Hundreds of millions of people around the world have received mRNA vaccines for COVID-19, providing them highly effective protection from developing serious illness from SARS-CoV-2 infection. This marks the dawn of a revolutionary new technology that has been years in development, and is poised to transform the treatment of not only viral infections but also many other diseases. At the Icahn Genomics Institute (IGI), we are developing new RNA therapeutics and nanomedicines for a broad range of diseases, including vaccines to prevent different viral infections, as well as cancer vaccines and adjuvants that direct a patient’s immune system to eliminate malignant cells and put cancers in long-term remission.

Beyond vaccines, scientists at the IGI are utilizing RNA for other types of therapeutics. This includes the development of short interfering RNA (siRNA) for the treatment of genetic diseases such as the porphyrias, and antisense oligonucleotides to alter the exon usage of specific genes involved in cancers, and treatments aimed at disorders of the central nervous system, such epilepsy.

A critical factor for the current and future success of RNA therapeutics is delivery. Getting mRNAs and oligonucleotides into cells of the body requires efficient delivery vehicles and modifications. Extensive work is ongoing in the institute to develop new nanoparticle formulations for more efficient and targeted delivery of RNAs and small molecules to desired cell types and tissues. This is enabling diverse applications that include non-invasive immunoimaging, reprogramming immune cells to promote tumor immunity, and modulation of inflammatory responses.

RNA therapeutics and nanomedicines researchers include:

• Manisha Balwani, MD, MS
• Nina Bhardwaj, MD, PhD
• Michael S Breen, PhD
• Margo S Breilyn, MD
• Brian D. Brown, PhD
• Joshua Brody, MD
• Robert J. Desnick, PhD, MD
• Eva Gonzalez Diaz, MD
• Navneet Dogra, PhD
• Yizhou Dong, PhD
• Ernesto Guccione, PhD
• Tingting Jiang, PhD
• Louai Labanieh, PhD
• Ivan Marazzi, PhD
• Jordi Ochando, PhD
• Anne Schaefer, MD, PhD
• Michael Schotsaert, PhD
• Xiaoqi Sun, PhD
• Abraham Teunissen, PhD, MSc, BASc
• Nicolas Vabret, PhD
• Lior Zangi, PhD

We have made great strides in our ability to treat disease through genetic and cellular engineering. Viral and non-viral vectors enable us to introduce synthetic genes into cells to reprogram cell functions. A potent example of this is the engineering of T cells to express a chimeric antigen receptor (CAR) that directs the T cells to kill cancer cells. With the development of CRISPR/Cas9 and its derivatives as a gene editing technology, researchers can now modify DNA and RNA at desired locations. Whether by knocking out a gene, turning on or off a gene, or adding or altering specific nucleotide sequences, we can change the blueprint of a cell, and use the technology to discover the functions of any gene or establish new disease treatments.  

The Icahn Genomics Institute (IGI) is using CRISPR gene editing to engineer stem cells to create important new models of complex human diseases. This includes using CRISPR to turn pluripotent stem cells into neurons to study synaptic plasticity and its dysfunction in Fragile X syndrome and association with autism. We are also reprogramming cells through CRISPR to generate human pluripotent stem cell models of blood diseases, such as myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML), in order to understand disease mechanisms and develop new therapeutic targets.

Scientists in the IGI are also developing new cell engineering and CRISPR technologies, including technologies to target the expression of therapeutic genes in cell-state dependent manners, and rationally designed CRISPR/Cas9 variants that improve the efficiency of therapeutic applications, such as base editing for the correction of deleterious mutations and treatment of inherited genetic diseases.

Gene, CRISPR, and cell engineering researchers include:

• Jalal Ahmed, MD
• Joshua Brody, MD
• Brian D. Brown, PhD
• Navneet Dogra, PhD
• Yizhou Dong, PhD
• Alison Goate, DPhil
• Tingting Jiang, PhD
• Wenyan Jiang, PhD
• Kiyotake Ishikawa, MD
• Samuele Marro, PhD
• Eirini Papapetrou, MD, PhD
• hXiaoqi Sun, PhD

Viruses and bacteria can be a devastating cause of disease, but bioengineers, virologists, and microbiologists in the Icahn Genomics Institute (IGI) and elsewhere are working to harness these organisms to create powerful new medical treatments for a wide variety of diseases. Through extensive investigation, scientists have removed harmful genes from adenoviruses, adeno-associated virus (AAV), retroviruses, lentiviruses, and other viruses and turned them into vehicles for delivering synthetic genes into cells to reprogram cellular functions or to replace defective genes. This has led to highly effective treatments for congenital blindness, immunodeficiencies, bleeding disorders, spinal muscular atrophy, and cancer.

Viruses and virus derivatives can also be used to create vaccines to prevent infectious diseases or as powerful immunotherapy treatments that kill cancer cells and recruit the immune system to eliminate tumors. Work by Dr. Adolfo Garcia-Sastre and others at Mount Sinai have turned New Castle Disease Virus (NDV) into an effective new COVID-19 vaccine as well as an anti-cancer agent, harnessing NDV’s potent ability to turn on a type I interferon response and stimulate the immune system.

Commensal bacteria—the bacteria that live in our gut, our mouths, and on our skin—are also being used to treat disease. Studies at Mount Sinai have found that a person’s unique microbiome composition can have a profound impact on health, including associations with asthma and food allergy. Scientists in the IGI have generated one of the largest biobanks of human gut bacteria in the world and are using it to identify the specific microbes that affect inflammation and metabolism, and promote different diseases, including inflammatory bowel disease (IBD). They are also using these biobanks to manufacture microbiome cocktails that will undergo clinical trials to assess their ability to improve patient outcomes in IBD and other inflammatory diseases as well as the immunotherapy response in cancer.

Viral and microbial therapeutics researchers include:

• Joshua Brody, MD
• Nina Bhardwaj, MD, PhD
• Jose C. Clemente Litran, PhD
• Sara Cuadrado, PhD
• Eva Gonzalez Diaz, MD
• Jeremiah Faith, PhD
• Adolfo Garcia-Sastre, PhD
• Ari Grinspan, MD
• Wenyan Jiang, PhD
• Louai Labanieh, PhD
• Ivan Marazzi, PhD
• Nicolas Vabret, PhD

Gene and cell therapy are providing new avenues for the treatment of cancer. One of the most exciting developments in this area is the use of gene engineering to introduce Chimeric Antigen Receptors (CAR) into T cells that reprogram them to target and kill cancer cells. There are already several FDA-approved CAR T cells therapies in the clinic that are highly effective at treating aggressive blood cancers such as B cell leukemia, lymphoma, and multiple myeloma. Scientists and oncologists in the Icahn Genomics Institute (IGI) are working together to understand how resistance can form to CAR T cell therapy, as well as other cancer immunotherapies, and creating powerful new CAR T cell therapies to treat solid organ tumors, such as lung and ovarian cancers.

The IGI is also developing ways to use RNA and DNA based therapies to target the immune system against these cancers. This includes using genomics analysis to identify shared antigens within patient tumors that can be incorporated into the design of novel cancer vaccines. The IGI is helping to pioneer novel cancer vaccines that use immunostimulatory RNA and oncolytic viruses, such as Newcastle Disease Virus (NDV), to activate innate immunity and prime anti-tumor immune responses—in situ—at the tumor site. This novel ‘in situ’ vaccine approach has already proved to be effective in inducing long-lasting tumor remissions in patients with disseminated lymphoma.

Cancer gene and cell therapy researchers include:

• Jalal Ahmed, MD
• Joshua Brody, MD
• Brian D. Brown, PhD
• Nina Bhardwaj, MD, PhD
• Diego Chowell, PhD
• Navneet Dogra, PhD
• Yizhou Dong, PhD
• Adolfo Garcia-Sastre, PhD
• Kuan-Lin Huang, PhD
• Louai Labanieh, PhD
• Samir Parekh, MBBS
• Xiaoqi Sun, PhD
• Nicolas Vabret, PhD
• Guo-Cheng Yuan, PhD

Monogenic diseases arise from inherited genetic mutations. They can be severe, life-long, and lethal. Many also have no treatment options. Gene and cell therapies offer a new avenue of treatment and over the past decade there has been monumental success in using gene therapy to treat highly debilitating genetic diseases, including the hemophilias, immunodeficiencies (ADA-SCID, X-SCID, WAS), lysosomal storage disorders (MLD, ALD), sickle cell anemia, and spinal muscular atrophy. This is just the beginning.

In synergy with Mount Sinai’s clinical genetic efforts, scientists and physician scientists in the Icahn Genomics Institute (IGI) are working to develop novel gene therapies to treat genetic disease. Our clinical genetics group, led by Manisha Balwani, MD, MS, ran Phase I/II and Phase III clinical trials of givosiran, a short interfering RNA (siRNA) drug that works by RNA interference (RNAi). They demonstrated that givosiran can successfully treat the debilitating genetic diseases called acute hepatic porphyrias, leading to the second FDA-approved RNAi drug. The concept for this drug began at Mount Sinai with work in preclinical models showing that RNAi could be an effective treatment for the porphyrias, representing a bench-to-bedside success.

New gene therapies are also being developed at the IGI to treat more complex diseases, including cardiac disease, immunodeficiencies, and epilepsy, using a variety of modalities such as AAV gene delivery, CRISPR gene editing, and antisense oligonucleotides.

Genetic disease gene and cell therapy researchers include:

• Manisha Balwani, MD, MS
• Margo S Breilyn, MD
• Louis J. Cohen, MD
• Robert J. Desnick, PhD, MD
• Navneet Dogra, PhD
• Ernesto Guccione, PhD
• Kiyotake Ishikawa, MD
• Tingting Jiang, PhD
• Louai Labanieh, PhD
• Samuele Marro, PhD
• Anne Schaefer, MD, PhD
• Makiko Yasuda, MD, PhD

To develop new therapies, we need to identify actionable molecular targets of disease. These are the genes, cells, or molecules driving disease that can be ‘drugged’ to return a tissue to homeostasis. At the Icahn Genomics Institute (IGI) we are uncovering novel disease targets through a multiscale approach that includes comprehensive analysis of patient tissues at the gene, transcript, cell, and organ level, employing functional genomics to establish causal factors of disease, and applying data science and artificial intelligence (AI) to identify pivotal nodes in convoluted biological networks.

Through extensive analysis of patient genetics, gene expression, and single cell data we can identify variations between healthy and disease states and use these insights to improve patient treatment. Since the data is highly complex, the IGI is developing and employing advanced computational approaches, including AI and machine learning, to decrypt the disease drivers, as well as uncover novel biomarkers to inform precision treatments. This has already started to transform patient care. Using advanced molecular techniques, scientists in the IGI have been able to resolve the disease etiology of different patients with undiagnosed conditions. In one case, it was determined that a patient’s immune disorder was caused by deficiencies in USP18, a negative regulator of JAK/STAT signaling, and subsequently, they were able to repurpose a JAK inhibitor and effectively treat the patient’s life-threatening condition.

Functional genomics, using CRISPR screens, is also being used to identify novel drug targets. Scientists at the IGI have invented a powerful new technology for functional genomics, which enables, for the first time, CRISPR screens to be resolved in situ with spatial resolution. This greatly expands target discovery by enabling the disease-causing role of genes operating extrinsically, such as cytokines, to be determined and represents a new frontier for identifying drug targets in cancer and other diseases by functional genomics. 

As our knowledge of diseases mechanisms increases, we will find and develop new therapeutics to many diseases that have previously defied treatment.

Therapeutic target discovery researchers include:

• Carmen Argmann, PhD
• Brian D. Brown, PhD
• Michael S Breen, PhD
• Supinda Bunyavanich, MD
• Alexander Charney, MD, PhD
• Judy H. Cho, MD
• Jose C. Clemente Litran, PhD
• Ron Do, PhD
• Jeremiah Faith, PhD
• Gang Fang, PhD
• Christian Forst, PhD
• Adolfo Garcia-Sastre, PhD
• Alison Goate, DPhil
• Ernesto Guccione, PhD
• Zeynep H. Gumus, PhD
• Ke Hao, PhD
• Gabriel E. Hoffman, PhD
• Sander Houten, PhD
• Kuan-Lin Huang, PhD
• Yuval Itan, PhD
• Wenyan Jiang, PhD
• Eimear E. Kenny, PhD
• Robert J. Klein, PhD
• Avi Ma’ayan, PhD
• Ivan Marazzi, PhD
• Edoardo Marcora, PhD
• Samuele Marro, PhD
• Eirini Papapetrou, MD, PhD
• Inga Peter, PhD
• Lauren Peters, PhD
• Dalila C. Pinto, PhD
• Towfique Raj, PhD
• Boris A. Reva, PhD
• Panagiotis Roussos, MD, MS, PhD
• Robert P. Sebra, PhD
• Andrew J. Sharp, PhD
• Honoratus (Harm) Van Bakel, PhD
• Minghui Wang, PhD
• Pei Wang, PhD
• Guo-cheng Yuan, PhD
• Bin Zhang, PhD

RNA NanoCore is a Core Facility at the Icahn Genomics Institute (IGI), which is part of the Icahn School of Medicine at Mount Sinai. In general, the Institute is working to create new DNA- and RNA-based therapies for a broad range of diseases. RNA NanoCore concentrates more specifically on using lipid nanoparticles and RNA technology to develop new therapeutics and nanomedicines.

Lipid nanoparticles are small lipid spheroids - approximately 100 nm in diameter – that encapsulate biological molecules such as RNA. They serve as a powerful non-viral gene delivery vehicle. This technology has already etched its mark in medicine by playing a pivotal role in the success of the COVID-19 vaccines and demonstrating the great potential and efficacy of this new class of nanotherapeutics.

RNA therapeutics are a new class of medicine in which RNA-based molecules are used for treatment or prevention of human diseases. RNA therapy can target specific cellular transcripts, genes and proteins or encode new genetic information. This broadens the druggable targets and enables development of new landscapes in the treatment of a variety of ailments, including cancers and genetic disorders. In addition, RNA based therapies use an accelerated development process that enables us to craft drugs in significantly reduced timelines compared to conventional drug development methods.

At RNA NanoCore, we package custom-made RNA in curated lipid nanoparticle formulation to allow researchers to develop next generation therapeutics. NanoCore’ channels IGI expertise to create a hub where science meets innovation. The continuous crosstalk between IGI and NanoCore positions us at the forefront of lipid nanoparticle and RNA technology so that we can offer innovative delivery systems for next-generation genetic medicine.

RNA NanoCore Co-Directors include:

• Angelo Ambile, PhD
• Yizhou Dong, PhD

Technology and Applications

RNA NanoCore, a Core Facility of the Icahn Genomics Institute (IGI), focuses on the use of lipid nanoparticles and RNA-based approaches to develop new gene therapies.

Lipid Nanoparticles

Lipid nanoparticles (LNPs) are the most advanced non-viral gene delivery system used in the clinic. They are composed of a set of lipids that can encapsulate different class of RNA molecules in nanovescicles. Four components are generally critical for LNP formulations, which include an ionizable cationic lipid, a helper lipid, cholesterol, and a PEG-lipid. Briefly, ionizable cationic lipids are a key component; they interact with RNA and promote RNA endosomal escape in cells. Helper lipids and cholesterol promote formulation stability and delivery efficiency. PEG-lipid prevents particle aggregation and prolong circulation time in vivo.

To prepare LNPs, the lipids and RNA are dissolved separately in ethanol and acidic aqueous solution, respectively. Next, the two solutions are mixed with an automated microfluidic device. Then, ethanol is removed by dialysis. The final LNP/RNA formulation is characterized based on the percentage of RNA encapsulation, the diameter of the LNP, and the polydispersity index, which measure the heterogeneity of the LNP composition. These are all services provided at RNA NanoCore. LNPs enhance the stability and delivery efficiency of mRNA, allowing customization for targeted applications, including vaccines or therapies for diverse diseases. This technology has been proven effective with the recent COVID-19 vaccines, which deliver mRNAs in vivo, thereby overcoming major barriers in genetic medicines.

RNA Therapeutics

RNA therapy is an emerging class of genetic medicine that uses the unique properties of RNA molecules to treat or prevent human diseases. RNA-based therapeutics include antisense oligonucleotides (ASOs), small interfering RNA (siRNA), microRNA (miRNA), RNA aptamers, and messenger RNA (mRNA). While ASOs, siRNA, and miRNA can theoretically target any cellular transcripts, mRNA therapeutics can be used to express functional proteins for vaccination, protein replacement therapy, and so on. RNA aptamers can directly bind specific receptors or inhibit protein activity similar to small molecule inhibitors and blocking antibody therapies. By acting on proteins, transcripts, and genes, RNA therapeutics tremendously expand the repertoire of druggable targets providing the foundations for the development of new therapeutic strategies.

RNA therapy possesses many advantages. For example, once the nucleic acid chemistry and the delivery method are established, the production of new and personalized RNA-based drugs can be achieved in a relatively short period using these pre-established methodologies. This rapid development process, as seen in the creation of the COVID-19 vaccines, minimizes the risk of genotoxicity. Overall, RNA therapy is rapidly emerging as one of the leading technologies in medicine with the potential to revolutionize the clinical outcomes of an endless number of diseases.

Services and Products

RNA NanoCore, a Core Facility of the Icahn Genomics Institute (IGI), provides a variety of services and products to assist researchers in pursuing their investigations. They are available to researchers both within and outside of the Icahn School of Medicine at Mount Sinai.

Services

RNA NanoCore offers a wide range of services tailored to meet the diverse needs of researchers in various fields. Key offerings include:

• Customized Lipid Nanoparticle (LNP) Synthesis: Production of lipid nanoparticles tailored to specific research requirements, including for in vitro and in vivo delivery of mRNA and CRISPR gRNA.
• RNA Production and Optimization: Synthesis and optimization of RNA molecules for various applications, including vaccine development, CRISPR gene editing, and protein expression.
• Collaborative Research and Consultation: Our team is available for consultations, research projects, and technical support, enabling seamless integration of our services into your research endeavors.

We have advanced facilities and expert staff to ensure reliable production, characterization, and quality control of mRNA and lipid nanoparticle (LNP)-mRNA formulations. Our core is equipped with state-of-the-art technology to produce high-quality mRNA and LNP-mRNA formulations.

Our meticulous approach includes comprehensive optimization of sequences and structural elements, such as untranslated regions, to boost mRNA stability and translational efficiency. We employ purification technologies to eliminate residual components and byproducts, ensuring the production of high-quality IVT mRNA transcripts and LNP-mRNA formulations.

We are spearheading the development of new ionizable lipids and LNP-mRNA formulations, establishing platforms for mRNA synthesis, purification, and quality control. Our commitment to innovation is reflected in our ongoing efforts to bring the latest technologies to Mount Sinai and develop new formulations for a range of medical fields including cancer, infectious disease, and genetic disorders as well as cardiovascular disease.

Products

• Reporter mRNA: We provide reporter mRNA for tracking delivery efficiency and/or duration of expression in vitro and in vivo. Our IVT mRNA resembles fully mature mRNA with 5’ cap, UTR, and 3’ polyA.
• eGFP mRNA, mCherry mRNA, Luciferase mRNA, and Cre mRNA: We can manufacture our catalog mRNA with modified nucleotides, such as N¹-methylpseudouridine, or capping technologies such as CleanCap® AG analog, within 2-3 weeks. Please inquire for information.
• Custom-made mRNA: We provide cloning services of DNA templates for custom-made mRNA sequence.
• LNP/mRNA formulation: We provide LNP/mRNA formulations with different chemical compositions optimized for specific applications and tissues of interest.
• SM-102 LNP, ALC-0315 LNP, and GenVoy LNP: We also provide customized LNP with other ionizable lipids and/or mRNA for specific application. We invite you to explore the services that our facility can offer to your academic pursuits. Whether you are working on experimental research projects, drug development, or vaccine design, our expertise and services are at your disposal.

Please contact us at nanocore@mssm.edu for additional product information.