Virginia Based AMPEL BioSolutions’ Machine Learning Breakthrough Predicts Drug Options for Inflammatory Skin Diseases

Published on the Biohealth Innovation Website on May 3, 2022:

AMPEL BioSolutions today announces a breakthrough in precision and personalized medicine that could revolutionize the way doctors treat inflammatory skin diseases, such as Lupus, Psoriasis, Atopic Dermatitis and Scleroderma. Revealed in the peer-reviewed journal Science Advances, the paper details AMPEL’s breakthrough machine learning approach to characterize disease activity from gene expression data obtained from patient skin biopsies. The lab test, only a concept for the last few years, is now ready for development for practical use. AMPEL’s initial focus was Lupus, but the test can be used for many autoimmune or inflammatory skin diseases that affect more than 35 million Americans.

AMPEL’s innovative machine learning approach, which is now ready to be developed as a decision support biomarker test, could greatly impact health care by allowing physicians to identify the cause of patient disease symptoms and select appropriate treatment more precisely.  AMPEL’s approach is sufficiently sensitive to detect changes in clinically uninvolved skin so that early intervention may prevent systemic flares and skin damage apparent in lesions.  The application of AMPEL’s machine learning approach could also assist pharmaceutical companies in drug development and clinical trials.

Patients with chronic skin diseases often suffer from unpredictable disease activity that impacts daily activities like work and family life. Since unpredictable symptoms often result in trips to the Emergency Room, the ability to predict worsening disease and systemic involvement with routine skin biopsies has important health care and health economics implications. 

Paired with AMPEL’s pipeline of tools to analyze very large and complex clinical datasets (“Big Data”), AMPEL’s machine learning program is a significant step towards implementing a routine skin test for monitoring disease activity and providing decision support for treatment based on a patient’s gene expression. This will transform the way doctors treat chronic skin diseases by using the information gathered by the lab test and analyzed by machine learning to diagnose, characterize the precise molecular abnormalities and treat skin diseases before damage begins, saving patients from pain and inconvenience of a disease that otherwise drastically affects their lives.

Pharmaceutical companies test drugs in clinical trials and face the challenge of enrolling patients that have the best potential to respond to the treatment being tested.  Enrolling the “wrong” patients can result in trial failure, often leading to cancellation of a drug’s development towards FDA approval that may have benefit in a sub-group of the overall patient population. AMPEL’s skin test will help pharmaceutical companies identify the patients most likely to respond to specific treatments, thereby helping improve outcomes in clinical trials.

Dr. Peter Lipsky, Chief Medical Officer and Co-Founder, AMPEL BioSolutions: “There is currently no other application that can precisely predict disease activity and propose appropriate treatments, and we are very encouraged by this breakthrough reported in Science Advances.  For those patients suffering with chronic skin diseases, meaningful innovation in treatments can’t come soon enough.  Following the development of our machine learning concept, we can now move forward in working with our partners to develop this skin test that could transform the way doctors can help patients with chronic skin disease manage their condition by offering better and more precise treatments based on individual patient data rather than a general approach.”

Dr. Amrie Grammer, Chief Scientific Officer and Co-Founder, AMPEL BioSolutions: ““Our team has developed a tool that can conceivably transform the way patients with skin conditions are treated.  As a precision medicine company, AMPEL is changing the paradigm of treatment in autoimmune and inflammatory diseases.  We are proud to be doing this work in Virginia and will continue to recruit talent and grow our business here.”

Dr. Wright Caughman, Professor, Department of Dermatology, Emory School of Medicine, and Exec VP for Health Affairs (Emeritus), Emory University: “AMPEL’s highly innovative skin biopsy test will provide an excellent new tool for the diagnosis and management of autoimmune and inflammatory diseases of the skin.  AMPEL is presenting this work at the Society for Investigative Dermatology meeting later this month.  Once AMPEL’s clinical genomic test is CLIA certified, physicians will be able to quickly identify the best medications for each individual patient and obtain faster and safer control of their disease.”

Dr. Kimberly Showalter Lakin, Rheumatologist, Associate Professor, Hospital for Special Surgery, Weill Cornell Medical College: “AMPEL’s Science Advances study is groundbreaking for physicians that take care of autoimmune patients with skin disease.  AMPEL’s work highlights the systemic nature of these conditions and identifies the molecular pathways in areas of skin that show no outward damage allowing early intervention.  Although there are numerous FDA-approved drugs that target different parts of the immune system, as a physician, I have no way of knowing which medications will work in which patients.  Management strategies often end up being ‘trial and error’ treatment decisions, and physicians and patients will greatly benefit from a tool like this that will allow for more precise treatments. Because not all medications work in all patients, currently, it can take many months and suffering before we are able to determine a treatment’s effectiveness.  This is very exciting and I look forward to the results of further studies.”

Dr. Dan Wallace, Rheumatologist, Board of Governors, Cedars-Sinai Medical Ctr and UCLA: “Lupus care will greatly benefit from more precise evaluation of patients, especially those with skin involvement.  This novel approach is an important step in that direction.  Precision medicine is a long overdue approach to determine immunological disease status and treatment of this devastating disease by focusing on each patient’s gene expression profile.” 

Dr. J. Michelle Kahlenberg, MD PhD, Rheumatologist, University of Michigan: “These data show the power of informatics research and the importance of sharing datasets to further the knowledge in the field. It amplifies what many of us in the skin autoimmune research field have been saying: that normal skin is not ‘normal’ in our patients and that we will learn a lot about disease pathogenesis by studying the skin.  A test that can help us to identify patients at risk of flare will be a very useful tool indeed!”

Deidre Baptista and Kirsten Maeda, “GEE Twins for Lupus” and Lupus Foundation of Northern California (LFNC) Board Members: “AMPEL’s precision medicine work published in Science Advances in a game-changer for autoimmune patients and a huge step forward in treating patients’ skin disease.  We have so much appreciation for AMPEL’s “out-of-the-box” thinking and unwavering dedication to improve patient’s lives.”

Jay Blanton, Psoriasis Patient: “The biggest challenge with living with Psoriasis for over a decade is finding medications that keep my disease stable.  I’ve experienced severe systemic flares over the years that erupt suddenly and without warning.  I am eager to see AMPEL’s novel RNA-based precision medicine test available to allow me to get ahead of my symptoms and provide suggestions for medicines that have the best chance of controlling my disease.”

Angel Williams, Lupus Patient and Lupus Foundation of America DC/MD/VA Ambassador: “Getting precise treatment after a skin biopsy from unaffected areas has the potential to decrease the number of scars a patient has from their disease damaging their skin.  Hair loss from skin damage and scars on your face are two of the most socially distressing outcomes of autoimmune disease.   I am looking forward to the day when AMPEL’s skin test for lupus patients is available.”

Jay Remley, Vice-Chair, LFNC (Lupus Foundation of Northern California) and former Executive Google Cloud: “Lupus is a complex auto-immune disease that is often mis-diagnosed and therefore, mis-treated for years.  This causes additional pain and anxiety for lupus patients.  DermaGENE® is a major breakthrough by addressing multiple autoimmune/inflammatory diseases (Psorisasis, Scleroderma, and Atopic Dermatitis).  By combining the broader autoimmune intelligence of DermaGENE® with precision medicine, not only will physicians be able to more accurately treat their patients, but this will significantly reduce patients being mis diagnosed and remove stress and anxiety from the diagnosis experience.”

Background Information

Machine learning is an analytic technique to train computers to assess information and make predictions. AMPEL has used this approach in a novel way to train a computer to analyze data obtained from assessing a kind of “Big Data”, namely that obtained by assessing gene expression information, to predict whether an individual living with lupus, psoriasis, atopic dermatitis or scleroderma is experiencing a flare in disease activity. Gene expression analysis examines the number and pattern of the genes expressed at a given moment and can provide insight into the entire spectrum of genomic abnormalities.

Many chronic diseases have unexpected flares that dramatically affect patient quality of life. Further, treatments for chronic disease have been developed based on a patient population as a group, so some individuals will respond differently or not at all to available treatments.  For the past nine years, the scientists and clinicians at AMPEL have been working on ways to address this problem, by designing concepts to personalize treatments for an individual patient as opposed to a patient population. The paper published in Science Advances confirms the practicality of AMPEL’s concept, which can now go into the development phase.

AMPEL’s initial focus was lupus but the test can be used for many autoimmune or inflammatory diseases.  AMPEL’s skin test will confirm or establish the diagnosis and provide decision support  for their physician with the most appropriate drugs for the patient at that moment in time.

Next steps include developing the physical lab test and rigorously examining the results in a clinical trial.  AMPEL’S goal is to have their test available for routine use by physicians within the next few years.

BioSolutions LLC (2013-present)

Harnessing Data to Improve Lives through Genomics AMPEL BioSolutions is a technology company with CRO capabilities based in Charlottesville Virginia.  AMPEL was founded to bring personalized precision medicine to patients with diseases involving the immune system and inflammation.  AMPEL develops clinical genomic tests to predict flares and drug options for a patient based on machine learning of gene expression.  Products expected to launch in 2022-2023 include LuGENE®, a blood test for Lupus, and DermaGENE® a skin biopsy test for Lupus, Psoriasis, Atopic Dermatitis and Scleroderma.

LuGENE®️ Blood Test Expected To Launch In 2022

LuGENE®️ Blood Test Expected to Launch in 2022

Machine Learning Approaches to Predict Lupus Disease Activity from Gene Expression Data

The integration of gene expression data to predict systemic lupus erythematosus (SLE) disease activity is a significant challenge because of the high degree of heterogeneity among patients and study cohorts, especially those collected on different microarray platforms. Here we deployed machine learning approaches to integrate gene expression data from three SLE data sets and used it to classify patients as having active or inactive disease as characterized by standard clinical composite outcome measures. Both raw whole blood gene expression data and informative gene modules generated by Weighted Gene Co-expression Network Analysis from purified leukocyte populations were employed with various classification algorithms. Classifiers were evaluated by 10-fold cross-validation across three combined data sets or by training and testing in independent data sets, the latter of which amplified the effects of technical variation. A random forest classifier achieved a peak classification accuracy of 83 percent under 10-fold cross-validation, but its performance could be severely affected by technical variation among data sets. The use of gene modules rather than raw gene expression was more robust, achieving classification accuracies of approximately 70 percent regardless of how the training and testing sets were formed. Fine-tuning the algorithms and parameter sets may generate sufficient accuracy to be informative as a standalone estimate of disease activity.

Eight Innovative, Virginia Life Science Startups To Know. AMPEL Makes The List!

Eight Innovative, Virginia Life Science Startups to Know. AMPEL Makes the List!

At BioBuzz, we’re dedicated to bringing you interesting and important stories that emerge from the thriving life sciences ecosystem that is the BioHealth Capital Region (BHCR). 

The heart of the BHCR biohealth cluster is Maryland, with its vast network of government research agencies, the strong university system, and a deep network of established, emerging, and startup life science companies across a wide range of fields, including cell and gene therapy, advanced biomanufacturing, phage therapy, medical devices and more traditional biotech and pharma organizations. That’s not even to mention the remarkable efforts of myriad Maryland vaccine companies to develop the first approved, safe, and efficacious SARS-CoV-2 vaccine.

Maryland is certainly the most mature market within the wider BHCR, and the one we tend to cover the most, especially recently, but it isn’t the only growing and thriving BHCR sector. 

In addition to exciting developments in Washington, DC, Charlottesville, Virginia is quietly emerging as an exciting hub for life science companies and promising startups that have spun out of the University of Virginia (UVA). UVA and CVilleBioHub, which was founded in 2016 by biotech industry leaders to support the growing biohealth ecosystem in and around Charlottesville, Virginia, have been catalysts for growth in what they call the CVille ecosystem. CVilleBioHub’s mission is to double the size of the biohealth cluster it serves by 2030 through strong engagement, deft resourcing, valuable programming, and grassroots advocacy.

It seems the collaboration between UVA and CVilleBioHub is working. There are a host of exciting, innovative startup companies that call Charlottesville home. We’re excited to highlight these nine innovative Charlottesville, Virginia startup companies and look forward to telling their stories well into the future.  

CBS19 News 5:00 & 6:00 Broadcast June 12, 2020

CBS19 News 5:00 & 6:00 Broadcast June 12, 2020

  • June 15, 2020
  • News

Charlottesville-based company develops COVID-19 test
CHARLOTTESVILLE, Va. (CBS19 NEWS) — A Charlottesville-based precision medical company has developed a new approach to predicting the severity of the coronavirus. Link to the full broadcast:

AMPEL BioSolutions has developed technology to determine how severely a person will react to coronavirus and identify the best, FDA-approved treatment options. The company has been working since March to develop a new test amid the COVID-19 pandemic.

“AMPEL’s goal is to accelerate getting effective treatments to COVID patients to be able to blunt that serious illness that leads to lung damage and death,” said  Dr. Amrie Grammer, Co-Founder, COO, and CSO of AMPEL BioSolutions.

Grammer, a double University of Virginia-graduate, said the company began work quickly to get results, publishing a paper in just five weeks.

“We started working around the clock and were able to get some results in five weeks to be able to suggest drugs that would blunt that very serious illness that leads to lung damage,” she said.

The genomic test, CovGENE, uses bodily fluids from a nasal swab or blood for testing. A partnership with a diagnostic company could expedite the test’s timeline.

“To partner with an existing diagnostic company that has a test on the market for COVID, to be able to license that, and they could very quickly bring this to market, with the right company it could be available in a matter of months,” Grammer said.

AMPEL’s focus has shifted slightly over the past few months.

“Our goal was bringing new drugs to patients with serious illness, initially Lupus, a very serious auto-immune disease that affects women,” Grammer said.

Amidst the coronavirus pandemic, she felt an obligation to focus on COVID-19 research.

“A contribution to the scientific community and we felt an obligation to bring that forward, especially in these very difficult COVID-19 pandemic times,” Grammer said.

AMPEL BioSolutions is working to get its lupus treatment, LuGENE, a gene-based diagnostic for patients to determine disease status, predict flares ups, and match patients with the best drug options, to market by 2022. The company is currently securing funding.