Resource requirements to accelerate clinical applications of next generation sequencing and radiomics: Workshop commentary and review.

The National Institutes of Health (NIH)/U.S. Food and Drug Administration (FDA) Joint Leadership Council Next-Generation Sequencing (NGS) and Radiomics Working Group (NGS&R WG) was formed by the NIH/FDA Joint Leadership Council to promote the development and validation of innovative NGS tests, radiomic tools, and associated data analysis and interpretation enhanced by artificial intelligence (AI) and machine-learning (ML) technologies. A two-day workshop was held on September 29-30, 2021 to convene members of the scientific community to discuss how to overcome the "ground truth" gap that has frequently been acknowledged as one of the limiting factors impeding high-quality research, development, validation, and regulatory science in these fields. This report provides a summary of the resource gaps identified by the WG and attendees, highlights existing resources and the ways they can potentially be leveraged to accelerate growth in these fields, and presents opportunities to support NGS and radiomic tool development and validation using technologies such as AI and ML.

A Neuroradiologist's Guide to Operationalizing the Response Assessment in Neuro-Oncology (RANO) Criteria Version 2.0 for Gliomas in Adults.

Radiographic assessment plays a crucial role in the management of patients with central nervous system (CNS) tumors, aiding in treatment planning and evaluation of therapeutic efficacy by quantifying response. Recently, an updated version of the Response Assessment in Neuro-Oncology (RANO) criteria (RANO 2.0) was developed to improve upon prior criteria and provide an updated, standardized framework for assessing treatment response in clinical trials for gliomas in adults. This article provides an overview of significant updates to the criteria including (1) the use of a unified set of criteria for high and low grade gliomas in adults; (2) the use of the post-radiotherapy MRI scan as the baseline for evaluation in newly diagnosed high-grade gliomas; (3) the option for the trial to mandate a confirmation scan to more reliably distinguish pseudoprogression from tumor progression; (4) the option of using volumetric tumor measurements; and (5) the removal of subjective non-enhancing tumor evaluations in predominantly enhancing gliomas (except for specific therapeutic modalities). Step-by-step pragmatic guidance is hereby provided for the neuroradiologist and imaging core lab involved in operationalization and technical execution of RANO 2.0 in clinical trials, including the display of representative cases and in-depth discussion of challenging scenarios.ABBREVIATIONS: BTIP = Brain Tumor Imaging Protocol; CE = Contrast-Enhancing; CNS = Central Nervous System; CR = Complete Response; ECOG = Eastern Cooperative Oncology Group; HGG = High-Grade Glioma; IDH = Isocitrate Dehydrogenase; IRF = Independent Radiologic Facility; LGG = Low-Grade Glioma; KPS = Karnofsky Performance Status; MR = Minor Response; mRANO = Modified RANO; NANO = Neurological Assessment in Neuro-Oncology; ORR = Objective Response Rate; OS = Overall Survival; PD = Progressive Disease; PFS = Progression-Free Survival; PR = Partial Response; PsP = Pseudoprogression; RANO = Response Assessment in Neuro-Oncology; RECIST = Response Evaluation Criteria In Solid Tumors; RT = Radiation Therapy; SD = Stable Disease; Tx = Treatment.

RANO 2.0: Update to the Response Assessment in Neuro-Oncology Criteria for High- and Low-Grade Gliomas in Adults.

PURPOSE: The Response Assessment in Neuro-Oncology (RANO) criteria for high-grade gliomas (RANO-HGG) and low-grade gliomas (RANO-LGG) were developed to improve reliability of response assessment in glioma trials. Over time, some limitations of these criteria were identified, and challenges emerged regarding integrating features of the modified RANO (mRANO) or the immunotherapy RANO (iRANO) criteria. METHODS: Informed by data from studies evaluating the different criteria, updates to the RANO criteria are proposed (RANO 2.0). RESULTS: We recommend a standard set of criteria for both high- and low-grade gliomas, to be used for all trials regardless of the treatment modalities being evaluated. In the newly diagnosed setting, the postradiotherapy magnetic resonance imaging (MRI), rather than the postsurgical MRI, will be used as the baseline for comparison with subsequent scans. Since the incidence of pseudoprogression is high in the 12 weeks after radiotherapy, continuation of treatment and confirmation of progression during this period with a repeat MRI, or histopathologic evidence of unequivocal recurrent tumor, are required to define tumor progression. However, confirmation scans are not mandatory after this period nor for the evaluation of treatment for recurrent tumors. For treatments with a high likelihood of pseudoprogression, mandatory confirmation of progression with a repeat MRI is highly recommended. The primary measurement remains the maximum cross-sectional area of tumor (two-dimensional) but volumetric measurements are an option. For IDH wild-type glioblastoma, the nonenhancing disease will no longer be evaluated except when assessing response to antiangiogenic agents. In IDH-mutated tumors with a significant nonenhancing component, clinical trials may require evaluating both the enhancing and nonenhancing tumor components for response assessment. CONCLUSION: The revised RANO 2.0 criteria refine response assessment in gliomas.

Harnessing imaging tools to guide immunotherapy trials: summary from the National Cancer Institute Cancer Imaging Steering Committee workshop.

As the immuno-oncology field continues the rapid growth witnessed over the past decade, optimising patient outcomes requires an evolution in the current response-assessment guidelines for phase 2 and 3 immunotherapy clinical trials and clinical care. Additionally, investigational tools-including image analysis of standard-of-care scans (such as CT, magnetic resonance, and PET) with analytics, such as radiomics, functional magnetic resonance agents, and novel molecular-imaging PET agents-offer promising advancements for assessment of immunotherapy. To document current challenges and opportunities and identify next steps in immunotherapy diagnostic imaging, the National Cancer Institute Clinical Imaging Steering Committee convened a meeting with diverse representation among imaging experts and oncologists to generate a comprehensive review of the state of the field.

Meta-Analysis of the Test-Retest Repeatability of [18F]-Fluorodeoxyglucose Standardized Uptake Values: Implications for Assessment of Tumor Response.

PURPOSE: Currently, guidelines for PET with 18F-fluorodeoxyglucose (FDG-PET) interpretation for assessment of therapy response in oncology primarily involve visual evaluation of FDG-PET/CT scans. However, quantitative measurements of the metabolic activity in tumors may be even more useful in evaluating response to treatment. Guidelines based on such measurements, including the European Organization for Research and Treatment of Cancer Criteria and PET Response Criteria in Solid Tumors, have been proposed. However, more rigorous analysis of response criteria based on FDG-PET measurements is needed to adopt regular use in practice. EXPERIMENTAL DESIGN: Well-defined boundaries of repeatability and reproducibility of quantitative measurements to discriminate noise from true signal changes are a needed initial step. An extension of the meta-analysis from de Langen and colleagues (2012) of the test-retest repeatability of quantitative FDG-PET measurements, including mean, maximum, and peak standardized uptake values (SUVmax, SUVmean, and SUVpeak, respectively), was performed. Data from 11 studies in the literature were used to estimate the relationship between the variance in test-retest measurements with uptake level and various study-level, patient-level, and lesion-level characteristics. RESULTS: Test-retest repeatability of percentage fluctuations for all three types of SUV measurement (max, mean, and peak) improved with higher FDG uptake levels. Repeatability in all three SUV measurements varied for different lesion locations. Worse repeatability in SUVmean was also associated with higher tumor volumes. CONCLUSIONS: On the basis of these results, recommendations regarding SUV measurements for assessing minimal detectable changes based on repeatability and reproducibility are proposed. These should be applied to differentiate between response categories for a future set of FDG-PET-based criteria that assess clinically significant changes in tumor response.

Criteria for the translation of radiomics into clinically useful tests.

Computer-extracted tumour characteristics have been incorporated into medical imaging computer-aided diagnosis (CAD) algorithms for decades. With the advent of radiomics, an extension of CAD involving high-throughput computer-extracted quantitative characterization of healthy or pathological structures and processes as captured by medical imaging, interest in such computer-extracted measurements has increased substantially. However, despite the thousands of radiomic studies, the number of settings in which radiomics has been successfully translated into a clinically useful tool or has obtained FDA clearance is comparatively small. This relative dearth might be attributable to factors such as the varying imaging and radiomic feature extraction protocols used from study to study, the numerous potential pitfalls in the analysis of radiomic data, and the lack of studies showing that acting upon a radiomic-based tool leads to a favourable benefit-risk balance for the patient. Several guidelines on specific aspects of radiomic data acquisition and analysis are already available, although a similar roadmap for the overall process of translating radiomics into tools that can be used in clinical care is needed. Herein, we provide 16 criteria for the effective execution of this process in the hopes that they will guide the development of more clinically useful radiomic tests in the future.

Formulation, biopharmaceutical evaluation and in-vitro screening of polyherbal phytosomes for breast cancer therapy.

Saudi Arabia has a rich culture of folk medicines and three such common herbs used by Saudi people for therapy of breast cancer are Turmeric (Kurkum) Curcuma longa, Chamomile (Babunaj) Matricaria chamomilla, and Aswaghantha (Aswaghadh) Withania somnifera. Hence, the present study aims to develop a polyherbal phytosome formulation by thin film hydration technique with a synergistic anti-cancer effect for the treatment of breast cancer. The phytosomes were standardized for their phytoconstituents by HPTLC and showed the best optimal properties with a mean vesicle diameter of less than 200 nm, zeta potential in the range of -24.43 to -35.70 mV, and relatively integrated structure with fairly uniform size on TEM. The in vitro MTT assay on MCF-7 breast cancer cell lines and MDA MB 231 breast adenocarcinoma cell lines was carried out. MTT assay on MCF-7 breast cancer cell lines indicated that plant extract-loaded phytosomes exhibited enhanced cytotoxic effects at IC50 values. of 55, 50, 45, 52, 42, 44, and 20 µg/mL compared to the extracts of C. longa, M. chamomilla, W. somnifera, and their combined extracts (80, 82, 74, 60, 70, 60, and 35 µg/mL respectively). Moreover, intracellular reactive oxygen species production was found to be higher for phytosomes treated cells at respective IC50 concentrations when compared to extracts. Overall, the developed polyherbal phytosomes were found to be effective and afford synergistic effects for breast cancer therapy.

A Randomised Study To Compare Palonosetron With Ondansetron for Prophylaxis of Postoperative Nausea and Vomiting (PONV) Following Laparoscopic Gynecological Surgeries.

Background Incidence of postoperative nausea and vomiting (PONV) in susceptible patients can be unacceptably high (70-80% reported incidence). This study was designed to evaluate the effect of palonosetron and ondansetron in preventing PONV in high-risk patients undergoing gynecological laparoscopic surgery. Methodology In this randomized, controlled, double-blind trial, non-smoking females aged 18-70 years, weighing 40-90 kg, and posted for elective laparoscopic gynecological surgeries were enrolled into ondansetron (Group A, n = 65) and palonosetron (Group B, n = 65) groups. Palonosetron (1 mcg/kg IV) or ondansetron (0.1 mg/kg IV) were administered just before induction. Postoperatively, the incidence of nausea, vomiting, PONV (scored on a scale of 0-3), need for rescue antiemetic, complete response, patient satisfaction, and adverse effects were evaluated up to 48 h following surgery. Normally distributed continuous variables were compared using Student's t-test. In addition, the Chi-squared test or Fisher's exact test were used to compare nominal categorical data as deemed appropriate. P-value <0.05 was observed as statistically significant. Results The overall PONV scores and postoperative nausea scores during 0-2 and 24-48 hours were comparable, but PONV scores (p = 0.023) and postoperative nausea scores (p = 0.010) during 2-24 hours were significantly lesser in Group B compared to Group A. There was no statistically significant difference in the postoperative vomiting score or retching during 0-48 hours. The amount of first-line rescue antiemetic used during 2-24 hours was significantly higher in Group A (56%) than in Group B (31%) (p = 0.012; p <0.05). A complete response to the drug during 2-24 hours was significantly higher (p = 0.023) in Group B (63%) compared to Group A (40%), whereas response was comparable during 0-2 and 24-48 hours. Both groups had a comparable incidence of adverse effects and patient satisfaction scores. Conclusion Palonosetron has a superior anti-nausea effect, less need for rescue antiemetics, and lesser incidence of total PONV compared to ondansetron during 2-24h and comparable effect to ondansetron during 0-2h and 24-48h postoperative period in high-risk patients undergoing gynecological laparoscopic surgery.

Considerations on Integrating Prostate-Specific Membrane Antigen Positron Emission Tomography Imaging Into Clinical Prostate Cancer Trials by National Clinical Trials Network Cooperative Groups.

PURPOSE: As prostate-specific membrane antigen (PSMA) positron emission tomography (PET) becomes increasingly available in the United States, the greater sensitivity of the technology in comparison to conventional imaging poses challenges for clinical trials. The NCI Clinical Imaging Steering Committee (CISC) PSMA PET Working Group was convened to coordinate the identification of these challenges in various clinical scenarios and to develop consensus recommendations on how best to integrate PSMA PET into ongoing and upcoming National Clinical Trials Network (NCTN) trials. METHODS: NCI CISC and NCI Genitourinary Steering Committee members and leadership nominated clinicians, biostatisticians, patient advocates, and other imaging experts for inclusion in the PSMA PET Working Group. From April to July 2021, the working group met independently and in conjunction with the CISC to frame challenges, including stage migration, response assessment, trial logistics, and statistical challenges, and to discuss proposed solutions. An anonymous, open-ended survey was distributed to members to collect feedback on challenges faced. Representatives from each NCTN group were invited to present an overview of affected trials. From these discussions, the consensus document was developed and circulated for the inclusion of multiple rounds of feedback from both the Working Group and CISC. RESULTS: The current consensus document outlines the key challenges for clinical prostate cancer trials resulting from the increasing availability of PSMA PET. We discuss implications for patient selection and definition of end points and provide guidance and potential solutions for different clinical scenarios, particularly with regard to best practices in defining eligibility criteria and outcome measures. RECOMMENDATIONS: This article provides guidance regarding clinical trial design and conduct, and the interpretation of trial results.

A Comparative Study of Palonosetron with Ondansetron for Prophylaxis of Postoperative Nausea and Vomiting (PONV) Following Laparoscopic Gynaecological Surgeries.

Background: Incidence of postoperative nausea and vomiting (PONV) in susceptible patients can be unacceptably high (70-80% reported incidence). This study was designed to evaluate the effect of palonosetron and ondansetron in preventing PONV in high-risk patients undergoing gynaecological laparoscopic surgery. Methodology: In this randomised, controlled, double-blind trial, nonsmoking females 18-70 years and weighing 40-90 kg, scheduled for elective laparoscopic gynaecological surgeries, were enrolled into the ondansetron (Group A, n=65) or palonosetron (Group B, n=65) group. Palonosetron (1 mcg/kg 4) or ondansetron (0.1 mg/kg 4) were administered just before induction. Postoperatively, incidence of nausea, vomiting, PONV (scored on a scale of 0-3), need for rescue antiemetic, complete response, patient satisfaction, and adverse effects were evaluated for up to 48 h following surgery. Results: The overall PONV scores and postoperative nausea score during 0-2 h and 24-48 h were comparable, but PONV scores (P=0.023) and postoperative nausea scores (P=0.010) during 2-24 h were significantly lesser in Group B compared to Group A. There was no statistically significant difference in the postoperative vomiting score or retching during 0-48 h. The amount of first-line rescue antiemetic used during 2-24 h was significantly higher in Group A (56%) than in Group B (31%) (P=0.012; P<0.05). Complete response to the drug during 2-24 h was significantly higher (P=0.023) in Group B (63%) compared to Group A (40%), whereas response was comparable during 0-2 h and 24-48 h. Both groups had comparable incidences of adverse effects and patient satisfaction scores. Conclusion: Palonosetron has superior antinausea effect, less need of rescue antiemetics, and lesser incidence of total PONV in comparison to ondansetron during 2-24 h and comparable effect to ondansetron during the 0-2 h and 24-48 h postoperative periods in high-risk patients undergoing gynaecological laparoscopic surgery.

Quorum quenching Bacillus spp.: an alternative biocontrol agent for Vibrio harveyi infection in aquaculture.

Quorum sensing (QS) is a type of cell to cell communication in bacteria that can also regulate the virulence potential in pathogenic strains. Hence, QS disruption, i.e. the quorum quenching (QQ) mechanism, is presently being explored as a novel bio-control strategy to counter bacterial infections. In the present study, we characterized the QQ ability of Bacillus spp. strains to reduce the expression of some virulence factors of a shrimp pathogen, Vibrio harveyi. We screened a total of 118 spore-forming bacterial isolates from aquaculture ponds and mangrove soil for their ability to degrade the synthetic N-acyl-homoserine lactones (AHLs) C4-HSL, C6-HSL, C8-HSL, and C10-HSL. We then selected the top 17 isolates with high AHL-degradation ability for further study. Among them, B. subtilis MFB10, B. lentus MFB2, and B. firmus MFB7 had the highest ability for degradation. These 3 isolates suppressed the expression of virulence genes encoding protease, lipase, phospholipase, caseinase, chitinase, and gelatinase, and potentially inhibited the biofilm formation of V. harveyi MFB32. The reduction in expression of virulence genes like those coding for metalloprotease, serine protease, and haemolysin were confirmed by real-time PCR analysis. Moreover, in an in vivo challenge experiment, these Bacillus spp. protected Penaeus monodon post-larvae against V. harveyi MFB3 infection. Our results demonstrate the potential application of AHL-degrading Bacillus spp. as an alternative to antibiotics in shrimp hatcheries to control luminescent vibriosis. This novel bio-therapeutic method is a promising approach towards disease control in shrimp aquaculture.

Characterization of V. cholerae O1 biotype El Tor serotype Ogawa possessing the ctxB gene of the classical biotype isolated from well water associated with the cholera outbreak in Kerala, South India.

We investigated 22 water samples (17 well water and five pipe water - both chlorinated) and six soil samples from the surroundings of wells of the households of suspected patients from Palakkad district, Kerala (India), from where a cholera outbreak was reported during June-July 2016. A total of 25 Vibrio cholerae isolates were collected from three well water samples during a recent cholera outbreak. Biochemical and serological studies revealed that all of the isolates belonged to serogroup O1, biotype El Tor, serotype Ogawa. PCR assays confirmed the occurrence of ctxB, ctxA, hlyA, tcpA El Tor,VPI, ace, zot, ompW, rfbO1 and toxR genes in all isolates. The presence of the ctxB gene of the classical biotype in all of the El Tor isolates suggests that it is a new variant of El Tor biotype. Antibiogram profile of all V. cholerae O1 isolates revealed resistance towards five classes of antibiotics island and indicates that they were multidrug resistant. ERIC-PCR and PFGE finger prints showed the clonal relationship among the V. cholerae O1 isolates. The results of this study revealed the emergence of a new variant of El Tor biotype in the water samples from Palakkad district, from where a cholera outbreak was reported.

Vibrio harveyi virulence gene expression in vitro and in vivo during infection in black tiger shrimp Penaeus monodon.

Luminescent Vibrio harveyi is common in sea and estuarine waters. It produces several virulence factors and negatively affects larval penaeid shrimp in hatcheries, resulting in severe economic losses to shrimp aquaculture. Although V. harveyi is an important pathogen of shrimp, its pathogenicity mechanisms have yet to be completely elucidated. In the present study, isolates of V. harveyi were isolated and characterized from diseased Penaeus monodon postlarvae from hatcheries in Kerala, India, from September to December 2016. All 23 tested isolates were positive for lipase, phospholipase, caseinase, gelatinase and chitinase activity, and 3 of the isolates (MFB32, MFB71 and MFB68) showed potential for significant biofilm formation. Based on the presence of virulence genes, the isolates of V. harveyi were grouped into 6 genotypes, predominated by vhpA+ flaB+ ser+ vhh1- luxR+ vopD- vcrD+ vscN-. One isolate from each genotype was randomly selected for in vivo virulence experiments, and the LD50 ranged from 1.7 ± 0.5 × 103 to 4.1 ± 0.1 × 105 CFU ml-1. The expression of genes during the infection in postlarvae was high in 2 of the isolates (MFB12 and MFB32), consistent with the result of the challenge test. However, in MFB19, even though all genes tested were present, their expression level was very low and likely contributed to its lack of virulence. Because of the significant variation in gene expression, the presence of virulence genes alone cannot be used as a marker for pathogenicity of V. harveyi.

Strain variability and pathogenic potential of tdhcarrying Vibrio parahaemolyticus isolated from diseased Penaeus monodon.

A disease outbreak in 42-d-old black tiger shrimp Penaeus monodon juveniles from a commercial aquaculture farm in Kerala, India, was investigated. The cause of the disease outbreak was confirmed as Vibrio parahaemolyticus by biochemical tests, PCR targeting the toxR gene and pathogenicity testing of the isolates. All of the isolates tested negative by PCR specific for V. parahaemolyticus associated with acute hepatopancreatic necrosis disease (AHPND), implicating vibriosis unrelated to AHPND as the cause of mortality. Among the 19 isolates obtained, 2 possessed the tdh gene (coding for thermo-stable hemolysin), whereas none of the isolates possessed trh. The LD50 value of 8 isolates of V. parahaemolyticus from diseased and apparently healthy shrimp ranged from 2.7 × 104 to 4.9 × 105 CFU ml-1 by immersion challenge of P. monodon postlarvae. BOX-PCR and dendrogram analysis of the bacterial isolates revealed that the isolates from moribund and apparently healthy shrimp formed separate clusters, indicating that these isolates originate from separate clones. The isolates from moribund shrimp including tdh-positive V. parahaemolyticus clustered together. The present study represents the first report of tdh-positive V. parahaemolyticus causing disease in a shrimp farm.

Prevalence, molecular characterization, genetic heterogeneity and antimicrobial resistance of Listeria monocytogenes associated with fish and fishery environment in Kerala, India.

The prevalence of Listeria monocytogenes in the retail fish markets of the Kerala, India was investigated by screening 227 samples comprising of marine finfish (n = 97) shellfish (n = 19), ready-to-cook fish products (n = 47), ready-to-eat fish products (n = 10), dried fish (n = 11) and retail ice (n = 43). The prevalence of L. monocytogenes and L. innocua was 2·7% and 17·2% respectively. Sample category wise, prevalence of L. monocytogenes was higher in marine finfish (1·8%) and retail ice (0·9%). All the L. monocytogenes isolates carried virulent genes namely inlA, inlC, inlJ, hlyA, iap, plcA, prfA genes and majority (82%) belonged to 1/2a, 3a serogroups. L. monocytogenes isolates were multidrug-resistant and showed resistance to ampicillin, penicillin, erythromycin, tetracycline and clindamycin. Enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR) delineated 58% genetic heterogeneity among the L. monocytogenes strains. The study reports that genetic similarities of the isolates were interlinked to their serogroup and sample origin. SIGNIFICANCE AND IMPACT OF THE STUDY: Prevalence of Listeria monocytogenes, in the retail fish markets of Kerala, India was low but their relatively higher presence in marine finfish and retail ice and virulent nature of the isolates signifies food safety concerns. Moreover, multidrug-resistant nature of these isolates may potentially lead to spread of antimicrobial resistance. This study identified retail ice as a vehicle for entry of L. monocytogenes in retail fish and hence, there is a need to ensure quality of retail ice used for maintaining the cold-chain.

Correction to: a Phase 2 Study of 16α-[18F]-Fluoro-17ß-Estradiol Positron Emission Tomography (FES-PET) as a Marker of Hormone Sensitivity in Metastatic Breast Cancer (MBC).

Two data points from Table 1. (continued) were published in error. The corrected data in Table 1. (continued) are shown, in italic, below.