Newly combined digital pathology, artificial intelligence (AI), and omics technologies are providing anatomic pathologists and medical laboratory scientists with powerful diagnostic tools
Add “spatial transcriptomics” to the growing list of “omics” that have the potential to deliver biomarkers which can be used for earlier and more accurate diagnoses of diseases and health conditions. As with other types of omics, spatial transcriptomics might be a new tool for surgical pathologists once further studies support its use in clinical care.
Among this spectrum of omics is spatial transcriptomics, or ST for short.
Spatial Transcriptomics is a groundbreaking and powerful molecular profiling method used to measure all gene activity within a tissue sample. The technology is already leading to discoveries that are helping researchers gain valuable information about neurological diseases and breast cancer.
Marriage of Genetic Imaging and Sequencing
Spatial transcriptomics is a term used to describe a variety of methods designed to assign cell types that have been isolated and identified by messenger RNA (mRNA), to their locations in a histological section. The technology can determine subcellular localization of mRNA molecules and can quantify gene expression within anatomic pathology samples.
In “Spatial: The Next Omics Frontier,” Genetic Engineering and Biotechnology News (GEN) wrote, “Spatial transcriptomics gives a rich, spatial context to gene expression. By marrying imaging and sequencing, spatial transcriptomics can map where particular transcripts exist on the tissue, indicating where particular genes are expressed.”
In an interview with Technology Networks, George Emanuel, PhD, co-founder of life-science genomics company Vizgen, said, “Spatial transcriptomic profiling provides the genomic information of single cells as they are intricately spatially organized within their native tissue environment.
“With techniques such as single-cell sequencing, researchers can learn about cell type composition; however, these techniques isolate individual cells in droplets and do not preserve the tissue structure that is a fundamental component of every biological organism,” he added.
“Direct spatial profiling the cellular composition of the tissue allows you to better understand why certain cell types are observed there and how variations in cell state might be a consequence of the unique microenvironment within the tissue,” he continued. “In this way, spatial transcriptomics allows us to measure the complexity of biological systems along the axes that are most relevant to their function.”
According to 10x Genomics, “spatial transcriptomics utilizes spotted arrays of specialized mRNA-capturing probes on the surface of glass slides. Each spot contains capture probes with a spatial barcode unique to that spot.
“When tissue is attached to the slide, the capture probes bind RNA from the adjacent point in the tissue. A reverse transcription reaction, while the tissue is still in place, generates a cDNA [complementary DNA] library that incorporates the spatial barcodes and preserves spatial information.
“Each spot contains approximately 200 million capture probes and all of the probes in an individual spot share a barcode that is specific to that spot.”
“The highly multiplexed transcriptomic readout reveals the complexity that arises from the very large number of genes in the genome, while high spatial resolution captures the exact locations where each transcript is being expressed,” Emanuel told Technology Networks.
Spatial Transcriptomics for Breast Cancer and Neurological Diagnostics
In that paper, the authors wrote “we envision that in the coming years we will see simplification, further standardization, and reduced pricing for the ST protocol leading to extensive ST sequencing of samples of various cancer types.”
Spatial transcriptomics is also being used to research neurological conditions and neurodegenerative diseases. ST has been proven as an effective tool to hunt for marker genes for these conditions as well as help medical professionals study drug therapies for the brain.
“You can actually map out where the target is in the brain, for example, and not only the approximate location inside the organ, but also in what type of cells,” Malte Kühnemund, PhD, Director of Research and Development at 10x Genomics, told Labiotech.eu. “You actually now know what type of cells you are targeting. That’s completely new information for them and it might help them to understand side effects and so on.”
The field of spatial transcriptomics is rapidly moving and changing as it branches out into more areas of healthcare. New discoveries within ST methodologies are making it possible to combine it with other technologies, such as Artificial Intelligence (AI), which could lead to powerful new ways oncologists and anatomic pathologists diagnose disease.
“I think it’s going to be tricky for pathologists to look at that data,” Kühnemund said. “I think this will go hand in hand with the digital pathology revolution where computers are doing the analysis and they spit out an answer. That’s a lot more precise than what any doctor could possibly do.”
Spatial transcriptomics certainly is a new and innovative way to look at tissue biology. However, the technology is still in its early stages and more research is needed to validate its development and results.
Nevertheless, this is an opportunity for companies developing artificial intelligence tools for analyzing digital pathology images to investigate how their AI technologies might be used with spatial transcriptomics to give anatomic pathologists a new and useful diagnostic tool.
Hello primary diagnosis of digital pathology images via artificial intelligence! Goodbye light microscopes!
Digital pathology is poised to take a great leap forward. Within as few as 12 months, image analysis algorithms may gain regulatory clearance in the United States for use in primary diagnosis of whole-slide images (WSIs) for certain types of cancer. Such a development will be a true revolution in surgical pathology and would signal the beginning of the end of the light microscope era.
A harbinger of this new age of digital pathology and automated image analysis is a press release issued last week by Ibex Medical Analytics of Tel Aviv, Israel. The company announced that its Galen artificial intelligence (AI)-powered platform for use in the primary diagnosis of specific cancers will undergo an accelerated review by the Food and Drug Administration (FDA).
FDA’s ‘Breakthrough Device Designation’ for Pathology AI Platform
Ibex stated that “The FDA’s Breakthrough Device Designation is granted to technologies that have the potential to provide more effective treatment or diagnosis of life-threatening diseases, such as cancer. The designation enables close collaboration with, and expedited review by, the FDA, and provides formal acknowledgement of the Galen platform’s utility and potential benefit as well as the robustness of Ibex’s clinical program.”
“All surgical pathologists should recognize that, once the FDA begins to review and clear algorithms capable of using digital pathology images to make an accurate primary diagnosis of cancer, their daily work routines will be forever changed,” stated Robert L. Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report. “Essentially, as FDA clearance is for use in clinical care, pathology image analysis algorithms powered by AI will put anatomic pathology on the road to total automation.
“Clinical laboratories have seen the same dynamic, with CBCs (complete blood counts) being a prime example. Through the 1970s, clinical laboratories employed substantial numbers of hematechnologists [hematechs],” he continued. “Hematechs used a light microscope to look at a smear of whole blood that was on a glass slide with a grid. The hematechs would manually count and record the number of red and white blood cells.
“That changed when in vitro diagnostics (IVD) manufacturers used the Coulter Principle and the Coulter Counter to automate counting the red and white blood cells in a sample, along with automatically calculating the differentials,” Michel explained. “Today, only clinical lab old-timers remember hematechs. Yet, the automation of CBCs eventually created more employment for medical technologists (MTs). That’s because the automated instruments needed to be operated by someone trained to understand the science and medicine involved in performing the assay.”
Primary Diagnosis of Cancer with an AI-Powered Algorithm
Surgical pathology is poised to go down a similar path. Use of a light microscope to conduct a manual review of glass slides will be supplanted by use of digital pathology images and the coming next generation of image analysis algorithms. Whether these algorithms are called machine learning, computational pathology, or artificial intelligence, the outcome is the same—eventually these algorithms will make an accurate primary diagnosis from a digital image, with comparable quality to a trained anatomic pathologist.
How much of a threat is automated analysis of digital pathology images? Computer scientist/engineer Ajit Singh, PhD, a partner at Artiman Ventures and an authority on digital pathology, believes that artificial intelligence is at the stage where it can be used for primary diagnosis for two types of common cancer: One is prostate cancer, and the other is dermatology.
“It is now possible to do a secondary read, and even a first read, in prostate cancer with an AI system alone. In cases where there may be uncertainty, a pathologist can review the images. Now, this is specifically for prostate cancer, and I think this is a tremendous positive development for diagnostic pathways,” he added.
Use of Digital Pathology with AI-Algorithms Changes Diagnostics
Pathologists who are wedded to their light microscopes will want to pay attention to the impending arrival of a fully digital pathology system, where glass slides are converted to whole-slide images and then digitized. From that point, the surgical pathologist becomes the coach and quarterback of an individual patient’s case. The pathologist guides the AI-powered image analysis algorithms. Based on the results, the pathologist then orders supplementary tests appropriate to developing a robust diagnosis and guiding therapeutic decisions for that patient’s cancer.
In his interview with The Dark Report, Singh explained that the first effective AI-powered algorithms in digital pathology will be developed for prostate cancer and skin cancer. Both types of cancer are much less complex than, say, breast cancer. Moreover, the AI developers have decades of prostate cancer and melanoma cases where the biopsies, diagnoses, and downstream patient outcomes create a rich data base from which the algorithms can be trained and tuned.
This webinar is organized as a roundtable discussion so participants can interact with the expert panelists. The Chair and Moderator is Ajit Singh, PhD, Adjunct Professor at the Stanford School of Medicine and Partner at Artiman Ventures.
The panelists (above) represent academic pathology, community hospital pathology, and the commercial sector. They are:
Because the arrival of automated analysis of digital pathology images will transform the daily routine of every surgical pathologist, it would be beneficial for all pathology groups to have one or more of their pathologists register and participate in this critical webinar.
The roundtable discussion will help them understand how quickly AI-powered image analysis is expected be cleared for use by the FDA in such diseases as prostate cancer and melanomas. Both types of cancers generate high volumes of case referrals to the nation’s pathologists, so potential for disruption to long-standing client relationships, and the possible loss of revenue for pathology groups that delay their adoption of digital pathology, can be significant.
On the flip side, community pathology groups that jump on the digital pathology bandwagon early and with the right preparation will be positioned to build stronger client relationships, increase subspecialty case referrals, and generate additional streams of revenue that boost partner compensation within their group.
Also, because so many pathologists are working remotely, Dark Daily has arranged special group rates for pathology practices that would like their surgical pathologists to participate in this important webinar and roundtable discussion on AI-powered primary diagnosis of pathology images. Inquire at email@example.com or call 512-264-7103.
Acceptance of digital pathology and whole-slide imaging is now almost universal among academic health center pathology departments and the nation’s largest pathology companies
Across the United States, many private practice anatomic pathology groups now recognize that digital pathology is the path forward for the entire profession. During the past decade, most academic pathology departments and large pathology lab companies have incorporated digital pathology (DP) and whole-slide imaging (WSI) into many of their labs’ daily activities.
However, in community hospital-based anatomic pathology groups, there have been barriers to even the partial adoption of digital pathology. The two biggest barriers are well-known and discussed frequently at conferences and in the literature.
Some Pathologists Reluctant to Give Up Light Microscopes
One recognized barrier to wider adoption of DP is the reluctance of many long-serving pathologists to give up their familiar light microscopes and glass slides so they can make the transition to reading pathology images on a computer screen. These pathologists remain loyal to the tools and workflows that have served them well throughout their careers.
They generally oppose their group’s move to digital pathology when the subject is discussed in partner meetings and strategic retreats. Since many pathology groups require 100% of partners or shareholders to approve major business decisions, even one recalcitrant and stubborn pathologist-partner can block the motion to adopt digital pathology that is supported by most partners.
The second barrier is the fully-loaded cost to acquire, validate, implement, and use a digital pathology system with whole-slide imaging. A full-featured scanner can cost $250,000 or more and acquiring all the software, systems, and tools needed by a group to fully incorporate digital pathology into daily workflow can easily total $500,000 to $1,000,000.
This substantial commitment of a pathology group’s capital can trigger the same intense debates as the original question of whether the pathologists in the group should adopt DP and WSI. And, not surprisingly, in most pathology groups the same dynamics come into play when votes are tallied on the motion for the pathology group to commit the funds necessary to acquire a digital pathology system, the scanners, and associated tools.
Just one or two partner holdouts can block the decision to spend the money, despite that most of the pathologist partners are ready to make the commitment.
More Community Pathology Groups Considering Digital Pathology
Yet, the momentum in favor of adopting DP and WSI continues to build. “Those pathology labs that are early adopters report multiple clinical and financial benefits. These can include generating positive financial outcomes—including the ability to attract new clients, increasing case referrals, and generating new sources of revenue to the group. In turn, the increased revenue can allow the group to increase pathologist compensation,” said Robert L. Michel, Editor-in-Chief of Dark Daily and its sister publication The Dark Report.
“We are in a time when health insurers are hammering away at the reimbursement paid to anatomic pathologists,” Michel continued. “Year after year, payers cut reimbursement for technical component and professional component services. They exclude many pathology groups from payer networks. That is why more community pathology groups are recognizing several important benefits with the use of DP and WSI that can increase a pathology group’s revenue and boost its pathologist compensation.
Community Pathology Groups Can Use Digital Pathology to Add Value
Equally important, there are specific ways that digital pathology and whole-slide imaging increase the value of the clinical services pathologists deliver to their client physicians. These dual benefits of DP are often overlooked—or not discussed—when community pathology groups conduct their annual retreats and debate the key points of when to adopt—and how to fund—a digital pathology system for their group. These benefits range from giving physicians a faster diagnostic answer on their cancer cases to helping the group’s subspecialist pathologists get more case referrals from physicians in other states.
“It’s important for all surgical pathologists to recognize several realities in today’s pathology marketplace,” Michel noted. “First, almost every sector in healthcare is digitizing itself. Reinforcing this trend is the federal government’s mandates for interoperability across EHRs, HISs, and LISs. Any private pathology group practice that lags in its adoption of digital capabilities and digital images will find itself falling farther and farther behind as physicians switch their case referrals to other pathology labs that have converted to digital pathology and whole-slide images.
“Second, pathology groups that adopt DP and WSI put themselves in a position to build market share in their service region, while at the same time increasing case referrals for their in-house subspecialist pathologists from throughout the United States,” Michel continued. “Also, when the histology is done locally, the local pathology group can deliver faster diagnostic answers and provide digital images as appropriate to referring physicians and hospitals in that region without the need to transport glass slides by couriers.
“Third—and this is an often-overlooked benefit of digital pathology—the local pathology group with DP and WSI can recruit today’s graduating pathology residents and fellows who have trained on DP and WSI. These new pathologists typically limit their job search to pathology groups that have gone digital,” Michel noted. “Millennial pathologists trained with digital images in their residency program. They are eager to work with the automated image analysis algorithms now coming to market.”
Recognizing the significant capital investment needed to acquire and deploy digital pathology and WSI, one goal of the webinar’s panel of experts is to identify ways that pathology groups can go digital on a budget. “We will do our best to identify different ways that pathology groups with limited financial resources can get into digital pathology,” said Keith Kaplan, MD, Chief Medical Officer at Corista in Concord, Mass., who will chair the upcoming webinar. “This may be the first public presentation where there is candid information about different financial strategies that your pathology group can utilize to acquire the scanners, the DP systems, and the associated tools needed for a full conversion to daily digital pathology.”
Don’t overlook how your participation in this webinar can be the foundation for helping your pathology group practice develop a timely, cost-effective path forward to introduce digital pathology and whole-slide imaging. Use of DP and WSI can become an important factor in helping your group offset payer prices cuts, develop new clients and sources of revenue, and increase pathologist compensation.
Click HERE to register today (or copy and paste this URL into your browser: https://www.darkdaily.com/webinar/adopting-digital-pathology-on-a-budget/). Make sure to have your pathology practice administrator and your histology manager join you for this important webinar.
Because of ‘shelter in place’ orders, many anatomic pathologists are reviewing digital images from home during the COVID-19 outbreak and demonstrating the value of whole slide imaging, digital pathology, and CMS’ recent amended remote sign-out policy
COVID-19 is already triggering many permanent changes in the way healthcare is organized and delivered in the United States. However, not until the SARS-CoV-2 pandemic eases will the full extent of these changes become visible. This will be particularly true for anatomic pathology and the profession’s expanded use of telepathology, digital pathology, and whole-slide imaging.
Since early March, specimen referrals and revenues have collapsed at anatomic pathology groups and laboratories across the nation. Dark Daily’s sister publication, The Dark Report (TDR), was first to quantify the magnitude of this collapse in tissue referrals to pathology groups. In an interview with The Dark Report, Kyle Fetter, Executive Vice President and General Manager of Diagnostic Services at XIFIN, Inc., explained that pathology clients using XIFIN’s revenue cycle management services were seeing an average 40% decrease in specimens. And, for certain pathology sub-specialties, the drop-off in specimen referrals was as much as 90%. (See TDR, “From Mid-March, Labs Saw Big Drop in Revenue,” April 20, 2020.)
The College of American Pathologists (CAP) appealed to the Centers for Medicare and Medicaid Services (CMS) to allow pathologists to work remotely. In response, CMS issued a memorandum which stated, “Due to the public health emergency posed by COVID-19 and the urgent need to expand laboratory capacity, CMS is exercising its enforcement discretion to adopt a temporary policy of relaxed enforcement in connection with laboratories located at temporary testing sites under the conditions outlined herein.”
Since then, many physicians, including pathologists, have quickly adapted to working remotely in some form.
Push for Remote Pathology Services Acknowledges Anatomic Pathologist Shortage
The CMS memorandum (QSO-20-21-CLIA), which the federal agency issued to laboratory surveyors on March 26, 2020, notes that CMS will exercise “enforcement discretion to ensure pathologists may review pathology slides remotely” if certain defined conditions are met.
CMS’ decision, which “is applicable only during the COVID-19 public health emergency,” is intended to increase capacity by allowing remote site review of clinical laboratory data, results, and pathology slides.
Ordinarily, CLIA regulations for cytology (a branch of study that focuses on the biological structure of cells) state that cytology slide preparations must be evaluated on the premises of a laboratory that is certified to conduct testing in the subspecialty of cytology. However, a fast-acting Congressional letter sent by 37 members of Congress to US Department of Health and Human Services (HHS) Secretary Alex Azar II, MD, states, “it is unwise and unnecessary to overburden the remaining pathologists with excess work due to staffing shortages, thereby increasing the risk of burnout, medical error, and further shortages in staffing due to exposure. The number of COVID-19 cases will increase and peak over the next two months and will stretch existing healthcare systems to their limits.”
Decreasing Number of ‘Active Pathologists’ Drives Adoption of Telepathology, Digital Pathology, and Whole-slide Imaging
The current COVID-19 outbreak is just the latest factor in support of enabling remote review of anatomic pathology images and cases. The trend of using telepathology, whole-slide imaging (WSI), and digital pathology systems has been gathering momentum for several years. Powerful economic forces support this trend.
TDR noted that these findings imply there are fewer pathologists in the United States today in active practice to handle the steady increase in the number of cases requiring diagnostic review. In turn, this situation could lead to delays in diagnoses detrimental to patient care.
Distinct Forces Beginning to Reshape Anatomic Pathology
In recent years, the anatomic pathology profession has faced growing financial pressure, a shrinking workforce, and a surge in the global demand for pathology—issues that come at a time when biopsies and cancer diagnostics require greater expertise.
The UCSF School of Medicine started with frozen slide sections and moved to the broader volume of pathology slides. Since 2015, UCSF’s School of Medicine has moved toward a fully digital pathology operation and has serialized the adoption by specialty, according to Zoltan Laszik, MD, PhD, attending physician at UCSF and Professor of Clinical Pathology in UCSF’s Departments of Pathology and Laboratory Medicine.
Laszik is among a handful of specialists and digital pathology early adopters who collaborated on the new Dark Daily white paper, which is available for free download.
Through the adoption of digital pathology, glass slides are digitized using a whole-slide image scanner, then analyzed through image viewing software. Although the basic viewing functionality is not drastically different than that provided by a microscope, digitization does bring improvements in lab efficiency, diagnostic accuracy, image management, workflows, and revenue enhancements.
Additionally, artificial intelligence (AI)-based computational applications have emerged as an integral part of the digital pathology workflow in some settings, the white paper explains.
“These developments are important to anatomic pathologists because the traditional pathology business model continues to transform at a steady pace,” noted Robert L. Michel, Editor-in-Chief of The Dark Report.
Anthony Magliocco, MD, FRCPC, FCAP, President and CEO of Protean BioDiagnostics and former Professor and Chair of Pathology at Moffitt Cancer Center, is featured in the white paper as well. His new pathology service model provides routine pathology services, precision oncology, second opinions, liquid biopsies, genetics, and genomics to cancer centers from a Florida-based specialty laboratory.
To register for this important learning opportunity, click here or place this URL in your web browser: https://www.darkdaily.com/webinar/streamlined-operations-increased-revenue-higher-quality-of-care-conclusive-evidence-on-the-value-of-adopting-digital-pathology-in-your-lab/.
These digital pathology technologies represent an innovative movement shaping the present and future of pathology services. Pathologists wanting to learn more are encouraged to sign up for the May 13 webinar, which will build on the body of evidence and commentary that is included in the new white paper, and which will be available for free on-demand download following the live broadcast.
Increased use of telemedicine may create opportunities for clinical laboratories to deliver increased value to both physicians and nurses
Recent data shows widespread employer adoption of telehealth services may soon become a reality. However, studies also show virtual provider visits and other telemedicine technologies are unlikely to diminish the role of clinical laboratories in providing the data required for diagnosis and treatment decisions. Instead, laboratories and anatomic pathology groups will likely see changes in how samples are collected from patients using telemedicine and how medical laboratory test results are reported, as access to telemedicine grows.
A recent National Business Group on Health (NBGH) survey indicates that in 2018 “virtually all [large] employers (96%) will make telehealth services available in states where it is allowed.” The survey was conducted between May and June 2017, with 148 large employers participating.
In an article she penned for MedCityNews, Smalley calls provider-to-provider telemedicine the “most evolved to-date” segment of the telehealth trend. She highlights ICU stroke care with remote consults and monitoring as an example of its “success,” and notes a large potential for growth in remote patient monitoring (RPM). Smalley cites a Berg Insight report that estimates 50-million patients will use remote monitored devices by 2021. However, Smalley also notes consumer acceptance of patient-to-provider telemedicine has fallen short of industry expectations.
While virtual office visits—where patients have access to physicians via telephone or videoconferencing—grab headlines, Smalley argues that “several factors” are hindering adoption.
“Reimbursement is not yet universal,” she notes. “But consumers are growing used to paying more out-of-pocket with high-deductible plans. Physicians have long resisted change in how they practice, and many remain lukewarm at best about telemedicine. It’s no coincidence that many of the innovations and pioneering models have come from outside of healthcare delivery … The barriers that loom the largest may likely be consumer awareness and trial.”
The Center for Connected Health Policy (CCHP) reports that 35 states have laws governing private payer reimbursement of telehealth, a number that has not changed since 2016. According to a CCHP press release, some state laws require reimbursement be equal to in-person visits, though not all laws mandate reimbursement.
Adopting Existing Retail Models to Promote Telemedicine to Patients
Smalley contends “smart marketing” will be needed to get consumers to leverage the telemedicine options that are becoming available to them. She says simply offering video or telephone visits is not enough. She encourages integrated delivery systems to take a page out of retailers’ playbooks.
“Look at how retailers, like Walmart, integrate online shopping and the store experience by offering side-by-side options supporting product delivery and in-store pickup. Telemedicine options ultimately need to be offered in a way that feels integrated and seamless to the health consumer,” she suggested, in her MedCityNews article. One example, she notes, would be providing an easy-to-navigate link to a virtual visit on a healthcare network’s urgent care webpage.
Healthcare Spending Could Increase Due to Telehealth
While health plans have zeroed in on telehealth as a way to drive down healthcare costs, a 2017 RAND Corp. study published in Health Affairs found virtual visits to physicians might not decrease spending, though access to care is improved.
“Instead of saving money by substitution [replacing more expensive visits to physician offices or EDs], direct-to-consumer telehealth may increase spending by new utilization [increasing the total number of patient visits],” a MedCityNews article suggests.
“Given that direct-to-consumer telehealth is even more convenient than traveling to retail clinics, it may not be surprising that an even greater share of telehealth services represents new medical use,” noted Lori Uscher-Pines, PhD, a RAND Policy Researcher. “There may be a dose response with respect to convenience and use: the more convenient the location, the lower the threshold for seeking care and the greater the use of medical services.”
Telehealth in Clinical Laboratories
Will telehealth services offered by hospital networks and healthcare providers impact clinical laboratories? While a physical visit is still required for drawing blood, collecting urine, or performing pathology testing, interpretive digital pathology, such as Whole Slide Imaging (AKA, Virtual Slide), does enable pathologists to provided distance interpretation services of blood tests to remote and/or resource deficient areas of the world, as Dark Daily reported in past e-briefings. This could become a substantial revenue stream in the future if telepathology’s global popularity continues to rise.