Lucid Diagnostics Provides Updates on Newly Published Esophageal Precancer Clinical Guideline and Proposed Medicare Local Coverage Determination

On April 4, 2022 Lucid Diagnostics Inc. (Nasdaq: LUCD) ("Lucid", the "Company"), a commercial-stage, cancer prevention medical diagnostics company, and majority-owned subsidiary of PAVmed Inc. (Nasdaq: PAVM, PAVMZ) ("PAVmed"), reported that a newly updated American College of Gastroenterology ("ACG") clinical guideline supports esophageal precancer ("Barrett’s Esophagus", "BE") screening to prevent highly lethal esophageal cancer ("EAC") utilizing its EsoGuard DNA Test on samples collected with its EsoCheck Cell Collection Device (Press release, Lucid Diagnostics, APR 4, 2022, View Source [SID1234611415]). It also provided an update on, and planned response to, a proposed Local Coverage Determination on molecular testing for esophageal precancer and cancer published by Medicare Administrative Contractor ("MAC") Palmetto GBA’s MolDX Program, triggering a comment period in advance of a public meeting.

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Updated ACG Guideline
An ACG clinical guideline entitled "Diagnosis and Management of Barrett’s Esophagus: An Updated ACG Guideline," the first such update since 2016, was published online last week in the American Journal of Gastroenterology. Lead author Nicholas J. Shaheen, M.D., Bozymski-William Heizer Distinguished Professor of Medicine at the University of North Carolina, chairs Lucid’s Medical Advisory Board (MAB) and serves as principal investigator of its ESOGUARD BE-1 and BE-2 clinical trials. Co-author Gary W. Falk, M.D., Professor of Medicine at the University of Pennsylvania School of Medicine, also serves on the Lucid MAB and as principal investigator of its eosinophilic esophagitis clinical trials.

The clinical guideline first reiterates the ACG’s long-standing recommendation for esophageal precancer screening in at-risk patients with gastroesophageal reflux disease ("GERD"), commonly known as chronic heartburn, acid reflux, or simply reflux.

Recommendation 5: We suggest a single screening endoscopy in patients with chronic GERD symptoms and 3 or more additional risk factors for BE, including male sex, age >50 yr, White race, tobacco smoking, obesity, and family history of BE or EAC in a first-degree relative.

For the first time, however, the clinical guideline also endorses nonendoscopic biomarker screening as an acceptable alternative to costly and invasive endoscopy.

Recommendation 6: We suggest that a swallowable, nonendoscopic capsule device combined with a biomarker is an acceptable alternative to endoscopy for screening for BE.

The clinical guideline specifically mentions EsoCheck, along with Lucid’s EsophaCap device, as such swallowable, nonendoscopic esophageal cell collection devices, as well as methylated DNA biomarkers such as EsoGuard. The summary of evidence for this recommendation cites the seminal NIH-funded, multicenter, case-control study published in 2018 in Science Translational Medicine, which demonstrated that EsoGuard is highly accurate at detecting esophageal precancer and cancer, including on samples collected with EsoCheck.

"Publication of this updated ACG clinical guideline is a critical milestone which has the potential to save many lives by, for the first time, driving widespread screening to prevent esophageal cancer deaths through the early detection of esophageal precancer," said Lishan Aklog M.D., Lucid’s Chairman and Chief Executive Officer. "Although, for over a decade, gastroenterology clinical guidelines have recommended esophageal precancer screening in GERD patients with long-established risk factors, very few patients undergo endoscopic screening—making the many thousands of annual esophageal deaths in the U.S. a profound and preventable tragedy. EsoGuard and EsoCheck represent the only ‘swallowable, nonendoscopic capsule device combined with a biomarker’ currently available in the U.S. to serve as such a widespread screening tool to prevent these tragic deaths."

Proposed MAC Local Coverage Determination
A proposed Local Coverage Determination ("LCD") DL39256, entitled "Molecular Testing for Detection of Upper Gastrointestinal Metaplasia, Dysplasia, and Neoplasia" was published last week on the Center for Medicare and Medicaid Services ("CMS") website by MAC Palmetto GBA. The proposed LCD is a further step in Lucid’s efforts to secure Medicare coverage and payment for EsoGuard.

In 2019, Lucid secured EsoGuard’s Proprietary Laboratory Assay (PLA) code 0114U Gastroenterology (Barrett’s esophagus), VIM and CCNA1 methylation analysis, esophageal cells, algorithm reported as likelihood for Barrett’s esophagus. EsoGuard then completed CMS’s Clinical Laboratory Fee Schedule ("CLFS") process, culminating in a final Medicare payment determination of $1,938.01, effective January 1, 2021.

Lucid also engaged directly with the Molecular Diagnostic Services ("MolDX") Program, coordinated by MAC Palmetto GBA, to secure EsoGuard coverage through an LCD. Noridian Healthcare Solutions, the MAC which covers LucidDx Labs (Lucid’s Lake Forest, California CLIA-certified laboratory), participates in the MolDX program. In May 2020, following multiple meetings with the MolDX team, Lucid submitted detailed dossiers providing data and justifications supporting EsoGuard coverage. In October 2021, as part of its LCD development process, MolDX held an open Contractor Advisory Committee ("CAC") meeting on the topic of molecular testing for certain gastrointestinal cancers, including EsoGuard, where the expert gastroenterologist panel voiced staunch support for esophageal precancer screening in at-risk GERD patients. Shortly thereafter, Lucid submitted comments to support EsoGuard’s role in such screening.

The proposed LCD, which the CMS website explicitly characterizes as a "work in progress" for "public review," outlines criteria that MolDX expects upper gastrointestinal precancer and cancer molecular diagnostic tests to meet. These criteria include active GERD with at least two risk factors, as well as evidence of analytic validity, clinical validity, and clinical utility. Although it found that no currently existing test has fulfilled all these criteria, it indicated that it will "monitor the evidence and will provide coverage based on the pertinent literature and society recommendations." Notably, the proposed LCD pre-dated, and therefore does not include consideration of, the most recent ACG clinical guideline update endorsing swallowable, nonendoscopic capsule devices combined with a biomarker, such as EsoCheck and EsoGuard. The publication of the proposed LCD triggers a written comment period which extends until May 14, 2022. MolDX will also hold an open meeting on May 10, 2022, during which stakeholders and other interested parties will have the opportunity to address the proposed LCD. A final LCD will not be issued until the MAC has had the opportunity to assess and consider these comments.

"We are on an unrelenting mission to end a profound tragedy—over 16,000 preventable esophageal deaths in the U.S. each year, a substantial portion of which are Medicare beneficiaries," said Dr. Aklog. "Decades of research have blessed us with modern noninvasive molecular diagnostic tools, such as EsoGuard and EsoCheck, which finally give us the opportunity to prevent these deaths through early detection of esophageal precancer. Clinical practice guidelines have now endorsed such tools as part of a widespread early detection cancer prevention program, which seeks to have the same impact on esophageal cancer deaths as similar programs have had in breast, colon, and cervical cancer. A necessary element to achieve the Administration’s recently announced "Cancer Moonshot" goal of reducing cancer deaths by 50% will be reducing deaths from our second most lethal cancer, esophageal cancer. We have the tools to do so and will not relent until we have achieved that goal."

"With a proposed LCD now published, we are very much looking forward to re-engaging with the MolDX team in the coming weeks as part of the process leading to the publication of a final LCD," Dr. Aklog added. "We will utilize the written comment process and the open meeting to bring to MolDX essential information that was not incorporated into the proposed LCD. These include: the updated ACG clinical guideline; the fact that EsoGuard’s published performance is at or above accepted performance criteria for detection of lower gastrointestinal cancers in approved and currently effective Medicare coverage determinations; and data from ongoing clinical utility studies Lucid and clinical investigators are performing. We are actively recruiting key stakeholders to submit comments and participate in the open meeting, including key opinion leaders in academia and the diagnostic industry, clinicians currently utilizing EsoGuard and EsoCheck to successfully detect esophageal precancer in at-risk patients, patient advocacy organizations, and industry associations with strong interest in certain policy implications of this proposed LCD."

About EsoGuard and EsoCheck
Millions of patients with GERD are at risk of developing esophageal precancer and a highly lethal form of esophageal cancer ("EAC"). Over 80% of EAC patients die within five years of diagnosis, making it the second most lethal cancer in the U.S. The mortality rate is high even in those diagnosed with early stage EAC. The U.S. incidence of EAC has increased 500% over the past four decades, while the incidences of other common cancers have declined or remained flat. In nearly all cases, EAC silently progresses until it manifests itself with new symptoms of advanced disease. All EAC is believed to arise from esophageal precancer, which occurs in approximately 5% to 15% of at-risk GERD patients. Early esophageal precancer can be monitored for progression to late esophageal precancer which can be cured with endoscopic esophageal ablation, reliably halting progression to cancer.

Esophageal precancer screening is already recommended by clinical practice guidelines in millions of GERD patients with multiple risk factors, including age over 50 years, male gender, White race, obesity, smoking history, and a family history of esophageal precancer or cancer. Unfortunately, fewer than 10% of those recommended for screening undergo traditional invasive endoscopic screening. The profound tragedy of an EAC diagnosis is that likely death could have been prevented if the at-risk GERD patient had been screened and then undergone surveillance and curative treatment.

The only missing element for a viable esophageal cancer prevention program has been the lack of a widespread screening tool that can detect esophageal precancer. Lucid believes EsoGuard and EsoCheck are the missing element and constitute the first and only commercially available test capable of serving as a widespread screening tool to prevent esophageal cancer deaths through the early detection of esophageal precancer in at-risk GERD patients.

EsoGuard is a bisulfite-converted NGS DNA assay performed on surface esophageal cells collected with EsoCheck which quantifies methylation at 31 sites on two genes, Vimentin (VIM) and Cyclin A1 (CCNA1). The assay was evaluated in a 408-patient, multicenter, case-control study published in Science Translational Medicine and showed greater than 90% sensitivity and specificity at detecting esophageal precancer and cancer.

EsoCheck is an FDA 510(k) and CE Mark cleared noninvasive swallowable balloon capsule catheter device capable of sampling surface esophageal cells in a less than five-minute office procedure. It consists of a vitamin pill-sized rigid plastic capsule tethered to a thin silicone catheter from which a soft silicone balloon with textured ridges emerges to gently swab surface esophageal cells. When vacuum suction is applied, the balloon and sampled cells are pulled into the capsule, protecting them from contamination and dilution by cells outside of the targeted region during device withdrawal. Lucid believes this proprietary Collect+Protect technology makes EsoCheck the only noninvasive esophageal cell collection device capable of such anatomically targeted and protected sampling. The sample is sent by overnight express mail to Lucid’s third-party CLIA-certified laboratory partner for EsoGuard testing.

Bruker Expands dia-PASEF® on the timsTOF 4D Proteomics and Epiproteomics Platform to Identify up to 13,000 Protein Groups with 1% FDR

On April 4, 2022 Bruker Corporation (Nasdaq: BRKR) reported expanded capabilities for deeper proteomic and epiproteomic coverage, including enhanced phosphopeptide analysis using the innovative TIMScore algorithm, which is now a part of the new PaSER 2022 GPU-based platform (Press release, Bruker, APR 4, 2022, View Source [SID1234611414]). The novel TIMScore algorithm takes advantage of machine learning (ML) to predict CCS values of tryptic and phosphorylated peptides. Experimentally measured CCS values are referenced against the predicted CCS value to call the most probable assignment, thereby increasing peptide confidence and coverage in high sensitivity applications. The TIMScore algorithm is especially adept in identifying phosphopeptides even at the strictest false localization rate (1% FLR) using LuciPHOr1, where it typically identifies 10%-25% more phosphopeptides.

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The human kinome comprises over 500 kinases and is essential for catalyzing protein phosphorylation, which during dysregulation is a known contributor to oncogenesis.2 In a previous human cancer cell line study by Mann et. al., at least three-fourths of the detected proteome (7832 out of 10,801 proteins) were found to be phosphorylated3. In a recent study performed in the Tenzer Lab at the University Medical Center of the Johannes Gutenberg University Mainz, some 27,768 phosphopeptides contained 4,672 isobaric phosphopeptide pairs of which 51% were chromatographically coeluting. TIMScore could separate 19% of the coeluting isomer pairs, refining the view of the phosphoproteome of a human osteosarcoma cell line.

Dr. Stefan Tenzer is Professor of Quantitative Proteomics and the Head of the Mass Spectrometry Core Facility at the University Medical Center of the Johannes Gutenberg University Mainz. Dr. Tenzer commented: "In our lab we use four timsTOF systems to understand posttranslational modifications and signaling pathways. TIMScore in PaSER uses machine learning to predict CCS values of phosphopeptides to decrease peptide ambiguity. The integration of the TIMScore model in PaSER allows for the seamless search of our data and provides an impressive increase of over 25% in the number of identified unique phosphopeptides, enabling deeper phosphoproteome coverage."

TIMScore complements the capabilities of TIMS DIA-NN. Both have been integrated in PaSER 2022 for "Run & Done" dda-PASEF and dia-PASEF workflows. Using TIMScore and dda-PASEF acquisitions of K562 and MOLT-4 cell lines, 40 fractions run at short (35 min) and long (120 min) gradients and filtered to a 1% FDR4 resulted in the identification of more than 513,000 precursors and 13,114 protein groups. With access to this experimentally derived and statistically filtered ultra-deep library, TIMS DIA-NN and short, 35-minute gradient dia-PASEF runs routinely identify >8000 protein groups and >100,000 precursors, setting the stage for high-throughput translational proteomics.

Dr. Rohan Thakur, President of the Bruker Life-Science Mass Spectrometry division, added: "It is exciting to see this greater depth in the biologically relevant phosphoproteome using mass spectrometry. With ultra-deep protein libraries of over 13k protein groups (PGs), our customers are now able to quantify over 8000 PGs with dia-PASEF, using TIMS DIA-NN, short-gradients and small sample amounts for human cell-line studies in single runs. Since mass spectrometry is a direct high-specificity readout of actual peptides and their modifications, and not a surrogate epitope-binding measurement with unknown FDRs, it has become the high-specificity method of choice for the study of the phosphoproteome. With the release of TIMScore and TIMS DIA-NN, large-scale, high-throughput, label free quantitative phosphoproteomic studies essential for cell signaling pathway analysis are now feasible. This will further enhance biomarker discovery in kinase signaling processes for understanding pathobiology, including in cancer."

The PaSER 2022 software includes TIMScore and TIMS DIA-NN for processing dda-PASEF and dia-PASEF workflows on timsTOF Pro 2, timsTOF SCP and timsTOF fleX systems. PaSER utilizes data streaming for dia-PASEF workflows in real-time, supporting ‘run & done’ for high-throughput 4D proteomics and 4D epiproteomics workflows.

References:

Fermin D., Walmsley SJ, Gringras AC., Choi, H., Nesvizhskii AI (2013). LuciPHOr: algorithm for phosphorylation site localization with false localization rate estimation using modified target-decoy approach. Mol. Cell Proteomics. Nov 12(11): 3409-19. Doi 10.1074/mcp/. PMID: 23918812.
Human Kinome study, Savage SR, Zhang B. Using phosphoproteomics data to understand cellular signaling: a comprehensive guide to bioinformatics resources. Clin Proteomics. 2020 Jul 11;17:27. doi: 10.1186/s12014-020-09290-x. PMID: 32676006; PMCID: PMC7353784.
Sharma K, D’Souza RC, Tyanova S, Schaab C, Wiśniewski JR, Cox J, Mann M. Ultradeep human phosphoproteome reveals a distinct regulatory nature of Tyr and Ser/Thr-based signaling. Cell Rep. 2014 Sep 11;8(5):1583-94. doi: 10.1016/j.celrep.2014.07.036. Epub 2014 Aug 21. PMID: 25159151.
Elias JE, Gygi SP. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry. Nat Methods. 2007 Mar;4(3):207-14. doi: 10.1038/nmeth1019. PMID: 17327847.

ATCC Announces Expansion of its Bioinformatics Data Platform with QIAGEN

On April 4, 2022 ATCC, the world’s premier biological materials management and standards organization, reported that it has entered into an agreement with QIAGEN, a recognized leader in bioinformatics solutions, to provide them with sequencing data from its collection of cell lines, and animal and human biological materials (Press release, Qiagen, APR 4, 2022, View Source [SID1234611413]). QIAGEN Digital Insights, the bioinformatics unit of QIAGEN, will establish a database from this information to develop and deliver high-value digital biology content for the biotechnology and pharmaceutical industries, enabling the use of authenticated biological data sets to uncover new disease pathways and discover novel therapeutic targets.

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"This first-of-its-kind arrangement will allow ATCC to provide data provenance that is traceable, standardized and authenticated to its original source," said Raymond H. Cypess, D.V.M., Ph.D., chairman and CEO of ATCC. "We are embracing this digital biotechnology to be able to share our expertise in advancing authentication to the research community."

"Our expertise in bioinformatics software and services, combined with ATCC’s sequencing data, will further expand our genomics knowledge and OmicSoft Land databases, thus empowering scientists from around the world with actionable insights into the discovery and development of precision therapeutics," said Jonathan Sheldon, Senior Vice President and Head of QIAGEN Digital Insights. "We are honored to be collaborating with ATCC on this project."

Cell lines form the cornerstone of cell-based experimentation studies that help researchers understand the underlying mechanisms of normal and disease biology, including cancer. However, it is commonly acknowledged that inaccurate public datasets and contamination may adversely affect biomedical research and development and the effective use of bioinformatics platforms.

ATCC will initially produce fully authenticated transcriptome (RNAseq) and whole exome sequencing (WES) datasets from the most highly utilized human and animal cell lines found in ATCC’s collection. These datasets will include multiple biological and technical replicates that will help establish a baseline for a wide range of cell lines under typical cell culture conditions. Users will also be able to request datasets to be included in the database in the future.

"This agreement will enable a data-driven drug discovery process to take shape – where the data representing biological materials can be searched, analyzed and incorporated into existing research pipelines," said Ruth Cheng, Ph.D., Chief Innovation and Strategy Officer & Vice President of Corporate Development. "This will, in turn, enable researchers to discover new cell lines in our collection to include in their research that previously may have remained largely hidden from view."

QIAGEN Digital Insights provides solutions that enable its customers within healthcare, forensics, academia, and the pharmaceutical and biotechnology industries to gain valuable molecular insights from samples containing the building blocks of life. Their sample and assay technologies isolate and process DNA, RNA and proteins from blood, tissue and other materials and make these biomolecules visible and ready for analysis. Bioinformatics software and knowledge bases interpret data to report relevant, actionable insights, tied together in seamless and cost-effective workflows through automation solutions.

Genialis ResponderID to Use Xerna™ TME Panel to Improve Targeted Therapy Selection

On April 4, 2022 Genialis, a leader in applied data science for the development of precision medicines, reported it will leverage its proprietary ResponderID AI platform technology to provide retrospective analysis to customers and collaborators to help classify patients for targeted therapy using the OncXerna Xerna TME Panel, an RNA-based pan-tumor biomarker shown to be predictive of responses to multiple immune-targeted cancer therapies (Press release, Genialis, APR 4, 2022, View Source [SID1234611412]).

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Targeted therapies today provide benefit only to a fraction of the patients for a given disease indication because current laboratory models do not faithfully represent patient biology. ResponderID starts at the end—with the patients. The platform’s computational models of disease biology embrace the complexity that defines each patient. The TME Panel measures approximately 100 genes by RNA sequencing and applies machine learning to decipher the therapeutically relevant patterns in those data. The TME Panel can enrich patient response to different classes of therapy (e.g. immune checkpoint inhibitors and anti-angiogenics) in several cancer types, including gastric and ovarian.

"Inclusion of the TME Panel algorithm within ResponderID will create a valuable starting point for numerous potential research and commercial partnerships," said Rafael Rosengarten, Ph.D., CEO of Genialis. "By offering our customers and collaborators the opportunity to quickly and comprehensively analyze their retrospective data, together we will be able to define and implement the most effective precision medicine strategy."

Collaborators that wish to use the Xerna TME Panel for future clinical studies and/or prospective research will be referred to one of OncXerna’s commercial diagnostic partners.

"We have a mounting body of evidence that suggests the Xerna TME Panel may be applicable to virtually any solid tumor type, and can be helpful to find the right patients for drugs that target the immune system," commented OncXerna CEO Laura Benjamin. "Genialis has the opportunity to evaluate the TME Panel across many of these disease types and for different therapeutic mechanisms."

ResponderID defines, models and validates disease models for drug development and discovery programs. The platform is a technology suite for clinical and translational research, built from years of experience working with partners across the industry and advanced internal R&D. ResponderID incorporates technologies and proprietary tools for feature selection, data harmonization, machine learning modeling and interpretation of the models. ResponderID is already in use to improve the efficiency, effectiveness and success rate of drug development and discovery across the oncology space, with more therapeutic areas in the works. Through numerous collaborations, ResponderID is building computational models to help treat cancers like gastric, colorectal, ovarian, lung, melanoma, acute myeloid leukemia, mesothelioma, and others.

OncXerna and Genialis co-authored a poster to be presented at AACR (Free AACR Whitepaper) 2022 that describes application of the TME Panel across various cancer types and drug modalities. For more information on Genialis and how it uses data science to advance precision medicine, please visit www.genialis.com.

Checkpoint Therapeutics to Present at the Virtual Fortress Biotech R&D Summit Hosted by B. Riley Securities

On April 4, 2022 Checkpoint Therapeutics, Inc. ("Checkpoint") (NASDAQ: CKPT), a clinical-stage immunotherapy and targeted oncology company, reported that members of Checkpoint’s management team will participate in the two-day Fortress Biotech ("Fortress") Virtual R&D Summit taking place on Tuesday, April 5, 2022 and Wednesday, April 6, 2022 (Press release, Checkpoint Therapeutics, APR 4, 2022, View Source [SID1234611411]). The Summit will be hosted by the B. Riley Securities’ Healthcare Equity Research team and will feature multiple programs from Fortress’ diversified pipeline.

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Checkpoint will present a corporate overview and participate in a panel discussion on Wednesday, April 6, 2022 at 2:15 p.m. ET. Registration for the event is available here.

Following the meeting, the webcast will be available on the IR Calendar page under News & Events, located within the Investors section of Checkpoint’s website, View Source, for approximately 30 days following the meeting.