Introduction

Esophageal squamous cell carcinoma (ESCC) is associated with poor prognosis despite advances in neoadjuvant immunochemotherapy (NICT). With highly variable treatment responses, identifying reliable predictive biomarkers remains crucial. While gut microbiome influences on immunotherapy efficacy are increasingly recognized, the specific role of the fungal microbiome (mycobiome) in NICT outcomes for ESCC remains unexplored, representing a significant gap in developing personalized treatment strategies.

Aims & Methods

This study aimed to characterize gut mycobiome signatures in ESCC patients and develop fungal biomarker-based predictive models for NICT response. We conducted ITS2 sequencing on 136 fecal samples collected from 68 ESCC patients (pre- and post-NICT) and 19 healthy controls (HC). Patients were stratified as responders (R, n=26) or non-responders (NR, n=42) based on tumor regression grade (TRG) scores. We performed comprehensive analyses of mycobiome diversity, composition, co-occurrence networks, and functional pathways across groups. The Boruta algorithm was employed for feature selection to identify fungal biomarkers, followed by multilayer perceptron (MLP) machine learning with five-fold cross-validation to develop predictive models. Additionally, ESCC xenograft models were established to investigate gut mycobiome-immune interactions through fecal microbiota transplantation (FMT) and targeted fungal manipulation experiments.

Results

ESCC patients demonstrated significant mycobiome dysbiosis compared to healthy controls, characterized by reduced fungal alpha diversity and distinct beta diversity patterns. At baseline, ESCC patients showed enrichment of Rhodotorula minuta, Actinomucor elegans, and several Candida species. Responders exhibited significantly higher baseline fungal diversity than non-responders, with enrichment of Meyerozyma, Candida boidinii, Trichosporon dermatis, and Cryptococcus species, whereas non-responders showed predominance of Saccharomyces, Nakaseomyces, and pathogenic Candida species (C. glabrata, C. parapsilosis, C. albicans). Responders also displayed more complex, stable fungal co-occurrence networks with higher density and clustering coefficients. Post-NICT, both groups showed partial recovery of mycobiome diversity, with significant increases in beneficial fungal taxa. Functional pathway analysis revealed distinct metabolic profiles between responders and non-responders. Using the Boruta algorithm, we identified 23 genus-level and 22 species-level fungal biomarkers that demonstrated high predictive value. The MLP model based on genus-level markers achieved AUCs of 90.2% (training) and 91.9% (test), while the species-level model showed comparable performance. In animal experiments, mice receiving R-FMT exhibited reduced tumor growth and enhanced CD8+ T cell infiltration compared to NR-FMT recipients. Notably, Candida boidinii supplementation synergized with anti-PD-1 therapy, while Saccharomyces depletion enhanced treatment sensitivity.

Conclusion

Our findings establish the gut mycobiome as a powerful predictor of NICT response in ESCC, with machine learning models achieving >90% accuracy using fungal biomarkers. Experimental validation not only confirms mechanistic links between specific fungi and antitumor immunity but also demonstrates that targeted mycobiome modulation can enhance immunotherapy efficacy. This dual approach of prediction and intervention offers a novel framework for precision oncology in ESCC, potentially transforming clinical decision-making and treatment outcomes in this challenging malignancy.

References

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Introduction

The use of patient-centric monitoring modalities for assessing therapies, such as vedolizumab (VDZ), are of growing interest to optimize disease outcomes in patients with Crohn’s disease (CD). Transmural healing is an emerging outcome assessed by intestinal ultrasonography (IUS), which allows frequent evaluation of CD.^1,2 Real-world evidence on the effectiveness of current treatments for induction and maintenance of a transmural response to inform treatment decisions is limited.

Aims & Methods

The SUNRISE study aims to describe patients with CD treated with VDZ achieving a composite outcome of complete remission, and transmural response, utilizing IUS. SUNRISE is an ongoing observational, prospective study (NCT05192863) being conducted across 10 sites in Canada, Israel and Italy. Adults with moderately to severely active CD, with a bowel wall thickness of > 3 mm based on IUS, and who newly initiated intravenous VDZ are eligible. Complete remission (defined as a composite endpoint of clinically corticosteroid-free [Harvey–Bradshaw Index score of < 5 points and no concomitant corticosteroids], biochemical [C-reactive protein and faecal calprotectin normalization] and transmural remission [assessed by IUS]) and transmural response after VDZ treatment are reported after induction with VDZ (Weeks 10/14) and every 6 months until Month 18 or early discontinuation. In addition, health-related quality of life (as measured by the Short Inflammatory Bowel Disease Questionnaire), healthcare resource utilization and patient satisfaction with IUS are reported.

Results

This interim analysis included 70 patients; median (interquartile range [IQR]) age was 50.0 (39.0–67.0) years, time since CD diagnosis was 4.0 (0.9–17.2) years and treatment duration (n = 69) was 5.0 (3.2–6.1) months. At Month 6 after VDZ initiation, the proportion of patients achieving complete remission, and transmural remission and response were 3/11 (27.3%), 9/28 (32.1%) and 12/28 (42.9%) patients, respectively; data at Weeks 10/14 are shown in the Table. Median (IQR) Short Inflammatory Bowel Disease Questionnaire total score was 4.3 (3.7–5.6) at baseline, 4.5 (3.4–5.3) at Week 10, 4.7 (3.9–5.6) at Week 14 and 5.0 (4.4–6.1) at Month 6. At Month 6, 10/21 patients (47.6%) ranked IUS as their preferred test over colonoscopy, magnetic resonance elastography and computed tomography enterography. Of 40 patients with available data at Month 6, 6 (15.0%) discontinued treatment, 5 (12.5%) switched to subcutaneous VDZ and 1 (2.5%) skipped ≥ 1 dose of VDZ. During the observation period, 2/70 patients (2.9%) had a CD-related hospitalization, and 1/70 patient (1.4%) each had a CD-related emergency room visit or CD-related surgery (fistula removal).

Table​

Conclusion

The SUNRISE study provides real-world evidence for the use of VDZ to achieve transmural healing in patients with CD and supports patient preference for IUS over other monitoring modalities. Additional follow-up data are required to confirm these findings.
This abstract was previously presented at the European Crohn’s and Colitis Organisation (ECCO) 2025 congress. This study and medical writing support was funded by Takeda Pharmaceuticals International AG, Zurich, Switzerland.

References

1. Ilvemark J.F.K.F. et al. J Crohns Colitis 2022;16:554–80.
2. Turner D. et al. Gastroenterol 2021;160:1570–83.

Disclosure

D.C. has received speaker’s fees and/or research support from AbbVie, Janssen, Takeda and Taro, and consultancy fees from AbbVie, Takeda and Taro.
G.F. has received personal fees from AbbVie, Abivax, AlfaSigma, Celltrion, Ferring, Galapagos, Janssen, Lilly, Pfizer, Sandoz, STADA and Takeda.
P.B. is an employee and stockholder of Takeda Pharmaceuticals International AG, Zurich, Switzerland.
F.C. is an employee of the contract research organization IQVIA Solutions Italy s.r.l., hired by Takeda Pharmaceuticals International AG for the following activities: project and site management, data management, quality control and statistical analysis.
M.M. is an employee and stockholder of Takeda Pharma AG, Zurich, Switzerland.
K.L.N. has received advisory board fees from AbbVie, Bristol Myers Squibb, Celltrion, Ferring, Janssen and Pfizer, and speaker’s fees and research support from AbbVie, Janssen and Pfizer.
U.K. has received advisory and speaker’s fees from AbbVie, Bristol Myers Squibb, Celltrion, Janssen, Medtronic, Pfizer and Takeda, and research support from Janssen, Medtronic and Pfizer.