies for childhood cancer survivors, integrating polygenic risk profiling to complement traditional clinical factors such as cancer treatment history and cardiac imaging surveillance. By refining individual risk prediction models, clinicians could identify individuals at greatest risk for late cardiomyopathy, enabling earlier intervention and potentially modifying lifestyle or treatment plans to mitigate cardiac deterioration.

Furthermore, the research underscores the complexity of childhood cancer survivorship as a distinct clinical domain requiring dedicated genomics-driven investigation. It draws attention to the necessity for longitudinal studies that combine large-scale genetic data with deep phenotyping and treatment exposure records. Future studies expanding upon these findings could explore gene-environment interactions, epigenetic modifications, and potential therapeutic targets to preserve cardiac function in this growing population.

Funded by multiple grants from the National Institutes of Health and supported by the American Lebanese Syrian Associated Charities (ALSAC), the study represents a collaborative effort among experts from institutions including the University of Minnesota, Baylor College of Medicine, Fred Hutchinson Cancer Center, University of Alabama at Birmingham, Northwestern University, and others, reflecting a multidisciplinary approach imperative for unraveling such complex disease processes.

As survival rates continue to improve for children diagnosed with cancer—with overall survival now surpassing 80% due to advances pioneered at institutions like St. Jude—the imperative to understand and prevent long-term adverse outcomes like cardiomyopathy grows ever more urgent. This research marks a pivotal step toward that goal, illuminating distinct genetic pathways that could inform precision medicine approaches aiming to improve quality of life and cardiovascular health in childhood cancer survivors worldwide.

In summary, this landmark study delineates a clear genetic divergence between early- and late-onset cardiomyopathy forms in childhood cancer survivors, identifying common variant protective effects within TTN and BAG3 and nullifying the presumed role of rare variants in late-onset cases. These insights change the landscape of cardiotoxicity research and bear profound implications for clinical practice, genetic counseling, and future therapeutic development.

Subject of Research: Genetic risk factors for late-onset cancer therapy-related cardiomyopathy in long-term survivors of childhood cancer

Article Title: TTN and BAG3 in Cancer Therapy–Related Cardiomyopathy Among Long-Term Survivors of Childhood Cancer

News Publication Date: June 20, 2025

Web References:

• St. Jude Lifetime Cohort (SJLIFE)
• Childhood Cancer Survivor Study (CCSS)
• Yadav Sapkota profile at St. Jude
• Epidemiology & Cancer Control Department at St. Jude
• DOI link to article

Image Credits: St. Jude Children’s Research Hospital

Keywords: Cardiomyopathy, childhood cancer survivorship, TTN, BAG3, genetic variants, late-onset cardiomyopathy, cancer therapy cardiotoxicity, dilated cardiomyopathy, cancer survivor genetics

The newly developed tool, named Spot imager with pseudo single-cell resolution histology (Spotiphy), utilizes generative artificial intelligence to enhance the resolution of sequencing-based spatial transcriptomics without sacrificing gene coverage. This innovative algorithm represents a significant advancement in the field, allowing for a more detailed and accurate representation of gene expression in various tissues. The findings, published in the prestigious journal Nature Methods, signal a remarkable shift in how researchers can approach spatial transcriptomics.

Co-senior author Jiyang Yu, PhD, who spearheaded the research at St. Jude, emphasized the tool’s significance by stating, "We’ve made the first generative algorithm that can predict spatial gene expression of whole transcriptomics at the single-cell level.” This statement points to the algorithm’s unique capability to integrate data from both single-cell RNA sequencing and histological imaging. By leveraging generative modeling techniques, Spotiphy can provide a complete transcriptome coverage while simultaneously offering insights at the single-cell resolution.

Traditionally, spatial transcriptomics has relied on analyzing fixed “spots” on a grid, where each spot can encompass multiple cells and diverse cellular populations. This poses challenges in pinpointing precise gene expression profiles, particularly in heterogeneous tissues. Spotiphy tackles this limitation head-on, employing a machine learning framework capable of extrapolating cell-type proportions and gene expression data to effectively interpolate the spaces between these predefined spots.

To illustrate this process, Junmin Peng, another co-senior author involved in the study, provided a compelling analogy. He suggested envisioning a photograph missing a central section—by employing the learned rules from its training, Spotiphy reconstructs the absent details, effectively filling in the gaps in spatial data. This crucial advancement ensures that researchers can visualize cellular landscapes with enhanced clarity and resolution, leading to more accurate scientific conclusions.

One of the notable applications of Spotiphy has been in the study of neurodegenerative diseases, particularly Alzheimer’s disease. The ability to discern subtle variations in gene expression among specific cell types, such as astrocytes, offers fresh avenues for understanding disease mechanisms. Previous methods often resulted in low-resolution outputs that combined multiple cells into a single spot, obscuring essential details. With Spotiphy, researchers have achieved a true single-cell resolution paired with high gene coverage, enabling a thorough exploration of cellular behavior in disease contexts.

In experimental models, Spotiphy validated existing findings concerning Alzheimer’s disease while also uncovering new insights regarding the spatial distribution of various cell types within the brain. For instance, the tool demonstrated that distinct subsets of astrocytes were associated with specific brain regions, thereby enhancing knowledge about neuroinflammatory responses and potential therapeutic targets. Additionally, it highlighted the presence of disease-associated microglia in affected brain areas, reinforcing previous observations implicating microglial dysfunction in Alzheimer’s pathology.

Beyond applications in neurobiology, Spotiphy has shown versatility in tackling other biomedical questions, including those related to cancer biology. The research team successfully applied the tool to analyze tumor microenvironments, illuminating spatial interactions between tumors and adjacent tissues. This newfound understanding of the dynamic interplay between cancer cells and their supporting stroma presents exciting possibilities for refining treatment strategies and improving patient outcomes.

The researchers’ commitment to the scientific community is clear; Spotiphy has been made freely available for use, democratizing access to this groundbreaking tool. Scientists and researchers interested in spatial transcriptomics can explore Spotiphy’s capabilities and apply them to their specific research contexts, further contributing to the growth of this evolving field.

As the landscape of genomics and cell biology continues to expand, tools like Spotiphy promise to redefine how researchers perceive and investigate complex biological systems. The capacity to visualize cellular arrangements coupled with an understanding of their gene expression profiles opens avenues for discovering new biological insights that were previously obscured by technological limitations.

In conclusion, the development of Spotiphy represents a monumental advance in the domain of spatial transcriptomics. It not only resolves a prominent limitation in achieving both resolution and coverage but also emphasizes the power of generative models in biological research. Scientists are now better equipped to uncover intricate details within biological tissues, paving the way for breakthroughs in understanding both normal physiology and complex disease states. The collaborative efforts of institutions like St. Jude Children’s Research Hospital and the University of Wisconsin-Madison exemplify the innovative spirit in biomedical research, revealing a future where tools and technologies continue to empower researchers in their quest for knowledge.

Subject of Research: Spatial transcriptomics and its applications in gene expression analysis
Article Title: Spotiphy enables single-cell spatial whole transcriptomics across the entire section
News Publication Date: 12-Mar-2025
Web References: Spotiphy GitHub Page
References: DOI: 10.1038/s41592-025-02622-5
Image Credits: Credit: St. Jude Children’s Research Hospital

Keywords: Spatial transcriptomics, Single-cell resolution, Gene expression, Computational biology, Neurodegenerative diseases, Alzheimer’s disease, Machine learning, Cancer biology, Biomedical innovation.