Development Of Clinical Biomarkers Research Articles

Abstract 7177: Development and validation of clinical pharmacodynamic biomarkers to assess treatment response to HPK1 inhibition and guide dosing decisions

Abstract Checkpoint inhibitors represent promising cancer therapeutics as they have the potential to reignite T cell activity and reverse T cell exhaustion, which is a critical mechanism of immune evasion by tumors. Hematopoietic progenitor kinase 1 (HPK1) is a negative regulator of T-cell signaling that has recently emerged as a novel target for cancer immunotherapy. Inhibition of HPK1 can restore T cell function and anti-tumor immune responses, and several HPK1 inhibitors are currently under pre-clinical development, or clinical evaluation. Identifying clinically useful pharmacodynamic (PD) biomarkers in response to HPK1 inhibition is critical to characterize exposure-response relationship in early-phase trials and inform dose selection for later-phase studies. However, development and implementation of clinical PD assays are challenging because high sensitivity and specificity are required. Here, we developed a multi-biomarker strategy that combines a proximal biomarker (SLP-76 (Ser376) phosphorylation, a specific substrate of HPK1) and distal biomarkers (cytokine production) to evaluate target engagement (TE) and establish proof of mechanism (POM) of HPK1 inhibitors to determine their comprehensive PD profile. These PD biomarker assays were developed using peripheral blood as a surrogate tissue to assess HPK1 inhibition-induced pSLP-76 level decrease and cytokine levels increase, thus reflecting drug inhibitory effects and T-cell activity recovery. However, the lack of basal levels of these biomarkers presented a challenge for clinical workflow, as ex-vivo T-cell receptor stimulation of the clinical specimen is required after collection. Phosphoflow cytometry was prioritized over several technology platforms evaluated for quantifying blood pSLP-76 levels because of superior assay performance and signal stability under the developed clinical workflow. Blood cytokines upregulated upon HPK1 inhibition were first identified using targeted proteomics. IFNγ, IL2, TNFα, and IL17A were next confirmed and validated using quantitative immunoassays. Both pSLP-76 and whole blood cytokine workflows were thoroughly optimized for every step of sample handling from specimen processing at clinical sites to sample analysis at testing lab to ensure standardized, precise, and robust assay performance for clinical application. In addition, consistent HPK1 inhibition potency values were achieved using blood from cancer patients, demonstrating that the established PD biomarker assays apply to the clinical target population. In conclusion, robust peripheral TE and POM biomarkers were successfully developed to support future phase I/II studies with HPK1 inhibitors. These are expected to enable characterization of the exposure-response relationships and help define the therapeutic window and optimal dose. Citation Format: Lin Jia, Yasmin Marikar-Coplin, Jeff Chen, Kevin Xu, Deanna A. Mele, Nadia Luheshi, Sonia Iyer, Anton I. Rosenbaum, Sonia Terrillon. Development and validation of clinical pharmacodynamic biomarkers to assess treatment response to HPK1 inhibition and guide dosing decisions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7177.

Abstract 1213: Tissue-specific thresholds and microenvironment correlates of tumor mutation burden associated with immunotherapy benefit and prognosis in microsatellite stable cancers

Abstract Background: Immune checkpoint inhibitors (ICIs) targeting anti-PD-1/L1 have expanded the treatment landscape against cancers, but are only effective in a subset of patients across all cancer types. Tumor mutation burden (TMB) is postulated to be a generic determinant of ICI dependent-tumor rejection. Here, we clarify the association between TMB and survival outcomes among microsatellite-stable cancers in a real-world clinicogenomic cohort including 70,698 patients distributed across 27 histologies. Methods: Patients were segregated into mutually exclusive anti-PD-1/L1 (N=14,736, immune checkpoint inhibitor, ICI) and non-ICI cohorts (N=55,962) if they had received pembrolizumab, nivolumab, atezolizumab, durvalumab, avelumab, or cemiplimab, and non-ICI therapies, respectively, during the course of treatment for individual cancer types. Patients treated with chemo-immunotherapy combination regimens were included in the ICI cohorts, but anti-CTLA-4 agents were excluded from both cohorts. For both ICI and non-ICI cohorts, patients were reiteratively categorized as TMB-high or -low using increasing TMB thresholds up to the 90th percentile TMB for individual cancer types. Outcomes were then assessed using Cox regression analyses of overall survival (OS). Results: Across 27 histologies, 12 cancer types had at least one TMB cutoff associated with survival benefit upon ICIs (melanoma, NSCLC, SCLC, bladder, cervical, colorectal, gastric, ovarian, head and neck, vulvar cancers, as well as carcinoma of unknown primary, and sarcoma), and these associations were generally conserved across sex and age groups, although not necessarily significant in all cases. In two cancer types (cholangiocarcinoma and neuroendocrine tumors), TMB cutoffs were associated with worse OS with ICIs. The lowest TMB cutoff in which a survival benefit could be detected with ICIs ranged from 2 mut/Mb in melanoma to 9 mut/Mb in colorectal cancer. TMB thresholds with the greatest predictive value (defined as the lowest survival hazard ratio) were frequently near the highest TMB examined for individual cancer types, suggesting that TMB may scale with ICI benefit. Conclusion: TMB was associated with survival benefit or detriment depending on tissue and treatment context. Detectable survival benefits were noted over a broad range of TMB cutoffs across cancer types, and a dose-dependent relationship between TMB and outcomes was observed in a subset of cancers. These results may have implications for cancer-agnostic and universal TMB cutoffs to guide the use of anti-PD-1/L1 therapies, and underline the importance of tissue context in the clinical development of ICI biomarkers. Citation Format: Maishara Muquith, Magdalena Espinoza, Andrew Elliott, Joanne Xiu, Andreas Seeber, Wafik El-Deiry, Emmanuel S. Antonarakis, Stephanie Graff, Michael J. Hall, Hossein Borghaei, Dave S. Hoon, Stephen V. Liu, Patrick C. Ma, Rana R. McKay, Trisha Wise-Draper, John Marshall, George W. Sledge, David Spetzler, Hao Zhu, David Hsieh. Tissue-specific thresholds and microenvironment correlates of tumor mutation burden associated with immunotherapy benefit and prognosis in microsatellite stable cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 1213.

NCI Resources for Cancer Immunoprevention Research.

Cancer prevention and early detection, the first two of the eight primary goals of the National Cancer Plan released in April 2023, are at the forefront of the nation's strategic efforts to reduce cancer incidence and mortality. The Division of Cancer Prevention (DCP) of the NCI is the federal government's principal component devoted to promoting and supporting innovative cancer prevention research. Recent advances in tumor immunology, cancer immunotherapy, and vaccinology strongly suggest that the host immune system can be effectively harnessed to elicit protective immunity against the development of cancer, that is, cancer immunoprevention. Cancer immunoprevention may be most effective if the intervention is given before or early in the carcinogenic process while the immune system remains relatively uncompromised. DCP has increased the emphasis on immunoprevention research in recent years and continues to expand program resources and interagency collaborations designed to facilitate research in the immunoprevention field. These resources support a wide array of basic, translational, and clinical research activities, including discovery, development, and validation of biomarkers for cancer risk assessment and early detection (Early Detection Research Network), elucidation of biological and pathophysiological mechanistic determinants of precancer growth and its control (Translational and Basic Science Research in Early Lesions), spatiotemporal multiomics characterization of precancerous lesions (Human Tumor Atlas Network/Pre-Cancer Atlas), discovery of immunoprevention pathways and immune targets (Cancer Immunoprevention Network), and preclinical and clinical development of novel agents for immunoprevention and interception (Cancer Prevention-Interception Targeted Agent Discovery Program, PREVENT Cancer Preclinical Drug Development Program, and Cancer Prevention Clinical Trials Network).

Report From the 2022 Mary Tyler Moore Vision Initiative Diabetic Retinal Disease Clinical Endpoints Workshop.

The Mary Tyler Moore Vision Initiative Diabetic Retinal Disease (DRD) Clinical Endpoints Workshop was held on October 22, 2022 to accelerate progress toward establishment of useful clinical and research endpoints and development of new therapeutics that have important relevance across the full spectrum of DRD pathology. More than 90 patient representatives, clinicians, scientists, funding and regulatory agencies, diagnostic, therapeutic and biotech industry representatives discussed the needs for new diagnostic and therapeutic approaches to prevent and restore retinal neurovascular unit integrity. Phase I of the MTM Vision Initiative plans, notably updating the DRD staging system and severity scale, establishing a human ocular biorepository and resource, and clinical endpoints and biomarker development and validation, was emphasized.

Autophagy and nuclear morphometry are associated with histopathologic features in esophageal squamous cell carcinoma.

Less than 15% of patients with esophageal squamous cell carcinoma (ESCC) survive 5years after diagnosis. A better understanding of the biology of these tumors and the development of clinical biomarkers is needed. Autophagy is a physiological mechanism involved in the turnover of cellular components that plays a key role in cancer. This study evaluated the differential levels of three key regulators of autophagy (SQSTM1, MAP1LC3B, and BECN1) in patients with ESCC, associating autophagy with histopathologic features, including the grade of differentiation, mitotic rate, inflammation score, and the intensity of tumor-infiltrating lymphocytes. Nuclear morphometry of the tumor parenchyma was also assessed, associating it with autophagy and histopathology. All three markers significantly increased in patients with ESCC compared to the control group. Based on the mean expression of each protein in the control group, 57% of patients with ESCC had high levels of all three markers compared to control patients (14%). The most frequent profiles found in ESCC were BECNhigh/MAP1LC3high and BECNhigh/SQSTM1high. According to the TCGA database, we found that the main autophagy genes were upregulated in ESCC. Moreover, high levels of autophagy markers were associated with a poor prognosis. Considering nuclear morphometry, ESCC samples showed a significant reduction in nuclear area, which was strongly negatively correlated with autophagy. Finally, the percentage of normal nuclei was associated with tumor differentiation, while poorly differentiated tumors showed lower SQSTM1 levels. ESCC progression may involve increased autophagy and changes in nuclear structure, associated with clinically relevant histopathological features. KEY MESSAGES: Autophagy markers are co-increased in primary ESCC. Autophagy negatively correlates with nuclear morphometry in ESCC parenchyma. Autophagy and nuclear morphometry are associated with histopathological features. Autophagy is increased in ESCC-TCGA database and associated with poor prognosis.

Phenotypic Features of Pediatric Bronchiectasis Exacerbations Associated With Symptom Resolution After 14 Days of Oral Antibiotic Treatment

Respiratory exacerbations in children and adolescents with bronchiectasis are treated with antibiotics. However, antibiotics can have variable interindividual effects when treating exacerbations. Can phenotypic features associated with symptom resolution after a 14-day course of oral antibiotics for a nonsevere exacerbation of bronchiectasis be identified? Combining data from two multicenter randomized controlled trials, we identified 217 children with bronchiectasis assigned to at least 14days of oral antibiotics to treat nonsevere (nonhospitalized) exacerbations. Univariable and then multivariable logistic regression were used to identify factors associated with symptom resolution within 14days of commencing antibiotics. Identified associations were re-evaluated by mediation analysis. Of the 217 study participants (52%male patients), 41%were Indigenous (Australian First Nations, New Zealand Māori, or Pacific Islander). The median age was 6.6 years (interquartile range, 4.0-10.1 years). By day 14, symptoms had resolved in 130 children (responders), but persisted in the remaining 87 children (nonresponders). Multivariable analysis found those who were Indigenous (adjusted OR [AOR], 3.59; 95%CI, 1.35-9.54) or showed new abnormal auscultatory findings (AOR, 3.85; 95%CI, 1.56-9.52) were more likely to be responders, whereas those with multiple bronchiectatic lobes at diagnosis (AOR, 0.66; 95%CI, 0.46-0.95) or higher cough scores when starting exacerbation treatment (AOR, 0.55; 95%CI, 0.34-0.90) were more likely to be nonresponders. Detecting a respiratory virus at the beginning of an exacerbation was not associated with antibiotic failure at 14days. Children with Indigenous ethnicity, milder bronchiectasis, mild exacerbations (low reported cough scores), or new abnormal auscultatory signs are more likely to respond to appropriate oral antibiotics than those without these features. These patient and exacerbation phenotypes may assist clinical management and development of biomarkers to identify those whose symptoms are more likely to resolve after 14days of oral antibiotics. Australian New Zealand Clinical Trials Registry; Nos.: ACTRN12612000011886 and ACTRN12612000010897; URL: https://www.anzctr.org.au.

Inability to suppress head rotation during the saccade test as a clinical biomarker for cognitive dysfunction in Parkinson’s disease

BackgroundThere is a need for development of reliable and accessible clinical biomarker for detecting cognitive dysfunction in PD. This study aimed to investigate whether involuntary head rotation during the saccade test could serve as a potential biomarker for screening cognitive dysfunction in PD. MethodsA total of 27 PD patients and nine age- and sex-matched healthy controls were prospectively enrolled in this study. A custom-designed gyroscope was attached to the forehead of each participant, and a saccade test consisting of 20 trials was conducted. The entire test was recorded on video, and two movement disorder experts independently rated the degree of head rotation, blinded to the patients' clinical information. The peak angular velocity of head rotation was derived from the gyroscope data. Participants underwent Montreal Cognitive Assessment (MoCA) as the cognitive evaluation. Correlation analysis was performed to assess the relationship between head rotation and MoCA scores. ResultsThe mean peak angular velocity of head rotation significantly correlated with the MoCA scores (R = -0.52, p = 0.0023) including age, sex, disease duration, and education duration as cofactors. The optimal peak angular velocity thresholds for head rotation, which aligned with the manual ratings, were determined to be 5°/s and 10°/s for raters 1 and 2, respectively. The MoCA scores exhibited significant correlations with the number of head rotations, using both the 5°/s (R = -0.36, p = 0.042) and 10°/s (R = -0.49, p = 0.0048) thresholds. Furthermore, the mean angular velocity of the head demonstrated a 100% positive predictive value and specificity for the detection of cognitive impairment (MoCA < 26), based on the cut-offs of 5°/s and 10°/s. ConclusionInability to suppress head rotation during saccades may serve as a potential clinical biomarker for screening cognitive dysfunction in PD.

Comparison of PARPi efficacy according to homologous recombination deficiency biomarkers in patients with ovarian cancer: a systematic review and meta-analysis.

Mutations in the BRCA1/2 (BRCA) genes are associated with response to poly(ADPribose) polymerase (PARP) inhibitors (PARPi). In addition, there are different homologous recombination deficiency (HRD) biomarkers available in clinical practice [e.g., genome-wide loss-of-heterozygosity (gLOH) and myChoice® score] that identify patients who can benefit from PARPi. Inconsistencies in biomarkers used in PARPi clinical trials make it challenging to identify clinically relevant predictive biomarkers. This study aims to compare clinically available HRD biomarkers in terms of benefits from PARPi. We performed database search for phase II or III randomized clinical trials comparing PARPi versus chemotherapy, and meta-analysis using generic inverse variance and a Random Effects model. Patients were classified according to their HRD status: (I) BRCAm (patients with BRCA mutation of germline or somatic origin); (II) non-BRCA HRD [patients BRCA wild-type (wt) with another HRD biomarker-gLOH or myChoice®]; and (III) homologous recombination proficiency (HRP) (BRCAwt and without HRD biomarkers). From those that were BRCAwt, we compared myChoice®+ with gLOH-high. Five studies (3,225 patients) analyzing PARPi in first line setting were included. Patients with BRCAmut had progression-free survival (PFS) with hazard ratio (HR) 0.33 [95% confidence interval (CI): 0.30-0.43]; patients with non-BRCA HRD had a PFS HR 0.49 (95% CI: 0.37-0.65), and patients with HRP had a PFS HR 0.78 (95% CI: 0.58-1.03). Eight studies (5,529 patients) with PARPi including first line and recurrence settings were included. BRCAmut had PFS HR 0.37 (95% CI: 0.30-0.48), BRCAwt & HRD 0.45 (95% CI: 0.37-0.55) and HRP 0.70 (95% CI: 0.57-0.85). Patients with BRCAwt & myChoice® ?42 had PFS HR 0.43 (95% CI: 0.34-0.56), similar to patients with BRCAwt & gLOH-high with PFS HR 0.42 (95% CI: 0.28-0.62). Patients with HRD derived significantly more benefit from PARPi when compared to patients with HRP. The benefit of PARPi in patients with HRP tumors was limited. Careful cost-effectiveness analysis, and alternative therapies or clinical trial enrollment should strongly be considered for patients with HRP tumors. Among patients with BRCAwt, a similar benefit was found in patients with gLOH-high and those myChoice®+. The clinical development of further HRD biomarkers (e.g., Sig3) may help identify more patients who benefit from PARPi.

A team science approach for the preclinical and clinical characterization and biomarker development for post‐traumatic epilepsy

AbstractObjectivePost‐traumatic epilepsy (PTE) is an acquired epilepsy that develops in the months or years following a traumatic brain injury (TBI) and can lead to substantial personal, financial, and societal burden. To date, PTE is rarely curable; current treatments are partially effective and often accompanied by adverse side effects. While research on PTE has expanded significantly in the last several years, there remain numerous challenges to identifying effective prevention and treatment strategies. In this paper, we describe advances from the CURE Epilepsy PTE Initiative, including its implementation and the emphasis on team science.MethodsThe CURE Epilepsy PTE Initiative funded six research teams to link preclinical and clinical studies to engage in the validation of experimental models, characterization of pathophysiology and biological pathways, and identification of risk factors associated with PTE. Three teams had projects with both a preclinical and a clinical component; these teams focused on: targeting the epileptogenic effects of subarachnoid blood, exploring the neuropathological mechanisms of epileptogenesis, and defining the role of extracellular matrix injury. Two teams undertook entirely preclinical projects: exploring the role of vascular injury, gliosis, and neurogenesis as drivers for PTE, and identifying genetic, proteomic, metabolomic, and microRNA biosignatures to improve the prediction of PTE. One team's project was entirely clinical and investigated genetic and protein biomarkers to improve the prediction of PTE.ResultsIn addition to scientific discoveries including characterization of a variety of animal models and progress towards the understanding of biological underpinnings and biomarkers for PTE, significant programmatic and personnel‐related processes were incorporated, including standardized, rigorous policies and procedures to ensure quality and accountability between and within groups.SignificanceWe propose CURE Epilepsy's team science approach as an effective way to bring together a diverse set of investigators to explore biological mechanisms that may lead to cures for the epilepsies.

Gene expression profiling of peripheral blood mononuclear cells from women with cervical lesions reveals new markers of cancer.

Cervical cancer (CC) is a multifactorial disease of which human papillomavirus (HPV) is the main etiological agent. Despite cervical Pap smear screening and anti‑HPV vaccination, CC remains a major public health issue. Identification of specific gene expression signatures in the blood could allow better insight into the immune response of CC and could provide valuable information for the development of novel biomarkers. The present study performed a transcriptomic analysis of peripheral blood mononuclear cells (PBMCs) from Senegalese patients with CC (n=31), low‑grade cervical intraepithelial neoplasia (CIN1; n=27) and from healthy control (CTR) subjects (n=29). Individuals in the CIN1 and CTR groups exhibited similar patterns in gene expression. A total of 182 genes were revealed to be differentially expressed in patients with CC compared with individuals in the CIN1 and CTR groups. The IL1R2, IL18R1, MMP9 and FKBP5 genes were the most upregulated, whereas the T‑cell receptor α gene TRA was the most downregulated in the CC group compared with in the CIN1 and CTR groups. The pathway enrichment analysis of the differentially expressed genes revealed pathways directly and indirectly linked to inflammation. To the best of our knowledge, the present study is the first large transcriptomic study on CC performed using PBMCs from African women; the results revealed the involvement of genes and pathways related to inflammation, most notably the IL‑1 pathway, and the involvement of downregulation of the T‑cell receptor α, a key component of the immune response. Several of the stated genes have already been reported in other cancer studies as putative blood biomarkers, thus reinforcing the requirement for deeper investigation. These findings may aid in the development of innovative clinical biomarkers for CC prevention and should be further replicated in other populations.

Priorities for research on neuromodulatory subcortical systems in Alzheimer's disease: Position paper from the NSS PIA of ISTAART.

The neuromodulatory subcortical system (NSS) nuclei are critical hubs for survival, hedonic tone, and homeostasis. Tau-associated NSS degeneration occurs early in Alzheimer's disease (AD) pathogenesis, long before the emergence of pathognomonic memory dysfunction and cortical lesions. Accumulating evidence supports the role of NSS dysfunction and degeneration in the behavioral and neuropsychiatric manifestations featured early in AD. Experimental studies even suggest that AD-associated NSS degeneration drives brain neuroinflammatory status and contributes to disease progression, including the exacerbation of cortical lesions. Given the important pathophysiologic and etiologic roles that involve the NSS in early AD stages, there is an urgent need to expand our understanding of the mechanisms underlying NSS vulnerability and more precisely detail the clinical progression of NSS changes in AD. Here, the NSS Professional Interest Area of the International Society to Advance Alzheimer's Research and Treatment highlights knowledge gaps about NSS within AD and provides recommendations for priorities specific to clinical research, biomarker development, modeling, and intervention. HIGHLIGHTS: Neuromodulatory nuclei degenerate in early Alzheimer's disease pathological stages. Alzheimer's pathophysiology is exacerbated by neuromodulatory nuclei degeneration. Neuromodulatory nuclei degeneration drives neuropsychiatric symptoms in dementia. Biomarkers of neuromodulatory integrity would be value-creating for dementia care. Neuromodulatory nuclei present strategic prospects for disease-modifying therapies.

VSOLassoBag: a variable-selection oriented LASSO bagging algorithm for biomarker discovery in omic-based translational research

Screening biomolecular markers from high-dimensional biological data is one of the long-standing tasks for biomedical translational research. With its advantages in both feature shrinkage and biological interpretability, Least Absolute Shrinkage and Selection Operator (LASSO) algorithm is one of the most popular methods for the scenarios of clinical biomarker development. However, in practice, applying LASSO on omics-based data with high dimensions and low-sample size may usually result in an excess number of predictive variables, leading to the overfitting of the model. Here, we present VSOLassoBag, a wrapped LASSO approach by integrating an ensemble learning strategy to help select efficient and stable variables with high confidence from omics-based data. Using a bagging strategy in combination with a parametric method or inflection point search method, VSOLassoBag can integrate and vote variables generated from multiple LASSO models to determine the optimal candidates. The application of VSOLassoBag on both simulation datasets and real-world datasets shows that the algorithm can effectively identify markers for either case-control binary classification or prognosis prediction. In addition, by comparing with multiple existing algorithms, VSOLassoBag shows a comparable performance under different scenarios while resulting in fewer features than others. In summary, VSOLassoBag, which is available at https://seqworld.com/VSOLassoBag/ under the GPL v3 license, provides an alternative strategy for selecting reliable biomarkers from high-dimensional omics data. For user's convenience, we implement VSOLassoBag as an R package that provides multithreading computing configurations.

Concomitant medications and circulating tumor cells: friends or foes?

The use of concomitant medications by patients with cancer is observed almost globally; however, little attention has been paid to this topic in the medical literature. Most clinical studies do not describe the type and duration of drugs used at the time of inclusion and during treatment or how these drugs may affect the experimental and/or standard therapy. Even less information has been published on the potential interaction between concomitant medications and tumor biomarkers. However, we do know that concomitant drugs can complicate cancer clinical trials and biomarker development, thus contributing to their interaction, leading to side effects, and resulting in suboptimal adherence to anticancer treatment. On the basis of these premises and moving from the study by Jurisova et al., which reported the effect of commonly used drugs on the prognosis of women with breast cancer and the detection of circulating tumor cells (CTCs), we comment on the role of CTCs as an emerging diagnostic and prognostic tool for breast cancer. We also report the known and hypothesized mechanisms of CTC interplay with other tumor and blood components, possibly modulated by widespread drugs, including over-the-counter compounds, and discuss the possible implications of commonly used concomitant medications on CTC detection and clearance. After considering all these points, it is conceivable that concomitant drugs are not necessarily a problem, but on the contrary, their virtuous mechanisms can be exploited to reduce tumor spread and enhance the effect of anticancer therapies.

The Effect of Biomarkers on Clinical Trial Risk in Gastric Cancer.

This study examined clinical trial success rates for new drug developments in gastric cancer since 1998. We also examined the clinical trial design features that may mitigate the risk of clinical trial failure. Clinical trial data was obtained from clinicaltrials.gov. Drugs were included if they entered testing between January 1, 1998 and January 1, 2022 and were excluded if they did not have a completed phase I trial or treated secondary effects of gastric cancer. Transition probabilities were calculated for each phase and compared with industry averages. Success rates were determined based on biomarker usage, drug target, type of therapy, and drug chemistry. Upon screening 1990 trials, 219 drugs met our inclusion criteria. The probability of a drug completing all phases of testing and obtaining FDA approval was 7%, which is below the 11% industry average. The use of biomarkers in clinical development resulted in nearly a 2-fold increase in the cumulative success rate. Biologics also exhibited higher success rates (17%) as opposed to small molecules (1%). This was true even when we compared both drug types that shared the same target. When comparing only receptor-targeted therapies, biologics (62%) continued to outperform small molecules (18%). Similarly, when narrowed down to drugs targeting solely HER2 receptors, biologics continued to prevail (64% vs. 24%). Implementing biomarkers, receptor-targeted therapies, and biologics in clinical development improves clinical trial success rates in gastric cancer. Thus, physicians should prioritize the enrollment of gastric cancer patients in clinical trials that incorporate the aforementioned features.

Biochemical Predictors of Acute Kidney Injury in Critically Ill COVID-19 Patients.

It is estimated that 50% of patients with coronavirus disease 2019 (COVID-19) have varying degrees of renal involvement. In this clinical biomarker development research, we examined in a retrospective study design the temporal changes in biochemical laboratory parameters in relation to the development of acute kidney injury (AKI). In a sample of 399 patients admitted from May 2020 to May 2021 to a tertiary health care intensive care unit (ICU), the incidence of AKI was 27.3%, and the median time to AKI was on 7th day of ICU admission. Most common etiology of AKI was kidney hypoperfusion. Within 72 h of developmental of low blood pressure, 63.76% developed AKI. The likelihood of AKI was higher in those with elevated serum ferritin, aspartate transaminase, and thrombocytopenia (low platelet count). A cutoff value of 750.3 ng/mL [area under the ROC curve (AUC) = 0.777] for serum ferritin, and 40.05 U/L for alanine aminotransferase (AUC = 0.677) 1 day before development of AKI displayed, respectively, a sensitivity of 76.2% and 64.3%, whereas the specificity was 69.5% and 64.1%, respectively, for these two biochemical predictors. A cutoff value of platelets (152.50 × 109/L [AUC = 0.75]) measured 4 days before development of AKI, displayed 83.3% sensitivity and 16.4% specificity. Taken together, our study thoroughly examined the temporal association of various clinical and laboratory parameters with AKI and prediction models were developed as per results of the time series data. These observations in a tertiary health care setting contribute to ongoing efforts for biomarker discovery and development using routine biochemical tests so as to forecast AKI in patients with COVID-19.

The best and worst of times in therapy development for myasthenia gravis.

Within the last 5 years, the US Food and Drug Administration (FDA) has approved complement and neonatal Fc receptor (FcRN) inhibitors for treatment of generalized myasthenia gravis, and several other therapies are in late-stage clinical trials or under regulatory review. However, questions about which patients are most likely to benefit from which therapies, and the relative effectiveness of these very expensive drugs, has resulted in uncertainty around the place that they should occupy in the existing therapeutic armamentarium. MGNet (a Rare Diseases Clinical Research Consortium funded by the National Institute of Neurological Diseases and Stroke) held two meetings during the 14th International Conference of the Myasthenia Gravis Foundation of America to discuss the most critical needs for clinical trial readiness and biomarker development in the context of therapy development for myasthenia gravis. Herein we provide a summary of these discussions, but not a consensus opinion, and offer a series of recommendations to guide focused research in the most critical areas. We welcome ongoing discussion through comments on this work.

Whole-exome sequencing analysis identifies distinct mutational profile and novel prognostic biomarkers in primary gastrointestinal diffuse large B-cell lymphoma

BackgroundDiffuse large B-cell lymphoma (DLBCL) is the most common aggressive non-Hodgkin lymphoma, and about 10% of DLBCL cases primarily occur in the gastrointestinal tract. Previous reports have revealed that primary gastrointestinal-DLBCL (pGI-DLBCL) harbors different genetic mutations from other nodal or extranodal DLBCL. However, the exonic mutation profile of pGI-DLBCL has not been fully addressed.MethodsWe performed whole-exome sequencing of matched tumor tissues and blood samples from 53 pGI-DLBCL patients. The exonic mutation profiles were screened, and the correlations between genetic mutations and clinicopathological characteristics were analyzed.ResultsA total of 6,588 protein-altering events were found and the five most frequent mutated genes in our pGI-DLBCL cohort were IGLL5 (47%), TP53 (42%), BTG2 (28%), P2RY8 (26%) and PCLO (23%). Compared to the common DLBCL, significantly less or absence of MYD88 (0%), EZH2 (0%), BCL2 (2%) or CD79B (8%) mutations were identified in pGI-DLBCL. The recurrent potential driver genes were mainly enriched in pathways related to signal transduction, infectious disease and immune regulation. In addition, HBV infection had an impact on the mutational signature in pGI-DLBCL, as positive HBsAg was significantly associated with the TP53 and LRP1B mutations, two established tumor suppressor genes in many human cancers. Moreover, IGLL5 and LRP1B mutations were significantly correlated with patient overall survival and could serve as two novel prognostic biomarkers in pGI-DLBCL.ConclusionsOur study provides a comprehensive view of the exonic mutation profile of the largest pGI-DLBCL cohort to date. The results could facilitate the clinical development of novel therapeutic and prognostic biomarkers for pGI-DLBCL.

Advances in Our Understanding of the Interaction of Drugs with T-cells: Implications for the Discovery of Biomarkers in Severe Cutaneous Drug Reactions.

Drugs can activate different cells of the immune system and initiate an immune response that can lead to life-threatening diseases collectively known as severe cutaneous adverse reactions (SCARs). Antibiotics, anticonvulsants, and antiretrovirals are involved in the development of SCARs by the activation of αβ naïve T-cells. However, other subsets of lymphocytes known as nonconventional T-cells with a limited T-cell receptor repertoire and innate and adaptative functions also recognize drugs and drug-like molecules, but their role in the pathogenesis of SCARs has only just begun to be explored. Despite 30 years of advances in our understanding of the mechanisms in which drugs interact with T-cells and the pathways for tissue injury seen during T-cell activation, at present, the development of useful clinical biomarkers for SCARs or predictive preclinical in vitro assays that could identify immunogenic moieties during drug discovery is an unmet goal. Therefore, the present review focuses on (i) advances in the understanding of the pathogenesis of SCARs reactions, (ii) a description of the interaction of drugs with conventional and nonconventional T-cells, and (iii) the current state of soluble blood circulating biomarker candidates for SCARs.

Evaluation of homologous recombination deficiency biomarkers in patients with ovarian cancer treated with PARP inhibitors.

e17615 Background: Germline BRCA1/2 mutations are associated with response to Poly(ADP-ribose) polymerase inhibitors (PARPi). In addition to BRCA1/2 mutations, there are other Homologous Recombinations Deficiency (HRD) biomarker candidates already available in clinical practice including genome-wide loss-of-heterozygosity (gLOH) and myChoice score. Inconsistencies in biomarkers used in clinical trials with PARPi are a challenge to clinical interpretation. This study aims to compare clinically available HRD biomarkers in terms of benefits from PARPi. Methods: We performed database search for phase II or III randomized clinical trials comparing PARPi versus chemotherapy, and meta-analysis using generic inverse variance and a random-effects model. Patients were classified into three categories according to their HRD status: 1) BRCAmut (patients with BRCA1/2 mutation of germline or somatic origin), 2) non-BRCA HRD (patients BRCA wild-type (wt) with a different HRD biomarker - gLOH or myChoice); and 3) homologous recombination proficiency (HRP) (BRCAwt and without HRD biomarkers). From those that were BRCAwt, we compared myChoice+ with gLOH-high. Results: Eight studies (n = 4372 patients) with PARPi as first-line and recurrence settings were included. BRCAmut had PFS HR 0.29 (95%CI, 0.24-0.35), BRCAwt &amp; HRD 0.43 (95%CI, 0.34-0.53) and HRP 0.74 (95%CI, 0.62-0.89). In a secondary analysis by HRD stratification method, patients with BRCAwt &amp; myChoice &gt; = 42 had PFS HR 0.43 (95%CI, 0.34-0.56), similar to patients with BRCAwt &amp; gLOH-high with PFS HR 0.42 (95%CI, 0.28-0.62). Conclusions: Patients with BRCA mutations benefited the most from PARPi. From patients with BRCA1/2 wild-type, a similar benefit was found in patients with gLOH-high and those myChoice+, which was superior to HRP patients. The clinical development of further HRD biomarkers (i.e. Sig3, HRDetect) may help identify more patients who benefit from PARPi.

OP0074 DISTINCT CIRCULATING LYMPHOCYTE SUBSETS DISTINGUISH FLARE FROM DRUG-FREE REMISSION IN RHEUMATOID ARTHRITIS

BackgroundRheumatoid arthritis (RA) is characterised by relapsing joint and systemic inflammation, yet the immunopathological basis of these disease flares and their clinical prediction remain uncertain.ObjectivesUsing mass cytometry and single cell RNA sequencing, we aimed to identify circulating lymphocyte subsets associated with RA flare, and identify potential cellular biomarkers to predict flare versus drug-free remission (DFR).MethodsWe analysed peripheral blood mononuclear cells (PBMCs) from patients recruited to the BioRRA study (Figure 1), a prospective clinical trial of conventional synthetic disease-modifying anti-rheumatic drug (csDMARD) cessation.[1] Patients with RA in clinical (DAS28-CRP &lt; 2.4) and ultrasound (absence of power Doppler signal in 7 joints) remission stopped csDMARDs, with flare defined as DAS28-CRP ≥ 2.4 during 6 month follow-up. A 44-marker mass cytometry panel was used to profile PBMCs from 36 patients (20 flare, 16 DFR) at two time points each (baseline, and flare onset / month 6 DFR). In a subset of patients (n = 12: 8 flare, 4 DFR), fluorescence-activated cell sorting of T and B cells was followed by single cell sequencing (n = 81,923 cells) incorporating 320 immune genes, 34 oligo-tagged surface protein antibodies, and TCR/BCR CDR3 sequence. Clones were defined as ≥2 cells with identical CDR3 nucleotide sequence, and clonal expansion as a significant increase in proportion from baseline to final study visit. Statistical significance was assessed after Benjamini-Hochberg multiple test correction (adj p &lt; 0.05).Figure 1.ResultsMass cytometry revealed 31 distinct cell clusters: notably, greater proportions of memory (CD45RO+/PD1hi) CD4+ and CD8+ T cells, and memory (CD27+/CD21-) B cells, were observed at onset of flare versus baseline (Table 1).Table 1.Mass cytometry (n = 20 flare + 16 DFR)ContrastClusterMedian %Adj. p (GLMM)Flare onset vs baseline: Flare patientsCD4+/CD45RO+/PD1+ memory T cells2.14 vs 0.24&lt;0.001CD8+/CD45RO+/PD1+ memory T cells6.64 vs 0.07&lt;0.001CD19+/CD27+/CD21- memory B cells2.39 vs 0.03&lt;0.001Single cell RNAseq (n = 8 flare + 4 DFR)ContrastClusterMedian %Adj. p (Wilcoxon)Flare onset vs baseline: Flare patientsIgA+ plasma cells0.37 vs 0.210.020Flare vs DFR patients: BaselineCD4+/CD25+/Foxp3+ Treg cells0.55 vs 1.270.022To better characterise these flare-associated subsets, single cell sequencing of CD45RO+/PD1hi CD4+ and CD8+ T cells, and CD19+ B cells, was performed and identified 21 distinct clusters. CDR3 sequencing revealed significant clonal expansion (Fisher exact, adj. p &lt; 0.05) at flare onset within five unique CD8+ clones (4 patients), one CD4+ clone (1 patent), and no B clones. Overall, there was a significantly greater proportion of IgA+ plasma cells at flare onset versus baseline. In contrast, a significantly lower proportion of CD25+/FoxP3+ regulatory T cells were present at csDMARD cessation (baseline) in subsequent flare versus DFR patients (Table 1), suggesting biomarker potential.To further assess the predictive performance of CD4+ Tregs as a biomarker for flare versus DFR, we analysed PBMCs from an independent cohort of 50 patients (25 flare, 25 DFR) stopping csDMARDs in the ongoing BIO-FLARE study.[2] By flow cytometry, we confirmed a lower proportion of CD4+/CD25hi Tregs at baseline in flare vs DFR (median 4.74 versus 6.37%, Wilcoxon p = 0.037; AUC: 0.67). In this cohort, stopping csDMARDs only in patients with elevated (&gt; 6.11% total CD4) baseline Tregs would have prevented drug cessation in 18/25 (72%) of flare patients; 9/25 (36%) of DFR patients would have continued csDMARDs unnecessarily.ConclusionWe present a detailed longitudinal characterisation of circulating lymphocyte surface phenotype, gene expression, and clonal expansion in RA flare vs DFR. Furthermore our data, across two independent cohorts, suggests a role for CD4+ Tregs in promoting drug-free remission meriting further investigation, with potential for future clinical biomarker development.