Abstract 6689: Whole genome cell-free tumor DNA mutational signatures from blood for early detection of recurrence of low stage lung adenocarcinoma

Introduction: Lung cancer remains the leading cause of cancer-related deaths. Surgery is the best option for early lung cancer, and the role of adjuvant therapy remains controversial. Liquid biopsy offers a noninvasive approach to monitor cancer burden. Targeted sequencing of circulating cell free tumor DNA (ctDNA) in blood has shown success for diagnosis; however, low tumor burden and dynamic evolution of low stage disease is challenging for targeted panels. Thus, we hypothesized that a whole genome sequencing (WGS)-derived patient specific mutational signature from a matched tumor-normal WGS can provide sensitive and specific approach to detect mutations and copy numbers in ctDNA for monitoring of lung adenocarcinoma patients.

Methods: We successfully profiled 50 Stage 1 or 2 lung adenocarcinomas. ctDNA was extracted from 1-2 mL of plasma, tumor DNA was extracted from pathology tissue and normal germline DNA from the white blood cells. WGS using was performed on matched tumor and normal DNA, and ctDNA extracted from plasma. WGS coverage was 40x for matched tumor-normal and 20x for ctDNA. We derived a personalized mutational pattern for each tumor and used an AI-based error suppression model for quantification and ultra-sensitive detection of ctDNA in plasma samples. A patient-specific personalized genome-wide compendium of somatic mutations and copy numbers was established and ctDNA tested at 3 to 18 available time points during the therapy or follow up. A personalized mutational signature for detection ctDNA from WGS was quantified and the ctDNA Tumor Fraction (TF) was compared to the clinical status and time to recurrence.

Results: Tumor specific signatures were derived from matched tumor-normal samples with >5% tumor purity and <30% duplications rate. Out of all patients, 33 patients showed no recurrence and 12 recurred. Tumor-specific signatures detected the presence of the tumor signature in plasma with TF as low as 10−5. Based on positive minimal residual disease in plasma, the recurrence prediction sensitivity was 0.75 and specificity 0.82, with positive predictive value of 0.6 and negative predictive value 0.9. WGS ctDNA predicted recurrence with a median lead time of 508 days before clinical/imaging recurrence. In one case we were able to identify the second primary by deconvoluting known and novel ctDNA mutations. ctDNA mutational profiles enabled identification of smoking mutational signature matching clinical history, and APOBEC and ageing signatures as well as tumor mutational burden.

Conclusions: Patient-specific WGS tumor signature from plasma derived ctDNA enables specific and ultrasensitive tracking of minimal residual disease in low stage lung adenocarcinoma patients. Molecularly positive status can be used to predict recurrence and identify patients with clinical low stage disease that may benefit from adjuvant therapy.

Citation Format: Ivy Tran, Alejandro Vargas, Reid Wilkins, Isabella Pizzillo, Kenneth Tokoro, Danielle Afterman, Tomer Lauterman, Maja Kuzman, Santiago Gonzalez, Dunja Glavas, James Smadbeck, Dillon Maloney, Jurica Levatic, Samuel Phillips, Sunil Deochand, Michael Yahalom, Ryan Ptashkin, Iman Tavassoly, Zohar Donenhirsh, Eric White, Ravi Kandasamy, Ury Alon, Paz Polak, Boris Oklander, Asaf Zviran, Matija Snuderl, Harvey I. Pass. Whole genome cell-free tumor DNA mutational signatures from blood for early detection of recurrence of low stage lung adenocarcinoma. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6689.

Outcomes of traumatic brain injury in the patient of 60 years and above: a single centre retrospective study

INTRODUCTION

The elderly is at risk for traumatic brain injury (TBI), but local data on their morbidity and mortality outcomes was lacking. This study aims to assess the outcome in mortality and functional outcome, Glasgow Outcome Scale (GOS) and factors associated with poor outcomes in patients with TBI more than 60 years old.

MATERIALS AND METHODS

This single centre retrospective cohort study was carried out involving patients age 60 years old and above with TBI between June 2018 to May 2021. The mortality and GOS at hospital discharge, 30th day, and 90th day of trauma were analysed. The simple logistic regression (SLR) and multiple logistic regression (MLR) were performed to determine factors associated with poor outcomes and mortality.

RESULTS

A total of 248 patients were analysed. The mean age was 67.5 ± 6.31 years. 156 (62.9%), 26 (10.5%), and 66 (26.6%) had mild, moderate, and severe TBI, respectively. The overall mortality rate was 9.7% and the median(IQR) GOS score were 4(2); p<0.001 at hospital discharge, 30th day and 90th day. There was significant difference in GOS outcomes after 90 days χ2(2) = 136.76 p<0.001. Upon MLR, there was a significant association of polytrauma, Adj. OR 11.04 (2.503-48.711); p < 0.002 and TBI severity: moderate TBI, Adj. OR 71.44(13.028-391.782); p < 0.001 and severe TBI, Adj OR 2533.51 (213.050-30127.644); p<0.001 towards poor outcome. However, only severity of TBI: moderate TBI, Adj. OR 19.48 (1.899-199.094); p=0.012 and severe TBI, Adj OR 26.42 (2.864-243.722); p=0.004 is associated with mortality.

CONCLUSION

Polytrauma and moderate-severe head injury are associated with poor outcomes and moderate-severe head injury is associated with high mortality.

Abstract 3401: Whole genome cell-free tumor DNA mutational signatures for noninvasive monitoring of pediatric brain cancers

Introduction: Liquid biopsy offers a noninvasive approach to monitor cancer burden during therapy and surveillance period. However, in pediatric brain cancers, liquid biopsy methods from the blood have been unsuccessful due to a low tumor burden and low number of mutations in coding regions. We hypothesized that a whole genome sequencing (WGS)-derived patient specific mutational signature from a matched tumor-normal WGS can provide a sensitive and specific approach to detect mutations in circulating cell free tumor DNA (ctDNA) and provide blood-based monitoring in pediatric patients with brain tumor.

Methods: All tumors were analyzed and molecularly subclassified using whole genome DNA methylation profiling and machine learning classifier. Tumor DNA was extracted from pathology tissue and normal germline DNA from the white blood cells, while ctDNA was extracted from 1-2 mL of post-surgery or follow-up plasma samples, WGS was applied to sequence DNA from matched tumor-normal and plasma samples. WGS coverage was 40x for matched tumor-normal DNA and 20x for ctDNA. Using the C2i assay, we derived a personalized mutational pattern for each tumor and used an AI-based error suppression model for quantification and ultra-sensitive detection of ctDNA in plasma samples. A patient-specific personalized genome-wide compendium of somatic mutations was established and ctDNA tested at 1 to 3 available time points during the therapy or surveillance period. An AI-based error suppression model was implemented to filter out the noise in the cell free DNA (cfDNA) while the personalized mutational signature was used to detect the ctDNA in the cfDNA and to amplify the somatic signal contained in it. The ctDNA Tumor Fraction (TF) was compared to the clinical status and MR-based imaging.

Results: We profiled 7 pediatric brain tumors, including 2 medulloblastomas (one Group 3, one Group 4), 3 pediatric glioblastomas IDH wild-type, 1 ependymoma PFA subtype and one low grade ganglioglioma. Tumor specific signatures were identified and detected in the plasma of 5 patients with clinical disease with a TF range 0.02-0.0005 but not in 2 patients with no tumor at the time of blood collection. In two children with a medulloblastoma and glioblastoma, the decrease of tumor fraction in ctDNA over 2 (TF: 0.002 to 0.0009) and 3 time points (TF: 0.0005 to undetectable), respectively, correlated with response to therapy based on imaging.

Conclusions: Patient-specific WGS tumor signature in ctDNA from blood can be used for sensitive monitoring of children with brain tumors.

Citation Format: Ivy Tran, Kristyn Galbraith, Guisheng Zhao, Robyn Borsuk, Joyce Varkey, Sharon Gardner, Jeffrey Allen, David Harter, Jeffrey Wisoff, Eveline T. Hidalgo, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, G. Praveen Raju, Theodore Nicolaides, Asaf Zviran, Matija Snuderl. Whole genome cell-free tumor DNA mutational signatures for noninvasive monitoring of pediatric brain cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3401.

Abstract 1959: Sensitive detection of circulating tumor DNA by whole genome sequencing: Validation of MRDetect using serial blood samples from stage III colorectal cancer patients

Background: While detection of circulating tumor DNA (ctDNA) is associated with poor cancer prognosis, the clinical utility for guiding treatment decisions is unresolved. Patients with minimal residual disease (MRD) often have less than one genome equivalent of ctDNA per 10 mL blood. Consequently, it is stochastic whether a 10 mL sample contains ctDNA from a particular genomic locus. Consequently, the sensitivity of ctDNA detection methods targeting a limited number of tumor loci is heavily affected by sampling bias. To overcome this challenge, we developed MRDetect; a whole genome sequencing (WGS) approach, which detects ctDNA using the patient-specific cumulative signal from tens of thousands of mutations throughout the genome. Recently, we showed how MRDetect found ctDNA fractions down to 10-4. Here, we performed a validation study to confirm the prognostic impact of MRDetect.

Aim: Validation of MRDetect for sensitive ctDNA detection to monitor residual disease in stage III colorectal cancer (CRC) patients treated with curative intent.

Methods: From a large, uniform cohort of stage III CRC patients n = 146), we had plasma samples collected every third month (n = 938, median = 9 per patient) and a median follow-up of 34 months. For each patient, a genome-wide mutational signature was established by WGS of tumor and matched normal DNA. Enhanced by an AI-based error suppression model, this signature was used to detect ctDNA in 1-2 mL plasma samples using WGS (20x coverage). We used de-novo point mutation and copy number variation analysis to investigate cancer evolution after treatment. To evaluate the reproducibility of MRDetect, aliquot samples (n = 2x190 samples) from 5 recurrence and 10 non-recurrence patients were processed and sequenced at two independent laboratories. Outcome measures: ctDNA status, tumor fraction, false positive rate, Time To ctDNA Recurrence (TTcR), and Time To radiological Recurrence (TTrR).

Results: Analysis of paired samples showed great reproducibility with high agreement between both ctDNA status calls (Cohens Kappa = 0.81) and the estimated tumor fractions (r2 = 0.99). MRDetect revealed post-operative ctDNA in all recurrence patients (5/5) with detected tumor fractions down to 2 x 10-4. Median TTcR was 0.9 month (range 0.5 - 7.3 months) while median TTrR was 12.8 months (range 11.3 - 31.1 months). The false positive rate was 1% (1/100), assessed in longitudinal samples from the 10 non-relapsing patients. Tumor evolution dynamics in plasma samples revealed novel amplification and deletions, which were absent in the primary tissue but confirmed in metachronous metastases. We will present results from the full cohort at AACR 2022.

Conclusion: MRDetect detects ctDNA with high sensitivity and specificity and enables effective postoperative assessment of MRD, cancer evolution dynamics and early relapse detection.

Citation Format: Amanda Frydendahl, Thomas Reinert, Jesper Nors, Sunil Deochand, Dillon Maloney, Noah Friedman, Tomer Lauterman, Danielle Afterman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Ravi Kandasamy, Iman Tavassoly, Jonathan Rosenfeld, Anders Husted Andersen, Uffe S. Løve, Per V. Andersen, Ole Thorlacius-Ussing, Lene Hjerrild Iversen, Kåre Andersson Gotschalck, Boris Oklander, Asaf Zviran, Claus Lindbjerg Andersen. Sensitive detection of circulating tumor DNA by whole genome sequencing: Validation of MRDetect using serial blood samples from stage III colorectal cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1959.

Abstract 540: Genome-wide circulating tumor DNA for monitoring treatment response and metastatic relapse in bladder cancer

Background: Neoadjuvant chemotherapy (NAC) followed by radical cystectomy (CX), is gold standard treatment in localized muscle-invasive bladder cancer (MIBC). About 45% of patients with MIBC develop metastatic relapse within 2 years after CX. The response rate to chemotherapy and immune checkpoint inhibitors (ICI) is relatively low, and biomarker tests for monitoring response are needed. Furthermore, biomarkers for early detection of minimal residual disease (MRD) after CX is needed to enable earlier treatment initiation. Tumor-informed detection of mutations in cell-free DNA (cfDNA) from peripheral blood has shown promising results in its ability to monitor MRD. However, the low tumor fraction after surgery and limited input material obtained from a typical plasma sample limits the probability of detecting low metastatic burden scenarios. Here we implemented and applied locally a whole-genome sequencing (WGS) approach to circulating tumor DNA (ctDNA) monitoring for improving ctDNA detection.

Methods: A total of 140 MIBC patients undergoing NAC and CX were enrolled, including a test cohort (n=19) and a validation cohort (n=120). cfDNA was extracted from ~1mL plasma (n=1100) and procured from longitudinal plasma sampling during NAC (response measure), pre-cystectomy (response measure), post-surgery (relapse monitoring) and during immunotherapy (ICI treatment). WGS was applied to tumor/germline pairs (coverage &gt;30x/20x) and plasma cfDNA (&gt;20x) facilitating detection of genome wide genomic alterations and quantification of ctDNA using the MRDetect method.

Results: We developed a personalized tumor-informed WGS model by integrating genome-wide mutation and copy number variation data coupled with advanced signal processing and AI-based error suppression. Patient-specific somatic variant patterns were then used for detecting and measuring the ctDNA levels in low-input blood samples by WGS. The assay sensitivity allowed for detection of tumor fractions down to 8*10-5. Furthermore, in our test cohort of 19 patients, we detected ctDNA after CX in 7 of 8 patients with clinical relapse (88% sensitivity) and detected no ctDNA in 11 of 11 patients with no clinical relapse (100% specificity). We observed a positive lead-time for MRD-based recurrence detection compared to CT-based reccurence detection (9 months on average). The full dataset is currently being processed and will be presented at the AACR 2022 meeting.

Conclusions: For precision oncology, we need to develop quantitative and non-invasive methodologies to help tailor the treatments to individual patients and monitor them for further clinical decision-making. The results indicate the clinical potential of personalized genome-wide mutation integration as an ultra-sensitive, non-invasive method for MRD detection and treatment response monitoring which could aid in clinical management of patients with bladder cancer.

Citation Format: Iver Nordentoft, Karin Birkenkamp-Demtröder, Emil Christensen, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Sia Viborg, Mads Agerbæk, Jørgen Bjerggaard Jensen, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, Asaf Zviran, Lars Dyrskjøt. Genome-wide circulating tumor DNA for monitoring treatment response and metastatic relapse in bladder cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 540.

Abstract 5114: Ultra-sensitive detection of minimal residual disease (MRD) through whole genome sequencing (WGS) using an AI-based error suppression model in resected early-stage non-small cell lung cancer (NSCLC)

Background: Early detection of recurrence and monitoring of MRD post-surgery is critical for clinical decision-making to tailor adjuvant therapy. In early-stage NSCLC, circulating tumor DNA (ctDNA) detection is especially challenging, requiring highly sensitive and specific assays. Therefore, we used a WGS approach (MRDetect) for ultra-sensitive ctDNA detection in NSCLC patients (pts) undergoing curative surgery.

Methods: We conducted a pilot study to evaluate the MRDetect approach in serial plasma samples (including pre-surgery, post-surgery and follow-up [f/u] timepoints) from resected stage IB-IIIA NSCLC pts. Pts underwent routine surveillance by computed tomography scans. ctDNA was extracted from ~1mL plasma. MRDetect uses WGS by a tumor-informed approach (sequencing coverage 40x for tumor, 20x for plasma DNA) combined with AI-based error suppression models (trained and calibrated with a non-cancer cohort, n=17) to increase the signal to noise ratio for precise ctDNA detection, and improve the accuracy of readouts especially for low tumor burden scenarios. The assay reports the detection and quantification of ctDNA burden in blood with a prognostic value for risk of recurrence. The ability of the assay to predict recurrence from a single sample, taken at the clinical landmark point (median 1.6 mths post-surgery, range 0.1-6.5) was evaluated.

Results: Overall, 52 NSCLC pts were enrolled (n=88 plasma samples) with median clinical f/u of 32.6 mths (range 3.1-98.6). There were 43 pts with post-surgery landmark samples, with median age 62 years, 70% were male, 79% were adenocarcinoma and 49% were EGFR mutated. 26% were stage IB and 37% each were stage II and III. There were 15/18 (sensitivity 83%) pts with confirmed radiological recurrence in which MRDetect was positive, including 6/7 (86%) EGFR mutated pts. The median RFS in MRDetect positive pts was 15.2 mths (range 3.7-33.4). Among 25 pts with no recurrence (median f/u 25.6 mths), MRDetect reported 4 pts to be MRD positive (specificity 84%). These results were consistent between EGFR mutated (sensitivity 86%, specificity 86%) and wildtype pts (sensitivity 82%, specificity 82%). For longitudinal samples (n=17 pts), negative ctDNA was associated with absence of recurrence in 14/15 pts (specificity 93%). At the AACR meeting, results from a planned larger validation study will be presented.

Conclusion: Using a robust WGS implemented AI-based computational platform (MRDetect), we demonstrate high sensitivity and specificity detection of MRD in both EGFR mutated and wildtype NSCLC. With an increasing number of therapeutic options in the adjuvant setting for NSCLC, an ultra-sensitive MRD assay has the potential to facilitate personalized clinical decision-making for tailoring both the need and choice of adjuvant therapies.

Citation Format: Aaron C. Tan, Stephanie P. Saw, Gillianne G. Lai, Kevin L. Chua, Angela Takano, Boon-Hean Ong, Tina P. Koh, Amit Jain, Wan Ling Tan, Quan Sing Ng, Ravindran Kanesvaran, Tanujaa Rajasekaran, Sunil Deochand, Dillon Maloney, Danielle Afterman, Tomer Lauterman, Noah Friedman, Imane Bourzgui, Nidhi Ramaraj, Zohar Donenhirsh, Ronel Veksler, Jonathan Rosenfeld, Ravi Kandasamy, Iman Tavassoly, Boris Oklander, Asaf Zviran, Wan-Teck Lim, Eng-Huat Tan, Anders J. Skanderup, Mei-Kim Ang, Daniel S. Tan. Ultra-sensitive detection of minimal residual disease (MRD) through whole genome sequencing (WGS) using an AI-based error suppression model in resected early-stage non-small cell lung cancer (NSCLC) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5114.

Lab validation of an ultrasensitive ctDNA pan-cancer MRD assay using whole-genome sequencing

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Background: Minimal residual disease (MRD) monitoring using liquid biopsy for solid tumors requires a highly sensitive and specific assay that can overcome the limitation of low abundance cfDNA in a standard blood draw. We developed a whole-genome sequencing (WGS)-based assay to detect the presence of circulating tumor DNA (ctDNA) in plasma. The C2i assay is a tumor-informed assay that uses personalized tumor signature, advanced noise models, and artificial intelligence (AI) modalities to interrogate plasma for the presence of ctDNA longitudinally. Methods: The C2i test was developed in accordance with CAP/CLIA and New York state validation principles. We used contrived samples to establish analytical validation of the assay performance, which was then validated with a large clinical cohort of early-stage patients across various cancer types. Briefly, aggregated tumor signatures derived from cancer cell lines were fragmented and spiked into a contrived healthy plasma pool; the mixed samples were used to assess the presence of tumor DNA signature down to tumor fractions of 10e-4. Positive samples are identified by tumor-derived variants detected above the noise levels. Noise modeling was established using a panel of normal (PON) approach. We assessed the analytical sensitivity, specificity, and accuracy using 348 contrived samples derived from five different cancer cell lines. Reproducibility and precision were assessed with multiple replicates, and statistical concordance was reported. This validation was complemented by a cohort of 200 patients and ̃1000 plasma samples across a variety of cancer types including, NSCLC, MIBC, CRC, GBM, Breast Cancer, and a mixture of other cancer types. Results: Cancer cell lines, representing the five most prevalent disease indications, used for determining analytical sensitivity are as follows: CRC HT-29, Breast SK-BR3, Bladder HT-1376, Lung HCI-H526, and Prostate LNCaP. The cell line DNA was enzymatically fragmented and size-selected to mimic ctDNA. This ctDNA was spiked into cfDNA extracted from healthy volunteers at various dilution levels, varying from 10e0 to 10e-4. The 95% probability of detecting ctDNA was established at 10e-4. The reproducibility of tumor signature between replicates was assessed to be greater than 90%. The assay was performed using both normal and maximum input amounts. These performance estimates were then validated on a cohort of plasma collected from early-stage (stage I-III) patients across various cancer types. Conclusions: C2i MRD test is an ultrasensitive pan-cancer MRD monitoring assay used in several clinical trials across the world. We present an extensive analytical and clinical validation of the assay supporting its high performance.

Biomodeling for Controlling the Spread of Coronavirus 2019

Wuhan has informed an outbreak of a typical lungs infection created by the 2019 novel coronavirus (2019-nCoV) in December 2019. Infections have been consigned to other cities, along with internationally which aggressing to trigger a global epidemic. In the past four years, coronavirus infections have become the most dangerous infections since of the event of some fresh deaths caused by corona infections in Saudi Arabia. Coronavirus infections may be planted in and spread out of Saudi Arabia by inbound and outbound Umrah visitors and non-Umrah visitors. The impact of fundamental reproductive number and zoonotic strength of infectivity on susceptible, exposed and infected peoples rate was assessed using Runge–Kutta–Felhberg strategy with shooting method. In this investigation, the vulnerable people's rate is significantly climbing in the brief interval of period owing to overwhelming and mean inactive period. Our examination shows the transmissibility of coronavirus is more grounded as contrasted and the Asia continent countries respiratory confusion. Middle East Respiratory Syndrome coronavirus is already spread in creature and human pools in Ethiopia. The Severe Acute Respiratory Syndrome coronavirus-2 growth in the Saudi Arabia may have a solemn crash on genetic assortment, interspecies circulation of these infections mostly with the reference to the alteration and recombination expectation of coronaviruses. Researches of the molecular mechanisms and genetics of this infection are provided in the component can act an important part of this project to follow tactics to prevent subsequent coronavirus outbreak.

Mathematical Modeling: Zoonotic Strength of Infectivity on COVID-19

Coronavirus 2019 (COVID-19) is an emerging contagious disease that has led to the global epidemic and is caused by severe acute respiratory syndrome, Coronavirus-2 (SARS-CoV-2). Zoonotic is an infection that is transmitted from animals to humans. Significantly changing animal infection is the best amplifying mask of pathogens. The power of animal infection is a contagious virus that usually spreads from vertebrate animals to humans and vice versa. The physical health of an animal depends on the normal vulnerability of its population and the change in actual animal health against infection over time, and is assessed based on previous circumstances in the population. After compiling the effect of virulence of the animal infection on the size of the susceptible, exposed and infected subjects, an investigation was made using MAPLE 18 with RK Fehlberg technique. This study discusses the stimulation of animal influences on the novel coronavirus infection that is reliable to be infectious. It analyzes all incoming and outgoing air passengers worldwide and in the country is keen on spreading the abnormally degenerate coronavirus. The zoonotic strength was applied to coronavirus infection and the rates of SEIR individuals terminated by secondary coronavirus infection were estimated. The transmission ability of coronavirus infection is associated with a lack of the perceived respiratory system in conservative people and global warming.

#3105 How does self-report of mood symptoms compare with observer assessments after acquired brain injury

Objectives

Post acquired brain injury (ABI) depression has been implicated in different patient outcomes such as prospective cognition, cognitive impairment, rehabilitation outcome, and quality of life. However, there have been no studies identified in the literature, investigating post ABI insight into depression across varied cognitive abilities. Here we looked at ABI patient insight into their depression across a range of cognitive abilities and compared this to an observed or an objective measure of depression.

Methods

A retrospective cohort of 24 individuals with ABI (depressed and non-depressed) seen in a neuropsychiatry outpatient clinic between 2019 and 2020 completed a Patient Health Questionnaire-9 (PHQ-9), self-reported depression scale and had a Neuropsychiatry Inventory Questionnaire(NPI-Q), an observer assessment with a depression domain. The patients also underwent a formal cognitive examination using the Montreal Cognitive Assessment (MoCA).

Results

Non-depressed ABI and depressed ABI individuals with a wide range of cognitive abilities demonstrated good insight into their depression when matched to the observer rating. Chi-Square Test showed little variation between the PHQ-9 and NPI-Q Depression data sets; Wilcoxon Signed Ranks Test: Z Test -4.08, p<0.001, Effect Size 0.87 and Spearman’s rho showed positive correlation between the two data sets (Correlation Coefficient 0.527, P<0.008). Therefore, there was a statistically significant agreement between the subjective measure (PHQ-9) and the observed (objective) measure NPIQD and that there was a positive correlation between the two measurement scales for patients with ABI regardless of cognition (as measured by MoCAz score; range -6 to 2.21, mean: -1.17)

Conclusions

These findings indicate (1) self-reported measures of depression in ABI are consistent with observed (objective measures) thus can be used to assess depression in this cohort and (2) ABI patients with a wide range of cognitive abilities would appear to have good insight into their depression.

Genome-wide circulating tumor DNA monitoring for bladder cancer treatment management and organ preservation

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Background: Bladder cancer (BC) is the 9th most commonly diagnosed cancer worldwide and each year responsible for 165,000 deaths. Neoadjuvant combination chemotherapy, followed by radical cystectomy, is used for the management of localized muscle-invasive bladder cancer. One of the critical challenges in this therapeutic regimen is monitoring the tumor load to assess therapeutic efficacy – this is typically performed by assessing pathological downstaging in the cystectomy specimen. A high frequency of patients presents with T0N0 at cystectomy (no indication of residual disease), and consequently, it is vital to investigate organ preservation approaches to identify those patients who may qualify for bladder preservation. For precision oncology, we need to develop quantitative and non-invasive diagnostic methodologies to help the oncologist tailor the treatments to individual patients and monitor them for further clinical decision-making. Methods: Cell-free DNA (cfDNA) mutation detection has shown significant promise in its ability to monitor minimal residual disease and disease relapse by detection of cancer mutations in the peripheral blood. However, the combination of low tumor fraction and limited input material obtained from a typical plasma sample restricts the probability of detecting low metastatic burden in cfDNA through current deep targeted sequencing methods. Results: Here we present results from applying whole-genome sequencing (WGS) of cfDNA. We integrate a genome-wide mutation and copy number monitoring approach coupled with advanced signal processing and Artificial Intelligence (AI) for measuring the tumor load from low-input blood samples (̃1mL of plasma) with ultra-sensitive detection. The increased sensitivity allowed clinical detection of tumor fraction down to 8*10-5 and recurrence detection sensitivity achieving > 65% at the first two months post-surgery. The WGS cfDNA approach is being evaluated on a patient cohort of more than 50 bladder cancer patients with longitudinal plasma sampling during neoadjuvant chemotherapy (response measure), pre-cystectomy (complete response measure), and post-surgery (relapse monitoring). Conclusions: The results indicate the clinical potential of genome-wide mutation integration as an ultra-sensitive, non-invasive diagnostic method for bladder cancer clinical management and bladder organ preservation.

The use of magnetic resonance phase-contrast cine in Chiari malformation with syringomyelia

INTRODUCTION

Chiari malformation (CM) is a disorder of mesodermal origin and is commonly associated with syringomyelia. Foramen magnum decompression is the first-line of standard treatment in symptomatic patients with a confirmed radiographic diagnosis. Magnetic resonance (MR) cine allows accurate evaluation of cerebrospinal fluid (CSF) physiology at the craniovertebral junction but often this is under-utilised in Malaysia.

METHODS

In this series, we looked into nine cases of CM with syringomyelia from clinical and radiological perspective before and after surgery. The radiological parameters were herniated tonsillar length, syrinx: cord ratio, syrinx length and diameter. Flow velocity and morphologic changes in Chiari were illustrated.

RESULTS

Seven patients showed either reduction in syrinx length, syrinx: cord ratio or both postoperatively. Clinical recovery somewhat varied in motor and sensory symptoms. Four patients gained better functional grade in modified Rankin scale (MRS) while the rest remained similar. The study highlighted the advantage of CSF flow dynamics information over MR anatomical radiographic improvement in addressing the neurologic and functional recovery. We also discussed the practicality of cine sequence in preoperative patient selection, syrinx analysis and postoperative flow evaluation in anticipation of clinical outcome.

CONCLUSION

Phase-contrast cine MRI is a useful tool dictated by resource availability. We recommend its routine use in preoperative analysis and subsequent observational follow-up after surgery.

Abstract B61: High-dimensional analysis of tumor-resident CD4 and CD8 double-negative T-cell subset in multiple tumor types

Background: Checkpoint blockade therapies like PD-1 antibodies elicit durable long-lasting immunity in a subset of patients of certain tumor types. However, many patients across a range of tumor types are resistant to checkpoint blockade. Mechanisms that confer local response or resistance to checkpoint blockade are not well understood. Mounting evidence points to local suppression of T cell function as one of the most substantial barriers to effective antitumor immunity.

Methods: The study involved multiparametric flow cytometry and genomic characterization of a subset of T cells in the tumors and lymphoid organs of syngeneic tumors, genetically engineered mouse model of cancers and human tumors.

Results: A significant fraction (10-40%) of α/β TCR+ CD3+ T cells do not express CD4, CD8 or NKp46 in the tumors. The presence of double-negative T-cell subset (DN T cells) is restricted to tumor microenvironment and is relatively scarce in tumor draining lymph nodes and in spleen. To identify if DN T cells are antigen-specific, we performed AH-1 tetramer staining. While a substantial fraction of CD8 T cells are AH-1 tetramer positive, majority of DN T cells are AH-1 tetramer negative in CT26 tumors. Recently, it has been shown that higher frequency of CD39-negative bystander T cells correlated to lack of response to PD-1 therapy in non-small cell lung cancer patients. Mounting evidence also reveals presence of a specific subset of CD8 T cells with features of stem cell memory in tumors as defined by CXCR5 and TCF1 expression. Efforts are under way to understand if DN T cells exhibit bystander cell and/or memory stem-like phenotype. Majority of the DN T cells are proliferating (Ki67+) and express very low levels of PD-1 (in contrast to CD8 T cells) and Granzyme B. Treatment of mice bearing syngeneic tumors with PD-1 checkpoint blockade therapy does not impact the frequency of DN T-cell subset consistent with lower levels of PD-1 expression. Moreover, a substantial frequency (30-40%) of DN T cells in both syngeneic and KPC pancreatic GEMM tumors express CD103, a tissue resident marker. Furthermore, DN T cells are CD44+ CD127+ KLRG1- and may represent a memory precursor cell population. Upon ex vivo stimulation, these DN T cell subsets proliferate and express modest levels of PD-1. Preliminary analysis of single-cell RNA sequencing data from FACS sorted murine DN T cells reveals lack of CD4, CD8 expression and retention of CD2, CD44, CD69, CCR7 and CXCR5 expression. Flow cytometry analysis of human CD2+ TILs reveals presence of DN T cells in human tumors. Single-cell transcriptome analysis of CD2+ T cells isolated from human colorectal tumors revealed presence of DN T cells. Current efforts are focused on further characterization of this subset in both mouse and human tumors.

Conclusions: In this study, we describe a tumor-resident CD4 and CD8 double-negative T-cell subset that may represent a bystander cell population with features of memory precursors and potential implications in modulation of response to checkpoint blockade therapy in cancer.

Citation Format: Murali Gururajan, Ravi Kandasamy, Jessica Wong, Kalpit Shah, Shuoguo Wang, Adam Bata, Amy Truong, Sunil Kuppasani, Ching-Ping Ho, Robert Graziano, Michael Quigley, Anwar Murtaza, Jinqi Liu. High-dimensional analysis of tumor-resident CD4 and CD8 double-negative T-cell subset in multiple tumor types [abstract]. In: Proceedings of the AACR Special Conference on Tumor Immunology and Immunotherapy; 2018 Nov 27-30; Miami Beach, FL. Philadelphia (PA): AACR; Cancer Immunol Res 2020;8(4 Suppl):Abstract nr B61.

Bilateral subtentorial empyema complicated with nosocomial acinectobacter ventriculitis: a case report

Subtentorial subdural empyema is a rare and life threatening intracranial suppuration. It is usually an intracranial complication of otogenic infections. Early diagnosis and surgical drainage are the most important factors determining prognosis. The high mortality reported in the literature reflects the severity of subtentorial subdural empyema if proper management is delayed. Intracranial infections usually require between 4 to 6 weeks of intravenous antibiotics therapy. However, the prolonged duration of hospitalization as well as requirement for neurosurgically inserted indwelling devices may predispose these patients to new nosocomial infections.

Isatin down-regulates expression of atrial natriuretic peptide receptor A and inhibits airway inflammation in a mouse model of allergic asthma

Isatin, an endogenous indole compound, prevents atrial natriuretic peptide (ANP) from signaling through its cell-surface receptor, NPRA. Allergic airway inflammation has been linked to natriuretic peptide signaling and blocking this signaling axis in the lung prevents allergen-induced pathology. In this study we encapsulated isatin in chitosan nanoparticles and tested them in a mouse model of allergic asthma by intranasal delivery to the lung. Isatin nanocapsules reduced lung pathology by blocking ANP signaling, but surprisingly also by reducing the expression of NPRA. Ovalbumin-allergic mice were treated intranasally with isatin-containing chitosan nanocapsules either before or after allergen challenge, and lung function, cytokine levels, histopathology and cellular infiltration were determined. ANP activity was quantitated by measuring changes in intracellular cyclic GMP and changes in NPRA levels were determined. For comparison with isatin's effects, the expression of the receptor was inhibited with small interfering RNA against NPRA mRNA. Isatin nanocapsules administered locally to the lung reduced cGMP production and NPRA expression and protected allergic mice from airway hyperreactivity and lung inflammation when given either before or after allergen challenge. Leukocyte infiltration was reduced and lung cytokine profiles showed a repolarization from a Th2-like to a Th1-like phenotype. Isatin nanocapsules administered locally to the lung inhibit NPRA signaling but also are capable of lowering the expression of NPRA, thus effectively reducing inflammation in a mouse model of allergic asthma. Pharmacological intervention to reduce NPRA activity through the inflammatory natriuretic peptide axis in the lung may be a useful adjunct therapy for treating lung disease.

Psoas abscess: diagnosis and treatment

Psoas abscess is an uncommon presentation on the acute medical take. However recognition and appropriate treatment is essential. This review is designed to highlight the clinical features, microbiology, diagnostic tests and treatment for this condition. In order to illustrate some of the pitfalls and complexities in the management of psoas abscess we have included a case history of a patient who was recently treated in our department.

Tracheal intubation without muscle relaxant--a technique using sevoflurane vital capacity induction and alfentanil

This randomized controlled study examined intubating conditions and haemodynamic changes following sevoflurane nitrous oxide induction in four groups: three different doses of alfentanil compared with low-dose alfentanil and suxamethonium. All patients received atropine 0.3 mg i.v. before induction of anaesthesia with vital capacity breaths of sevoflurane 8% (more than 7% in the inspiratory gas) in 60% nitrous oxide and oxygen. Patients were allocated randomly to four groups of intravenous supplements: group SA20, alfentanil 20 microg x kg(-1); group SA25, alfentanil 25 microg x kg(-1); group SA30, alfentanil 30 microg x kg(-1); group SSA, alfentanil 10 microg x kg(-1) and suxamethonium 1 mg x kg(-1). Orotracheal intubation and assessment of intubating conditions was performed by one of the investigators who was blinded to the subject's group. Intubating conditions were satisfactory or excellent in 83%, 80%, 92% and 96% of patients in groups SA20, SA25, SA30 and SSA respectively. These differences were not statistically significant. The increase in heart rate associated with laryngoscopy and tracheal intubation was effectively attenuated in all groups. Mean arterial pressure decreased significantly and similarly after induction in all groups. Two minutes after intubation the mean arterial pressure was increased significantly (P<0.05) compared to the post-induction value in group SSA. The intubating conditions obtained with sevoflurane plus alfentanil 30 microg x kg(-1) were comparable to those provided by the sevoflurane, suxamethonium and alfentanil 10 microg x kg(-1) combination.

Anaesthesia for caesarean section in a patient with Eisenmenger's syndrome

Eisenmenger's syndrome was originally described in 1897 and redefined by Wood in 1958. This syndrome includes pulmonary hypertension with reversed or bi-directional shunt associated with septal defects or a patent ductus arteriosus. A 27-year-old G2 PO with Eisenmenger's syndrome presented to the hospital for management at 17 weeks of pregnancy. She was advised termination of pregnancy but she refused. An elective caesarean section was performed successfully under general anaesthesia uneventfully at 29 weeks due to severe intrauterine growth retardation (IUGR). Patient's postoperative complications like pulmonary thromboembolism, the advantages and disadvantages of anticoagulation are discussed. Pregnancy carries substantial maternal and fetal risk for patients with pulmonary hypertension and Eisenmenger's syndrome. Although pregnancy should be discouraged in women with Eisenmenger's syndrome it can be successful.

Use of sevoflurane in difficult airways

Inhalational induction is one of the recognized methods for the management of difficult airway. Halothane is the usual choice of agent for this purpose. The relatively new agent sevoflurane, which is the least irritant of all the available agents, is emerging as a choice of inhalational agent for both adult and pediatric populations. There are various reports for and against the use of sevoflurane for the management of difficult airway. We describe the use of sevoflurane for the management of difficult airway in four patients presenting with airway problems.

Conditions for laryngeal mask insertion. A comparison of propofol versus sevoflurane with or without alfentanil

One hundred unpremedicated ASA 1 or 2 patients scheduled for elective surgery were divided equally into four groups and recruited into this prospective, randomised parallel groups study. Induction was with propofol 2.5 mg.kg-1 or vital-capacity breath induction with sevoflurane (> 7% in the inspiratory gas) in 65% nitrous oxide and oxygen, or gaseous induction with sevoflurane plus alfentanil 5 micrograms.kg-1 or propofol 2.5 mg.kg-1 and alfentanil 5 micrograms.kg-1. The conditions for laryngeal mask insertion were assessed and graded on a three-point scale using six variables. The overall condition for laryngeal mask insertion was assessed as excellent, satisfactory or poor on the basis of total score in each group. Excellent or satisfactory conditions were observed in 25 (100%) patients in the sevoflurane-alfentanil group, 22 (88%) in the propofol-alfentanil group and 16 (64%) patients each in the propofol and sevoflurane groups (p < 0.001). A sevoflurane-alfentanil combination provides better conditions for laryngeal mask insertion when compared with sevoflurane alone, or a propofol-alfentanil combination.

Hybrid (COPP/ABV) therapy in childhood Hodgkin's disease: a study of 53 cases during 1989-1993 at the Cancer Institute, Madras

The optimal therapy for children with Hodgkin's disease is controversial. Between 1989 and 1993, 53 children under 14 years of age with Hodgkin's disease were treated with COPP/ABV (cyclophosphamide, vincristine, procarbazine, prednisolone/adriamycin, bleomycin, vinblastine) hybrid chemotherapy. The results were analyzed with the Kaplan-Meier product limit method for survival and the Logrank test for predicting statistical significance. Ten patients (18.87%) had early-stage disease (I to IIA) and 43 (81.13%) had advanced disease. Lymphocyte-predominant histology was seen in 20 (37.5%) patients, nodular sclerosis in 8 (15%), mixed cellularity in 21 (39.6%), and lymphocyte depletion in 4 (7.56%). The male:female ratio was 3.82:1. Complete responses were seen in 51 (96.22%) patients, with 47 (92.15%) of them in sustained first remission. The event-free survival rate is 90.3% to date. COPP/ABV hybrid chemotherapy is an effective primary therapy for all stages of Hodgkin's disease in children.

Functional characterization of three isoforms of the Na+/H+ exchanger stably expressed in Chinese hamster ovary cells. ATP dependence, osmotic sensitivity, and role in cell proliferation

Four distinct isoforms of the mammalian Na+/H+ exchanger (NHE) have been identified by molecular cloning. Three of these (NHE-1, NHE-2, and NHE-3) have been shown to be functionally active by heterologous expression. Their kinetic and pharmacological properties are well documented, yet comparatively little is known about their regulation. In this report, rat NHE-1, NHE-2, and NHE-3 were stably transfected into antiporter-deficient Chinese hamster ovary cells to study their role in cellular proliferation and their regulation by nucleotides and cell volume. Their ability to influence cell proliferation was assessed by measuring the growth of antiporter-deficient cells and of the different transfectants in media of varying pH. While antiporter-deficient cells were unable to grow at acidic pH levels, all three isoforms supported proliferation under these conditions. Therefore, while the epithelia-specific isoforms (NHE-2 and NHE-3) are thought to play primarily a role in transcellular ion transport, they can also contribute to intracellular pH (pHi) homeostasis and have a permissive role in cell growth. The activity of the three isoforms was markedly inhibited by depletion of cellular ATP. In the pHi 6.0-7.2 range, decreases in the affinity for internal H+ and/or the maximal rate of transport accounted for the inhibitory effect, depending on the isoform. The osmotic responsiveness of the three isoforms was also compared. As reported earlier, NHE-1 was stimulated by hypertonicity. Under similar conditions, NHE-2 was also stimulated to a comparable extent. Conversely, both isoforms were inhibited in hypotonic media. In contrast, NHE-3 was markedly inhibited by hypertonic cell shrinking but was unaffected by hypotonicity. Osmotic inhibition of NHE-3 was rapid, reversible, and apparent throughout the pH range studied. Osmotic inhibition of NHE-3 may play a role in the physiology and pathophysiology of epithelia.