Neoadjuvant systemic therapy (NST) is a standard treatment approach for patients with early-stage breast cancer, particularly those with stage II-III disease and aggressive subtypes such as HER2-positive and triple-negative breast cancer. While NST improves surgical outcomes and provides prognostic information, accurately assessing preoperative treatment response remains a clinical challenge. Circulating tumor DNA (ctDNA) has emerged as a promising non-invasive biomarker for monitoring disease dynamics and guiding therapeutic decisions. In this study, we aimed to evaluate whether ctDNA analysis in patients with stage II-III breast cancer (n = 20) could serve as a surrogate for invasive biopsies in molecular profiling and as a tool for monitoring response to NST. At baseline, ctDNA was detectable in the majority of patients by droplet digital (dd)PCR (15/18, 83%) and all patients with longitudinal follow-up had ctDNA clearance after NST (13/13; 100%). A positive correlation was observed between the allele fraction in ctDNA, histologic grade and molecular subtype, suggesting that ctDNA levels may be influenced by tumor biology. None of the three patients with undetectable baseline ctDNA had distant relapse, regardless of whether they achieved pathologic complete response (pCR), compared to 5/15 (33%) with detectable baseline ctDNA. These findings suggest that ctDNA assessment at baseline may provide additional prognostic information to define the risk of patients after NST. While ctDNA shows promise in capturing tumor burden and biological characteristics, its role in predicting pCR and long-term outcomes requires further investigation.

Circulating tumor DNA (ctDNA) has potential as a prognostic factor for predicting relapse in high-risk breast cancer (BC). This study investigates the utility of ctDNA assessment using a tumor-informed assay, in patients with high-risk BC treated with neoadjuvant chemotherapy (NAC). Thirty newly diagnosed patients with various high-risk BC subtypes participated, providing serial blood samples at multiple time points, including baseline, during NAC, and during follow-up. ctDNA was detected at baseline in 29/29 patients for whom an assay panel could be designed, with detection sensitivity reaching 0.0083% (variant allele frequency). Among patients with detectable baseline ctDNA, 94% showed clearance during treatment, correlating with improved outcomes. Additionally, ctDNA detection post-surgery or during follow-up predicted disease recurrence. These findings suggest that serial ctDNA monitoring throughout NAC and follow-up can effectively identify residual disease in BC and correlate with clinical outcomes.

Importance:Randomized trials established the safety of omitting axillary lymph node dissection (ALND) among patients with clinically node-negative breast cancer and less than 3 positive sentinel lymph nodes (+SLNs) having upfront surgery and adjuvant radiation. Patients with palpable mobile level I/II axillary adenopathy (cN1) were not eligible for these studies. Presently, more than 80% of patients with HR+/HER2- cN1 disease undergo ALND either at upfront surgery or after neoadjuvant therapy, despite evidence that 50% to 60% will have only 1 or 2 positive nodes. Objective:To determine upfront sentinel lymph node biopsy (SLNB) feasibility and evaluate ALND rate among patients with HR+/HER2- cN1 breast cancer selected with axillary ultrasound (AUS). Design, Setting, and Participants:This nonrandomized clinical trial involved patients with cTx/cT1-2 cN1 HR+/HER2- breast cancer with 3 or fewer morphologically abnormal nodes on AUS at 4 centers. The trial began on April 20, 2021, and the database for this report was frozen on September 26, 2024. Interventions:Patients underwent upfront lumpectomy/mastectomy and SLNB, with single/dual-tracer mapping. ALND was indicated for 3 or more positive SLNs. Main Outcomes and Measures:The primary outcome was ALND rate. Secondary outcomes were frequency of palpable nodes being radioactive/blue and locoregional recurrence. Results:Among 78 enrolled patients, the median (IQR) age was 58 (49.0-66.5) years. Most tumors were cT1 (37 [47%]) or cT2 (40 [51%]), 56 patients (72%) had ductal histology, and 59 tumors (76%) were moderately differentiated. On AUS, 39 patients (50%) had 1 abnormal-appearing node, 33 (42%) had 2, and 6 (8%) had 3. Median (IQR) pathologic tumor size was 2.3 (1.6-3.3) cm, 50 patients (64%) had lymphovascular invasion, and 54 (69%) had extracapsular extension. SLNB was performed with dual tracer in 68 (87%), and 3 or more SLNs were retrieved in 75 (96%). The palpable diseased nodes were blue and/or radioactive in 107 of 161 instances (66.5%). Overall, 24 patients (31%) had 1 +SLN, 30 patients (38%) had 2 +SLNs, and 24 patients (31%) had 3 or more +SLNs. SLNB alone was performed in 59 patients (76%), while 19 (24%) had ALND; indicated ALND was deferred in 5 cases. Among those with 12 months or more follow-up (n = 68; median, 25 months), there have been no isolated axillary or locoregional recurrences. Conclusions and Relevance:This study found that SLNB is feasible among patients with cN1 HR+/HER2- disease and that resection of palpable nodes is necessary to minimize false-negative rates. This approach affords the opportunity to omit ALND and minimize morbidity among patients with cN1 cancer and limited nodal burden. Trial Registration:ClinicalTrials.gov Identifier: NCT04854005.

This nonrandomized clinical trial analyzes data for patients who underwent upfront surgery to determine the feasibility of upfront sentinel lymph node biopsy and evaluate the rate of axillary lymph node dissection. QuestionWhat is the feasibility of upfront sentinel lymph node biopsy (SLNB) and the rate of axillary lymph node dissection (ALND) among patients with HR+/HER2- cN1 breast cancer selected with axillary ultrasound?FindingsIn this nonrandomized clinical trial including 78 consecutive patients with cTx/cT1-2 cN1 HR+/HER2- breast cancer with palpable, biopsy-proven nodal metastases, SLNB was feasible among patients with cN1 HR+/HER2- disease, with 3 or more SLNs retrieved in 96% of cases, and nearly 70% of patients meeting criteria for SLNB alone and able to avoid ALND.MeaningThis approach affords the opportunity to omit ALND and minimize morbidity among cN1 patients with limited nodal disease burden. ImportanceRandomized trials established the safety of omitting axillary lymph node dissection (ALND) among patients with clinically node-negative breast cancer and less than 3 positive sentinel lymph nodes (+SLNs) having upfront surgery and adjuvant radiation. Patients with palpable mobile level I/II axillary adenopathy (cN1) were not eligible for these studies. Presently, more than 80% of patients with HR+/HER2- cN1 disease undergo ALND either at upfront surgery or after neoadjuvant therapy, despite evidence that 50% to 60% will have only 1 or 2 positive nodes.ObjectiveTo determine upfront sentinel lymph node biopsy (SLNB) feasibility and evaluate ALND rate among patients with HR+/HER2- cN1 breast cancer selected with axillary ultrasound (AUS).Design, Setting, and ParticipantsThis nonrandomized clinical trial involved patients with cTx/cT1-2 cN1 HR+/HER2- breast cancer with 3 or fewer morphologically abnormal nodes on AUS at 4 centers. The trial began on April 20, 2021, and the database for this report was frozen on September 26, 2024.InterventionsPatients underwent upfront lumpectomy/mastectomy and SLNB, with single/dual-tracer mapping. ALND was indicated for 3 or more positive SLNs.Main Outcomes and MeasuresThe primary outcome was ALND rate. Secondary outcomes were frequency of palpable nodes being radioactive/blue and locoregional recurrence.ResultsAmong 78 enrolled patients, the median (IQR) age was 58 (49.0-66.5) years. Most tumors were cT1 (37 [47%]) or cT2 (40 [51%]), 56 patients (72%) had ductal histology, and 59 tumors (76%) were moderately differentiated. On AUS, 39 patients (50%) had 1 abnormal-appearing node, 33 (42%) had 2, and 6 (8%) had 3. Median (IQR) pathologic tumor size was 2.3 (1.6-3.3) cm, 50 patients (64%) had lymphovascular invasion, and 54 (69%) had extracapsular extension. SLNB was performed with dual tracer in 68 (87%), and 3 or more SLNs were retrieved in 75 (96%). The palpable diseased nodes were blue and/or radioactive in 107 of 161 instances (66.5%). Overall, 24 patients (31%) had 1 +SLN, 30 patients (38%) had 2 +SLNs, and 24 patients (31%) had 3 or more +SLNs. SLNB alone was performed in 59 patients (76%), while 19 (24%) had ALND; indicated ALND was deferred in 5 cases. Among those with 12 months or more follow-up (n = 68; median, 25 months), there have been no isolated axillary or locoregional recurrences.Conclusions and RelevanceThis study found that SLNB is feasible among patients with cN1 HR+/HER2- disease and that resection of palpable nodes is necessary to minimize false-negative rates. This approach affords the opportunity to omit ALND and minimize morbidity among patients with cN1 cancer and limited nodal burden.Trial RegistrationClinicalTrials.gov Identifier: NCT04854005

Abstract Background: The Breast Cancer Index (BCI) is a gene expression-based assay that stratifies patients based on their risk of overall (0-10 years) and late (beyond 5 years) distant recurrence. In addition , BCI can also predict the benefit of extended endocrine therapy in early-stage, HR+ breast cancer. In this study, we assessed the relationships between BCI and risk of distant recurrence and explored associations between BCI classification and the tumor genomic and transcriptomic profiles of HR+ patients who experienced metastatic relapse. Methods: Primary tumors from patients with metastatic or recurrent HR+ breast cancer underwent BCI testing, MSK-IMPACT targeted sequencing (up to 505 cancer genes), and mRNA sequencing. Time to DR (TTDR) was defined as the time from surgery to first distant recurrence. A 5-year cutoff was used to distinguish early versus late DR groups. Kaplan-Meier and Cox proportional hazards analyses were used to assess BCI’s prognostic value. Wilcoxon tests were applied for pairwise comparisons of BCI scores between early and late DR groups, and Fisher’s exact tests were used to identify genomic alterations differing by BCI groups as well as DR groups. Given the limited cohort size, multiple testing correction was not applied. Transcriptomic data (N=91) were analyzed for differentially expressed genes by comparing BCI high-risk vs. low-risk tumors and early vs. late DR groups (|log2FC|>1, adjusted p<0.05). Results: The study included 180 HR+ patients (47% post-menopausal, 61% N+, 65.3% grade 3). Most tumors were classified as BCI high risk (86.7%), and patients classified as high risk by BCI had earlier recurrence than those classified as low risk (median TTDR: 3.0 years vs. 4.7 years; HR = 1.89, 95% CI: 1.20-2.96; p = 0.0053). BCI scores differ significantly between early and late DR groups (p = 0.005). The genomic landscape was consistent with high-risk luminal tumors and showed frequent TP53 mutations (38%). PIK3CA and TBX3 mutations were more common in BCI low-risk tumors (71% vs. 41%, p=0.007; 21% vs. 5%, p=0.01). CDKN2A deletions and MCL1 amplifications were enriched in early DR, whereas ERBB2 and SPOP amplifications as well as NOTCH3, and MAP2K4 mutations were more frequent in late DR (p<0.05). Transcriptomic analysis revealed downregulation of cell cycle, p53 signaling, senescence, and progesterone-mediated oocyte maturation pathways in BCI high-risk tumors. The cell cycle pathway was also downregulated in late recurrences, suggesting reduced proliferative activity associated with delayed relapse. Conclusion: BCI remained a strong prognostic indicator in this HR+ metastatic cohort, with higher scores predicting shorter TTDR. Integrated genomic and transcriptomic profiling highlighted distinct molecular programs associated with BCI classification providing insight into biological mechanisms underlying early versus late relapse in HR+ breast cancer. Citation Format: Hong Zhang, Niloufar Khojandi, Natalia Siuliukina, Julia Ah-Reum An, Darya Dahi, Luca Boscolo Bielo, Subhiksha Nandakumar, Enrico Moiso, Edaise M. da Silva, Mehnaj Ahmed, Lisa Loudon, Konner Nelson, Kevin Murphy, Jade Oghoanina, Mark E. Robson, Sarat Chandarlapaty, George Plitas, Amanda K. L. Anderson, Yi Zhang, Pedram Razavi, Kai Treuner. Associations between Breast Cancer Index and MSK-IMPACT genomic and transcriptomic profiles in HR+ breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2026; Part 1 (Regular Abstracts); 2026 Apr 17-22; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2026;86(7 Suppl):Abstract nr 1188.

In hematopoietic cell transplant (HCT) patients, intestinal Candida parapsilosis expansion and translocation can cause life-threatening candidemia, yet whether commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a machine learning model on supernatant metabolomic profiles of Lachnospiraceae to identify bacteria-derived inhibitors of fungal growth, identifying valeric and butyric acids as top hits. Fecal samples from HCT patients supported this association, with valeric and butyric acid levels inversely correlating with C. parapsilosis growth. In cell culture and mice, valeric acid inhibited C. parapsilosis growth by increasing intracellular acidification. Administration of glycerol valerate, or free or microencapsulated valeric acid, to release valeric acid along the entire intestinal tract blunted C. parapsilosis growth at murine intestinal sites where valeric acid was detected. Thus, machine learning identified a mechanistic driver of trans-kingdom ecology limiting C. parapsilosis intestinal expansion and may inform strategies to reduce patient risk of candidiasis.

OBJECTIVE:To evaluate the association between living in disadvantaged neighborhoods in New York City (NYC) with tumor grade, a clinical proxy for proliferation and tumor aggressiveness, and breast cancer-specific survival (BCSS). BACKGROUND:Neighborhood disadvantage (ND) is associated with shorter BCSS, independent of individual-level, tumor, and treatment characteristics, highlighting unmeasured factors associated with this survival disparity. METHODS:Women with stage I to III breast cancer (BCa) living in NYC treated at Memorial Sloan Kettering Cancer Center from 2013 to 2024 were included. ND was stratified using the Area Deprivation Index (ADI). The median ADI for the cohort was 3 and was used as the cutoff between neighborhood advantage (NA, ADI 1-3) and ND (ADI 4-10). Multivariable logistic regression and Cox proportional hazards modeling, controlling for individual, tumor, and treatment factors, were used to determine the association between ND and tumor grade and BCSS, respectively. RESULTS:Five thousand four hundred fifty-two women with BCa were included. Three thousand four hundred seventy-nine (64%) lived in NA and 1973 (36%) in ND. On multivariable analysis, ND had higher odds of poorly versus well/moderately differentiated tumors (adjusted odds ratio: 1.23, CI: 1.03-1.48), independent of age, race/ethnicity, insurance, body mass index, smoking/alcohol, stage, and subtype. ND was also associated with shorter BCSS (adjusted hazard ratio: 1.56, CI: 1.05-2.38). CONCLUSIONS:Women living in ND in NYC were more likely to present with poorly differentiated tumors and have shorter BCSS. These findings merit further inquiry and lay the foundation for future translational studies to externally validate the mechanisms by which ND "gets under the skin" to impact aggressive BCa tumor biology, and ultimately survival.

Background: Adding pembrolizumab to neoadjuvant chemotherapy (NAC+P) for stage II-III triple-negative breast cancer (TNBC) improves pathologic complete response (pCR) rates and event-free survival compared to neoadjuvant chemotherapy (NAC) alone. Recurrence patterns and factors associated with disease-free survival (DFS) in a real-world cohort are not known. We compared recurrence rates and assessed factors associated with DFS in patients receiving NAC+P versus NAC for early-stage TNBC. Methods: This retrospective analysis compared two consecutive cohorts of patients with stage II-III TNBC: 344 treated with NAC+P from 6/1/21-4/30/24 based on the KEYNOTE-522 regimen and 513 treated with NAC from 7/1/09-3/15/19. Demographic, clinicopathologic characteristics, and recurrence data were collected. Tumor infiltrating lymphocytes (TILs) were scored on pre-treatment core needle biopsy for NAC+P only. Primary outcomes were local recurrence (LR), locoregional recurrence (LRR), and distant recurrence (DR). Secondary outcomes were DFS and factors associated with DFS. Kaplan-Meier time-to-event analyses assessed for DFS. Univariate and multivariable Cox regression models assessed for factors associated with DFS. Results: In the NAC+P group, most patients presented with cT2 (70%), cN0 (53%) disease at a median age of 52 years (IQR 41, 62). In the NAC group, most presented with cT2 (48%) or cT3/4 (28%), cN1 (52%) disease at a median age of 51 years (IQR 41, 60). Rates of breast, nodal, and overall pCR (58% vs 36%, p<0.001) were higher with NAC+P. At 1-year, crude LR rates were not different between NAC+P and NAC: 2.3% vs 4.3%, p=0.13. However, 1-year LRR and DR rates were lower with NAC+P: LRR (0.6% vs 4%, p=0.01) and DR (8% vs 12%, p=0.03). Thirty-one NAC+P patients had DR. The most common sites of first progression were liver (29%), lung (29%), or brain (26%). Among 121 NAC patients with DR, the most common sites of first progression were multiorgan (50%), lung (19%), or liver (12%). Of 61 patients with multiorgan DR, 36 (59%) had brain metastases.At a median follow-up of 1.2 years (IQR 0.8, 1.6), the 1-year disease recurrence rate for NAC+P was 10% (95% CI: 6%-13%). With a median follow-up of 6 years (IQR 3.3, 7.7), the 5-year disease recurrence rate for NAC was 24% (95% CI: 20%-28%). Factors associated with worse DFS for NAC+P included extreme breast density (HR 3.78, p=0.004) and cN1 disease (HR 2.68, p=0.04). On univariate analysis only, cN2/3 disease and comprehensive RT were associated with worse DFS, while lower cT stage, immune-related adverse events, breast pCR, nodal pCR, and overall pCR were associated with improved DFS. Using a 10% cutoff, stromal TILs on pre-treatment core needle biopsy were not associated with DFS. Factors associated with improved DFS for NAC were cT2 vs cT3/T4 (HR 0.56, p=0.01), ACT-based regimen (HR 0.61, p=0.02), and overall pCR (HR 0.32, p<0.001), while lymphovascular invasion on biopsy (HR 2.1, p<0.001) was associated with worse DFS. Univariate associations for worse DFS included cN1 and cN2/3 disease. Conclusions: Compared to NAC, NAC+P resulted in improved crude 1-year rates of LRR and DR, along with numerical improvements in DFS with shorter follow-up. Factors associated with DFS (including pCR) were not similar across cohorts and isolated brain metastases as a site of first progression were more common in patients treated with NAC+P who developed DR. Citation Format: Lauren Perry, Varadan Sevilimedu, Natalia Polidorio, Marisa Lazarus, Giacomo Montagna, Nour Abuhadra, Ellen Yang, Rachel Han, Hannah Y. Wen, Lior Braunstein, Monica Morrow, George Plitas, Stephanie Downs-Canner. Patterns and Predictors of Recurrence After Neoadjuvant Chemo-Immunotherapy in Early-Stage Triple-Negative Breast Cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P5-09-17.

Introduction: Presence of circulating tumor DNA (ctDNA) after treatment for early-stage breast cancer (EBC) is associated with poor outcomes, yet accurate detection of ctDNA clearance after treatment requires ultrasensitive methods. Here, we describe the clearance of ctDNA in EBC by multiple treatment modalities, including surgery and neoadjuvant chemotherapy (NAC), using an ultrasensitive ctDNA minimum residual disease (MRD) assay. Methods: The MSK-LINC study prospectively collected blood samples from EBC patients throughout their clinical care at MSK. MRD was monitored using Foresight CLARITY, an ultra-sensitive MRD research assay with LOD95 below 1 part-per-million (ppm). Whole genome sequencing (WGS) of primary tumor and WBC samples was used to identify tumor-derived phased variants. Personalized MRD assays were then designed to detect ctDNA. We assessed the relationship between ctDNA during distinct phases of treatment and clinical outcomes, including NAC, surgery, or adjuvant treatment. Results: We analyzed 390 samples from 50 EBC patients (Stages: I=22%, II=56%, III=22%) treated with curative-intent surgery for diverse subtypes (62% HR+/HER2-, 24% HER2+, 14% TNBC). Pretreatment ctDNA was present in 72% of patients, with a median variant allele frequency (VAF) of 100 ppm (range 8 - 226,000 ppm). Following neoadjuvant (44%) or adjuvant (48%) chemotherapy, 14% distant relapses were observed. Among 18 patients with detectable ctDNA before or during NAC, 56% cleared their ctDNA prior to surgery and remained disease free, with 60% of these achieving pathological complete response (pCR). In contrast, 44% of patients were ctDNA MRD positive (ctDNA+) at the last time-point prior to surgery (median 5 ppm, range: 3-12); 50% of these patients experienced disease recurrence and none achieved pCR. Clearance of ctDNA prior to surgery was associated with significantly improved DFS (p = 0.012). When considering the effect of surgery on patients with residual ctDNA after NAC, 63% had undetectable ctDNA at the first post-operative time-point while 38% did not, with ctDNA levels ranging from 0.9 to 322 ppm. All ctDNA+ patients experienced relapse. Among patients who cleared ctDNA at any postoperative timepoint, only one (13%) experienced relapse; ctDNA was detected in the next blood sample, 15 months prior to relapse. All patients experiencing relapse had ctDNA detected prior to recurrence by serial monitoring. Among evaluable patients not receiving NAC, 15 patients had ctDNA detected pre-surgery (median ctDNA level 40 ppm, range 8-913), with 87% achieving ctDNA clearance post-surgery. The two patients without ctDNA clearance post-surgery (VAF pre- vs post-surgery 124→3.8 ppm and 40→10 ppm) were HR+/HER2- and experienced no relapse. Interestingly, both patients received adjuvant chemotherapy and endocrine therapy, leading to ctDNA clearance at subsequent timepoints. Among 13 cases with ctDNA clearance post-surgery, 92% remain disease free. We observed a single late relapse at 54 mo in a patient with TNBC who cleared ctDNA at the post-operative landmark, with ctDNA detection re-emerging prior to relapse. Conclusion: In EBC, ctDNA clearance by NAC, surgery, or adjuvant therapy is strongly associated with favorable outcomes. Ultrasensitive MRD analysis demonstrates that surgery also leads to a high rate of ctDNA clearance, suggesting the ability to measure and differentiate responses to both local and systemic therapies. Ultrasensitive ctDNA in EBC is likely to become an important biomarker of response to therapeutic interventions and warrants further study. Citation Format: Luc Cabel, Julia Ah-Reum An, David Kurtz, Dara Ross, Esra Dikoglu, Enrico Moiso, Kevin Murphy, Kathleen Szuhany, Sierra Love Stowell, Dillon Maloney, Giselle Zamora-Chavez, Andre Schultz, Howard I. Scher, Jake Chabon, Mark E Robson, Monica Morrow, Bob T Li, Ash A Alizadeh, Sarat Chandarlapaty, George Plitas, Maximilian Diehn, Pedram Razavi. Circulating tumor DNA clearance by neoadjuvant chemotherapy or breast surgery detected using an ultrasensitive ctDNA MRD assay in early breast cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P2-01-25.

Spatial transcriptomic data enable study of cell-cell communication, yet current analysis tools often fail to provide dynamic, interpretable estimates of interactions and their spatial range across tissue. We present AMICI, an interpretable attention framework that jointly estimates interaction length scales, adaptively resolves sender-receiver subpopulations, and links communication to downstream gene programs. AMICI recovers ground-truth interactions in semi-synthetic data, uncovers gene programs linked to cell communication in the mouse cortex, and reveals length-scale-dependent tumor-immune signaling that reinforces estrogen receptor (ER) programs in breast cancer.

Metaplastic breast cancer (MpBC) treated with standard chemotherapy has low rates of complete pathological response (pCR)(2–23%). In this study, we evaluate the response to neoadjuvant chemo-immunotherapy (NACI) in early-stage MpBC. Thirty-two stage I-III MpBC patients treated with NACI (KEYNOTE-522 regimen) were prospectively enrolled in an institutional rare tumor program. All MpBC were triple negative; most were of chondromyxoid/matrix-producing (12/32, 38%). The majority had stage II (78%) tumors, 12/32 (37.5%) patients completed NACI, 11/32 (34%) progressed during NACI, and in the remaining 9, NACI was discontinued due to side effects. The pCR rate in the entire cohort was 22% (7/32) and it was statistically higher (5/8, 62%) among patients with high ( ≥ 60%) stromal tumor-infiltrating lymphocytes (sTILs) as compared to patients with < 60% sTILs (1/11, 9%). Most patients received adjuvant systemic therapy (capecitabine 16/32, pembrolizumab 20/32). At a median follow-up of 13 months, there were a total of 2 local recurrences, 10 distant recurrences, and 7 deaths. We demonstrated a modest pCR rate in MpBC with the addition of pembrolizumab (22%). Nonetheless, amongst patients with high sTILs, high pCR rates—comparable to those in the KEYNOTE-522 trial—were observed. These findings suggest that sTILs can be used to triage MpBC patients for NACI.

Background: The Breast Cancer Index (BCI) is a gene expression-based signature that stratifies patients based on the risk of overall (0-10 years) and late (post-5 years) distant recurrence (DR). BCI also predicts the likelihood of benefit from extended endocrine therapy in early-stage, HR+ breast cancer (BC). This study aims to explore the correlation between BCI and disease-free interval and possible associations between gene-expression-based classification by BCI and the genomic features of primary breast cancers in patients with HR+/HER2- breast cancer who developed metastatic relapse. Methods: Primary tumor samples from HR+/HER2- metastatic/recurrent BC patients underwent both BCI and MSK-IMPACT targeted sequencing. MSK-IMPACT identifies somatic mutations, rearrangements, and copy-number alterations in up to 505 cancer genes. Time to DR (TTDR) defined as the time between date of surgery and distant recurrence. Kaplan-Meier survival analysis and Cox proportional hazards regression were used to evaluate BCI's prognostic performance. Pearson’s correlation (R) was used for correlation between BCI score and TTDR. Fisher’s exact tests were used to identify genomic alterations with significant differences comparing BCI prognostic groups. Due to small sample size, comparisons were not adjusted for multiple testing. Results: The study includes 107 HR+/HER2- metastatic patients with primary tumors tested with both MSK-IMPACT and BCI: 44% post-menopausal, 60% T2/3, 64% grade 3, 56% lymph node positive (LN+). Consistent with the nature of this cohort (all experienced DR), BCI classified the majority of the patients (n=94, 88%) as high-risk for DR. The BCI score was negatively correlated with TTDR (R=-0.24, p=0.011). Patients classified as high-risk by BCI tended to have DR earlier than low-risk patients (median TTDR: 2.8y vs. 3.4y; HR=1.95 with 95% CI: 1.05-3.62; p=0.031). Overall, the genomic profile of the cohort was consistent with high-risk luminal primary tumors, with higher than expected rate of TP53 mutations (35%). Analysis of somatic genomic alterations by MSK-IMPACT revealed a trend that there are more mutations in PIK3CA and TBX3 in the BCI low-risk group compared to the high-risk group (77% vs 46%, p=0.038) and (38 vs 3%, p=0.020), respectively. Conclusion: In this cohort of high-risk BC patients who all had a DR event, BCI remained prognostic with lower BCI scores associated with longer TTDR. Initial findings from the genomic correlative analysis suggested an association of BCI with certain genomic features. Further analyses with additional samples are ongoing to substantiate these findings. Citation Format: Hong Zhang, Li Ma, Anton Safonov, Natalia Siuliukina, Julia Ah-Reum An, Subhiksha Nandakumar, Enrico Moiso, Edaise da Silva, Mehnaj Ahmed, Lisa Loudon, Konner Nelson, Kevin Murphy, Jade Oghoanina, Mark Robson, Sarat Chandarlapaty, George Plitas, Yi Zhang, Kai Treuner, Pedram Razavi. Associations between Breast Cancer Index Classifications and MSK-IMPACT Genomic Profiles in HR+/HER2- Breast Cancer [abstract]. In: Proceedings of the San Antonio Breast Cancer Symposium 2024; 2024 Dec 10-13; San Antonio, TX. Philadelphia (PA): AACR; Clin Cancer Res 2025;31(12 Suppl):Abstract nr P1-11-07.

Flat epithelial atypia (FEA), a rare breast proliferative lesion, is often diagnosed following core biopsy (CB) of mammographic microcalcifications. In the prospective multi-institution TBCRC 034 trial, we investigate the upgrade rate to ductal carcinoma in situ (DCIS) or invasive cancer following excision for patients diagnosed with FEA on CB. Patients with a breast imaging reporting and data system (BI-RADS) ≤ 4 imaging abnormality and a concordant CB diagnosis of FEA were identified for excision. Upgrade rates were determined on the basis of local and central pathology review. The prespecified threshold to omit excision of FEA on CB was an upgrade rate of ≤ 3

BACKGROUND:The combination of pembrolizumab with neoadjuvant chemotherapy (NAC) for triple-negative breast cancer (TNBC) improves pathologic complete response (pCR) rates and event-free survival. Yet it is unclear which patients benefit most from the addition of immunotherapy. This study aims to identify predictive factors for pCR in patients with TNBC receiving chemo-immunotherapy (chemo-IO). PATIENTS AND METHODS:This single-institution retrospective analysis included 283 consecutive patients with TNBC treated with neoadjuvant chemo-IO from 1 June 2021 to 20 January 2023. The primary outcome was overall pCR; secondary outcomes were breast pCR and nodal pCR. Univariate and multivariable logistic regression models assessed for characteristics associated with overall, breast, or nodal pCR. RESULTS:Most patients presented with cT2 (71%) cN0 (54%) disease. The overall pCR rate was 57%, breast pCR was 58%, and axillary pCR was 67% among biopsy-proven cN+ patients. Race, pathogenic BRCA mutations, backbone chemotherapy regimen, immune-related adverse events, and disruptions in immunotherapy were not associated with pCR. Univariate associations with overall pCR were younger age (p = 0.04), lower clinical T stage (p = 0.01), ductal histology (p < 0.001), poor differentiation (p < 0.001), and unifocality (p < 0.001). Breast and axillary pCR had similar associations. Nodal pCR also had univariate associations with normal body mass index (BMI) (p = 0.04) and absence of lymphovascular invasion (LVI) (p = 0.04). On multivariable analyses, ductal histology and unifocality remained independently associated with overall and breast pCR. CONCLUSIONS:This analysis showed few clinical variables to be independently associated with pCR after neoadjuvant chemo-IO for TNBC. Thus, predicting chemo-IO response to personalize treatment and minimize morbidity may instead lie in ongoing basic and translational research to assess for useful biomarkers.

In hematopoietic cell transplant patients, intestinal Candida parapsilosis expansion and translocation cause life-threatening candidemia, yet how commensal intestinal bacteria prevent Candida expansion remains incompletely defined. Here, we trained a machine learning model on supernatant metabolomic profiles of commensal bacteria to identify bacteria-derived inhibitors of fungal growth, with valeric and butyric acid as top hits. Experimental validation confirmed in silico predictions in three systems. First, in patient fecal samples, valeric and butyric acid levels inversely correlated with C. parapsilosis growth. Second, in vitro, valeric acid potently inhibited C. parapsilosis growth by causing intracellular acidification. Third, administration of glycerol valerate, and free or microencapsulated valeric acid blunted C. parapsilosis growth at murine intestinal sites where valeric acid could be detected. Thus, machine learning could identify a mechanistic driver of trans-kingdom ecology limiting C. parapsilosis intestinal expansion and may inform strategies to reduce patient risk of developing candidiasis during high-risk periods. ### Competing Interest Statement E.G.P. has received speaker honoraria from Bristol-Myer Squibb, Celgene, Seres Therapeutics, MedImmune, Novartis, and Ferring Pharmaceuticals; is an inventor on patent application no. WPO2015179437A1, entitled Methods and compositions for reducing Clostridium difficile infection and no.WPO2017091753A1, entitled Methods and compositions for reducing vancomycin-resistant Enterococci infection or colonization; and holds patents that receive royalties from Seres Therapeutics. M. P. is an employee at SILA Advanced Nutrition. The remaining authors declare no competing interests.