Using algorithmic technology designed for mapping the stars, the scientists have created an imaging/spatial location platform called AstroPath which may help oncologists develop immunotherapies that work best on specific cancers. Such a capability is key to effective precision medicine techniques.
Dark Daily has regularly pointed out that technologies developed in other fields of science will eventually be brought into anatomic pathology and clinical laboratory medicine. Use of the star-mapping technology in oncology and the diagnosis of cancer is one such example.
In “Analysis of Multispectral Imaging with the AstroPath Platform Informs Efficacy of PD-1 Blockade,” published in the journal Science, the multi-institution research team wrote, “Here, we present the AstroPath platform, an end-to-end pathology workflow with rigorous quality control for creating quantitative, spatially resolved mIF [multiplex immunofluorescence] datasets. Although the current effort focused on a six-plex mIF assay, the principles described here provide a general framework for the development of any multiplex assay with single-cell image resolution. Such approaches will vastly improve the standardization and scalability of these technologies, enabling cross-site and cross-study comparisons. This will be essential for multiplex imaging technologies to realize their potential as biomarker discovery platforms and ultimately as standard diagnostic tests for clinical therapeutic decision-making.
“Drawing from the field of astronomy, in which petabytes of imaging data are routinely analyzed across a wide spectral range, [the researchers] developed a platform for multispectral imaging of whole-tumor sections with high-fidelity single-cell resolution. The resultant AstroPath platform was used to develop a multiplex immunofluorescent assay highly predictive of responses and outcomes for melanoma patients receiving immunotherapy,” the researchers added.
Using Star Mapping Software to Fight Cancer
“The application of advanced mapping techniques from astronomy has the potential to identify predictive biomarkers that will help physicians design precise immunotherapy treatments for individual cancer patients,” said Michele Cleary, PhD, CEO of the Mark Foundation for Cancer Research, in a Johns Hopkins news release.
Although the universe we live in and the universe of a cancerous tumor may not seem related, the fact is the same visualization technology can be used to map them both.
“What should be pointed out is that astronomy is mapping the sky in three dimensions, so keeping the spatial relationships while also identify each heavenly body is the goal of these algorithms,” said Robert Michel, Publisher and Editor-in-Chief of Dark Daily and its sister publication The Dark Report.
“Both aspects of that information technology have value in surgical pathology, where the spatial relationship of different cells and cell structures is relevant and important while also having the ability to identify and characterize different types of cells and cell structures. This technology appears to also be capable of identifying multiple biomarkers,” he added.
AstroPath Provides 1,000 Times the Information Content from A Single Biopsy
According to the news release, “[The researchers] characterized the immune microenvironment in melanoma biopsies by examining the immune cells in and around the cancer cells within the tumor mass and then identified a composite biomarker that includes six markers and is highly predictive of response to a specific type of an immunotherapy called Anti-PD-1 therapy.”
This is where the use of AstroPath is truly innovative. Previously, researchers could only identify those biomarkers one at a time, through a painstaking process.
“For the last 40 years, pathology analysis of cancer has examined one marker at a time, which provides limited information,” said Drew Pardoll, MD, PhD, Director of the Bloomberg-Kimmel Institute for Cancer Immunotherapy and a Johns Hopkins professor of oncology, in the news release. “Leveraging new technology, including instrumentation to image up to 12 markers simultaneously, the AstroPath imaging algorithms provide 1,000 times the information content from a single biopsy than is currently available through routine pathology,” he added.
More information about a cancerous tumor means clinicians have more tools to combat it. Treatment becomes less about finding the right immunotherapy and more about treating it immediately.
“This facilitates precision cancer immunotherapy—identifying the unique features of each patient’s cancer to predict who will respond to a given immunotherapy, such as anti-PD-1, and who will not. In doing so, it also advances diagnostic pathology from uniparameter to multiparameter assays,” Pardoll said.
Big Data and Data Analysis Is the Future of Precision Medicine
The use of data in science is changing how researchers, clinicians, pathologists, and others provide healthcare in the modern world. When it is properly collected and analyzed, data holds the key to precision medicine’s personalized and targeted patient care.
“Big data is changing science. There are applications everywhere, from astronomy to genomics to oceanography,” said Alexander S. Szalay, PhD, Bloomberg Distinguished Professor and Professor in the Department of Computer Science at Johns Hopkins University, and Director of the Institute for Data Intensive Engineering and Science (IDIES), in the news release.
“Data-intensive scientific discovery is a new paradigm. The technical challenge we face is how to get consistent, reproducible results when you collect data at scale. AstroPath is a step towards establishing a universal standard,” he added.
Should AstroPath prove to be a clinically safe and accurate method for developing precision medicine cancer therapies, anatomic pathologists can look forward to exciting new ways to diagnose cancer and determine the best courses of treatment based on each patient’s unique medical needs.
Following a nearly two-year disruption due to the SARS-CoV-2 pandemic, pathologists and clinical laboratory professionals once again have an opportunity to gather and learn from each other
It is good news that the daily number of new cases of COVID-19 continue declining here in the United States. That fact, and the growing number of vaccinations, have encouraged state and federal officials to lift many restrictions on business and social activities.
Clinical laboratories are watching a big drop in the daily number of COVID-19 tests they perform, even as routine test volumes climb and more patients show up in doctors’ offices for the typical mix of ailments and health conditions.
It’s true that many familiar routines are back. But it is also true that things are not exactly the way they were pre-pandemic. And that’s the rub. Going forward, what should medical laboratory managers and pathologists expect to be the “post-pandemic normal” in how patients access care and how providers deliver clinical services? How will healthcare in this country be different from what it was pre-pandemic?
Preparing Clinical Lab Leaders for What Comes Next
These questions and more will be front and center when the Executive War College on Lab and Pathology Management returns on Nov. 2-3, 2021, at the Hyatt Riverwalk Hotel in San Antonio. The theme of this first live gathering since the spring of 2019 will be “Preparing Your Clinical Laboratory and Pathology Group for Post-Pandemic Success.”
“Today, lab managers have the interesting challenge of understanding the new opportunities they can use to advance their labs, both clinically and financially,” stated Robert L. Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report, and founder of the Executive War College. “It isn’t that the pandemic changed healthcare in fundamental ways. Rather, it is that the pandemic accelerated changes that were underway before the outbreak began.
“That’s true of telehealth as well, for example,” he continued. “Once the nation was locked down, utilization of virtual physician visits and telehealth services skyrocketed. Today, national surveys confirm that as many as 50% of all patients and physicians have used a telehealth service, are comfortable with this type of appointment, and are ready to continue to use virtual office visits.
“Another trend accelerated by the pandemic is patient self-testing at home,” Michel added. “Government health officials saw the benefit of clearing for clinical use different specimen collection systems and COVID-19 test methods designed for use by consumers in the comfort of their home. Today, consumers can choose from multiple specimen collection products and SARS-CoV-2 tests designed for in-home use. Clinical laboratory managers should consider this development to be a consumer home-test baseline. Federal officials have created a regulatory pathway that will make it easier and faster for federal regulators to clear other types of diagnostic tests for consumer home use.”
What if the FDA Approves More Consumer At-Home Tests?
There are implications to each of the two trends described above. In the case of telehealth, if patients see their doctors virtually and the doctors order medical tests, how do clinical laboratories access these patients to collect the specimens needed to do this testing?
Similarly, if, in coming years, the federal Food and Drug Administration (FDA) increases the number of diagnostic test specimen-collection kits that consumers can use from home, how should local clinical laboratories position themselves to receive those kits and perform those tests?
These are two examples of important questions to be answered at sessions scheduled for the Executive War College in San Antonio on Nov. 2-3. Case studies by innovative lab leaders will address topics ranging from high-level strategy to daily management, operations, marketing, and managed care contracting.
Attendance Limited at This Fall’s Executive War College
At the first live edition of the Executive War College since May 2019, attendees will notice one significant difference from earlier years. By design, and for the safety and well-being of attendees, the number of attendees will be limited to 300. The hotel follows the Centers for Disease Control and Prevention (CDC) guidelines and is prepared to adjust those numbers as CDC guidance evolves. Thus, those interested in attending this year’s conference are advised to register early to guarantee their place and avoid being disappointed.
Suggestions for session topics and speakers are welcome and can be sent to info@darkreport.com. Conference details, session topics, and speakers will be updated regularly at www.executivewarcollege.com.
So, register today because seating is limited at the 2021 Executive War College Presents “Preparing Your Clinical Laboratory and Pathology Group for Post-Pandemic Success.” To ensure your place at this valuable conference, click HERE or place this URL (https://dark.regfox.com/2021-ewc-presents) into your browser.
The rapid diagnostic test costs less than $5 per unit and can be adapted for other diseases, the developers say, which opens a slew of possibilities for clinical laboratories
Just as the SARS-CoV-2 coronavirus spurred deployment of new vaccine technology based on messenger RNA (mRNA), the COVID-19 pandemic also could prove to be a watershed for in vitro diagnostics (IVD) innovation in ways that benefit clinical laboratories.
A Penn Medicine news release noted that “The RAPID technology … transforms the binding event between the SARS-CoV-2 viral spike protein and its receptor in the human body, the protein ACE2 (which provides the entry point for the coronavirus to hook into and infect human cells), into an electrical signal that clinicians and technicians can detect. That signal allows the test to discriminate between infected and healthy human samples. The signal can be read through a desktop instrument or a smartphone.”
Though still in its early stages, the technique potentially offers dramatically lower costs and faster results than traditional RT-PCR (reverse transcription polymerase chain reaction) molecular tests. Moreover, the RAPID technology might be useful for identifying other types of biomarkers and could be the basis for diagnostic tests that help reduce the cost-per-test in medical laboratory testing while providing comparable sensitivity and specificity to existing methodologies.
Clinical trials began on January 5, 2021, and the Penn Medicine researchers say the IVD test technology can be applied to other infectious diseases, which, if proven accurate, would be a boon to clinical laboratory testing.
Diagnostic Test Results in Four Minutes for Less than $5/Test
According to the news release, the RAPID 1.0 (Real-time Accurate Portable Impedimetric Detection prototype 1.0) biosensor test costs less than $5 and can deliver results in four minutes. The researchers reported overall accuracy of 87.1% on (139) nasal swab samples and 90% on (50) saliva samples.
The technology uses electrodes that can be mass-produced at low cost on commercially-available screen printers, the researchers said. Results can be read on electronic devices connected to a PC or smartphone.
Does Penn Medicine’s RAPID 1.0 Test Replace Traditional RT-PCR Testing?
In their published study, the Penn Medicine researchers cited the need for “fast, reliable, inexpensive, and scalable point-of-care diagnostics.”
RT-PCR tests, they said, “are limited by their requirement of a large laboratory space, high reagent costs, multistep sample preparation, and the potential for cross-contamination. Moreover, results usually take hours to days to become available.”
Researchers who have studied the SARS-CoV-2 coronavirus know that it uses a spike-like protein to bind to angiotensin-converting enzyme 2 (ACE2) receptors on the surfaces of human cells.
As described in Penn Medicine’s published study, the biosensor contains ACE2 and other biochemical agents anchored to an electrode. When the SARS-CoV-2 coronavirus attaches to the ACE2, the biosensor transforms the chemical reaction into an electrical signal that can be measured on a device known as a potentiostat.
The researchers tested their RAPID 1.0 technology with two commercially available potentiostat models:
The researchers initially developed the electrode as a printed circuit board, which is relatively expensive. To reduce costs, they constructed a version that uses filter paper as the main component. The researchers noted that one screen printer in a lab can produce 35,000 electrodes per day, including time needed to incorporate the chemical elements. “However, it must be noted that these steps can be fully automated into a production line for industrial purposes, drastically reducing time requirements,” they wrote.
The test can be performed at room temperature, they added, and total cost per unit is $4.67. Much of that—$4.50—is for functionalizing the ACE2 recognition agent. The cost for the bare electrode is just seven cents.
“The overall cost of RAPID may be further reduced through recombinant production of ACE2 and ACE2 variants,” the researchers said, adding that the RAPID 1.0 test can detect the SARS-CoV-2 coronavirus at low concentrations correlating to the earliest stages of the COVID-19 disease.
Testing Penn Medicine’s RAPID 1.0 Test
The researchers evaluated the technology in blinded tests with clinical samples from the Hospital of the University of Pennsylvania. The evaluation included 139 nasal swab samples, of which 109 were determined to be COVID-19 positive by RT-PCR tests and clinical assessments. Among these, the RAPID test successfully detected the SARS-CoV-2 coronavirus in 91 samples, for a sensitivity rate of 83.5%. One sample was from a patient diagnosed with the highly contagious SARS-CoV-2 Alpha variant B.1.1.7, which the test correctly identified as positive.
Among the 30 samples determined to be COVID negative, the RAPID test scored a specificity rate of 100%, meaning no false positives. Overall accuracy, including sensitivity and specificity, was 87.1%.
The researchers also analyzed 50 saliva samples: 13 COVID-positive and 37 COVID-negative. The test correctly identified all 13 positive samples but produced five false-positives among the 37 negative samples, for a specificity rate of 86.5%. The researchers speculated that this could be due to interactions between ACE2 and other biomolecules in the saliva but suggested that performance “will improve when using fresh saliva samples at the point-of-care.”
Are There Other Applications for the RAPID Test?
The Penn Medicine news release said the RAPID technology can be adapted to detect other viruses, including those that cause Influenza and sexually-transmitted diseases.
Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report, said the test points to one silver lining in the COVID-19 pandemic. “Researchers around the world intensified their work to find ways to identify the SARS-CoV-2 virus that are faster, cheaper, and more accurate than the diagnostic technologies that existed at the time of the outbreak. In this regard, the COVID-19 pandemic may have accelerated the development and refinement of useful diagnostic technologies that will disrupt long-established methods of testing.”
Marcelo Der Torossian Torres, PhD, postdoctoral researcher at Penn Medicine and lead author of the study, said in the news release, “Quick and reliable tests like RAPID allow for high-frequency testing, which can help identify asymptomatic individuals who, once they learn they are infected, will stay home and decrease spread.
“We envision this type of test being able to be used at high-populated locations such as schools, airports, stadiums, companies—or even in one’s own home,” he added.
Clinical laboratory managers may want to stay current on the development and possible commercialization of the RAPID 1.0 (Real-time Accurate Portable Impedimetric Detection prototype 1.0) biosensor test by the research team at Penn Medicine.
Researchers found that early in life intestinal microorganisms “educate” the thymus to develop T cells; findings could lead to improved immune system therapeutics and associated clinical laboratory tests
The researchers published their findings in Nature. They used engineered mice as the test subjects and say the study could lead to a greater understanding of human conditions such as Type 1 and Type 2 diabetes and inflammatory bowel disease (IBD). In turn, this new knowledge could lead to new diagnostic tests for clinical laboratories.
“From the time we are born, our immune system is set up so that it can learn as much as it can to distinguish the good from the bad,” Matthew Bettini, PhD, Associate Professor of Pathology said in a University of Utah news release.
Does Gut Bacteria ‘Educate’ the Immune System?
The researchers were attempting to learn how the body develops T cells specific to intestinal microorganisms. T cells, they noted, are “educated” in the thymus, an organ in the upper chest that is key to the adaptive immune system.
“Humans and their microbiota have coevolved a mutually beneficial relationship in which the human host provides a hospitable environment for the microorganisms and the microbiota provides many advantages for the host, including nutritional benefits and protection from pathogen infection,” they wrote in their study. “Maintaining this relationship requires a careful immune balance to contain commensal microorganisms within the lumen, while limiting inflammatory anti-commensal responses.”
Findings Challenge Earlier Assumptions about Microbiota’s Influence on Immunity
The researchers began by seeding the intestines of mice with segmented filamentous bacteria (SFB), which they described as “one of the few commensal microorganisms for which a microorganism-specific T-cell receptor has been identified.” In addition, SFB-specific T cells can be tracked using a magnetic enrichment technique, they wrote in Nature.
They discovered that in young mice, microbial antigens from the intestines migrated to the thymus, resulting in an expansion of T cells specific to SFB. But they did not see an expansion of T cells in adult mice, suggesting that the process of adapting to microbiota happens early.
“Our study challenges previous assumptions that potential pathogens have no influence on immune cells that are developing in the thymus,” Bettini said in the news release. “Instead, we see that there is a window of opportunity for the thymus to learn from these bacteria. Even though these events that shape which T cells are present happen early in life, they can have a greater impact later in life.”
For example, T cells specific to microbiota can also protect against closely related harmful bacteria, the researchers found. “Mice populated with E. coli at a young age were more than six times as likely to survive a lethal dose of Salmonella later in life,” the news release noted. “The results suggest that building immunity to microbiota also builds protection against harmful bacteria the body has yet to encounter.”
According to the researchers, in addition to protecting against pathogens, “microbiota-specific T cells have pathogenic potential.” For example, “defects in these mechanisms could help explain why the immune system sometimes attacks good bacteria in the wrong place, causing the chronic inflammation that’s responsible for inflammatory bowel disease,” they suggested.
Other Clinical Laboratory Research into the Human Microbiome
All of this suggests the potential in the future “for clinical laboratories and microbiologists to do microbiome testing in support of clinical care,” said Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report. Of course, more research is needed in these areas.
“We believe that our findings may be extended to areas of research where certain bacteria have been found to be either protective or pathogenic for other conditions, such as Type 1 and Type 2 diabetes,” Bettini said in the University of Utah news release. “Now we’re wondering, will this window of bacterial exposure and T cell development also be important in initiating these diseases?”
Some experts question the usefulness of Pap testing going forward. But how would cutting back on Pap testing affect clinical laboratory revenue and is it safe for cancer patients?
Recently, a major medical society issued its findings that cervical cancer in the United States has been on a sustained decline for more than a decade and a half. This confirms what cytopathologists and cytotechnologists have watched as the development of new clinical laboratory tests, and the introduction of a vaccine for HPV (human papillomavirus) about 15 years ago, contributed to a reduction in the number of cervical cancer deaths annually here in the United States and in several other nations.
As incidences of cervical cancer declined, so have orders for Pap tests. Thus, clinical laboratory revenues in this area also have declined. This is a change from the 1990s and early 2000s, when Pap tests were the primary screening tool for cervical cancer. About 55 million Pap tests were performed annually during those years and many labs maintained sizeable numbers of cytotechs to perform these tests.
HPV Testing Drove Decreases in Cervical Cancer, Decline in Pap Testing
For at least the past decade, there are pathologists, cytotechnologists, and medical laboratory scientists who graduated from their training programs and began working in labs unaware that, since the 1990s, conventional Pap testing as a major source of test referrals and revenue for clinical laboratories and pathology groups has been on the decline.
What is the reason for the decline? Advances in several areas of medicine, implemented over the past 25 years, have greatly altered how we screen for cervical cancer today. And, in a stepwise fashion, the HPV test and HPV vaccine steadily reduced the role of Pap tests as a primary screening tool.
HPV, a common sexually-transmitted virus, is linked to not only cervical cancer, but also cancers of the vulva, vagina, penis, and anus, according to the Centers for Disease Control and Prevention (CDC) data, which recorded 43 million HPV infections in the US in 2018.
Cervical Cancer Down, But Other HPV Cancers Up
Though cervical cancer incidence is down, other HPV-related cancers may need additional screening standards to head off rising cancer cases, the ASCO study suggests.
To conduct their study, the ASCO researchers analyzed data for 657,317 people in the US Cancer Statistics (USCS) program from 2001 to 2017. The researchers reported their findings at the 2021 ASCO Annual Meeting held online in June. They include:
Cervical cancer incidence rate decreased each year by 1.03% annually over 16 years.
In the 20 to 24 age group, a “disproportionately higher decrease” of 4.6% per year in cervical cancer incidence rate suggested “potential effect of vaccinations.”
Without screenings, HPV-related cancers incidence increased in women over 16 years.
Oropharyngeal, anal, rectal, and vulvar cancer increased 1.3% in women per year.
In men, oropharyngeal cancer incidence represented 81% of all HPV-related cancers—five times more than cases for women over 16 years.
HPV-related cancers in men increased 2.36% per year over 16 years, and oropharyngeal cancer had the biggest increase.
“Without standardized screening, HPV-related cancers—such as oropharyngeal cancers and anal rectal cancers—are increasing. To reduce these trends and achieve success comparable to what we’re seeing with cervical cancer we must develop effective screening strategies and determine vaccine efficacy in these patient populations,” Liao said in the news release.
Should PAP Tests Be Dropped as a Primary Screen for Cervical Cancer?
Today’s American Cancer Society (ACS) guidelines for cervical cancer screening denote the primary (FDA-designated) HPV test as the “preferred test” for people 25 to 65 years of age. A Pap test (or Pap smear) can be done at the same time, or in instances when a primary HPV test is not available, the ACS said.
HPV screening aims to detect high risk strains of HPV by looking for DNA in cervical cells and the Pap test involves collecting cells from the cervix for review in the medical laboratory for cancer and pre-cancer, the ACS added.
However, pathologists and cytotechnologists who have examined Pap smear slides for many years know that indications of cervical cancer are not always detected by HPV screening. A Pap test often picks up indications of cervical cancer that might not have been detected by the HPV test.
One reason is HPV tests only monitor about 20 of the genetic mutations known to cause cervical cancer. There are about 80 mutations that can cause cervical cancer, but most are so rare, it does not pay to include them in the HPV test panel.
“The Pap is not something that we should look at as replaceable. In some circumstances, we can get a Pap smear that has some significant cellular changes on it,” Jessica Shepherd, MD, an obstetrician and gynecologist at Baylor University Medical Center in Dallas, told USA Today.
Medicine Advancing, Pap Referrals Not So Much
In the 1990s, Pap tests were the front line for cervical cancer screening and a source of about 55 million referrals to clinical laboratories each year, recalls Robert Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report.
“Interestingly, in the past decade, many cytotechnologists and laboratory scientists who started work in labs at the time of the new HPV screening guidelines and vaccination were unaware of the Pap test’s impact on revenue for clinical labs and pathology groups,” he said.
Medical advancements over the past 25 years have altered how providers screen women for cervical cancer and help them prevent it. And as HPV screening and HPV vaccination gained prominence, the standard Pap test became a kind of “co-pilot” to HPV testing. Unfortunately, this meant less oncology referrals to medical labs.