Citations

Imaging-based, single-cell, spatial transcriptomics (iSCST) of FFPE tissue enables comprehensive analysis of archived specimens while preserving spatial context, critical to an understanding of ulcerative colitis (UC) pathology. Here, we deployed a robust framework for applying iSCST to clinical FFPE mucosal biopsies from patients with UC or immune checkpoint inhibitor–induced colitis, as well as patients serving as healthy controls. iSCST using custom Xenium gene panels enabled precise detection of diverse cell subsets and disease-specific genes. We mapped transcriptionally distinct fibroblast subsets within mucosal niches, including inflammation-associated fibroblasts (IAFs), and identified colitis-specific neighborhoods formed by IAFs, monocytes, and neutrophils. Transcriptional signatures and spatial neighborhoods uncovered through iSCST were associated with vedolizumab (VDZ) response, with nonresponders exhibiting either an innate IAF-monocyte-neutrophil signature or adaptive gut-associated lymphoid tissue signature, while responders showed enrichment of an epithelial cellular neighborhood. These signatures were validated in an internal and an external dataset, supporting the existence of 2 distinct archetypes of treatment resistance to VDZ in UC. This iSCST framework provides a powerful approach for analyzing FFPE tissues, offering insights into colitis-associated cellular networks and identifying biomarkers to enhance patient risk stratification in routine clinical workflows.

Abstract The lung, one the largest branching organs in our body and vital for survival at first breath, is commonly known as the gas-exchange organ. Recent novel findings on lung sensing cells, molecules, and lung-brain crosstalk in the emerging discipline of interoception have highlighted the consideration of the lung as a sensory organ. Acknowledging the central importance of lung sensing to human health and disease, NHLBI convened a workshop to synthesize the past, current, and future of lung sensing research, with in-person presentations by ∼20 interdisciplinary experts and a large virtual audience. Here, we highlight the key topics discussed and summarize a blueprint for the future in this important field.

The recent approval of encorafenib, cetuximab, and FOLFOX based on the phase III BREAKWATER trial has introduced a new standard of care for the first-line treatment of BRAF V600E–mutated metastatic colorectal cancer (mCRC). However, its safety and efficacy in patients with significant liver dysfunction remains unclear and, as such, patients are often excluded from pivotal clinical trials. This report presents a case of BRAF V600E–mutated mCRC presenting with extensive hepatic involvement and liver dysfunction. Despite the absence of guidelines, the patient was initiated on full-dose encorafenib, cetuximab, and FOLFOX. He experienced a rapid clinical and biochemical response, with near-normalization of liver enzymes after cycle 1, and complete functional recovery by cycle 3. Treatment was well tolerated, with no significant adverse events throughout 9 cycles. He subsequently transitioned to maintenance 5-FU, cetuximab, and encorafenib. Posttreatment blood-based next-generation sequencing revealed no residual actionable mutations. The patient then successfully underwent complete surgical resection of his primary tumor and metastatic disease with negative margins. This case highlights the importance of considering encorafenib-based therapy in select patients with BRAF V600E–mutated mCRC in the setting of compromised liver function.

LBA514 Background: Preclinical and clinical data show that antibody-drug conjugates (ADCs) such as T-DXd may synergize with immunotherapy. Rilvegostomig (R) is a monovalent, Fc-reduced, dual checkpoint bispecific IgG1 monoclonal antibody against PD-1 and TIGIT receptors. R + T-DXd was evaluated as neoadjuvant therapy for up to 4 cycles. Methods: I-SPY2.2 is a phase II neoadjuvant trial with three neoadjuvant sequences (Blocks A/B/C). All HER2-negative subtypes were eligible for R + T-DXd in Block A. Predicted responders at the end of Block A or B could undergo surgery; otherwise, they continued to Block B +/- C. Block B pts received paclitaxel +/- carboplatin +/- pembrolizumab and Block C pts doxorubicin + cyclophosphamide (AC) +/- pembrolizumab, HR+ immune+ received IO in Blocks B/C. Results are analyzed by receptor and response predictive subtypes (RPS), that include expression-based immune, and luminal signatures with hormone receptor (HR) and HER2 status. Some pts were randomized to a control regimen (skipping R + T-DXd in block A and starting in block B). To minimize risk of interstitial lung disease (ILD) that could lead to treatment discontinuation, pts underwent pulmonary function tests and high-resolution chest CTs every 6 weeks. Abnormalities were reviewed in real time. The primary endpoint was pathologic complete response (pCR), within each RPS and HR/HER2 signature, with estimated pCR (EpCR) rates compared to subtype-specific block A goal rates and control pts in those groups. Other endpoints included safety and treatment discontinuation. Results: 105 pts were treated with R + T-DXd in block A, while 31 pts were randomized to the control regimen. Block A EpCR rate was 57% in the 12 HR+Immune+ pts vs a pre-specified goal of 15% (posterior probability, PP > .99). In 35 HR-Immune+ pts EpCR was 52% vs a pre-specified goal of 40% (PP = .87). No other groups (Immune-) had a PP > .85 for their respective pCR goal rate. HER2-IHC was 0 (27.6%), 1+ (49.5%) and 2+ (22.9%) in the treatment arm vs. 37.7%, 37.7%, and 24.7% in the control arm, with no difference in distribution between arms in immune subtypes. The most common adverse events in Block A were fatigue (84.8%), nausea (81.0%) and alopecia (58.1%). ILD was the most common adverse event of special interest in Block A and overall, occurring in 12 pts (11.4%; 7G1, 4G2, 1G3) during Block A and in 3 pts (G1, 2.9%) in other Blocks. 8 pts discontinued T-DXd + R due to ILD and proceeded to the next Block. Conclusions: When considering the full treatment strategy including block B and C regimens, experimental strategies had similar EpCR rates vs. controls in immune+ subtypes but block A rates exceeded pre-defined goal thresholds. This infers that treatment beginning with R + T-DXd has equivalent efficacy to standard of care for immune+ pts, but 64% pts with pCR skip chemotherapy (Block B) and 97% avoid AC (Block C). R + T-DXd participants avoided persistent ILD. Clinical trial information: NCT01042379 .

TPS3678 Background: Advanced and metastatic colorectal cancer (CRC) remains an area of significant unmet clinical need, particularly for patients with MSS/MSI-L tumors. In recent years, there have been several advancements in the treatment of solid tumors with T cell engagers. Our ATLAS scRNA-seq based discovery platform identified LY6G6D as a highly-specific tumor-associated antigen in advanced and metastatic CRC. CBI-1214, a CD3 bispecific T cell engager targeting LY6G6D with potent in vitro and in vivo activity even at low LY6G6D expression levels of ~300 copies/cell ( Yigit B et al, AACR 2025 ), is being developed for the treatment of patients with advanced or metastatic MSS/MSI-L CRC. Methods: This ongoing, open-label FIH study (CBI-1214-001) is being conducted to evaluate the safety, tolerability, pharmacokinetics (PK), and anti-tumor activity of CBI-1214 and to determine the maximum tolerated dose (MTD) and/or optimal biological dose (OBD) in participants with advanced or metastatic MSS/MSI-L CRC who have exhausted at least one prior line of systemic treatment and do not qualify for available targeted treatment options for actionable genomic alterations. Additional eligibility criteria include: at least 18 years of age, measurable disease (as defined by RECIST v1.1), available archival tumor tissue sample or a fresh tumor sample, ECOG PS 0 or 1, as well as adequate hematologic and organ functions. Patients whose CRC tumor tissues have been identified as dMMR or MSI-H are excluded. The study is conducted in two parts: Part 1 dose escalation, which starts with Part 1a as accelerated dose escalation, followed by Part 1b escalation, which is based on a modified toxicity probability interval (mTPI-2) design, and Part 2, which is designed as a randomized dose optimization study to select the final recommended phase 2 dose (RP2D). For both parts of the study, the study intervention is administered as monotherapy, given as an intravenous (IV) infusion, in 21-day treatment cycles, with a step-up option. After an up-to-28-day screening period, eligible patients receive study medication and are followed for their entire treatment period plus a follow-up period of approximately 90 days. The study is open for recruitment in the United States (NCT07321106). Clinical trial information: NCT07321106 .

e23510 Background: There is minimal data comparing the prognostic models (PM) developed to predict recurrence of Gastrointestinal stromal tumors (GIST). Current PM include tumor size, location, and mitotic index (MI) but lack genotypic data. This analysis compares the performance of the National Institute of Health, Armed Forces Institute of Pathology, and Memorial Sloan Kettering Cancer Center models for predicting tumor recurrence with and without adjustment for c-kit Exon 11 mutation status (MS). Methods: This is an IRB-approved single-institution retrospective analysis. Adults with GIST mentioned in their medical records from 2014 – 2025 at the authors’ institution were identified. 330 patients with documented biopsy-proven GIST were included. Data was collected by manual review. PM were evaluated using multivariate analysis, adjusting for surgical resection, systemic therapy, and c-Kit exon 11 MS. Predictive performance was measured by area under the curve (AUC) and receiver operating characteristics (ROC) analysis. Results: Mean age at diagnosis was 64.6 years (SD =13.1 years). 46.7 % of patients were male. Primary GIST was most common in the stomach (63.9%) and small bowel (23.6%). Primary tumors were an average of 6.5 cm (SD 5.6 cm) with a MI of 6.6/50 HFU (SD = 13.4 50/HFU). Patients received resection (80.9%) and first-line systemic therapy with imatinib (43.3%). Recurrence occurred in 17.9% of patients. 19.4% of patients completed genetic testing, of which 51.6% were c-Kit exon 11 mutation positive. The predictive performance of all PM was not statistically different with (p value = 0.16) or without (p value = 0.18) adjustment for c-Kit exon 11 MS (Table 1). However, adjusting for c-Kit exon 11 MS improved AUC for all PM. Conclusions: Adjusting PM for c-KIT exon 11 status improved the predictive performance of all PM, although the results were not significant. This study found no significant difference in the performance of PM that predict GIST recurrence, which aligns with the one other study on this topic. Lack of significance may be due to a small sample size, which also limited the multivariate analysis. Including genotypes in PM that predict GIST recurrence should be further explored with larger multi-center datasets that can adjust for multiple mutations. Multivariate analysis comparing prognostic models for gastrointestinal stromal tumors at predicting recurrence with and without adjustment for c-KIT exon 11 genotypes using receiver operating characteristic. Without c-Kit exon 11 AUC (95% Confidence Interval) P value NIH 0.86 (0.81,0.90) 0.18 AFIP 0.87 (0.82,0.91) MSKCC 0.89 (0.84,0.94) With c-Kit exon 11 genotype NIH 0.80 (0.67,0.93) 0.16 AFIP 0.84 (0.73,0.95) MSKCC 0.90 (0.80,0.99) NIH: National Institute of Health, AFIP: Armed Forces Institute of Pathology, MSKCC: Memorial Sloan Kettering Cancer Centre. AUC: Area under the curve.

Context.— In 2016, the College of American Pathologists published an evidence-based guideline to develop recommendations for interpretive diagnostic error reduction in anatomic pathology. New evidence, together with evolving practice environments and the continued adoption of digital technologies, including artificial intelligence, has prompted a review of the guideline. Objective.— To assess evidence published since the release of the original guideline and update evidence-based recommendations for the reduction of diagnostic errors. Design.— The College of American Pathologists, in collaboration with the Association of Directors of Anatomic and Subspecialty Pathology, convened a panel of experts to update the 2016 evidence-based guideline. A systematic literature review was conducted to address 4 key questions. Using the Grading of Recommendations Assessment, Development and Evaluation approach, recommendations were created based on the available evidence, certainty of that evidence, and key judgments as defined in the Grading of Recommendations Assessment, Development and Evaluation framework. Results.— Two strong recommendations and 4 good practice statements were established for the reduction of diagnostic error. Conclusions.— The expert panel recommends that anatomic pathologists implement procedures for the review of pathology cases to detect and correct potential interpretive errors to improve patient outcomes.