Biomarkers Of Clinical Response Research Articles

Low CD86 expression is a predictive biomarker for clinical response to the therapeutic HPV vaccine, IGMKK16E7: Results of a post-hoc analysis

Abstract Background Although therapeutic HPV vaccines could offer a non-invasive treatment for patients with cervical intraepithelial neoplasia (CIN), none have been clinically implemented. Oral administration of the therapeutic HPV vaccine, IGMKK16E7, results in the histological regression of HPV16-positive CIN2/3 to normal (complete response: CR). Here, we investigated biomarkers that could predict CR after oral administration of IGMKK16E7. Methods Forty-two patients administered with high-dose oral IGMKK16E7 in a Phase I/II trial were included. Cervical-exfoliated cells were collected before administration. Gene expression of CD4, CD8, Foxp3, PD-1, CTLA-4, CD103, CD28, CD80, CD86, and PD-L1 in the cells were measured by quantitative RT-PCR. ROC curve analysis and Mann-Whitney tests were used to explore potential biomarkers. Pearson correlation coefficient analysis was used to correlate gene expression profiles with clinical outcome. Results The only predictive biomarker of vaccine response for which ROC curve analysis showed significant diagnostic performance with histological CR was CD86 (AUC 0.71, 95%XI 0.53-0.88, p = .020). CR patients had significantly lower CD86 expression (CD86-low) than non-CR patients (p = .035). The CR rate for CD86-low and CD86-high cases was 50% and 19%, respectively, and CD86-low cases had a significantly higher CR rate (p = .047). Compared to all patients, the CD86-low group had a 1.5-fold increase in CR rate. Gene expression of CD86 and CTLA-4 showed the strongest positive correlation with clinical outcomes in the non-CR group (p < .001). Conclusion Low expression of CD86 in exfoliated cervical cells can be used as a pre-treatment biomarker to predict histological CR after IGMKK16E7 use.

XENTURION is a population-level multidimensional resource of xenografts and tumoroids from metastatic colorectal cancer patients

The breadth and depth at which cancer models are interrogated contribute to the successful clinical translation of drug discovery efforts. In colorectal cancer (CRC), model availability is limited by a dearth of large-scale collections of patient-derived xenografts (PDXs) and paired tumoroids from metastatic disease, where experimental therapies are typically tested. Here we introduce XENTURION, an open-science resource offering a platform of 128 PDX models from patients with metastatic CRC, along with matched PDX-derived tumoroids. Multidimensional omics analyses indicate that tumoroids retain extensive molecular fidelity with parental PDXs. A tumoroid-based trial with the anti-EGFR antibody cetuximab reveals variable sensitivities that are consistent with clinical response biomarkers, mirror tumor growth changes in matched PDXs, and recapitulate EGFR genetic deletion outcomes. Inhibition of adaptive signals upregulated by EGFR blockade increases the magnitude of cetuximab response. These findings illustrate the potential of large living biobanks, providing avenues for molecularly informed preclinical research in oncology.

Peripheral blood T-cell modulation by omalizumab in chronic urticaria patients.

Chronic spontaneous urticaria (CSU) is a highly prevalent and difficult to manage cutaneous disease characterized by the presence of recurrent urticaria, angioedema, or both, for a period of 6 weeks or longer. One of the biological treatments used for patients with CSU with an autoimmune background and bad control of the disease is omalizumab, an anti-IgE monoclonal antibody. The understanding of the mechanism of action of this biological drug in CSU along with the identification of potential biomarkers of clinical response can be helpful in the personalized management of the disease. The purpose of this study was to analyze the effect of omalizumab on peripheral blood lymphocyte subpopulations in patients with CSU in order to identify potential biomarkers of treatment response. We analyzed 71 patients with CSU [33 under omalizumab and 38 under non-immunomodulatory drugs (treated with antihistamines; NID)] and 50 healthy controls. An exhaustive immunophenotyping of whole blood T-cell subpopulations, including naïve, central memory, effector memory, effector cells, Th1, Th2, and Th17 was performed by multiparametric flow cytometry. Moreover, in CSU patients, we analyzed markers of inflammation (ESR, DD, CRP), atopy (prick test, IgE quantification), and autoimmunity (anti-thyroid antibodies and indirect basophil activation test).To evaluate the clinical activity, the Urticaria Activity Score 7 (UAS 7) test was used. In patients with CSU under treatment with omalizumab, there was a significant decrease in the percentage of naïve and an increase in the percentage of central memory CD4 T cells as well as a decrease in the percentage of naïve and increase in the percentage of effector CD8 T-cell subsets. Moreover, patients under treatment with omalizumab had higher percentages of Th1 and Th2 cells than patients under treatment with NID. The immune monitoring of T-cell subpopulations in patients with CSU starting omalizumab, may be a useful strategy to analyze treatment response in the clinical practice.

Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models.

Ovarian cancers are still largely treated with platinum-based chemotherapy as the standard of care, yet few biomarkers of clinical response have had an impact on clinical decision making as of yet. Two particular challenges faced in mechanistically deciphering platinum responsiveness in ovarian cancer have been the suitability of cell line models for ovarian cancer subtypes and the availability of information on comparatively how sensitive ovarian cancer cell lines are to platinum. We performed one of the most comprehensive profiles to date on 36 ovarian cancer cell lines across over seven subtypes and integrated drug response and multiomic data to improve on our understanding of the best cell line models for platinum responsiveness in ovarian cancer. RNA-seq analysis of the 36 cell lines in a single batch experiment largely conforms with the currently accepted subtyping of ovarian cancers, further supporting other studies that have reclassified cell lines and demonstrate that commonly used cell lines are poor models of high-grade serous ovarian carcinoma. We performed drug dose response assays in the 32 of these cell lines for cisplatin and carboplatin, providing a quantitative database of IC 50 s for these drugs. Our results demonstrate that cell lines largely fall either well above or below the equivalent dose of the clinical maximally achievable dose (C max ) of each compound, allowing designation of cell lines as sensitive or resistant. We performed differential expression analysis for high-grade serous ovarian carcinoma cell lines to identify gene expression correlating with platinum-response. Further, we generated two platinum-resistant derivatives each for OVCAR3 and OVCAR4, as well as leveraged clinically-resistant PEO1/PEO4/PEO6 and PEA1/PEA2 isogenic models to perform differential expression analysis for seven total isogenic pairs of platinum resistant cell lines. While gene expression changes overall were heterogeneous and vast, common themes were innate immunity/STAT activation, epithelial to mesenchymal transition and stemness, and platinum influx/efflux regulators. In addition to gene expression analyses, we performed copy number signature analysis and orthogonal measures of homologous recombination deficiency (HRD) scar scores and copy number burden, which is the first report to our knowledge applying field-standard copy number signatures to ovarian cancer cell lines. We also examined markers and functional readouts of stemness that revealed that cell lines are poor models for examination of stemness contributions to platinum resistance, likely pointing to the fact that this is a transient state. Overall this study serves as a resource to determine the best cell lines to utilize for ovarian cancer research on certain subtypes and platinum response studies, as well as sparks new hypotheses for future study in ovarian cancer.

Nasal Epithelium Transcriptomics Predict Clinical Response to Elexacaftor/Tezacaftor/Ivacaftor.

Elexacaftor/tezacaftor/ivacaftor (ETI) has made a substantial positive impact for people living with CF (pwCF). However, there can be substantial variability in efficacy, and we lack adequate biomarkers to predict individual response. We thus aimed to identify transcriptomic profiles in nasal respiratory epithelium that predict clinical response to ETI treatment. We obtained nasal epithelial samples from pwCF prior to ETI initiation and performed a transcriptome-wide analysis of baseline gene expression to predict changes in FEV1 (∆FEV1), year's best FEV1 (∆ybFEV1), and body mass index (∆BMI). Using the top differentially expressed genes (DEGs), we generated transcriptomic risk scores (TRS) and evaluated their predictive performance. The study included 40 pwCF aged ≥6 years (mean 27.7 [SD=15.1] years; 40% female). After ETI initiation, FEV1 improved ≥5% in 22 (61.1%) participants and ybFEV1 improved ≥5% in 19 (50%). TRS were constructed using top over-expressed and under-expressed genes for each. Adding the ∆FEV1 TRS for to a model with age, sex, and baseline FEV1 increased the AUC from 0.41 to 0.88; the ∆ybFEV1 TRS increased the AUC from 0.51 to 0.88; and the ∆BMI TRS increased the AUC from 0.46 to 0.92. Average accuracy was thus ~85% in predicting the response to the three outcomes. Results were similar in models further adjusted for F508del zygosity and previous CFTR modulator use. In conclusion, we identified nasal epithelial transcriptomic profiles that help accurately predict changes in FEV1 and BMI with ETI treatment. These novel TRS could serve as predictive biomarkers for clinical response to modulator treatment in pwCF.

Antitumor mechanisms of OncoTherad (MRB-CFI-1) nanoimmunotherapy involving monoamine oxidases: Clinical implications in BCG-unresponsive non-muscle invasive bladder cancer.

e14597 Background: Bacillus Calmette-Guérin (BCG) immunotherapy has been the gold standard treatment for non-muscle invasive bladder cancer (NMIBC) for nearly half a century. However, many high-risk patients experience recurrence, including those who progress and eventually become unresponsive to BCG. The emergence of new immunotherapeutic agents has revolutionized the treatment of various tumor types, including urothelial carcinoma. In this context, our research group has developed OncoTherad (MRB-CFI-1) immunotherapy, which has shown promising results in cancer treatment, particularly in NMIBC. Given the inherent complexity of the immune response, patient selection and the development of biomarkers to guide the identification of individuals who will derive the greatest benefit from a specific immunotherapy remain crucial. Over the past years, several studies have demonstrated the upregulation of monoamine oxidases (MAOs) in tumor progression and metastasis. Therefore, the objectives of this present study were to characterize the effects of OncoTherad (MRB-CFI-1) on the modulation of MAOs (MAO-A and MAO-B) in the bladder of patients with BCG-unresponsive NMIBC. Methods: A total of 40 bladder biopsies from patients with BCG-unresponsive NMIBC treated with OncoTherad (MRB-CFI-1) were collected and analyzed from Paulínia Municipal Hospital (HMP). These samples were then divided into two groups (n=20 per group): Group 1 (biopsy before OncoTherad treatment) and Group 2 (biopsy after OncoTherad treatment). Subsequently, the samples underwent immunohistochemical analyses for MAO-A and MAO-B. The retrospective anonymous study was approved by the local ethics committee (Clinical Trial: RBR-6swqd2). Results: Our results demonstrated high immunoreactivities for both MAO-A and MAO-B in the bladder tumor microenvironment prior to OncoTherad (MRB-CFI-1) treatment, confirming that the pattern reported in literature studies can also be observed in NMIBC. Total immunoreactivities for MAO-A did not differ statistically between bladder biopsies of Groups 1 and 2, indicating that this treatment does not interfere with the action of MAO-A in bladder tissue. In contrast, immunoreactivities for MAO-B were significantly lower (p<0.05) in the Group 2 when compared to Group 1 suggesting that this immunotherapy reversed the immunosuppressive state and tumor progression induced by MAO-B. Conclusions: Taken together, our results support the use of MAO-B as a biomarker for clinical response to OncoTherad (MRB-CFI-1) immunotherapy.

Advancing Evidence Generation for Circulating Tumor DNA: Lessons Learned from A Multi-Assay Study of Baseline Circulating Tumor DNA Levels across Cancer Types and Stages.

Circulating tumor DNA (ctDNA) holds promise as a biomarker for predicting clinical responses to therapy in solid tumors, and multiple ctDNA assays are in development. However, the heterogeneity in ctDNA levels prior to treatment (baseline) across different cancer types and stages and across ctDNA assays has not been widely studied. Friends of Cancer Research formed a collaboration across multiple commercial ctDNA assay developers to assess baseline ctDNA levels across five cancer types in early- and late-stage disease. This retrospective study included eight commercial ctDNA assay developers providing summary-level de-identified data for patients with non-small cell lung cancer (NSCLC), bladder, breast, prostate, and head and neck squamous cell carcinoma following a common analysis protocol. Baseline ctDNA levels across late-stage cancer types were similarly detected, highlighting the potential use of ctDNA as a biomarker in these cancer types. Variability was observed in ctDNA levels across assays in early-stage NSCLC, indicative of the contribution of assay analytical performance and methodology on variability. We identified key data elements, including assay characteristics and clinicopathological metadata, that need to be standardized for future meta-analyses across multiple assays. This work facilitates evidence generation opportunities to support the use of ctDNA as a biomarker for clinical response.

Biomarkers of immunotherapy in glioblastoma.

Glioblastoma (GBM) is the most common primary brain cancer, comprising half of all malignant brain tumors. Patients with GBM have a poor prognosis, with a median survival of 14-15 months. Current therapies for GBM, including chemotherapy, radiotherapy, and surgical resection, remain inadequate. Novel therapies are required to extend patient survival. Although immunotherapy has shown promise in other cancers, including melanoma and non-small lung cancer, its efficacy in GBM has been limited to subsets of patients. Identifying biomarkers of immunotherapy response in GBM could help stratify patients, identify new therapeutic targets, and develop more effective treatments. This article reviews existing and emerging biomarkers of clinical response to immunotherapy in GBM. The scope of this review includes immune checkpoint inhibitor and antitumoral vaccination approaches, summarizing the variety of molecular, cellular, and computational methodologies that have been explored in the setting of anti-GBM immunotherapies.

Abstract 219: Molecular and therapeutic characterization of a large-scale collection of metastatic colorectal cancer patient-derived xenografts and matched organoids for translational oncology

Abstract Strong evidence supports the use of patient-derived xenografts (PDXs) as faithful models reflecting patient outcomes. Since not all research can support the use of animals, exploiting patient-derived in vitro models such as organoids (also know as tumoroids) is essential. However, current biobanks of metastatic colorectal cancer (mCRC) tumoroids have important limitations, such as small sample size and a lack of systematic in vivo validation with paired xenografts, which decreases the translational value of tumoroid-based pipelines. Here we describe XENTURION, a unique open-science resource of XENografts and Tumoroids for Research In ONcology that encompasses 129 sibling pairs of mCRC PDXs and PDX-derived tumoroids (PDXTs) with accompanying molecular and therapeutic characterization.The vast majority of XENTURION models were analyzed for mutations (targeted next-generation sequencing of 116 relevant CRC genes), gene copy number architecture (DNA shallow sequencing) and global transcriptomics (RNAseq) and benchmarked against large patient datasets (TCGA and MSK-IMPACT). Results showed that the PDX-PDXT collection proved to be representative of the genetic heterogeneity of mCRCs and displayed high genetic and transcriptional similarity between matched pairs. A PDXT-based population trial with the clinically approved anti-EGFR antibody cetuximab was performed in 116 PDXTs, revealing variable sensitivities that were consistent with clinical response biomarkers and with tumor growth changes in 79 matched PDXs. Cetuximab response profiles also recapitulated the outcome of EGFR knock-out by CRISPR-Casp9 technology in 13 representative PDXTs. Adaptive signals upregulated by EGFR blockade both in tumoroids and PDXs were computationally and functionally prioritized. Top candidates were screened in PDXTs and 3 surviving compounds were identified as actionable co-extinction targets with cetuximab in 12 PDXT models. Results were finally validated in PDXs.To our knowledge, this is the first large-scale study in which a systematic comparison of molecular and therapeutic profiles between PDXT-PDX pairs was attempted. As a publicly available resource, XENTURION will offer a knowledge base of disseminatable methods, resources and information to streamline preclinical studies and accelerate new treatments for patients with mCRC. Citation Format: Simonetta M. Leto, Elena Grassi, Marco Avolio, Valentina Vurchio, Francesca Cottino, Martina Ferri, Eugenia R. Zanella, Laura Di Blasio, Alberto Puliafito, Luca Primo, Andrea Bertotti, Livio Trusolino. Molecular and therapeutic characterization of a large-scale collection of metastatic colorectal cancer patient-derived xenografts and matched organoids for translational oncology [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 219.

Abstract 3695: Monitoring response to immunotherapy using cell free DNA fragmentomes

Abstract BACKGROUND: The rapid detection of disease progression in patients receiving immune checkpoint inhibitors (ICIs) is challenging since there are no reliable biomarkers of clinical response. Liquid biopsy assays may address this unmet need by using cell-free DNA (cfDNA) to monitor treatment responses. Current targeted next-generation sequencing cfDNA assays are costly and have limited assay sensitivity for detection of cancer-specific mutations at low mutant allele frequency (MAF). Here, we demonstrate the utility of DELFI Tumor Fraction (DELFI-TF), a tumor- and mutation-independent cfDNA fragmentome approach to monitor treatment response in patients with metastatic non-small cell lung cancer (mNSCLC). METHODS: Overall, 422 longitudinal blood samples were collected from 141 mNSCLC patients of which 109 were treated with immunotherapy and 32 with targeted therapy (TT). Plasma-derived cfDNA was processed with whole genome sequencing at low coverage (~4x). Circulating tumor burden was quantified as the maximum MAF (maxMAF) of tumor-derived variants detected using a 500+gene panel. Matched white blood cells were used to filter out germline and clonal hematopoietic variants. A random forest regression model was trained with maxMAF as the response using fragmentation-derived features. The accuracy of DELFI-TF was assessed using leave one patient out cross-validation in the ICI cohort and holdout validation in the cohort of patients receiving TT. For survival analyses, we used the median baseline scores to define low/high DELFI-TF and maxMAF. RESULTS: In the ICI cohort, DELFI-TF scores were strongly correlated with the maxMAF (r=0.94, p<0.001, Pearson). At baseline, DELFI-TF and maxMAF both differentiate responding from non-responding tumors (p = 0.01 and p = 0.001 for DELFI-TF and maxMAF respectively; Wilcoxon). Patients with high DELFI-TF or maxMAF had significantly shorter progression-free survival (PFS) compared to low DELFI-TF or maxMAF (17.0 vs 4.7 months, p < 0.001; 17.0 vs 4.6 months, p < 0.001; Log-Rank respectively) and similar overall survival (OS) (DELFI-TF high 11.4 vs low 34.1 months, p<0.001; maxMAF high 10.9 vs low 34.1 months, p < 0.001, Log-Rank). Changes in DELFI-TF and maxMAF at the earliest timepoint were highly correlated (n=109; r=0.90; Pearson). In the validation cohort of TT patients, DELFI-TF at baseline outperformed maxMAF in distinguishing patients with PFS and OS benefits (DELFI-TF PFS 36.4 vs 11.5 months, p = 0.03; maxMAF PFS 21.9 vs 15.9 months, p=0.6; Log-Rank) (DELFI-TF OS high 37 months vs low not reached (NR), p < 0.05; Max MAF OS high 37 vs NR, p = 0.1, Log-Rank). The majority of TT patients (81%) had consistent changes with DELFI-TF and maxMAF from baseline to the earliest timepoint. CONCLUSIONS: DELFI-TF is a tumor and mutation independent approach that is cost-efficient with high performance comparable to current ctDNA assays for estimating tumor burden and monitoring response in cancer patients. Citation Format: Bahar Alipanahi, Lavanya Sivapalan, Jamie Medina, Zachary L. Skidmore, Paola Ghanem, Erica Peters, Gavin Pereira, Nisha Rao, Kavya Velliangiri, Alissa Konicki, Stephen Cristiano, Laurel Millberg, Jacob Carey, Keith Lumbard, Noushin Niknafs, Bryan Chesnick, Jennifer Tom, Alessandro Leal, Benjamin Levy, Patrick Forde, Peter Bach, Nicholas C. Dracopoli, Robert B. Scharpf, Victor Velculescu, Lorenzo Rinaldi, Valsamo Anagnostou. Monitoring response to immunotherapy using cell free DNA fragmentomes [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 3695.

Abstract B030: PARP-1 inhibition results in ovarian and endometrial cancer cell death by disrupting the nucleolar localization of the RNA helicase DDX21 which is associated with decreased survival outcomes

Abstract Cancer cells with DNA repair defects (e.g., BRCA1/2 mutant cells) are vulnerable to PARP inhibitors (PARPi) due to induction of synthetic lethality. However, recent clinical evidence has shown that PARPi can prevent the growth of some cancers irrespective of their BRCA1/2 status, suggesting alternative mechanisms of action. One such mechanism involves DDX21, an RNA helicase that localizes to the nucleoli of cells. When ADP-ribosylated by PARP-1, DDX21 promotes rDNA transcription leading to ribosome biogenesis, protein translation, and ultimately the growth of breast cancer cells. Validating this pathway in other tumor types may lead to the expanded use of PARPi as a cancer therapeutic and the potential use of DDX21 nucleolar localization as a biomarker of clinical response to PARPi. For our first aim, we hypothesized that PARPi also blocks the DDX21/PARP-1/ribosome biogenesis pathway in ovarian and endometrial cancers and can thus be used to inhibit their growth. To test this, we are determining the effect of Niraparib, an inhibitor targeting PARP-1 activity, on DDX21 subcellular localization, ribosome biogenesis, and cell growth in different ovarian (OVCAR3, OVCAR4, and HCC5012) and endometrial (KLE, Ishikawa, and HEC-1-A) cancer cell lines. We are using Western blotting to assess the levels of DDX21 and ADP-ribosylation, and immunofluorescent staining to assess the localization of DDX21 to nucleoli before and after treatment with Niraparib. We are also using qPCR to determine the levels of rRNAs and Puromycin incorporation assays to monitor ribosome translation activity before and after treatment with Niraparib. Moreover, we are using cell growth assays to determine the effect of Niraparib on the proliferation of the ovarian and endometrial cancer cell lines. Our cell-based results indicate that the nucleolar localization of DDX21 is disrupted by Niraparib treatment, leading to a pan-nuclear distribution. Furthermore, Niraparib treatment in ovarian cancer cell lines causes decreased rRNA transcription, decreased protein translation, and decreased cell proliferation. For our second aim, we are assessing possible associations among DDX21 nucleolar localization, PARP-1 protein levels, and clinical outcomes in cancer samples from patients using immunohistochemical (IHC) staining for DDX21 and PARP-1. Analysis of endometrial cancer patient samples suggests a significant association among high DDX21 nucleolar localization, high PARP-1 expression, and decreased survival. Overall, our results suggest that Niraparib works, in part, by blocking the DDX21/PARP-1/ribosome biogenesis pathway leading to endometrial and ovarian cancer cell death. The potential use of DDX21 localization as a biomarker of response to PARPi and as a prognostic factor will be further explored by conducting additional laboratory and clinical studies. Citation Format: Marwa W. Aljardali, Kevin M. Kremer, Jessica Parker, Jayanthi S. Lea, W. Lee Kraus, Cristel V. Camacho. PARP-1 inhibition results in ovarian and endometrial cancer cell death by disrupting the nucleolar localization of the RNA helicase DDX21 which is associated with decreased survival outcomes [abstract]. In: Proceedings of the AACR Special Conference on Ovarian Cancer; 2023 Oct 5-7; Boston, Massachusetts. Philadelphia (PA): AACR; Cancer Res 2024;84(5 Suppl_2):Abstract nr B030.

Effects of electroconvulsive therapy on cortical thickness in depression: a systematic review.

Electroconvulsive therapy (ECT) is one of the most studied and validated available treatments for severe or treatment-resistant depression. However, little is known about the neural mechanisms underlying ECT. This systematic review aims to critically review all structural magnetic resonance imaging studies investigating longitudinal cortical thickness (CT) changes after ECT in patients with unipolar or bipolar depression. We performed a search on PubMed, Medline, and Embase to identify all available studies published before April 20, 2023. A total of 10 studies were included. The investigations showed widespread increases in CT after ECT in depressed patients, involving mainly the temporal, insular, and frontal regions. In five studies, CT increases in a non-overlapping set of brain areas correlated with the clinical efficacy of ECT. The small sample size, heterogeneity in terms of populations, comorbidities, and ECT protocols, and the lack of a control group in some investigations limit the generalisability of the results. Our findings support the idea that ECT can increase CT in patients with unipolar and bipolar depression. It remains unclear whether these changes are related to the clinical response. Future larger studies with longer follow-up are warranted to thoroughly address the potential role of CT as a biomarker of clinical response after ECT.

Clinical Utility and Implementation of Pharmacogenomics for the Personalisation of Antipsychotic Treatments.

Decades of pharmacogenetic research have revealed genetic biomarkers of clinical response to antipsychotics. Genetic variants in antipsychotic targets, dopamine and serotonin receptors in particular, and in metabolic enzymes have been associated with the efficacy and toxicity of antipsychotic treatments. However, genetic prediction of antipsychotic response based on these biomarkers is far from accurate. Despite the clinical validity of these findings, the clinical utility remains unclear. Nevertheless, genetic information on CYP metabolic enzymes responsible for the biotransformation of most commercially available antipsychotics has proven to be effective for the personalisation of clinical dosing, resulting in a reduction of induced side effects and in an increase in efficacy. However, pharmacogenetic information is rarely used in psychiatric settings as a prescription aid. Lack of studies on cost-effectiveness, absence of clinical guidelines based on pharmacogenetic biomarkers for several commonly used antipsychotics, the cost of genetic testing and the delay in results delivery hamper the implementation of pharmacogenetic interventions in clinical settings. This narrative review will comment on the existing pharmacogenetic information, the clinical utility of pharmacogenetic findings, and their current and future implementations.

CD74 is associated with inflamed tumor immune microenvironment and predicts responsiveness to PD-1/CTLA-4 bispecific antibody in patients with solid tumors

IntroductionCadonilimab (AK104) is a first-in-class tetravalent bispecific antibody that targets both PD-1 and CTLA-4, showing a manageable safety profile and favorable clinical benefits. This study aimed to identify the biomarkers of clinical response and explore the immune response within the tumor microenvironment upon the AK104 therapy in advanced solid tumors.Material and methodsGene expression profiles of paired pre- and post-treatment tumor tissues from twenty-one patients were analyzed. The association of gene expression levels with either clinical efficacy or prognosis was evaluated and subsequently validated with published datasets using log-rank for Kaplan–Meier estimates. Comparative immune profile analyses of tumor microenvironment before and after AK104 treatment were conducted. The visualization of tumor-infiltrating lymphocytes was performed using multiplex immunohistochemistry. The predictive value of CD74 was further validated with protein expression by immunohistochemistry.ResultsBaseline CD74 gene expression was associated with favorable patient outcomes (overall survival [OS], HR = 0.33, 95% CI 0.11–1.03, p = 0.0463), which was further confirmed with the published datasets. Tumors with high CD74 gene expression at baseline were more likely to exhibit an immune-inflamed microenvironment. AK104 efficiently enhanced the infiltration of immune cells in the tumor microenvironment. Additionally, high CD74 protein expression (≥ 10% of the tumor area occupied by CD74 stained immune cells) at baseline was associated with better progressive-free survival (HR = 0.21, 95% CI 0.06–0.68, p = 0.0065) and OS (HR = 0.35, 95% CI 0.12–1.08, p = 0.0615).ConclusionsOur findings demonstrate that CD74 is a promising predictive biomarker for AK104 therapeutic response in advanced solid tumors.Trial registration number NCT03261011.

DOP22 Predictive biomarkers of therapeutic response in Inflammatory Bowel Disease: a step towards personalized medicine

Abstract Background Inflammatory bowel diseases are complex conditions characterized by heterogeneity at clinical, immunological, molecular, genetic, and microbial levels. The most effective approaches to induce clinical remission and control inflammation in these diseases are biologic and JAK-inhibitor therapies. However, a significant proportion of patients do not respond to treatment. Consequently, the identification of predictive biomarkers of clinical response to the different available therapies could improve the selection of patients who may benefit from the most appropriate treatment. Methods A multiomic study (transcriptomic, proteomic, metabolomic and metagenomic) was performed in 53 patients with active Crohn´s disease (CD) and 50 patients with active ulcerative colitis (UC) before and after 14 weeks of treatment (anti-TNFα, ustekinumab, vedolizumab or tofacitinib). Responders and non-responders patients were categorized based on endoscopic findings. Samples (serum, urine, stool and intestinal biopsies) were used for RNA-seq analysis, liquid chromatography-mass spectrometry, nuclear magnetic resonance, and 16S rRNA gene sequencing. Results Our findings revealed multiple mRNAs, proteins and metabolites associated with the response to different treatments (Table 1). Differential gene expression analyses in intestinal tissue showed that the main differences were detected between responders versus non-responders UC patients to anti-TNF, vedolizumab and tofacitinib. Proteomic analysis found numerous differentially expressed proteins between the study groups. Additionally, ROC curves revealed two proteins with good predictive value to discriminate between CD and UC patients responders versus non-responders to anti-TNF treatment (AUC=0.81 and AUC=0.96, respectively). Metabolomics showed up-regulation of 21 lipoproteins in serum from CD patients responders to ustekinumab compared to non-responders. Metabolic analysis pathways identified enrichment in ketone and butyrate metabolism, mitochondrial electron transport chain, carnitine synthesis, and oxidation of chain fatty acids. Regarding metagenomic results, only differences were found in microbial composition in responders versus non-responders UC patients treated with anti-TNF (Figure 1). Conclusion This study provides early insights into shifts in gene and protein expression in intestinal tissue, alterations in serum and urine metabolites, and changes in gut microbiota as potential predictors of response to biologics and JAK-inhibitor treatment. Further research is needed to validate these results and asses their clinical significance in identifying patients most likely to benefit from each therapeutic approach.

Response to Fingolimod in Multiple Sclerosis Patients Is Associated with a Differential Transcriptomic Regulation.

Fingolimod is an immunomodulatory sphingosine-1-phosphate (S1P) analogue approved for the treatment of relapsing-remitting multiple sclerosis (RRMS). The identification of biomarkers of clinical responses to fingolimod is a major necessity in MS to identify optimal responders and avoid the risk of disease progression in non-responders. With this aim, we used RNA sequencing to study the transcriptomic changes induced by fingolimod in peripheral blood mononuclear cells of MS-treated patients and their association with clinical response. Samples were obtained from 10 RRMS patients (five responders and five non-responders) at baseline and at 12 months of fingolimod therapy. Fingolimod exerted a vast impact at the transcriptional level, identifying 7155 differentially expressed genes (DEGs) compared to baseline that affected the regulation of numerous signaling pathways. These DEGs were predominantly immune related, including genes associated with S1P metabolism, cytokines, lymphocyte trafficking, master transcription factors of lymphocyte functions and the NF-kB pathway. Responder and non-responder patients exhibited a differential transcriptomic regulation during treatment, with responders presenting a higher number of DEGs (6405) compared to non-responders (2653). The S1P, NF-kB and TCR signaling pathways were differentially modulated in responder and non-responder patients. These transcriptomic differences offer the potential of being exploited as biomarkers of a clinical response to fingolimod.

Elucidating the Heterogeneity of Immunotherapy Response and Immune-Related Toxicities by Longitudinal ctDNA and Immune Cell Compartment Tracking in Lung Cancer.

Although immunotherapy is the mainstay of therapy for advanced non-small cell lung cancer (NSCLC), robust biomarkers of clinical response are lacking. The heterogeneity of clinical responses together with the limited value of radiographic response assessments to timely and accurately predict therapeutic effect-especially in the setting of stable disease-calls for the development of molecularly informed real-time minimally invasive approaches. In addition to capturing tumor regression, liquid biopsies may be informative in capturing immune-related adverse events (irAE). We investigated longitudinal changes in circulating tumor DNA (ctDNA) in patients with metastatic NSCLC who received immunotherapy-based regimens. Using ctDNA targeted error-correction sequencing together with matched sequencing of white blood cells and tumor tissue, we tracked serial changes in cell-free tumor load (cfTL) and determined molecular response. Peripheral T-cell repertoire dynamics were serially assessed and evaluated together with plasma protein expression profiles. Molecular response, defined as complete clearance of cfTL, was significantly associated with progression-free (log-rank P = 0.0003) and overall survival (log-rank P = 0.01) and was particularly informative in capturing differential survival outcomes among patients with radiographically stable disease. For patients who developed irAEs, on-treatment peripheral blood T-cell repertoire reshaping, assessed by significant T-cell receptor (TCR) clonotypic expansions and regressions, was identified on average 5 months prior to clinical diagnosis of an irAE. Molecular responses assist with the interpretation of heterogeneous clinical responses, especially for patients with stable disease. Our complementary assessment of the peripheral tumor and immune compartments provides an approach for monitoring of clinical benefits and irAEs during immunotherapy.

42292 Plasma biomarkers for clinical response and disease severity identified from Hidradenitis Suppurativa patients in the phase II AURORA study

42292 Plasma biomarkers for clinical response and disease severity identified from Hidradenitis Suppurativa patients in the phase II AURORA study

Evaluation of a semi-automated approach for FDG PET image analysis for routine clinical application in patients with multiple myeloma

BackgroundFDG PET/CT is a tool for assessing response to therapy in various cancers, and may provide an earlier biomarker of clinical response. We developed a novel semi-automated approach for analyzing FDG PET/CT images in patients with multiple myeloma (MM) to standardize FDG PET application. MethodsPatients (n = 8) with relapsed/refractory MM from the Phase 2 study (NCT02899052) of venetoclax plus carfilzomib and dexamethasone underwent FDG PET/CT at baseline and up to two timepoints during treatment. Images were processed using an established automated segmentation algorithm, with the modification that a red marrow region in an unaffected lumbar vertebra was used to define background standardized uptake value normalized to lean body mass (SUL) threshold above which uptake was considered disease-specific uptake. This approach was compared to lesion segmentation, and to International Myeloma Working Group (IMWG) response criteria, including minimal residual disease (MRD). ResultsThe two FDG PET analysis techniques agreed on evaluation of patient-level SULpeak for 67% of scans. In the metabolic response assessment per PET Response Criteria in Solid Tumors (PERCIST), the two techniques agreed in 75% of patients. Differences between techniques occurred in low-uptake lesions due to greater reader sensitivity to lesions with uptake marginally above background. PERCIST outcomes were generally in agreement with IMWC and MRD. ConclusionsThis semi-automated analysis was in high agreement with standard approaches for detecting response to MM therapy. This proof-of-concept study suggests that larger studies should be conducted to confirm how FDG PET analysis may aid early response detection in MM.

LB1630 Modular analysis of the psoriasis transcriptome identifies biomarkers of clinical response to distinct classes of biologics and elucidates drug and disease endotypes across skin and blood

LB1630 Modular analysis of the psoriasis transcriptome identifies biomarkers of clinical response to distinct classes of biologics and elucidates drug and disease endotypes across skin and blood