Weinshilboum, Richard

Abstract Internal validation is the most popular evaluation strategy used for drug–target predictive models. The simple random shuffling in the cross-validation, however, is not always ideal to handle large, diverse and copious datasets as it could potentially introduce bias. Hence, these predictive models cannot be comprehensively evaluated to provide insight into their general performance on a variety of use-cases (e.g. permutations of different levels of connectiveness and categories in drug and target space, as well as validations based on different data sources). In this work, we introduce a benchmark, BETA, that aims to address this gap by (i) providing an extensive multipartite network consisting of 0.97 million biomedical concepts and 8.5 million associations, in addition to 62 million drug–drug and protein–protein similarities and (ii) presenting evaluation strategies that reflect seven cases (i.e. general, screening with different connectivity, target and drug screening based on categories, searching for specific drugs and targets and drug repurposing for specific diseases), a total of seven Tests (consisting of 344 Tasks in total) across multiple sampling and validation strategies. Six state-of-the-art methods covering two broad input data types (chemical structure- and gene sequence-based and network-based) were tested across all the developed Tasks. The best-worst performing cases have been analyzed to demonstrate the ability of the proposed benchmark to identify limitations of the tested methods for running over the benchmark tasks. The results highlight BETA as a benchmark in the selection of computational strategies for drug repurposing and target discovery.

Abstract Background: Hormone receptor-positive (HR+) breast cancer (BC) accounts for ~60-70% of all BC cases. CDK4/6i combined with endocrine therapy (ET) is the standard of care for first- and second-line therapy of patients with HR+ metastatic breast cancer (MBC) based on substantial improvements in progression free survival (PFS) and overall survival compared to ET alone. Unfortunately, most patients (pts) develop resistance to CDK4/6i. The mechanisms underlying CDK4/6i resistance have not been fully elucidated. Robust in vivo CDK4/6i resistant animal models from pts with de novo and acquired CDK 4/6i resistance are lacking. Patient-derived xenografts (PDXs) are important preclinical tools in oncology to advance our understanding of cancer biology and to evaluate drug response phenotypes. Unfortunately, the establishment of sustainable PDXs from pts with HR+ BC is much more difficult than from HR-negative BC. In order to obtain clinically relevant models that can be utilized to better understand mechanisms of primary and acquired resistance to ET and CDK4/6i, we report the development of PDXs from a prospective study in which percutaneous biopsies were obtained from women receiving palbociclib for the treatment of HR+ advanced or MBC (PROMISE; NCT03281902). Methods: PROMISE (Prospective Study to Evaluate the Role of Tumor Sequencing in Women Receiving Palbociclib for Advanced Hormone Receptor (HR)-Positive Breast Cancer) is a prospective trial which enrolled pts with HR+, HER2-negative MBC who planned to start treatment with palbociclib and letrozole (1st line [FL]) or palbociclib and fulvestrant (2nd line [SL]). For pts enrolled at Mayo Clinic Rochester (MCR), serial tumor biopsies were obtained prior to the start of treatment and at disease progression to establish PDXs. Because baseline take rate was low, we amended the protocol to attempt PDX generation after the 2nd cycle (C2) of therapy. Tissues were received within an hour of excision and were orthotopically implanted in the mammary fat pad of 6~8-week-old nonobese diabetic (NOD)/SCID/IL-2g-receptor null (NSG) mice. Tumor growth was defined as tumor volume ≥ 50 mm3. Tumor take rate was defined as percent of patients with development of at least one stably transplantable (passed at least for two generations) xenograft that was pathologically confirmed as BC. Results: Of the 50 pts enrolled at MCR, 37 were FL pts (2 ineligible) and 13 were SL pts (1 ineligible). Fresh tumor samples obtained pre-treatment from 43 eligible pts (32 FL), after C2 from 17 eligible pts (13 FL), and at disease progression from 10 eligible pts (5 FL) were implanted. Tumor growth was seen in at least one mouse from a pre-treatment specimen in 1 (3.1%) FL pt (confirmed BC) and 4 (36.4%) SL pts (2 confirmed BC); from end of C2 specimens in 2 (15.4%) FL pts and 2 (50%) SL pts (1 confirmed BC); and at progression in 1 (20%) FL pt and 2 (40%) SL pts (1 confirmed BC). The take rate from pre-treatment samples among FL pts was 1/32 (3.1%; 95% CI: 0.08-16.2%). Take rates in other groups are pending histological review. Discussion: In pts receiving palbociclib for HR+ MBC, the take rate using a pre-treatment percutaneous biopsy was low (3.1%) in the FL setting. However, higher growth rates were seen in the SL setting. The observation of higher growth rates at the end of C2 and at progression may relate to the activation of G1/S that occurs with withdrawal of palbociclib, and should be further studied. PDX remains a valuable tool for the evaluation of tumor biology and the development of new therapeutics, especially for those models established from pts with palbociclib and ET resistance. Proteogenomic and sequencing studies are ongoing to fully characterize these PDXs. Citation Format: Jia Yu, Vera J. Suman, Jun He, Jason P. Sinnwell, Ann M. Moyer, Bo Qin, Yayun Gu, Huan Zhang, Jodi M. Carter, Krishna R. Kalari, Brendan P. McMenomy, Minetta C. Liu, Tufia C. Haddad, Kathryn J. Ruddy, Fergus J. Couch, Alvaro Moreno-Aspitia, Donald W. Northfelt, Richard Weinshilboum, Ciara O'Sullivan, Matthew P. Goetz, Liewei Wang. Patient-derived xenografts (PDXs) generated from hormone receptor-positive breast cancer (BC) before and after cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i) treatment: Initial findings from the PROMISE study [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P5-01-07.

Abstract Introduction. The standard treatment for non-metastatic triple-negative breast cancer (TNBC) is neoadjuvant chemotherapy (NAC) and nearly 50% exhibit pathological complete response (pCR). However, patients with residual disease after NAC are at increased risk for recurrence and death. Prior studies examining the transcriptome of TNBC pre/post-NAC have examined a limited number of genes (<500) in heterogeneous subgroups of TNBC (e.g. LAR and non-LAR). We explored the transcriptome of androgen-receptor (AR) negative (non-LAR) TNBC subtype both pre/post NAC to identify pathways associated with NAC response. Methods. Tumors obtained pre/post NAC from TNBC patients enrolled in the Breast Cancer Genome Guided therapy study (BEAUTY) underwent RNA sequencing and reverse-phase protein array (RPPA). EdgeR was applied for differentially expressed (DE) analysis and regression methods for RPPA. Digital deconvolution method (CIBERSORTx) and TNBC single-cell data were used to obtain cell types. Pathway analysis was carried out using 2972 gene sets and gene set variation analysis (GSVA). Functional enrichment analysis was conducted with significant genes. Results. Of the 44 TNBC patients, 32 patients were excluded from the analysis cohort due to: LAR tumor (6 pts.), non-LAR tumor with pCR (23 pts.), and cell type issues with RNA-seq data (3 pt.). Paired RNA-Seq data were available for 12 TNBC patients (4 with progression <2 years [EP]) and 8 who were progression-free > 4 years [NP]) and paired RPPA data were available for 9 of these 12 patients. Differentially expressed genes, proteins and cell types between EP and NP in post-NAC. We identified 489 genes differentially expressed (DE) between EP and NP (logFC=|2|, FDR < 0.05). Analysis of cytobands from these 489 genes showed an enrichment of genes on chromosome 6p22.1-2 and 17q25.3 regions (enrichment ratio >5; p-value <10E-4). Critical genes identified in the AR- network (p-value < 10E-3) were IL1RN, SLAMF9, KRT81, BHLHE22, B3GALT5, PCP4, TREM1, AQP9, NRTN, and COL2A1.In addition, preliminary results from RPPA data of post-NAC tumors showed astrocytic phosphoprotein (PEA-15), involved in apoptosis, proliferation, glucose metabolism, as well as cell proliferation and Y box binding (YB1) proteins (involved in metastases), were more DE in EP than NP (p < 0.05). CIBERSORTx was applied to estimate the proportions of different cell types in post-NAC tumors. Cancer-associated fibroblasts iCAFs were low and myCAFs are high in EP vs NP. It is known that the cross-talk between CAFs and tumor cells may induce tumor resistance to chemotherapy. Differentially expressed pathways in post and pre-NAC EP tumors. Using genome-wide expression data from the paired 12 tumors and the GSVA method, we obtained individual pathway scores for 2972 pathways. One hundred ninety pathways were downregulated and 61 pathways were upregulated (p-value <= 0.05) in the post-NAC residual disease of EP relative to NP. We further examined these 190 pathways in the paired EPs and found 71% of those pathways were upregulated in the pre-NAC. These 190 downregulated pathways were enriched with FOXO, TGF-beta, PI3k, FGFR1, insulin and others. The 61 upregulated pathways in post-NAC EP tumors were enriched with mismatch repair, purine, tubulin, telomere, polymerase and gap-junction related pathways; 77% of those 61 pathways were downregulated in pre-NAC. Conclusions. Using a comprehensive “omics” approach, we have identified novel cancer and drug response pathways associated with recurrence in AR-TNBC disease. Further work to evaluate these as markers of outcome and potential drug targets is warranted. Citation Format: Krishna R Kalari, Vera J Suman, Xiaojia Tang, Jason P Sinnwell, Kevin J Thompson, Peter T Vedell, Jodi M Carter, Sarah A McLaughlin, Alvaro Moreno Aspitia, Donald W Northfelt, Richard J Gray, Richard Weinshilboum, Liewei Wang, Judy C Boughey, Matthew Goetz. Multi-omics data shows downregulation of mismatch repair, purin and tublin pathways in AR-negative triple-negative chemotherapy-resistant tumors [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P4-01-05.

Age at depressive onset (AAO) corresponds to unique symptomatology and clinical outcomes. Integration of genome-wide association study (GWAS) results with additional “omic” measures to evaluate AAO has not been reported and may reveal novel markers of susceptibility and/or resistance to major depressive disorder (MDD). To address this gap, we integrated genomics with metabolomics using data-driven network analysis to characterize and differentiate MDD based on AAO. This study first performed two GWAS for AAO as a continuous trait in (a) 486 adults from the Pharmacogenomic Research Network-Antidepressant Medication Pharmacogenomic Study (PGRN-AMPS), and (b) 295 adults from the Combining Medications to Enhance Depression Outcomes (CO-MED) study. Variants from top signals were integrated with 153 p180-assayed metabolites to establish multi-omics network characterizations of early (<age 18) and adult-onset depression. The most significant variant (p = 8.77 × 10−8) localized to an intron of SAMD3. In silico functional annotation of top signals (p < 1 × 10−5) demonstrated gene expression enrichment in the brain and during embryonic development. Network analysis identified differential associations between four variants (in/near INTU, FAT1, CNTN6, and TM9SF2) and plasma metabolites (phosphatidylcholines, carnitines, biogenic amines, and amino acids) in early- compared with adult-onset MDD. Multi-omics integration identified differential biosignatures of early- and adult-onset MDD. These biosignatures call for future studies to follow participants from childhood through adulthood and collect repeated -omics and neuroimaging measures to validate and deeply characterize the biomarkers of susceptibility and/or resistance to MDD development.

Major depressive disorder (MDD), the number one psychiatric disease and a major cause of medical disability worldwide, is a heterogeneous disease. Efforts to identify biomarkers for antidepressant therapy response by the use of genome‐wide association studies (GWAS) have generally yielded disappointing results, e.g. only a few markers have been replicated across studies. By applying a “pharmacometabolomics‐informed pharmacogenomic” research strategy, we previously identified a genome‐wide significant single‐nucleotide polymorphism (SNP) signal in the glutamate‐rich 3 ( ERICH3 ) gene that was associated with plasma serotonin concentrations which were themselves associated with selective serotonin reuptake inhibitor (SSRI) response in MDD patients enrolled in the Mayo Clinic PGRN‐AMPS SSRI trial. The same ERICH3 SNPs were associated with SSRI response in other GWAS, including the STAR*D and ISPC studies. However, the function of ERICH3 and the molecular mechanism(s) by which it might be associated with plasma serotonin concentrations and with SSRI response remain unknown. Functional characterization of ERICH3 and its encoded protein might make it possible to identify novel mechanisms of antidepressant treatment response. In the present study, ERICH3 mRNA and protein were studied in cell lines from human peripheral blood and brain. ERICH3 cDNA constructs and specific antibodies were generated to make it possible to study its function. Two ERICH3 mRNA splice variants and protein isoforms, one “full‐length” and the other encoding a C‐terminal protein, were identified in a variety of human cell lines and in human brain tissue. ERICH3 mRNA expression and immunofluorescent staining suggested both cytosolic and vesicular localizations for ERICH3 as well as co‐localization with serotonin and dopamine in both mouse and human neurons. Co‐immunoprecipitation studies identified several ERICH3 interacting proteins, including PIK3C2A, CLTC and AP2A2, proteins known to play a role in vesicular trafficking, as well as ALK and CUX1, both of which display genetic polymorphisms that have been associated with SSRI response in GWAS studies of antidepressant treatment response in MDD patients. This series of experiments suggests that ERICH3 may play a role in vesicular trafficking and, as a result, may influence neurotransmitter actions in the brain that are associated with antidepressant treatment response. Support or Funding Information This work was supported by the NIH grants U19 GM61388, R01 GM28157 and T32 GM008685. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Single nucleotide variants in the open reading frames (ORFs) of pharmacogenes are important causes of interindividual variability in drug response. Because of the very large number of missense variants in ORFs, it is difficult to link the genotypes of these variants to their phenotypes using “one at a time” expression systems. Therefore, the functional characterization of variants of unknown significance in clinically important pharmacogenes remains a major challenge in pharmacogenomics. Deep mutational scanning (DMS) is a high‐throughput technique that make it possible to analyze hundreds of different missense variants in a parallel and scalable fashion. Engineered “landing pad” HEK 293T cells were used as a platform to integrate pooled variant libraries, resulting in one variant per cell for further assessment. We adapted this DMS system to analyze the function of missense variants in the ORFs of CYP2C9 and CYP2C19 . The ORFs of CYP2C9 and CYP2C19 were fused to green fluorescent protein, and individual variants with different fluorescence intensities were used to indicate different levels of protein expression. Pooled variant libraries were generated by nicking mutagenesis, and we then used recombinase to integrate the libraries into landing pad cells, one per cell. Multiplexed functional selection performed with Fluorescence Activated Cell Sorting separated cells into different bins by fluorescence readout at the single–cell level. Amplicon sequencing of DNA collected in each bin, followed by computational analysis of the frequency of variants appearing in each bin, was used to determine levels of protein expression. To identify potentially severely damaging variants for these two important pharmacogenes, we studied 243 missense variants in the CYP2C9 and CYP2C19 ORFs that had been identified by the Exome Aggregation Consortium Project and by the Mayo Clinic RIGHT 1K Study. We found that 13 of 115 CYP2C9 and 25 of 128 CYP2C19 missense variants displayed less than approximately 25% of the wildtype protein expression, a level that may have clinical relevance for drug metabolism. Variant calling by the DMS method for the severely damaging variants was compared with the results of individual variant assay by western blot and with the predictions of computational algorithms such as Polyphen and SIFT. Our results suggest that DMS is an efficient method for the high‐throughput identification of damaging ORF variants that might have potential clinical application in pharmacogenomics. Support or Funding Information Funded by NIH grant U19 GM61388 (The Pharmacogenomics Research Network), R01 GM28157, R01 GM125633, T32 GM08685 and by the Mayo Clinic Center for Individualized Medicine This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Abstract Purpose: Patient-derived xenografts (PDX) are a research tool for studying cancer biology and drug response phenotypes. While engraftment rates are higher for tumors with more aggressive characteristics, it is uncertain whether engraftment is prognostic for cancer recurrence. Patients and Methods: In a prospective study of patients with breast cancer treated with neoadjuvant chemotherapy (NAC) with taxane ± trastuzumab followed by anthracycline-based chemotherapy, we report the association between breast cancer events and PDX engraftment using tumors derived from treatment naïve (pre-NAC biopsies from 113 patients) and treatment resistant (post-NAC at surgery from 34 patients). Gray test was used to assess whether the cumulative incidence of a breast cancer event differs with respect to either pre-NAC PDX engraftment or post-NAC PDX engraftment. Results: With a median follow-up of 5.7 years, the cumulative incidence of breast cancer relapse did not differ significantly according to pre-NAC PDX engraftment (5-year rate: 13.6% vs. 13.4%; P = 0.89). However, the incidence of a breast event was greater for patients with post-NAC PDX engraftment (5-year rate: 50.0% vs. 19.6%), but this did not achieve significance (P = 0.11). Conclusions: In treatment-naïve breast cancer receiving standard NAC, PDX engraftment was not prognostic for breast cancer recurrence. Further study is needed to establish whether PDX engraftment in the treatment-resistant setting is prognostic for cancer recurrence.

Abstract Background: The tamoxifen (TAM) metabolite, ENDX, demonstrated promising antitumor activity in endocrine resistant breast cancer (BC) in both phase I and phase II settings. Furthermore, ENDX resulted in superior in vivo antitumor activity compared to TAM and letrozole in aromatase-expressing aromatase inhibitor-sensitive and resistant MCF7AC1 models. Recently, we identified protein kinase C beta 1 (PKCβ1), which regulates cell proliferation and tumorigenic transformation, as a novel target of ENDX. ENDX-bound PKCβ1 at concentrations achieved in phase I/II ENDX studies (100-300 nM). In contrast, TAM binding to PKCβ1 occurred at concentrations 7-10 folds higher (2 μM) than achievable with TAM 20 mg/day dosing. However, the clinical relevance of targeting PKCβ1 kinase activity is unclear, since drugs that target PKCβ1 (enzastaurin) have been ineffective in BC and other solid tumors. Therefore, we sought to understand how ENDX altered PKCβ1 and to further compare and contrast ENDXs effects to that of PKCβ1 kinase inhibition in ERα+ BC. Methods: The effects of PKCβ1 silencing and ENDX treatment on gene expression was analyzed by RNAseq in MCF7AC1 cells. The impact of PKCβ1-silencing on cell cycle was evaluated by flow cytometry. Protein expression of cell cycle regulators in PKCβ1 and ENDX-treated MCF7AC1 and T47D cells were compared to TAM and enzastaurin in vitro and to letrozole, TAM or control in vivo. The effects of PKCβ1 and drugs on growth were analyzed by cell proliferation assays. PRKCB gene amplification was assessed in primary tumors using TCGA data and in metastatic tumors using whole-exome sequencing data from patients enrolled in the PROMISE study (NCT 03281902). Results: RNAseq analysis revealed E2F targets and G2M checkpoints as the top hallmark genesets significantly downregulated in both PKCβ1-silenced and ENDX-treated MCF7AC1 cells. Flow cytometry demonstrated that PKCβ1 silencing increased G1 and reduced S phases of the cell cycle. Western blot analyses of PKCβ1-silenced MCF7AC1 and T47D cells displayed reduced protein levels of the cell cycle regulators Cyclin D1, Retinoblastoma (Rb), phospho-RbS807/811, CDK4, Chk1 and E2F1 that regulate G1/S transition. While short term ENDX (48 hours) treatment did not alter PKCβ1 levels, prolonged in vitro ENDX treatment profoundly reduced PKCβ1 protein levels and the aforementioned cell cycle regulators, faithfully replicating PKCβ1 silencing effects. In contrast, enzastaurin had no impact on proliferation or cell cycle proteins in either model. Consistent with this finding, ENDX, but not TAM or letrozole, reduced protein levels of ERα and cell cycle regulators in vivo. Overexpression of PKCβ1 induced TAM, but not ENDX, resistance and had little impact on responsiveness to enzastaurin. While PRKCB gene amplification was uncommon in newly diagnosed ERα+/HER2- BC (5%, TCGA), PRKCB was amplified in 40% of metastatic ERα+/HER2- BC (PROMISE study). Conclusion: We have confirmed the relevance of a new ENDX target, PKCβ1, in ERα+/HER2- BC. While targeting PKCβ1 kinase activity elicited no anticancer effects in ERα+ cells, PKCβ1 downregulation, either by siRNA or ENDX, resulted in profound ERα turnover, reduced protein levels of essential cell cycle mediators and profoundly inhibited cell proliferation. Furthermore, PKCβ1 protein expression is associated with TAM, but not ENDX, resistance, a finding whose clinical relevance is further magnified by identification of PRKCB amplification in metastatic ERα+ BC, confirming its potential importance in progression. Efforts are currently underway to elucidate the mechanistic basis for ENDX-induced PKCβ1 and ERα degradation and the contribution of these effects to the superior antitumor activity of ENDX in ERα+ BC. Citation Format: Swaathi Jayaraman, Mary J Kuffel, Krishna R Kalari, Kevin J Thompson, Xiaojia Tang, Vera J Suman, Elizabeth S Bruinsma, Ciara C O'Sullivan, Liewei Wang, Richard Weinshilboum, James N Ingle, John R Hawse, Matthew P Goetz. Antitumor activity of Z-endoxifen (ENDX) is mediated via PKCβ1-dependent ERα loss and cell cycle arrest in ERα-positive breast cancer [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD8-04.

Abstract Introduction: The immune microenvironment of high-risk HR+ breast cancer (BC) is poorly understood. BEAUTY is a prospective neoadjuvant chemotherapy (NAC) study of stage I-III BC patients treated with neoadjuvant weekly taxane followed by anthracycline-based chemotherapy. Among clinical luminal B BC (St. Gallen criteria) from BEAUTY, we used high-plex digital spatial profiling (DSP) to characterize the intra-epithelial tumor and stromal immune landscapes to 1) assess the impact of NAC on these landscapes and 2) identify immune biomarkers predictive of response to NAC. Methods: The tissue set included FFPE sections of resected tumors from 35 patients (median 51y; range: 21-71y) with clinically-defined luminal B BC (ER &gt; 10%/grade 2/Ki67 ≥ 15% or ER &gt; 10%/grade 3), and 16 paired pre-NAC biopsies. Nanostring GeoMX DSP was used to quantitate 58 immune and BC biomarker proteins in intra-epithelial, cytokeratin-positive tumor segments and adjacent stromal (cytokeratin-negative/SYTO13 (nuclear stain)-positive) segments. Data were normalized using the geometric mean of two negative controls (RbIgG and MsIgG1). A general linear model with negative binomial identified differentially-expressed (DE) proteins in pre/post-NAC tumors. Based on DE protein data and biologic function, a targeted protein subset (N=19) was evaluated in pre-NAC biopsies for associations between protein abundance and residual cancer burden (RCB) class (0-II vs. III) (Wilcoxon-rank sum test: p-value &lt; 0.025 considered significant) or RCB ‘breast only’ index (Spearman correlation). Results: Comparing tumor segments in pre-NAC specimens, intra-epithelial segments were predictably enriched in cytokeratin, ER, PR and Ki-67, but also CD127 and NY-ESO-1; whereas stromal segments were enriched in proteins associated with T cell subsets (e.g. CD3, CD4, CD8), macrophages (CD68 and CD163), antigen presentation/dendritic cells (CD11c, HLA-DR) and immune checkpoint proteins (PD-L1, PD-L2, B7-H3, TIM-3, VISTA) among others. While NAC did not alter the spatial distribution of proteins (intra-epithelial vs. stromal segments), it markedly attenuated the immune landscape, with decreased abundance of functionally-diverse immune proteins (e.g. CD45, CD3, CD4, CD127, granzyme B, CTLA4; STING, B7-H3, CD11c, and CD68, log2FC: 0.27-1.52 p &lt; 0.05), including low abundance proteins PD-1, PD-L1, PD-L2, CD20, and OX40L (log 2FC: 0.15-1.16, p &lt; 0.05). Both PR and Ki-67 decreased in post-NAC tumors whereas ER was not significantly altered (p &lt; 0.05). CD8, CD14, CD163, HLA-DR, IDO-1 and TIM-3 were not significantly altered by NAC. In the pre-NAC biopsies (which had subsequent residual tumor burdens of RCB class 0 or I (n=1 each), II (n=6), and III (n=8), and median RCB ‘breast only’ index of 3.39 (range: 0.00-38.02), 19 proteins were used for RCB analysis (CD3, CD4, CD8, CD14, CD34, CD44, CD45, CD68, CD127, CD163, CTLA4, granzyme B, STING, B7-H3, fibronectin, Ki-67, HLA-DR, SMA and TIM3). Among them, stromal CD127 was significantly higher in RCB class III than RCB class 0-II (p=0.021) and RCB ‘breast only’ index was positively correlated with intra-epithelial granzyme B (rho = 0.61; p=0.012), and negatively correlated with intra-epithelial Ki-67 (rho= -0.71; p=0.0022). Conclusion: In this series of clinical luminal B BC, NAC markedly attenuated the tumoral immune landscapes with a small set of “NAC-resistant” immune proteins. Among a targeted set, stromal CD127 was significantly higher in RCB III, and RCB breast-only index was positively correlated with intra-epithelial granzyme B. These data provide insight into the impact of NAC on HR+ BC, and identify potential immune biomarkers to predict response to neoadjuvant chemotherapy. Citation Format: Jodi M Carter, Judy C Boughey, Jun He, Vera J Suman, Xue Wang, Jennifer M Kachergus, Krishna R Kalari, Liewei Wang, Richard Weinshilboum, Ann M Moyer, Sarah A McLaughlin, Alvaro Moreno-Aspitia, Donald W Northfelt, Richard J Gray, James N Ingle, E. Aubrey Thompson, Matthew P Goetz. Neoadjuvant chemotherapy selectively alters spatially-defined immune landscapes in clinical luminal B HR+/HER2- breast cancers: Analysis of the breast cancer genome guided therapy study (BEAUTY) [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PD7-05.