Predictive Biomarkers Of Response Research Articles

A comprehensive view of N-glycosylation as clinical biomarker in prostate cancer.

Alterations in the prostate cancer (PCa) N-glycome have gained attention as a potential biomarker. This comprehensive review explores the diversity of N-glycosylation patterns observed in PCa-related cell lines, tissue, serum and urine, focusing on prostate-specific antigen (PSA) and the total pool of glycoproteins. Within the context of PCa, altered N-glycosylation patterns are a mechanism of immune escape and a disruption in normal glycoprotein distribution and trafficking. Glycoproteins with PCa-induced N-glycosylation patterns tend to accumulate in prostate tissue and the bloodstream, thereby diminishing N-glycan proportions in urine. Based on literary observations, aberrations in N-glycan branching are probably a characteristic of metabolic reprogramming and (chronic) inflammation. Changes in (core) fucosylation, specific N-glycosylation structures (such as N,N'-diacetyllactosamine) and high-mannose glycans otherwise are more likely indicators of cancer development and progression. Further investigation into these PCa-specific alterations holds promise in the discovery of new diagnostic, prognostic and response prediction biomarkers in PCa.

Evaluation of EpiSwitch in predicting immunotherapy response in hepatocellular carcinoma and gastrointestinal tumors.

623 Background: The EpiSwitch Checkpoint Inhibitor Response Test (CiRT) is a blood-based assay that analyzes DNA conformations in immune cells to predict responses to immune checkpoint inhibitors (ICIs) targeting PD-L1/PD-1. CiRT has demonstrated superior predictive accuracy compared to traditional biomarkers, such as tumor mutational burden (TMB) and PD-L1 immunohistochemistry (IHC), for predicting responses in urothelial cancer (ESMO 2022). However, its role in hepatocellular carcinoma (HCC) and other gastrointestinal (GI) tumors remains unclear. As immunotherapy becomes more common in these cancers, identifying reliable predictive biomarkers is essential to optimize treatment outcomes. Methods: This retrospective study evaluates CiRT-predicted immunotherapy responses and clinical outcomes in patients with HCC and GI tumors, including cholangiocarcinoma, pancreatic adenocarcinoma, and gastric cancer. All patients received one or more lines of immunotherapy. CiRT responses were categorized into high probability (HP) and low probability (LP). Treatment response was assessed per RECIST 1.1 criteria. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), overall survival (OS), and progression-free survival (PFS) were analyzed. Results: 43 patients (24 HP, 19 LP) were included. HCC patients (n = 33) received varied immunotherapy regimens, such as combinations of bevacizumab with atezolizumab, tremelimumab with durvalumab, and nivolumab with ipilimumab. Non-HCC patients (n = 10) received combinations of immunotherapy and chemotherapy such as durvalumab with cisplatin and gemcitabine and nivolumab with oxaliplatin and capecitabine. Across all patients, CiRT revealed a sensitivity of 73.91%, a specificity of 65%, a PPV of 70.83%, and an NPV of 68.42%. In HCC, sensitivity was 70.59% and specificity was 68.75%. In non-HCC, sensitivity was 83.33% and specificity 50%. HP responders showed better treatment outcomes compared to LP responders, with higher rates of complete response (CR: 12.5% vs 0%), partial response (PR: 29.2% vs 21.1%), and stable disease (SD: 29.2% vs 10.5%), and a lower rate of progressive disease (PD: 29.2% vs 68.4%) (p = 0.0467). Overall, 70.83% of HP achieved CR, PR, or SD vs. 31.58% of LP (p = 0.0098). PFS was significantly better in HP (p = 0.044, Log-rank test; median PFS = 2.0 months for the LP group, mPFS not reached for the HP group). No statistically significant OS difference was noted due to the lack of events in the HP group. Conclusions: CiRT HP status was associated with improved response rates to immunotherapy, longer PFS, and better treatment outcomes in HCC and GI tumors. HP responders experienced notably better outcomes, suggesting that CiRT could serve as a promising predictive biomarker for immunotherapy response, addressing a critical unmet need for reliable biomarkers to treat HCC and other GI tumors.

Alteration of gut microbiota in patients with advanced hepatocellular carcinoma.

641 Background: Hepatocellular carcinoma (HCC) is the most common primary liver cancer and the third leading cause of cancer-related death worldwide. Despite advancements in treatment, such as novel combinations of immunotherapy and targeted therapy or dual immunotherapy, the prognosis remains poor due to a lack of predictive biomarkers for treatment response. Gut microbiota alterations have been proposed as both potential diagnostic biomarker and predictive biomarker. However, data in this field are not well-established and are mostly derived from studies conducted in China and Western countries, which may not fully reflect the situation in Thailand. Methods: Fecal samples were collected from pre-treated advanced HCC patients who visited medical oncology outpatient clinic at Srinagarind hospital, Khon Kaen University (HCC group = 27) and analyzed using 16S rRNA sequencing of gut microbiota. Additional sequenced data from a healthy population (Control group = 31) who had no underlying disease and had normal liver ultrasonography were retrieved from a previous study conducted by Khon Kaen University (Cholangiocarcinoma Screening and Care Program, CASCAP). The datasets were compared using the Wilcoxon rank-sum test to analyze the alteration of gut microbiota between HCC group and control group. Results: The HCC group exhibited significantly lower biodiversity index (p< 0.001) than control group in terms of richness, Shannon diversity index and Simpson’s index. The HCC group had significantly higher relative abundance of the phylum Proteobacteria (p< 0.001), Firmicutes (p< 0.001) and a lower abundance of the phylum Actinobacteria (p< 0.001) compared to the control group. Additionally, the HCC group had significantly higher relative abundance of Stenotrophomonas, Granulicatella, Ruminococcus, Blautia, Phascolarctobacterium, Butyricoccus, Streptococcus, Escherichia-Shigella, Flavonifractor, Haemophilus and Lachnospira at the genus level. Further analysis of relative abundance of gut microbiota at the genus level and clinical prognostic parameters showed positive correlation between Streptococcus and 6-month survival status. Conclusions: Gut microbiota profile in patients with advanced HCC was significantly altered from healthy control group. This could be the evidence of microbial dysbiosis and may potentially be biomarker for prognosis.

Unraveling the role of interferon-stimulated neutrophils: A promising biomarker for immunotherapy efficacy and prognosis in gastric adenocarcinoma.

472 Background: Despite significant advancements in immunotherapy, the identification of effective predictive biomarkers for treatment response in gastric adenocarcinoma (GAC) remains a critical challenge. Discovering such biomarkers could enhance patient stratification and improve therapeutic outcomes. Methods: We conducted a comprehensive analysis of 18 specimens obtained from 10 GAC patients, both prior to and following immunotherapy. Utilizing single-cell RNA sequencing, we compared the cellular composition and functional phenotypes of these specimens, with particular emphasis on tumor-infiltrating immune cells and the identification of previously uncharacterized neutrophil subclusters. Results: Our analysis identified eight distinct neutrophil subclusters, including Neu01_S100A12, Neu02_VEGF, Neu03_CCL3_CCL4, Neu04_IL1β, Neu05_CXCR4, Neu06_IFN-Stimulated, Neu07_Proliferative, and Neu08_B-cell_related. Notably, the presence of IFN-Stimulated neutrophils was positively correlated with the efficacy of immunotherapy in GAC, a finding that was further validated through analyses of public datasets and in-house cohort studies employing multiplex immunohistochemistry. Additionally, IFN-Stimulated neutrophils served as prognostic indicators across multiple datasets. Investigations revealed that these cells engage in significant cellular communication with other immune components within the tumor microenvironment, including CD8+ T cells, macrophages, and B cells, thereby promoting a pro-inflammatory and anti-tumor phenotype. Importantly, pan-cancer analyses demonstrated the consistent prognostic and immunotherapy efficacy-predicting potential of IFN-Stimulated neutrophils across various cancer types. Conclusions: IFN-Stimulated neutrophils represent a promising biomarker for predicting immunotherapy response and patient prognosis in GAC. Our findings offer novel insights into the underlying mechanisms of immunotherapy and highlight potential avenues for personalized treatment strategies in the management of GAC.

Circulating tumor DNA for predicting complete response to total neoadjuvant therapy in locally advanced rectal cancer: ENSEMBLE-2.

284 Background: Total neoadjuvant therapy (TNT) has dramatically shifted the paradigm in the treatment of locally advanced rectal cancer (LARC), prolonging survival with high rates of pathologic complete response (pCR) and introducing non-operative management (NOM). However, no predictive biomarkers of TNT efficacy, the regrowth of NOM, or prognosis have been developed. Circulating tumor DNA (ctDNA) is a minimally invasive biomarker used to detect molecular residual disease (MRD) and predict recurrence in colon cancer after curative resection. The effectiveness of ctDNA MRD status as a predictive biomarker for TNT was evaluated in the Phase II TNT study, ENSEMBLE-2 (jRCTs071210143), conducted in Japan. Methods: Patients with LARC undergoing TNT were enrolled in ENSEMBLE-2. Protocol treatment was defined as total mesorectal excision (TME) following long course chemoradiotherapy (LCCRT: 50.4Gy, capecitabine) plus four cycles of CAPOX. NOM was allowed if a clinical complete response (cCR) was achieved in the evaluation after TNT. ctDNA MRD was measured by Signatera (Natera, Inc.) at the following time points: baseline, after LCCRT, after TNT, post operative 4w, 12w, 24, 36 and 48w in the GALAXY trial (UMIN000039205). Results: A total of 28 patients were enrolled in the study. Treatment was discontinued at the patient's request in one case. After completing TNT, TME and NOM were performed in 21 (77.8%) and 6 (21.4%) patients, respectively. ctDNA positivity rates were 96.4. % (27/28) at baseline, 14.8% (4/27) after LCCRT, and 34.6 % (9/26) after TNT. Post-LCCRT ctDNA status was not significantly associated with cCR + near CR (nCR) vs. incomplete clinical response (iCR), pCR vs. non-pCR (p=0.065 and p=0.539, respectively). In contrast, ctDNA status after TNT was significantly associated with cCR + nCR vs. iCR (p=0.028), as well as pCR vs. non-pCR (p=0.038). Conclusions: Our study indicates that post TNT ctDNA status may be a predictive biomarker for TNT response in LARC patients. ctDNA negativity upon completion of neoadjuvant treatment may indicate a favorable response. Clinical trial information: jRCTs071210143 . Correlation with ctDNA, clinical response, treatment after TNT and pathological response. After LCCRT p value After TNT p value Clinical ResponsecCR + nCR vs. iCR (ctDNA -/+) cCR + nCR 18 / 1 0.065 cCR + nCR 15 / 4 0.028 iCR 5 / 3 iCR 2 / 5 Treatment after TNTNOM vs. TME (ctDNA -/+) TME 17 / 3 0.438 TME 11 / 9 0.063 NOM 6 / 0 NOM 6 / 0 Pathological response after TMEpCR vs. non pCR (ctDNA -/+) pCR 5 / 0 0.539 pCR 5 / 0 0.038 non pCR 12 / 3 non pCR 6 / 9 Fisher's exact test was used to statistically examine the correlation between ctDNA MRD status and the factors at each timing.

Revolutionizing lung cancer treatment: Introducing PROTAC therapy as a novel paradigm in targeted therapeutics.

This comprehensive review explores the transformative potential of PROTAC (Proteolysis-Targeting Chimeras) therapy as a groundbreaking approach in the landscape of lung cancer treatment. The introduction provides a succinct overview of current challenges in lung cancer treatment, emphasizing the significance of targeted therapies. Focusing on PROTAC therapy, the article elucidates its mechanism of action, comparing it with traditional targeted therapies and highlighting the key components and design principles of PROTAC molecules. In the context of lung cancer, the review meticulously summarizes preclinical evidence, emphasizing efficacy and specificity gleaned from studies evaluating PROTAC therapy. It delves into the implications of this preclinical data, discussing potential advantages over existing targeted therapies. An update on ongoing clinical trials involving PROTAC therapy for lung cancer offers a snapshot of the current progress, with a summary of key outcomes and advancements in early-phase trials. The mechanistic insights into PROTAC therapy's impact on lung cancer cells are explored, alongside a discussion on potential biomarkers for patient stratification and response prediction. The influence of tumor heterogeneity on PROTAC therapy outcomes is also addressed. Safety and tolerability assessments, encompassing preclinical and clinical studies, are comprehensively evaluated, including a comparative analysis with traditional targeted therapies and strategies to mitigate side effects. Looking forward, the article discusses the future perspectives of PROTAC therapy in lung cancer treatment and addresses ongoing challenges, providing a nuanced exploration of potential combination therapies and synergistic approaches. In conclusion, the review summarizes key findings and insights, underscoring the tremendous potential of PROTAC therapy as a promising and innovative avenue in pursuing more effective lung cancer treatments.

Kinomic profiling to predict sunitinib response of patients with metastasized clear cell Renal Cell Carcinoma.

Treatment with Sunitinib, a potent multitargeted receptor tyrosine kinase inhibitor (TKI) has increased the progression-free survival (PFS) and overall-survival (OS) of patients with metastasized renal cell carcinoma (mRCC). With modest OS improvement and variable response and toxicity predictive and/or prognostic biomarkers are needed to personalize patient management: Prediction of individual TKI therapy response and resistance will increase successful treatment outcome while reducing unnecessary drug use and expense. The aim of this study was to investigate whether kinase activity analysis can predict sunitinib response and/or toxicity using tissue samples obtained from primary clear cell RCC (ccRCC) from a cohort of clinically annotated patients with mRCC receiving sunitinib as first-line treatment. EuroTARGET partners collected ccRCC and matched normal kidney tissue samples immediately after surgery, snap-frozen and stored at -80°C until use. Phosphotyrosine-activity profiling was performed using PamChip® peptide microarrays (144 peptides derived from known phosphorylation sites in Protein Tyrosine Kinase substrates) of lysed tissue samples (5 µg protein input) of 163 mRCC patients. Evolve software Was used to analyze kinome profiles and Bionavigator was used for unsupervised and supervised clustering. The kinexus kinase predictor (www.phosphonet.ca) was used to analyze the peptide lists within the clusters. Kinome data was available from 94 patients who received sunitinib as 1st-line treatment and had complete follow-up of their clinical data (PFS, OS and toxicity) for at least 6 months. Matched normal tissue was available from 14 mRCC patients. Supervised clustering of basal kinome activity could correctly classify mRCC patients with PFS >9 months versus PFS<9 months with an accuracy of 61 %. Unsupervised hierarchical clustering revealed 3 major clusters related to immune signaling, VEGF pathway, and immune signaling/cell adhesion. Basal kinase activity levels of patients with short PFS were substantially higher compared to patients who experienced extended PFS. Based on kinase levels ccRCC tumors can be subdivided into 3 clusters which may reflect the aggressiveness of these tumors. The accuracy of response prediction of 61 % based on basal kinase levels is too low to justify implementation. STK assays may help to predict sunitinib toxicity and guide clinical management. Additionally, it is possible that mRCC patients with an immune kinase signature are better checkpoint inhibitor candidates, but this needs to be studied.

A prospective multi-site translational study investigating the association of gut microbiome (GM) diversity with pathological complete response (pCR) after neoadjuvant treatment in early stage rectal and esophageal cancer.

TPS849 Background: The diversity of the GM is defined as the number and relative abundance distribution of distinct types of microorganisms colonizing within the gut. Studies have suggested that dysbiosis of the GM confers a predisposition to certain malignancies and impacts response to immunomodulating therapies. The influence of the GM diversity on the pathological response after neoadjuvant chemotherapy and radiotherapy is unclear. Some studies have suggested that the GM may offer predictive biomarkers for response to chemoradiation in rectal cancer. Other studies in early-stage rectal cancer patients indicated an association between GM diversity and pathological outcomes following neo-adjuvant therapy (NAT). We hypothesize that a more diverse GM constitution at baseline leads to an improved pathological response at the time of definitive surgery. Methods: We designed a cross-institutional translational study investigating the impact of the GM diversity on the efficacy of NAT in GI cancers by assessing its association with pathological response. The study population includes patients with early-stage rectal or esophageal cancer due to commence NAT (including chemotherapy and chemoradiation) who are planned for definitive surgery. Exclusion criteria includes prior allogenic tissue/solid organ transplantation and prior receipt of anti-cancer therapy. The study assessments include fecal sampling of the GM prior to NAT, upon completion and again six months post completion of therapy. Fecal samples are analysed by 16S RNA sequencing. Pathological response will be examined at time of surgery and patients will be classified as responders (complete pathological response) or non-responders. The primary endpoint of the study is to examine the association between the GM diversity and pathological response. Exploratory analysis will include the assessment of the association between cf-DNA and the GM diversity as well as an assessment of the association between cf-DNA at baseline and pCR. Species richness (Alpha Diversity) will be analysed using the Shannon diversity index and Jaccard similarity index will be used to calculate beta diversity. Following planned study recruitment, classification and clustering analysis will be performed with Principal Component Analysis (PCA) and Random Forest analysis. Logistic regression analysis adjusting for potential confounding factors will be employed to assess the primary endpoint of the association between GM and complete pCR in the final statistical analysis. Adjusted odds ratios (OR) and 95% confidence intervals will be presented. This trial accrued 11 patients between May 2023 and Sept 2024. Out of the 11 patients enrolled, 9 patients have undergone their planned surgery. We are expecting to have 30 patients accrued prior to Jan 2025.

Updated results from the phase Ib/II study of fruquintinib combined with SOX and toripalimab in patients with advanced metastatic gastric/gastroesophageal junction adenocarcinoma (GC/GEJC).

423 Background: The efficacy of first-line treatment in advanced GC/GEJC patients (pts) with negative or low PD-L1 expression still needs to be improved. This phase Ib/II, open-label study (NCT05024812) evaluating fruquintinib (a highly selective VEGFR-1, -2, -3 inhibitor) plus toripalimab (anti-PD-1), and SOX has shown preliminary antitumor activity as first-line therapy in GC/GEJC. Here we update the results with longer follow-up duration and a specific focus on PD-L1 CPS features. Methods: The study of phase Ib employed a 3+3 dose escalation design, pts were treated with fruquintinib 3mg/d (dose level; DL1), 4mg/d (DL2), or 5mg/d (DL3) po, d1-14, in combination with fixed dose of toripalimab (240mg, iv, d1), oxaliplatin (130 mg/m 2 , iv, d1) and S-1 (40-60mg based on BSA, po, d1-14) every 3 weeks. It had been reported in phase Ib that fruquintinib 5mg/d was defined as the RP2D. In phase II, a further 64 pts would be treated with the same regimen. Primary endpoint of phase II was PFS per RECIST 1.1. Secondary endpoints included ORR, DCR, OS, DOR and safety. Results: As of August 15, 2024, 32 pts (9 in phase Ib; 23 in phase II) had been enrolled. Pts characteristics included: median age 62 (range 38–73); 66% male; 88% with ECOG PS 1, and 31% with liver metastasis. 31 pts had PD-L1 CPS available. 40.6% were CPS &lt; 1 and 68.8% were CPS &lt; 5. Of the 30 pts evaluable for tumor response, the ORR was 63.5% (95% CI 43.9–80.1) with 4 pts achieving complete responses and DCR was 96.7% (95% CI 82.8–99.9). After a median follow-up of 10.94 months, the median PFS was 9.33 (95% CI: 5.68–NA) months and OS result was not reached. Pts with CPS &lt; 5 were more likely to achieve higher response rate (65.0 vs 55.6%) and longer PFS than CPS ≥5 (12.68 vs 8.11 months). Similar trends were observed in pts with CPS &lt; 1 and CPS ≥1 (ORR: 75.0 vs 52.9%; PFS: 12.68 vs 8.11 months). Treatment-related adverse events (TRAEs) were mainly grade 1-2 and the most common ones were hypoalbuminemia (50%), neutrophil count decreased (34%), anemia (41%), platelet count decreased (34%) and white blood cell decreased (34%). Grade 4 TRAEs occurred in 2 pts (impaired liver function, hypertriglyceridemia). There were no treatment related deaths in the trial. Conclusions: Fruquintinib combined with SOX and toripalimab provided favorable efficacy and manageable toxicity profile as first-line therapy for pts with advanced metastatic GC/GEJC, especially in pts with negative or low PD-L1 expression. More data including the potential predictive response biomarkers would be further analyzed and reported. Clinical trial information: NCT05024812 .

Multimodal integration of blood RNA and ctDNA reflects response to immunotherapy in metastatic urothelial cancer.

Previously, we demonstrated that changes in circulating tumor DNA (ctDNA) are promising biomarkers for early response prediction (ERP) to immune checkpoint inhibitors (ICI) in metastatic urothelial cancer (mUC). In this study, we investigated the value of whole blood immunotranscriptomics for ERP-ICI and integrated both biomarkers into a multimodal model to boost accuracy. Blood samples of 93 patients were collected at baseline and after 2-6 weeks of ICI for ctDNA (N=88) and immunotranscriptome (N=79) analyses. ctDNA changes were dichotomized into increase or no increase, the latter including patients with undetectable ctDNA. For RNA model development, the cohort was split into a discovery (N=29), test (N=29) and validation set (N=21). Finally, RNA- and ctDNA-based predictions were integrated in a multimodal model. Clinical benefit (CB) was defined as progression-free survival beyond 6 months. Sensitivity (SN) and specificity (SP) of ctDNA increase for predicting non-CB (N-CB) was 59% and 92%, respectively. Immunotranscriptome analysis revealed upregulation of T-cell activation, proliferation and interferon signalling during treatment in the CB group, contrary to N-CB patients. Based on these differences a 10-gene RNA model was generated, reaching a SN and SP of 73% and 79% in the test and 67% and 67% in the validation set for predicting N-CB. Multimodal model integration led to superior performance with a SN and SP of 79% and 100% in the validation cohort. The combination of whole blood immunotranscriptome and ctDNA in a multimodal model showed promise for ERP-ICI in mUC and accurately identified patients with N-CB. 2016-3060, 2020-6778FUNDING. Eurostars grant E! 114908 - PRECISE, Paul Speth Foundation (Bullseye project).

Very Early Health Technology Assessment for Potential Predictive Biomarkers in the Treatment of Advanced Non-Small Cell Lung Cancer.

Immune checkpoint inhibitor (ICI)-containing treatment is currently prescribed as first-line treatment for all patients with advanced non-small cell lung cancer (NSCLC) without targetable driver mutations. However, only 30-45% of patients show no progression within 12 months after treatment start. Various biomarkers are being studied to save costly and potentially harmful treatment in non-responders. We evaluated the cost-effectiveness of implementing a hypothetical predictive biomarker for ICI-containing treatment response compared with standard of care (e.g., no implemented biomarker) for pembrolizumab-containing treatment in patients with advanced NSCLC in the Netherlands. Standard-of-care-based and predictive-biomarker-based strategies were compared using Markov models for three first-line pembrolizumab-containing treatments depending on a patient's tumor programmed cell death ligand-1 (PD-L1) expression and histology. A Dutch healthcare system perspective was adopted. Assuming a receiver operating characteristic-area under the curve of 1.0 in identifying responders, alternative treatments were offered for non-responders in the predictive-biomarker-based strategy. Parameters and assumptions were based on real-world data from surveys, literature using a targeted search, expert opinion, and registries. Outcomes included differences in costs, survival (life years (LYs)), and survival corrected for health-related quality of life (QoL) quality-adjusted life-years (QALYs) between the predictive-biomarker- and standard-of-care-based strategy. Implementing a predictive biomarker in pembrolizumab-carboplatin-paclitaxel treatment led to a mean survival reduction of 24 days (- 0.067 LYs) (18 days corrected for QoL (- 0.049 QALYs)), with cost savings of €22,606 compared with standard of care. Pembrolizumab monotherapy and pembrolizumab-pemetrexed-platinum treatments showed survival reductions of 4.5 and 3.9 months, respectively (3.6 and 2.8 months corrected for QoL), with cost savings of €24,345 and €28,456. Sensitivity analyses confirmed consistent cost savings and survival reductions. Survival losses were mainly observed due to the lower survival rates associated with the alternative first-line treatment options available for non-responders in the predictive-biomarker-based strategy within each pembrolizumab-containing treatment regimen. Pembrolizumab-carboplatin-paclitaxel treatment also showed survival gains under certain conditions related to QoL and survival estimates. Our study highlights the importance of careful de-implementation of ICI-treatments in advanced NSCLC, balancing costs reductions and side effects without comprising survival. In the pembrolizumab-carboplatin-paclitaxel treatment regimen, the survival loss could be considered negligible. Future research should define acceptable tradeoffs and thresholds for de-implementation, considering factors such as survival of alternative treatments and responder classification to guide predictive biomarker implementation and optimize health resource allocation.

Investigating the Impact of B Cell-Related Genes on Colorectal Cancer Immunosuppressive Environment and Immunotherapy Evasion.

We aimed to elucidate the prognostic and immunological roles of B cell-related genes in colorectal cancer (CRC). This study comprehensively integrated data from single-cell RNA-sequencing, TCGA, GEO, IMvigor210, GDSC, CancerSEA, HPA, and TISIDB databases to explore prognostic implications and immunological significance of B cell-related gene signature in CRC. We identified seven prognostically significant B cell-related genes for constructing a risk score. Clinical relevance analysis indicated that this risk score served as an independent prognostic factor, with the model accurately predicting patient outcomes. GSEA results implicated the risk score in immune function, cell cycle, and DNA replication. Immune infiltration analysis revealing lower levels of B cells, CD4+ cells, and CD8+ cells in the high-risk group, correlating with decreased immune activity and function. IMvigor210 and TIDE analysis indicated poorer prognosis among high-risk group patients receiving immune therapy. Additionally, the high-risk group exhibited lower sensitivity to immune therapy. Further analysis of drug sensitivity suggested higher resistance to common chemotherapy drugs among high-risk groups. Finally, we identified HSPA1A as the gene with the strongest association with immune and inflammatory responses. Validation of HSPA1A protein expression and prognosis demonstrated elevated expression in CRC compared to normal colorectal tissue, further reinforcing its association with poorer prognosis and higher tumor stage. The risk score exhibited substantial variations in clinical characteristics, functional mechanism, TMB, drug sensitivity, immune cell infiltration, and immune subtype. Our findings may aid in clinical decision-making by shedding light on novel and promising biomarkers for CRC prognosis and immunotherapy response prediction.

Prognostic and clinical heterogeneity of PD1 and PD-L1- immunohistochemical scores in endometrial cancers.

PD1/PD-L1 inhibition (ICi) has recently become a new standard of care for patients with advanced MMR-deficient (MMRd) endometrial cancers. Nevertheless, response to immunotherapy is more complex than the presence of a single biomarker and therefore it remains challenging to predict patients response to ICi beyond MMRd tumors. Elevated PD-L1 expression (CPS ≥ 1) is often used as a prognostic marker as well as a predictive biomarker of response to ICi in different tumor types. In a retrospective, patient derived study, we analyzed PD1- and PD-L1 staining and correlated the results of different scores to clinical data to evaluate the prognostic impact of these scores. Immunohistochemical analysis of the receptor PD1 and the receptor ligand PD-L1 were performed on TMAs of primary paraffin‑embedded tumor samples. All patients were treated for primary endometrial cancer in the Department of Gynecology and Obstetrics, University Medical Center Schleswig-Holstein, Campus-Lübeck, Germany between the years 2006-2018. The evaluation and determination of the tumor proportion scoring (TPS), the combined positive score (CPS) and the immune cell scoring (IC) was automatically assessed semi-quantitatively, and results were correlated with clinicopathological characteristics and survival. 130 samples were evaluable and 64% showed a positivity (IC > 0) for the receptor PD1 and 56% for the receptor ligand PD-L1. Patients with a PD1 IC Score ≥ 1 showed a significant longer disease-free survival of 140months (95% confidence interval (CI): 124-158) compared to patients with a lower IC < 1 for PD1 of 89months (95% confidence interval (CI): 69-110); p = 0.017). Furthermore, the disease-free survival for patients with a CPS ≥ 5 for PD1 was longer (153.7months (95% confidence interval (CI): 134-173.6) vs. 98.6months (95% confidence interval (CI): 83-114); p = 0.036). Additionally, a PD1 CPS ≥ 5 showed a better overall survival but the result was not statistically significant. No difference in survival was found between patients with PD-L1 higher or lower than CPS 5. In this study we pointed out that there are significant clinical differences among several immunohistochemical scoring systems. In our trial, a PD1-positivity with CPS ≥ 5 and IC ≥ 1 were significantly associated to a better disease-free survival while there was no association with TPS. The PD1-IC scoring was associated with MMRd while the TPS scoring was not. Therefore, PD1-IC could be more appropriate for endometrial carcinomas compared to TPS and could also add prognostic information beside the more established PD-L1-staining. Further prospective studies are needed for a validation of these scores in combination with other biomarkers.

P0093 Identification of metabolic predictive biomarkers of response to Inflammatory Bowel Disease treatment

Abstract Background The therapeutic goal in inflammatory bowel disease (IBD), which includes Crohn´s disease (CD) and ulcerative colitis (UC), is the control of the inflammatory process frequently through biologic and JAK-inhibitor therapies, which are generally expensive and may induce adverse effects. Unfortunately, only one-third of patients respond to these treatments, and there are no markers that accurately predict this response. The aim of this study was to identify potential serum and urinary metabolic biomarkers predictive of IBD response to different drugs at baseline (before treatment), which could facilitate the selection of the most appropriate therapy for each patient. Methods A prospective multicenter study was conducted including CD and UC patients who initiated biologic (anti-TNF, ustekinumab or vedolizumab) or JAK-inhibitor (tofacitinib) therapies. Patients were assessed at 14 weeks to determine if they had achieved an endoscopic response, based on the SES-CD and on the endoscopic sub-score of the Partial Mayo Score. The analyses of the serum and urine metabolome, along with the deconvolution of the serum lipoprotein profile into 110 subfractions, were performed using nuclear magnetic resonance for a quantitative differential analysis comparing the baseline serum samples of responders and non-responders. Results A total of 150 patients were included (30 CD anti-TNF, 30 UC anti-TNF, 30 CD ustekinumab, 30 UC vedolizumab and 30 UC tofacitinib). Metabolomics analysis identified 55 potential predictive biomarkers of IBD treatment response (11 common and 44 drug-specific), with significantly altered levels (p&amp;lt;0.05) in the baseline urine and serum samples of subsequent responders compared to non-responders (Figure 1). Moreover, based on ROC curves, some of these biomarkers showed good sensitivity and specificity for distinguishing between responders and non-responders before treatment (Figure 2). Finally, metabolite set enrichment analysis identified different biological pathways associated with the response to each of the treatments for IBD. Among the common ones, the citrate cycle and the metabolism of butanoate, alanine, aspartate, glutamate, and arginine stood out. Conclusion The present study represents a step towards personalized medicine in the selection of targeted therapies for IBD patients, addressing an important unmet need. Although further validation is needed, we have identified serum and urinary metabolic biomarkers with the potential to predict response to biologic and JAK-inhibitor therapies.

P0323 Serum leucine-rich α2-glycoprotein (LRG) and Monocyte chemoattractant protein-1 (MCP-1) as Novel Biomarkers for Predicting Vedolizumab Response in Ulcerative Colitis Patients

Abstract Background Close monitoring of disease activity is essential for the therapeutic management of inflammatory bowel disease. A minimally invasive and reliable serum biomarker is desirable, but its reliability and validity have not yet been fully evaluated. The purpose of this study (UMIN000043185) was to investigate the utility of leucine-rich α-2-glycoprotein (LRG) in the management of vedolizumab therapy in patients with ulcerative colitis (UC), and to identify mucosal signatures and surrogate biomarkers by using serum cytokine and mucosal transcriptome analysis. Methods Serum LRG, C-reactive protein (CRP), serum Mucosal Vascular Addressin Cell Adhesion Molecule 1(MadCAM1), serum vedolizumab levels, 19 serum cytokines, and fecal calprotectin (fCal) were measured over 54 weeks (week 0, 2, 6, 14, 30, and 54) (n=21). Clinical remission (Mayo score &amp;lt;= 2, all subscore &amp;lt; = 1) and mucosal healing (Mayo endoscopic subscore &amp;lt;= 1) at week 14 were compared between the clinical remission (CR) group (n=11) and non-clinical remission (non-CR) group (n=10), and between the mucosal healing (MH) group (n=14) and non-mucosal healing (non-MH) group (n=7). Differentially expressed gene (DEG) extraction was performed by stratifying data at week 0 and comparing two groups: CR (n=10) and non-CR (n=3), and complete MH (Mayo endoscopic subscore = 0) (n=8) and non-complete MH (n=6) at week 14. Results Serum LRG concentrations were significantly lower in CR group compared to the non-CR group at week 0 (19.0 vs. 29.0 ug/mL, p=0.027) and week 6 (13.4 vs. 19.6 ug/mL, p=0.034) and significantly lower in MH group compared to the non-MH group at week 6 (13.7 vs. 21.6 ug/mL, p=0.033). In contrast, there were no significant differences in serum CRP and fecal calprotectin levels at any time point for either CR or MH. Serum MCP-1 levels showed significant differences between CR and non-CR at week 0 (609.0 vs 403.4 pg/mL, p=0.0018), between MH and non-MH at week 0 (587.2 vs 358.9 pg/mL, p&amp;lt;0. 001), week 6 (606.9 vs 451.6 pg/mL, p=0.015). DEGs extracted from colon tissue included LRG1 and LRG-related cytokines, MCP-1, reflecting the effect of vedolizumab treatment. Conclusion Both serum LRG (lower in CR/ MH group) and serum MCP-1 (higher in CR/MH group) were suggested to be promising predictive biomarkers of vedolizumab treatment response in patients with UC. Further studies are needed to assess their reliability and validity as indicators of treatment effectiveness.

NLRP3 promoter methylation as a predictive biomarker for glucocorticoid response in patients with inflammatory bowel disease.

Glucocorticoids are used for inflammatory bowel disease (IBD) therapy; however nearly 50 % of IBD patients exhibit resistance or dependence. This study evaluates the relationship between methylation level at two CpG sites (cg21991396 and cg00448525) within NLRP3 promoter and glucocorticoid response of 94 IBD pediatrics (39 with Crohn's disease (40.4 %)) and 47 IBD adults (26 with Crohn's disease (55.3 %)). Disease activity scores were collected before the treatment, after the first full-dose reduction and after 3 months of therapy. Patients with active disease despite receiving a standard dose of prednisone were considered resistant, while those who initially responded but relapsed upon dose reduction were classified as dependent. The DNA methylation was investigated through sodium bisulfite conversion followed by pyrosequencing. In IBD adults, methylation levels at both NLRP3 CpG sites increased with patients' age (p = 0.0038 and p = 0.0018, respectively). In IBD pediatrics, the methylation level at both CpG sites negatively correlated with the disease activity score before treatment (p = 0.031 and p = 0.072, respectively) and after 1 month of therapy (p = 0.037 and p = 0.067, respectively). Furthermore, poor glucocorticoid response after one month of therapy in pediatric patients was associated with lower methylation levels at both CpG sites (p = 0.045 and p = 0.038, respectively). Crohn's disease patients had higher percentage of good responders compared to ulcerative colitis patients (p = 0.06). These findings indicate that NLRP3 methylation might change through patients' lifespan and could have different clinical implications for pediatric and adult IBD forms.

Expression of some circulating microRNAs as predictive biomarkers for prognosis and treatment response in glioblastoma

Glioblastoma multiforme (GBM) is the most prevalent, treatment-resistant, and fatal form of brain malignancy. It is characterized by genetic heterogeneity, and an infiltrative nature, and GBM treatment is highly challenging. Despite multimodal therapies, clinicians lack efficient prognostic and predictive markers. Therefore, new insights into GBM management are urgently needed to increase the chance of therapeutic success. Circulating miRNAs (miRs) are important regulators of cancer progression and are potentially useful for GBM diagnosis and treatment. This study investigated how miR-29a, miR-106a, and miR-200a affect the prognosis of GBM patients. This study was conducted on 25 GBM patients and 20 healthy volunteers as a control group. The expression levels of target miRs were analyzed pre- and post-treatment using qRT-PCR and evaluated in relation to both clinical GBM criteria and the patient’s survival modes. The diagnostic efficacy of target miRs was assessed using the receiver operating characteristic (ROC) curve. MiRs levels showed significant differences among the enrolled participants. All investigated miRs were significantly elevated in GBM patients with non-frontal lesions. Only miR-200a showed a significant difference in GBM patients older than 60 years with a tumor size ≥ 5 mm. Regarding miR-106a, a significant difference was detected based on the surgical strategy and use of an Eastern Cooperative Oncology Group (ECOG) performance status equal to 2. For miR-29a, a significant upregulation was detected according to the surgical strategy. All post-treatment miRs levels in GBM patients were significantly downregulated. In conclusion, circulating miRs revealed a significant role in predicting GBM patient treatment outcomes providing valuable insights for personalized therapeutic strategies.

Opportunities for predictive proteogenomic biomarkers of drug treatment sensitivity in epithelial ovarian cancer.

Genomic analysis has played a significant role in the identification of driver mutations that are linked to disease progression and response to drug treatment in ovarian cancer. A prominent example is the stratification of epithelial ovarian cancer (EOC) patients with homologous recombination deficiency (HRD) characterized by mutations in DNA damage repair genes such as BRCA1/2 for treatment with PARP inhibitors. However, recent studies have shown that some epithelial ovarian tumors respond to PARP inhibitors irrespective of their HRD or BRCA mutation status. An exclusive focus on the genome overlooks the significant insight that can be gained from other biological analytes, including proteins, which carry out cellular functions. Proteogenomics is the integration of genomics, transcriptomics, epigenomics and proteomics data. This review paper provides novel insight into the role of proteogenomics as an analytical approach to identify predictive biomarkers of drug treatment response in epithelial ovarian cancer. Proteogenomic analysis can facilitate the identification of predictive biomarkers of drug treatment response, consequently greatly improving the stratification of patients with EOC for treatment towards a goal of personalized medicine.

Associations of genetic polymorphisms with clinical response to tocilizumab in Chinese rheumatoid arthritis patients.

To examine the associations of single-nucleotide polymorphisms (SNPs) within interleukin-6 (IL6) and IL-6 receptor (IL6R) as well as several potential SNPs revealed in a genome-wide association study (GWAS) with clinical response to tocilizumab (TCZ) in Chinese rheumatoid arthritis (RA) patients. A total of 23 SNPs were genotyped in 68 RA patients receiving intravenous TCZ, who were prospectively followed for 6months to determine the clinical response based on several criteria, including clinical disease activity index (CDAI) low disease activity (LDA) and remission, disease activity score in 28 joint counts - erythrocyte sedimentation rate (DAS28-ESR) LDA and remission, European League Against Rheumatism (EULAR) good response and change in DAS28-ESR (ΔDAS28-ESR). The patients were on average 51.16 (13.23) years, and 55 were female (80.88%) and 47 were bDMARD-naïve (69.12%). After adjusting potential confounding factors, IL6R rs35717427 and GALNT18 rs4910008 were significantly associated with CDAI LDA, and IL6R rs11265621, rs6690230 were significantly associated with EULAR good response, DAS28-ESR LDA and remission. In addition, IL6 2069840 was found to be significantly associated with DAS28-ESR remission, and rs10108210, CLEC2D rs1560011 and KCNMB1 rs703505 were found to be significantly associated with ΔDAS28-ESR. Genetic polymorphisms hold the potential as predictive biomarkers for clinical response to TCZ, which might aid in individualized treatment with TCZ in Chinese patients with RA.

NKAP: A new m6A RNA binding protein predicts prognosis and immunotherapy response in head and neck squamous cell carcinoma.

This study aimed to investigate whether NKAP (nuclear factor κB activating protein) serves as a prognostic marker and predictive biomarker for immunotherapy response in head and neck squamous cell carcinoma (HNSCC). A retrospective cohort study combined with in vitro analyses was conducted. NKAP mRNA expression levels were assessed in 520 HNSCC tumor tissues and 44 normal tissues from the TCGA dataset and validated in a clinical cohort (n = 32). Clinical correlations with overall survival and immunotherapy outcomes were analyzed. The key pathological variables included tumor stage, grade, HPV status, and TP53 mutation. Appropriate statistics were calculated at a significant level (P<0.05). In this study, we have collected tissue samples from HNSCC patients (mean age: 52.65 ± 7.76; males 66%, females 34%). NKAP was upregulated in HNSCC tissues compared to adjacent normal tissues (P < 0.001). The high expression of NKAP correlated with advanced tumor stage, grade, and reduced survival (P < 0.05). High expression levels of NKAP were also associated with anti-PD-L1 therapy response (P < 0.05). Functional enrichment analysis revealed NKAP involvement in cell cycle regulation, mRNA processing, and chromatin remodeling pathways critical for cancer progression. NKAP represents a promising prognostic marker and therapeutic target for immunotherapy in HNSCC. Prospective studies are warranted to confirm these findings.