Comprehensive NGS profiling to enable detection of ALK gene rearrangements and MET amplifications in non-small cell lung cancer.

Introduction: Next-generation sequencing (NGS) is currently widely used for biomarker studies and molecular profiling to identify concurrent alterations that can lead to the better characterization of a tumor's molecular landscape. However, further evaluation of technical aspects related to the detection of gene rearrangements and copy number alterations is warranted. Methods: There were 12 ALK rearrangement-positive tumor specimens from patients with non-small cell lung cancer (NSCLC) previously detected via fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and an RNA-based NGS assay, and 26 MET high gene copy number (GCN) cases detected by FISH, selected for this retrospective study. All 38 pre-characterized cases were reassessed utilizing the PGDx™ elio™ tissue complete assay, a 505 gene targeted NGS panel, to evaluate concordance with these conventional diagnostic techniques. Results: The detection of ALK rearrangements using the DNA-based NGS assay demonstrated excellent sensitivity with the added benefit of characterizing gene fusion partners and genomic breakpoints. MET copy number alterations were also detected; however, some discordances were observed likely attributed to differences in algorithm, reporting thresholds and gene copy number state. TMB was also assessed by the assay and correlated to the presence of NSCLC driver alterations and was found to be significantly lower in cases with NGS-confirmed canonical driver mutations compared with those without (p=0.0019). Discussion: Overall, this study validates NGS as an accurate approach for detecting structural variants while also highlighting the need for further optimization to enable harmonization across methodologies for amplifications.

Dietary supplements to reduce symptom severity and duration in people with SARS-CoV-2: a double-blind randomised controlled trial.

BACKGROUND: COVID-19 has caused morbidity, hospitalisation and mortality worldwide. Despite effective vaccines, there is still a need for effective treatments, especially for people in the community. Dietary supplements have long been used to treat respiratory infections, and preliminary evidence indicates some may be effective in people with COVID-19. We sought to evaluate whether a combination of vitamin C, vitamin D3, vitamin K2 and zinc could improve overall health and decrease symptom burden in outpatients diagnosed with COVID-19. METHODS: Participants were randomised to receive either vitamin C (6 g), vitamin D3 (1000 units), vitamin K2 (240 µg) and zinc acetate (75 mg) or placebo daily for 21 days and were followed for 12 weeks. An additional loading dose of 50 000 units vitamin D3 (or placebo) was given on day one. The primary outcome was participant-reported overall health using the EuroQol Visual Assessment Scale summed over 21 days. Secondary outcomes included health status, symptom severity, symptom duration, delayed return to usual health, frequency of hospitalisation and mortality. RESULTS: 90 patients (46 control, 44 treatment) were randomised. The study was stopped prematurely due to insufficient capacity for recruitment. The mean difference (control-treatment) in cumulative overall health was -37.4 (95% CI -157.2 to 82.3), p=0.53 on a scale of 0-2100. No clinically or statistically significant differences were seen in any secondary outcomes. INTERPRETATION: In this double-blind, placebo-controlled, randomised trial of outpatients diagnosed with COVID-19, the dietary supplements vitamin C, vitamin D3, vitamin K2 and zinc acetate showed no clinically or statistically significant effects on the documented measures of health compared with a placebo when given for 21 days. Termination due to feasibility limited our ability to demonstrate the efficacy of these supplements for COVID-19. Further research is needed to determine clinical utility. TRIAL REGISTRATION NUMBER: NCT04780061.

Practical Assessment and Management of Vulnerabilities in Older Patients Receiving Systemic Cancer Therapy: ASCO Guideline Update.

PURPOSE: To update the ASCO guideline (2018) on the practical assessment and management of age-associated vulnerabilities in older patients undergoing systemic cancer therapy. METHODS: An Expert Panel conducted a systematic review to identify relevant randomized clinical trials (RCTs), systematic reviews, and meta-analyses from January 2016 to December 2022. RESULTS: A total of 26 publications met eligibility criteria and form the evidentiary basis for the update. RECOMMENDATIONS: The Expert Panel reiterates its overarching recommendation from the prior guideline that geriatric assessment (GA), including all essential domains, should be used to identify vulnerabilities or impairments that are not routinely captured in oncology assessments for all patients over 65 years old with cancer. Based on recently published RCTs demonstrating significantly improved clinical outcomes, all older adults with cancer (65+ years old) receiving systemic therapy with GA-identified deficits should have GA-guided management (GAM) included in their care plan. GAM includes using GA findings to inform cancer treatment decision-making as well as to address impairments through appropriate interventions, counseling, and/or referrals. A GA should include high priority aging-related domains known to be associated with outcomes in older adults with cancer: physical and cognitive function, emotional health, comorbid conditions, polypharmacy, nutrition, and social support. Clinical adaptation of the GA based on patient population, resources, and time is appropriate.The Panel recommends the Practical Geriatric Assessment as one option for this purpose (https://old-prod.asco.org/sites/new-www.asco.org/files/content-files/practice-patients/documents/2023-PGA-Final.pdf; https://youtu.be/jnaQIjOz2Dw; https://youtu.be/nZXtwaGh0Z0).Additional information is available at www.asco.org/supportive-care-guidelines.

Drug combinations identified by high-throughput screening promote cell cycle transition and upregulate Smad pathways in myeloma.

Drug resistance and disease progression are common in multiple myeloma (MM) patients, underscoring the need for new therapeutic combinations. A high-throughput drug screen in 47 MM cell lines and in silico Huber robust regression analysis of drug responses revealed 43 potentially synergistic combinations. We hypothesized that effective combinations would reduce MYC expression and enhance p16 activity. Six combinations cooperatively reduced MYC protein, frequently over-expressed in MM and also cooperatively increased p16 expression, frequently downregulated in MM. Synergistic reductions in viability were observed with top combinations in proteasome inhibitor-resistant and sensitive MM cell lines, while sparing fibroblasts. Three combinations significantly prolonged survival in a transplantable Ras-driven allograft model of advanced MM closely recapitulating high-risk/refractory myeloma in humans and reduced viability of ex vivo treated patient cells. Common genetic pathways similarly downregulated by these combinations promoted cell cycle transition, whereas pathways most upregulated were involved in TGFß/SMAD signaling. These preclinical data identify potentially useful drug combinations for evaluation in drug-resistant MM and reveal potential mechanisms of combined drug sensitivity.

A Multidisciplinary Approach for the Management of Portal Vein Thrombosis.

Portal venous thrombosis (PVT) is an uncommon disease associated with highly morbid conditions such as intestinal ischemia and portal hypertension. Patients at higher risk of developing PVT include those with cirrhosis, malignancy, or prothrombotic states. The mainstay of treatment is early initiation of anticoagulation. The first case is a 49-year-old female diagnosed with a cecal mass and PVT. She was started on anticoagulation and underwent a right hemicolectomy with several small bowel resections. She developed portal hypertension that required TIPS and mechanical thrombectomy. The second patient is a 65-year-old female found to have PVT. She was anticoagulated with heparin and given systemic TPA. She developed intestinal ischemia and portal hypertension requiring small bowel resection, TIPS, and mechanical thrombectomy. These cases give insight into the impact of a multidisciplinary team approach to PVT. The role and timing of endovascular treatment is not well established and needs to be further investigated.

Preservation fluids of heritage anatomical specimens - a challenge for modern science. Studies of the origin, composition and microbiological contamination of old museum collections.

Anatomical museums preserve specimens of great historical value and undiscovered scientific potential. However, frequently these collections lack documentation of the techniques of preparation and the composition of preservative substances (conservation principles). This poses a huge problem for the care and preservation of these materials, more so because understanding this issue requires knowledge of fundamentals from different scientific disciplines. The aim of the research was to obtain information about the composition of substances used to preserve historic specimens, as well as to conduct a microbiological assessment of the specimens to detect possible factors causing their deterioration. Furthermore, we wanted to fill an existing gap in the literature, as there is a lack of reports on analytical methods that could be successfully applied by anatomists involved in the daily care of museum collections in human anatomy departments. The starting point was the analysis of the sources and history of the collections, on which basis the choice of research methods was made. Methods based on simple chemical reactions and specialised methods (such as gas chromatography-tandem mass spectrometry, Fourier transform infrared spectroscopy, inductively coupled plasma optical emission spectroscopy) were used in the analyses of the composition of fluids. Microbiological analyses were based on culture and isolation methods, analysis of microscopy slides and matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry analysis. As a result of these analyses, some components of the preservative mixtures and their concentrations were determined. The presence of methanol, ethanol, formaldehyde and glycerol was detected, among other chemicals. The concentrations of these substances were different between the samples and their determination required the use of a variety of methods suitable for the individual components of the preservative mixture. In microbiological tests, both bacteria and fungi were isolated from swabs taken from anatomical specimens. The bacterial flora was less numerous than the fungal flora. Among the bacteria, environmental Gram-positive Bacillus cereus, Bacillus thuringiensis and a rare bacterium of the Cupriavidus genus were isolated, whereas among the fungal organisms, the yeast-like fungi Candida boidinii and Geotrichum silvicola as well as mould fungi Penicillium sp. and Fusarium sp. were detected. However, the microscopic evaluation showed a greater diversity of microorganisms, which may be related to the fact that many environmental bacteria cannot be cultured using classical methods, but can be observed under the microscope. The results of the research made it possible to draw conclusions about the mutual influence of physical, chemical, and microbiological factors on the condition of historical anatomical specimens. In the course of the research, information was obtained on the processes which could have taken place during the storage of these collections. Maintaining the integrity of a container housing a preserved anatomical specimen has a major impact on maintaining the concentration of preservative fluid and keeping the specimen environment sterile. Many conservation procedures for historical specimens carried out nowadays pose a risk of destroying valuable specimens, as well as a health risk for the person carrying out the work. The exploration of the topic of conservation of anatomical specimens, especially those that lack documentation of their origin, is a key issue in current research on historical collections of anatomical specimens.

Metastatic Colorectal Cancer Treatment Response Evaluation by Ultra-Deep Sequencing of Cell-Free DNA and Matched White Blood Cells.

PURPOSE: Circulating tumor DNA (ctDNA) has the potential to guide therapy selection and monitor treatment response in patients with metastatic cancer. However, germline and clonal hematopoiesis-associated alterations can confound identification of tumor-specific mutations in cell-free DNA (cfDNA), often requiring additional sequencing of tumor tissue. The current study assessed whether ctDNA-based treatment response monitoring could be performed in a tumor tissue-independent manner by combining ultra-deep targeted sequencing analyses of cfDNA with patient-matched white blood cell (WBC)-derived DNA. EXPERIMENTAL DESIGN: In total, 183 cfDNA and 49 WBC samples, along with 28 tissue samples, from 52 patients with metastatic colorectal cancer participating in the prospective phase III CAIRO5 clinical trial were analyzed using an ultra-deep targeted sequencing liquid biopsy assay. RESULTS: The combined cfDNA and WBC analysis prevented false-positives due to germline or hematopoietic variants in 40% of patients. Patient-matched tumor tissue sequencing did not provide additional information. Longitudinal analyses of ctDNA were more predictive of overall survival than standard-of-care radiological response evaluation. ctDNA mutations related to primary or acquired resistance to panitumumab were identified in 42% of patients. CONCLUSIONS: Accurate calling of ctDNA mutations for treatment response monitoring is feasible in a tumor tissue-independent manner by combined cfDNA and patient-matched WBC genomic DNA analysis. This tissue biopsy-independent approach simplifies sample logistics and facilitates the application of liquid biopsy ctDNA testing for evaluation of emerging therapy resistance, opening new avenues for early adaptation of treatment regimens.

Terra Incognita in anatomical museology - A literature review from the perspective of evidence-based care.

BACKGROUND: The care of historical collections in anatomical museums is a highly specialized subject requiring advanced knowledge. When searching for practical information on this subject, the authors were not able to find appropriate literature based on scientific research. The absence of this literature is probably due to the specialized nature of the subject and the poorly defined classification of this type of museum. The purpose of this study is to conduct a systematic literature review to identify (i) the current state of knowledge of anatomical museology and (ii) the nature and determinants of ongoing research on anatomical museum objects. MATERIALS AND METHODS: A systematic search of the main electronic databases (PubMed, Google Scholar, Scopus) was conducted to identify relevant studies. The records retrieved were categorized according to thematic similarity and scientific content. Based on these groupings, statistics were created based on the number of eligible papers in each particular group. RESULTS: 61 % of the papers retrieved addressed the history, social issues, or related aspects of contemporary museology; 8 % were technical papers; and 31 % research papers, of which only 8 % were focused on the museum object as the topic of the research. The paper retrieved showed a predominance of works in cultural studies, with surprisingly few applicable to museum practice. Furthermore, there was a lack of consensus in the literature regarding the classification of anatomical museums. CONCLUSIONS: Anatomical museology is a poorly defined concept in the scientific literature and it is a rare topic in contemporary work by anatomical practitioners. The literature review revealed that the debate about the fate of anatomical museums encompasses a broad spectrum of diverse, often disparate scientific fields as well as economic factors that influence the present status and future of these institutions. For these reasons, museum object research is problematic in design, may not be considered worthwhile, or is unattractive from an institutional perspective. The literature survey showed that there is a paucity of work in the available modern literature that provides significant support for museum anatomists.

Uptake and factors associated with direct-acting antiviral therapy for hepatitis C and treatment outcomes among Canadian immigrants: A retrospective cohort analysis.

Background: We sought to compare rates and factors associated with direct acting antiviral (DAA) treatment uptake and sustained virological response (SVR) between Canadian-born and foreign-born patients. Methods: The study was conducted utilizing a retrospective cohort of hepatitis C virus (HCV)-infected patients assessed at The Ottawa Hospital Viral Hepatitis Clinic between January 2015 and October 2021. Risk factors, income, and clinical characteristics of HCV infection associated with DAA therapy uptake and SVR were compared by immigration status using logistic regression. Results: Of 1,459 HCV-infected patients, 264 (18.1%) were born outside of the country. A median 17 years passed from immigration to first assessment at the clinic. The proportion of patients initiating DAA therapy was similar between groups (65.2% versus 69.5%, p = 0.17). Characteristics associated with DAA therapy uptake included age at first assessment (OR 1.02; 95% CI 1.01 to 1.03) and being cirrhotic (OR 3.19; 95% CI 1.99 to 2.13). Crude SVR rate was higher in immigrants than in Canadian-born patients (91.5% versus 83.7%, p = 0.01). After controlling for other variables, only advancing age was associated with the likelihood of achieving crude SVR (OR 1.04, 95% CI 1.02 to 1.05). Conclusions: We found that DAA therapy uptake and HCV cure rates were high in both groups suggesting equity of opportunity in those referred to our program. The older age at presentation suggests missed opportunities to diagnose and engage immigrants in HCV care. These findings emphasize the importance of early large-scale screening and engagement in care for HCV infection of immigrant populations to prevent future complications.

Social Justice and Equity: Why Older Adults With Cancer Belong-A Life Course Perspective.

The population of older adults with cancer in the United States is rapidly increasing, which will have a substantial impact on the oncology and public health workforces across the cancer continuum, from prevention to end of life. Unfortunately, inequities in existing social structures that cause increased psychosocial stressors have led to disparities in the incidence of cancer and the morbidity and mortality of cancer for individuals from marginalized backgrounds. It is imperative that older adults, especially those from historically marginalized backgrounds, be adequately represented in all stages of cancer research to address health inequities. Continued efforts and progress toward achieving social justice and health equity require a deeper commitment to and better understanding of the impact of social determinants of health within the cancer domain. Undoubtedly, a more holistic and integrated view that extends beyond the biologic and genetic factors of health must be adopted for health entities to recognize the critical role of environmental, behavioral, and social determinants in cancer health disparities. Against this backdrop, this paper uses a life course approach to present a multifactorial framework for understanding and addressing cancer disparities in an effort to advance social justice and health equity for racially and ethnically diverse older adults.

Automated next-generation profiling of genomic alterations in human cancers.

The lack of validated, distributed comprehensive genomic profiling assays for patients with cancer inhibits access to precision oncology treatment. To address this, we describe elio tissue complete, which has been FDA-cleared for examination of 505 cancer-related genes. Independent analyses of clinically and biologically relevant sequence changes across 170 clinical tumor samples using MSK-IMPACT, FoundationOne, and PCR-based methods reveals a positive percent agreement of >97%. We observe high concordance with whole-exome sequencing for evaluation of tumor mutational burden for 307 solid tumors (Pearson r = 0.95) and comparison of the elio tissue complete microsatellite instability detection approach with an independent PCR assay for 223 samples displays a positive percent agreement of 99%. Finally, evaluation of amplifications and translocations against DNA- and RNA-based approaches exhibits >98% negative percent agreement and positive percent agreement of 86% and 82%, respectively. These methods provide an approach for pan-solid tumor comprehensive genomic profiling with high analytical performance.

Dietary supplements to reduce symptom severity and duration in people with SARS-CoV-2: study protocol for a randomised, double-blind, placebo controlled clinical trial.

INTRODUCTION: COVID-19 has caused morbidity, hospitalisations and deaths worldwide. Despite four approved vaccines for COVID-19 in Canada, there is still a need for effective treatments, especially for people in the community. Vaccine efficacy is not 100% and long-term efficacy is still unknown. Furthermore, there are challenges to herd immunity including vaccine hesitancy and underlying conditions preventing vaccination. We aim to explore if the nutrients vitamin C, vitamin D, vitamin K2 and zinc are an effective treatment option for outpatients diagnosed with COVID-19. The primary outcome is the difference in participant-reported overall health; secondary outcomes include the effect on health status, symptom severity and duration, frequency and length of hospitalisations and mortality. METHODS AND ANALYSIS: This study is a two-arm, parallel-group, double-blind, placebo-controlled, phase III randomised controlled trial. 200 patients will be recruited remotely from COVID-19 test centres in Ottawa, Canada associated with The Ottawa Hospital. Overall health will be measured using the EuroQol Visual Assessment Scale; health status will be measured using the EuroQol 5-dimension 5-level questionnaire; symptom severity and duration will be measured using an independently developed questionnaire; analyses will use an area under the curve approach and compare mean scores using unadjusted t tests. Study data will be recorded on electronic case report forms using the Research Electronic Data Capture platform. An independent data safety and monitoring board will perform ongoing review of the study for feasibility and safety. ETHICS AND DISSEMINATION: This study has received ethical approval from the research ethics boards of the Canadian College of Naturopathic Medicine and the Ottawa Health Sciences Network, as well as regulatory approval from the Therapeutic Products Directorate and Natural and Non-Prescription Health Products Directorate of Health Canada. Results will be published in a peer-reviewed scientific journal with open access. TRIAL REGISTRATION NUMBER: NCT04780061.

Enduring Physical or Mental Suffering of People Requesting Medical Assistance in Dying.

BACKGROUND: Medical assistance in dying (MAiD) is available in Canada for patients with grievous and irremediable medical conditions causing unbearable physical or mental suffering. It is not known how the 'grievous and irremediable suffering' criteria is being interpreted and documented by physicians. METHODS: Retrospective chart review of MAiD assessments from patients who submitted written MAiD requests to The Ottawa Hospital from June 1, 2016 to September 18, 2018. We used inductive thematic analysis to determine themes and subthemes. RESULTS: Our sample included 52 patients with a mean age of 70.5 years (SD 14), 24/52 (46%) were male. We identified 5 themes: 1) patient's context and history (e.g., past experiences, lack of disease modifying treatments), 2) physical symptoms (e.g., chronic pain, fatigue), 3) psychosocial symptoms (e.g., social isolation, or inability to communicate), 4) sense of control and 5) irreversibility. These themes were used to create a framework that describes the suffering of patients requesting MAiD. Patients who request MAiD describe how their disease causes suffering through physical symptoms, psychological symptoms and loss of control that is irreversible. These domains of suffering interact with their personal history and context leading to a reality that is unacceptable and irreversible. CONCLUSION: MAiD assessors' working definition of 'grievous and irremediable suffering' as documented in their assessments is consistent with the body of literature on this topic. MAiD assessments could be enhanced with more information about existential aspects of suffering and the impact of illness on meaningful life roles.

Validation of a Circulating Tumor DNA-Based Next-Generation Sequencing Assay in a Cohort of Patients with Solid tumors: A Proposed Solution for Decentralized Plasma Testing.

BACKGROUND: Characterization of circulating tumor DNA (ctDNA) has been integrated into clinical practice. Although labs have standardized validation procedures to develop single locus tests, the efficacy of on-site plasma-based next-generation sequencing (NGS) assays still needs to be proved. MATERIALS AND METHODS: In this retrospective study, we profiled DNA from matched tissue and plasma samples from 75 patients with cancer. We applied an NGS test that detects clinically relevant alterations in 33 genes and microsatellite instability (MSI) to analyze plasma cell-free DNA (cfDNA). RESULTS: The concordance between alterations detected in both tissue and plasma samples was higher in patients with metastatic disease. The NGS test detected 77% of sequence alterations, amplifications, and fusions that were found in metastatic samples compared with 45% of those alterations found in the primary tumor samples (p = .00005). There was 87% agreement on MSI status between the NGS test and tumor tissue results. In three patients, MSI-high ctDNA correlated with response to immunotherapy. In addition, the NGS test revealed an FGFR2 amplification that was not detected in tumor tissue from a patient with metastatic gastric cancer, emphasizing the importance of profiling plasma samples in patients with advanced cancer. CONCLUSION: Our validation experience of a plasma-based NGS assay advances current knowledge about translating cfDNA testing into clinical practice and supports the application of plasma assays in the management of oncology patients with metastatic disease. With an in-house method that minimizes the need for invasive procedures, on-site cfDNA testing supplements tissue biopsy to guide precision therapy and is entitled to become a routine practice. IMPLICATIONS FOR PRACTICE: This study proposes a solution for decentralized liquid biopsy testing based on validation of a next-generation sequencing (NGS) test that detects four classes of genomic alterations in blood: sequence mutations (single nucleotide substitutions or insertions and deletions), fusions, amplifications, and microsatellite instability (MSI). Although there are reference labs that perform single-site comprehensive liquid biopsy testing, the targeted assay this study validated can be established locally in any lab with capacity to offer clinical molecular pathology assays. To the authors' knowledge, this is the first report that validates evaluating an on-site plasma-based NGS test that detects the MSI status along with common sequence alterations encountered in solid tumors.

Carnitine in Alcohol Use Disorders: A Scoping Review.

Recent studies in alcohol use disorders (AUDs) have demonstrated some connections between carnitine metabolism and the pathophysiology of the disease. In this scoping review, we aimed to collate and examine existing research available on carnitine metabolism and AUDs and develop hypotheses surrounding the role carnitine may play in AUD. A scoping review method was used to search electronic databases in September 2019. The database search terms used included "alcohol, alcoholism, alcohol abuse, alcohol consumption, alcohol drinking patterns, alcohol-induced disorders, alcoholic intoxication, alcohol-related disorders, binge drinking, Wernicke encephalopathy, acylcarnitine, acetyl-l-carnitine, acetylcarnitine, carnitine and palmitoylcarnitine." The inclusion criteria included English language, human-based, AUD diagnosis and measured blood or tissue carnitine or used carnitine as a treatment. Of 586 studies that were identified and screened, 65 underwent abstract review, and 41 were fully reviewed. Eighteen studies were ultimately included for analysis. Data were summarized in an electronic data extraction form. We found that there is limited literature available. Alcohol use appears to impact carnitine metabolism, most clearly in the setting of alcoholic cirrhosis. Six studies found carnitine to be increased in AUD, of which 5 were conducted in patients with alcoholic cirrhosis. Only 3 placebo-controlled trials were identified and provide some support for the use of carnitine in AUD to decrease cravings, anhedonia, and withdrawal and improve cognition. The increase in plasma carnitine in alcoholic cirrhosis may be related to disordered fatty acid metabolism and oxidative stress that occurs in AUD. The multiple possible therapeutic effects carnitine could have on ethanol metabolism and the early evidence available for carnitine supplementation as a treatment for AUD provide a foundation for future randomized control trials of carnitine for treating AUD.

Generic Protocols for the Analytical Validation of Next-Generation Sequencing-Based ctDNA Assays: A Joint Consensus Recommendation of the BloodPAC's Analytical Variables Working Group.

Liquid biopsy, particularly the analysis of circulating tumor DNA (ctDNA), has demonstrated considerable promise for numerous clinical intended uses. Successful validation and commercialization of novel ctDNA tests have the potential to improve the outcomes of patients with cancer. The goal of the Blood Profiling Atlas Consortium (BloodPAC) is to accelerate the development and validation of liquid biopsy assays that will be introduced into the clinic. To accomplish this goal, the BloodPAC conducts research in the following areas: Data Collection and Analysis within the BloodPAC Data Commons; Preanalytical Variables; Analytical Variables; Patient Context Variables; and Reimbursement. In this document, the BloodPAC's Analytical Variables Working Group (AV WG) attempts to define a set of generic analytical validation protocols tailored for ctDNA-based Next-Generation Sequencing (NGS) assays. Analytical validation of ctDNA assays poses several unique challenges that primarily arise from the fact that very few tumor-derived DNA molecules may be present in circulation relative to the amount of nontumor-derived cell-free DNA (cfDNA). These challenges include the exquisite level of sensitivity and specificity needed to detect ctDNA, the potential for false negatives in detecting these rare molecules, and the increased reliance on contrived samples to attain sufficient ctDNA for analytical validation. By addressing these unique challenges, the BloodPAC hopes to expedite sponsors' presubmission discussions with the Food and Drug Administration (FDA) with the protocols presented herein. By sharing best practices with the broader community, this work may also save the time and capacity of FDA reviewers through increased efficiency.

Mouse tumor susceptibility genes identify drug combinations for multiple myeloma.

Long-term genetic studies utilizing backcross and congenic strain analyses coupled with positional cloning strategies and functional studies identified Cdkn2a, Mtor, and Mndal as mouse plasmacytoma susceptibility/resistance genes. Tumor incidence data in congenic strains carrying the resistance alleles of Cdkn2a and Mtor led us to hypothesize that drug combinations affecting these pathways are likely to have an additive, if not synergistic effect in inhibiting tumor cell growth. Traditional and novel systems-level genomic approaches were used to assess combination activity, disease specificity, and clinical potential of a drug combination involving rapamycin/everolimus, an Mtor inhibitor, with entinostat, an histone deacetylase inhibitor. The combination synergistically repressed oncogenic MYC and activated the Cdkn2a tumor suppressor. The identification of MYC as a primary upstream regulator led to the identification of small molecule binders of the G-quadruplex structure that forms in the NHEIII region of the MYC promoter. These studies highlight the importance of identifying drug combinations which simultaneously upregulate tumor suppressors and downregulate oncogenes.

Structure, Hydration, and Interactions of Native and Hydrophobically Modified Phytoglycogen Nanoparticles.

Phytoglycogen is a highly branched polymer of glucose produced as soft, compact nanoparticles by sweet corn. Properties such as softness, porosity, and mechanical integrity, combined with nontoxicity and biodegradability, make phytoglycogen nanoparticles ideal for applications involving the human body, ranging from skin moisturizing and rejuvenation agents in personal care formulations to functional therapeutics in biomedicine. To further broaden the range of applications, phytoglycogen nanoparticles can be chemically modified with hydrophobic species such as octenyl succinic anhydride (OSA). Here, we present a self-consistent model of the particle structure, water content, and degree of chemical modification of the particles, as well as the emergence of well-defined interparticle spacings in concentrated dispersions, based on small-angle neutron scattering (SANS) measurements of aqueous dispersions of native phytoglycogen nanoparticles and particles that were hydrophobically modified using octenyl succinic anhydride (OSA) in both its protiated (pOSA) and deuterated (dOSA) forms. Measurements on native particles with reduced polydispersity have allowed us to refine the particle morphology, which is well described by a hairy particle (core-chain) geometry with short chains decorating the surface of the particles. The isotopic variants of OSA-modified particles enhanced the scattering contrast for neutrons, revealing lightly modified hairy chains for small degrees of substitution (DS) of OSA, and a raspberry particle geometry for the largest DS value, where the OSA-modified hairy chains collapse to form small seeds on the surface of the particles. This refined model of native and OSA-modified phytoglycogen nanoparticles establishes a quantitative basis for the development of new applications of this promising sustainable nanotechnology.

Hypomorphic mTOR Downregulates CDK6 and Delays Thymic Pre-T LBL Tumorigenesis.

PI3K/AKT/mTOR pathway hyperactivation is frequent in T-cell acute lymphoblastic leukemia/lymphoma (T-ALL/LBL). To model inhibition of mTOR, pre-T-cell lymphoblastic leukemia/lymphoma (pre-T LBL) tumor development was monitored in mice with T lymphocyte-specific, constitutively active AKT (Lck-MyrAkt2) that were either crossed to mTOR knockdown (KD) mice or treated with the mTOR inhibitor everolimus. Lck-MyrAkt2;mTOR KD mice lived significantly longer than Lck-MyrAkt2;mTOR wild-type (WT) mice, although both groups ultimately developed thymic pre-T LBL. An increase in survival was also observed when Lck-MyrAkt2;mTOR WT mice were treated for 8 weeks with everolimus. The transcriptional profiles of WT and KD thymic lymphomas were compared, and Ingenuity Pathway Upstream Regulator Analysis of differentially expressed genes in tumors from mTOR WT versus KD mice identified let-7 and miR-21 as potential regulatory genes. mTOR KD mice had higher levels of let-7a and miR-21 than mTOR WT mice, and rapamycin induced their expression in mTOR WT cells. CDK6 was one of the most downregulated targets of both let-7 and miR21 in mTOR KD tumors. CDK6 overexpression and decreased expression of let-7 in mTOR KD cells rescued a G1 arrest phenotype. Combined mTOR (rapamycin) and CDK4/6 (palbociclib) inhibition decreased tumor size and proliferation in tumor flank transplants, increased survival in an intravenous transplant model of disseminated leukemia compared with single agent treatment, and cooperatively decreased cell viability in human T-ALL/LBL cell lines. Thus, mTOR KD mice provide a model to explore drug combinations synergizing with mTOR inhibitors and can be used to identify downstream targets of inhibition.