Intrinsic Subtypes Research Articles

A comparison of invasive lobular carcinoma with other invasive breast cancers at Tygerberg Academic Hospital.

The second most common histological subtype of invasive breast carcinoma is invasive lobular carcinoma (ILC) occuring with a frequency 10-15% in Western countries and approximately 5%, in Africa, the Middle East and Asia (AMA). Combined hormone replacement therapy (CHRT) is a risk factor for the development of ILC which is infrequently diagnosed at our centre.This study aimed to investigate the incidence and clinicopathological characteristics of ILC as compared to invasive breast carcinoma of no special type (IBC-NST). Clinical and pathological data on breast carcinoma patients attending the breast and endocrine unit at Tygerberg Academic Hospital since 2017 have been recorded on a Stellenbosch University REDCap® database. IBC-NST was the most frequent subtype diagnosed (83.9%) and ILC the second most common subtype (5.2%). Most ILCs were of luminal B intrinsic subtype, and the median size was slightly smaller than IBC-NST. There were significantly more grade 2 ILCs than IBC-NSTs (81.5% vs 50.9%). There was no statistical difference between stage and histological subtype. ILC has clinicopathological differences when compared to IBC-NST, although these were less pronounced in this study. The prevalence of ILC was similar to numbers reported in AMA. We hypothesise that there may be a discrepancy in the prevalence of ILC between public and private healthcare systems in South Africa, and that it may be due to differing trends in prescribing CHRT.

A comparison of invasive lobular carcinoma with other invasive breast cancers at Tygerberg Academic Hospital

BACKGROUND: The second most common histological subtype of invasive breast carcinoma is invasive lobular carcinoma (ILC) occuring with a frequency 10-15% in Western countries and approximately 5%, in Africa, the Middle East and Asia (AMA). Combined hormone replacement therapy (CHRT) is a risk factor for the development of ILC which is infrequently diagnosed at our centre.This study aimed to investigate the incidence and clinicopathological characteristics of ILC as compared to invasive breast carcinoma of no special type (IBC-NST METHODS: Clinical and pathological data on breast carcinoma patients attending the breast and endocrine unit at Tygerberg Academic Hospital since 2017 have been recorded on a Stellenbosch University REDCap® database RESULTS: IBC-NST was the most frequent subtype diagnosed (83.9%) and ILC the second most common subtype (5.2%). Most ILCs were of luminal B intrinsic subtype, and the median size was slightly smaller than IBC-NST. There were significantly more grade 2 ILCs than IBC-NSTs (81.5% vs 50.9%). There was no statistical difference between stage and histological subtype CONCLUSION: ILC has clinicopathological differences when compared to IBC-NST, although these were less pronounced in this study. The prevalence of ILC was similar to numbers reported in AMA. We hypothesise that there may be a discrepancy in the prevalence of ILC between public and private healthcare systems in South Africa, and that it may be due to differing trends in prescribing CHRT

272TiP HARMONIA SOLTI-2101 / AFT-58: A head-to-head phase III study comparing ribociclib (RIB) and palbociclib (PAL) in patients (pts) with hormone receptor-positive/HER2-negative/HER2-enriched (HR+/HER2-/HER2-E) advanced breast cancer (ABC)

RIB and PAL are CDK4/6 inhibitors with efficacy and tolerability in pts with HR+/HER2- ABC when administered in combination with endocrine therapy (ET). RNA-based intrinsic subtyping has strong prognostic and predictive value in advanced HR+/HER2- tumors treated with ET. Non-Luminal subtypes, such as HER2-E and basal-like, are relatively endocrine-resistant and have poorer prognosis than luminal. tumors can switch subtypes over time to a more aggressive and less endocrine-responsive biology, which may also be reversed by effective treatment.

271P Eribulin (E) plus endocrine therapy (ET) in patients (pts) with HR[+]/HER2[-] metastatic breast cancer (mBC) after progression on previous ET: The REVERT study

Most pts with luminal mBC progress to ET +/- targeted therapy. E treatment promotes intrinsic subtype changes in the neoadjuvant setting, shifting luminal B to luminal A tumors. REVERT (NCT03795012) explores if E increases hormonal sensitivity in aromatase inhibitor (AI)-pretreated luminal mBC pts. REVERT is a multicenter, randomized, non-comparative phase II trial in which pts with AI-resistant, HR[+]/HER2[-], mBC were randomized (1:1) to receive E (1.23 mg/m2 on days 1 and 8 of every 21-day cycle) or E plus AI. Pts were stratified by previous CDK4/6 inhibitors. Pts must have received at least one anthracycline- and/or taxane-based regimen in the (neo)adjuvant setting and up to 3 prior lines of ET in the metastatic setting. Previous chemotherapy for mBC was not allowed. The primary endpoint was the overall response rate (ORR) as per RECIST v. 1.1 in E+AI arm. Secondary endpoints included ORR in E pts and progression-free survival (PFS) and safety as per the NCI-CTCAE v.4.0.3 in both arms. The target sample size was 60 pts. An interim analysis was planned with 22 recruited pts based on two-stage Simon design. Between June, 2019 and January, 2021, a total of 22 pts from 7 centers in Spain were enrolled. Median age was 63.0 (range 50-77) years, 21 (95.5%) pts had visceral disease and 8 (36.4%) pts presented ≥3 metastatic sites. The trial was terminated early on March 31, 2021 with 8 pts (36.4%) remained on treatment. ORR was achieved in 4 (26.7%; 95% CI: 7.8 to 55.1) of 15 pts in E+AI arm and 2 (28.6%; 95% CI: 3.7 to 71.0) of 7 pts in E arm (p=1). Median PFS was 6.3 months(mo) with E+AI and 6 mo with E alone (HR: 1.1; 95% CI, 0.3 to 3.9; p=0.932). A significant interaction (p=0.1) between treatment arm and pts with previous CDK4/6 inhibitor (HR= 0.3 favors E+AI) or without previous CDK4/6 inhibitor (HR = 3.2 favors E) was observed. All grade and grade ≥3 adverse events were similar in both arms, being neutropenia and fatigue the most frequent. Although superiority of E+AI over E single therapy seems unlikely in this scenario, E+AI combination deserves further investigation in pts with ET-resistant, HR[+]/HER2[-] mBC, after progression to CDK4/6 inhibitors.

LBA18 Final overall survival (OS) for abemaciclib plus trastuzumab +/- fulvestrant versus trastuzumab plus chemotherapy in patients with HR+, HER2+ advanced breast cancer (monarcHER): A randomized, open-label, phase II trial

Abemaciclib, an oral, selective CDK4 & 6 inhibitor, significantly improved PFS in HR+, HER2+ advanced breast cancer (ABC; locoregionally recurrent or metastatic) when combined with fulvestrant and trastuzumab, compared to trastuzumab plus chemotherapy in monarcHER (Tolaney 2020, Lancet Oncol.) Here, we report the OS results at the prespecified final analysis. monarcHER (NCT02675231) is a randomized, multicenter, open-label phase 2 trial. Randomization was 1:1:1 to arm A (abemaciclib 150mg PO BID, trastuzumab IV, fulvestrant 500mg IM), arm B (abemaciclib, trastuzumab), and arm C (trastuzumab, SOC chemotherapy). Stratification factors were number of prior systemic regimens for ABC and measurable disease. Exploratory biomarker analyses were also conducted, including evaluation of intrinsic subtypes by RNAseq. At the time of data cutoff (31 Mar 2022), of the 237 patients enrolled, 157 deaths had occurred across the treatment arms, 50 deaths (63%) arm A, 54 deaths (68%) arm B, and 53 deaths (67%) arm C. Median follow-up was 52.9 months. mOS was 30.3 months in arm A, 31.43 months in arm B and 22.7 months in arm C (A v C: HR 0.75 [95% CI 0.47, 1.21]; nominal 2-sided p-value 0.243; B v C: HR 0.73 [95% CI 0.46, 1.15]; nominal 2-sided p-value 0.177). In exploratory RNAseq analyses, luminal subtypes were associated with longer PFS (8.6 v 5.4 months [HR 0.54, 95% CI 0.38, 0.79]) and OS (31.7 v. 19.7 months [HR 0.68, 95% CI 0.46, 1]) compared to non-luminal. Updated PFS and safety findings were consistent with the primary analysis (data cutoff 8 Apr 2019). Abemaciclib plus trastuzumab ± fulvestrant numerically improved OS in women with HR+, HER2+ ABC compared to chemotherapy plus trastuzumab with a manageable safety profile.

Clustering Molecular Subtypes in Breast Cancer, Immunohistochemical Parameters and Risk of Axillary Nodal Involvement.

(1) Background: To establish similarities in the risk of axillary lymph node metastasis between different groups of women with breast cancer according to immunohistochemical (IHC) parameters. (2) Methods: Data was collected retrospectively, from 2000 to 2013, of 1058 node-positive breast tumours. All patients were divided according to the St Gallen 2013 criteria and IHC features. The proportion of axillary involvement (pN > pN0; pN > pN1mi; pN > pN1) was calculated for each group. Similarities in axillary nodal dissemination were explored by cluster analysis and association between IHC and risk of axillary disease was studied with multivariate analysis. (3) Results: Among clinico-pathological surrogates of intrinsic subtypes, axillary involvement was more frequent in Luminal-B like HER2 negative (45.8%) and less frequent in Luminal-B HER2 positive (33.8%; p = 0.044). Axillary macroscopic involvement was more frequent in Luminal-B like HER2 negative (37.9%) and HER2 positive (37.8%) and less frequent in Luminal-B HER2 positive (25.5%) and Luminal-A like (25.6%; p = 0.002). Axillary involvement ≥pN2 was significantly less frequent in Luminal-A like (7.4%; p < 0.001). Luminal-A with Luminal-B HER2 positive, and triple-negative with Erb-B2 overexpressing tumours were clustered together regarding any axillary involvement, macroscopic disease or ≥pN2. Among the defined subgroups, axillary metastases were more frequent when Ki67 was higher. In a multivariate analysis, Ki67>14% were associated with a risk of axillary metastases (HR: 1.31; 95% CI, 1.51–6.80; p < 0.037). (4) Conclusions: there are two lymphatic drainage pathways of the breast according to the expression of hormone receptor-related genes. Positive-ER tumors are associated with lower axillary involvement and negative-ER tumors and Ki67 > 14% with higher nodal involvement.

Multimodality imaging in lobular breast cancer: Differences in mammography, ultrasound, and MRI in the assessment of local tumor extent and correlation with molecular characteristics.

IntroductionInvasive lobular breast cancer (ILC) is a diagnostic challenge due to the diversity of morphological features. The objective of the study was to investigate the presentation and local extent of ILC using various imaging techniques and to assess the correlation between imaging and molecular profile.Materials and methodsWe reviewed 162 consecutive patients with ILC found on vacuum-assisted biopsy, who underwent evaluation of the lesion morphology and extent using ultrasound (US), mammography (MMG), and magnetic resonance imaging (MRI). Radiographic features were compared with ILC intrinsic subtype based on the expression of Ki-67 and estrogen, progesterone, and HER2 receptors.ResultsA total of 113 mass lesions and 49 non-mass enhancements (NMEs) were found in MRI. Masses were typically irregular and spiculated, showing heterogeneous contrast enhancement, diffusion restriction, and type III enhancement curve. NMEs presented mainly as the area of focal or multiregional distribution with heterogeneous or clumped contrast enhancement, diffusion restriction, and type III enhancement curve. Lesion extent significantly varied between MRI and MMG/ultrasonography (USG) (P < 0.001) but did not differ between MGF and ultrasonography (USG). The larger the ILC, the higher the disproportion when lesion extent in MRI was compared with MMG (P < 0.001) and ultrasonography (USG) (P < 0.001). In the study group, there were 97 cases of luminal A subtype (59.9%), 54 cases of luminal B HER2− (33.3%), nine cases of luminal B HER2+ (5.5%), and two cases of triple negative (1.2%). The HER2 type was not found in the study group. We did not observe any significant correlation between molecular profile and imaging.ConclusionMRI is the most effective technique for the assessment of ILC local extent, which is important for optimal treatment planning. Further studies are needed to investigate if the intrinsic subtype of ILC can be predicted by imaging features on MRI.

HER2-enriched subtype and novel molecular subgroups drive aromatase inhibitor resistance and an increased risk of relapse in early ER+/HER2+ breast cancer.

SummaryBackgroundOestrogen receptor positive/ human epidermal growth factor receptor positive (ER+/HER2+) breast cancers (BCs) are less responsive to endocrine therapy than ER+/HER2- tumours. Mechanisms underpinning the differential behaviour of ER+HER2+ tumours are poorly characterised. Our aim was to identify biomarkers of response to 2 weeks’ presurgical AI treatment in ER+/HER2+ BCs.MethodsAll available ER+/HER2+ BC baseline tumours (n=342) in the POETIC trial were gene expression profiled using BC360™ (NanoString) covering intrinsic subtypes and 46 key biological signatures. Early response to AI was assessed by changes in Ki67 expression and residual Ki67 at 2 weeks (Ki672wk). Time-To-Recurrence (TTR) was estimated using Kaplan-Meier methods and Cox models adjusted for standard clinicopathological variables. New molecular subgroups (MS) were identified using consensus clustering.FindingsHER2-enriched (HER2-E) subtype BCs (44.7% of the total) showed poorer Ki67 response and higher Ki672wk (p<0.0001) than non-HER2-E BCs. High expression of ERBB2 expression, homologous recombination deficiency (HRD) and TP53 mutational score were associated with poor response and immune-related signatures with High Ki672wk. Five new MS that were associated with differential response to AI were identified. HER2-E had significantly poorer TTR compared to Luminal BCs (HR 2.55, 95% CI 1.14–5.69; p=0.0222). The new MS were independent predictors of TTR, adding significant value beyond intrinsic subtypes.InterpretationOur results show HER2-E as a standardised biomarker associated with poor response to AI and worse outcome in ER+/HER2+. HRD, TP53 mutational score and immune-tumour tolerance are predictive biomarkers for poor response to AI. Lastly, novel MS identify additional non-HER2-E tumours not responding to AI with an increased risk of relapse.FundingCancer Research UK (CRUK/07/015).

Pan-cancer landscape of T-cell exhaustion heterogeneity within the tumor microenvironment revealed a progressive roadmap of hierarchical dysfunction associated with prognosis and therapeutic efficacy.

SummaryBackgroundT cells form the major component of anti-tumor immunity. A deeper understanding of T cell exhaustion (TEX) heterogeneity within the tumor microenvironment (TME) is key to overcoming TEX and improving checkpoint blockade immunotherapies in the clinical setting.MethodsWe conducted a comprehensive pan-cancer analysis of TEX subsets from 9564 tumor samples across 30 bulk solid cancer types. Pan-cancer TEX subtypes were identified using literature-derived hierarchical TEX-specific developmental pathway signatures. The potential multi-omics and clinical features involved in TEX heterogeneity were determined.FindingsOur study yielded a dynamic, progressive roadmap and a hierarchical dysfunction landscape regarding TEX within the TME. In total, we identified five pan-cancer TEX subtypes, revealing tissue/cancer type-specific TEX patterns in low immunogenic tumors. By contrast, highly immunogenic tumors tend to harbor high frequencies of progenitor TEX subsets. In addition, the TEX profile also revealed distinct prognoses, intrinsic molecular subtype distribution, immune microenvironment and multi-omics features among the cancers. Network analysis identified four previously unknown TEX-associated cancer genes (tolloid-like 1, myosin heavy chain 111, P2Y receptor family member 8 and protein kinase D2), the possible association with anti-PD-1 immunotherapy response was validated using a single-cell dataset. Finally, a machine learning-based gene signature was developed to model the hierarchical TEX stages, verified in single-cell and immunotherapy patient cohorts.InterpretationOur study provided a TEX-derived system that can be applied for the immune subtyping of cancers and may have implications for the further optimization of personalized cancer immunotherapy.FundingThis study was supported by the National Natural Science Foundation of China (Grant No. 62072341 and 61973240). The funders had no roles in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Dynamic changes in intrinsic subtype, immunity status, and risk score before and after neoadjuvant chemo- and HER2-targeted therapy without pCR in HER2-positive breast cancers: A cross-sectional analysis.

Very few studies have been done in HER2 positive patients without complete pathological response (pCR) after combined neoadjuvant chemo- and HER2-target therapy to investigate changes in intrinsic subtype, risk of recurrence (ROR) score, and immunity status before and after treatment.Patients with nonmetastatic HER2-positive breast cancer failed to achieve pCR after neoadjuvant chemotherapy plus trastuzumab were included in current study. We examined the distribution of PAM50 subtypes, ROR score and immunity score in 25 paired baseline and surgical samples. The Miller–Payne grading system was used to evaluate the efficacy of the neoadjuvant therapy. It was observed that the distribution of intrinsic subtype, ROR category and immunity subgroup varied according to hormone receptor (HR) status. HER2-enriched and basal-like subtypes, median-high ROR categories and immunity-weak subgroup were dominant in baseline tumors. Compared to baseline samples, conversion of intrinsic subtype, ROR categories and immunity subgroups were found in 15 (60.0%), 13(52.0%), and 11(44.0%) surgical samples, respectively. The PAM50 subtype, ROR category, and immunity subgroup were concordant between baseline and surgical samples where nonluminal subtypes, median-high ROR categories and i-weak subgroup were still common.In conclusion, the HER2-positive breast cancer is highly heterogeneous with a distribution of 72-gene expression varying according to HR co-expression. The dynamics of the 72-gene expression pre- and posttreatment may become novel biomarker for guiding adjuvant therapy and hence warrant further investigation.

BSCI-06 COMPREHENSIVE ANALYSIS OF THE IMMUNOGENOMICS OF TRIPLE NEGATIVE BREAST CANCER BRAIN METASTASES FROM LCCC1419

BACKGROUNDTriple negative breast cancer (TNBC) lacks expression of hormone receptors (estrogen and progesterone receptors, ER and PR) and HER2. Almost 50% of patients with metastatic TNBC will develop brain metastases (BrM), often with concurrent progressive extracranial disease. While immunotherapy has shown promise in the treatment of advanced TNBC, the immune profile of BrM remains largely unknown. To inform the development of immunotherapy strategies in this aggressive disease, we characterized the genomic and immune landscape of TNBC BrM and matched primary tumors.METHODSFormalin-fixed, paraffin-embedded samples of BrM and primary tumors of patients with clinical TNBC (n=25, n=9 matched pairs) from the LCCC1419 biobank at UNC-Chapel Hill were analyzed by whole exome (WES) and RNA sequencing, with matched blood DNA sequenced for identification of somatic variants. Mutational and copy number alteration analyses, neoantigen prediction, and transcriptomic analysis of the tumor immune microenvironment were performed.RESULTSPrimary and BrM tissues were confirmed as TNBC and of the basal intrinsic subtype. Compared to primary tumors, BrM demonstrated higher tumor mutational burden. Neoantigen prediction showed elevated cancer testis antigen- and endogenous retrovirus-derived MHC class I-binding peptides in both primary tumors and BrM, and predicted single nucleotide variants (SNV)-derived peptides were significantly higher in BrM. BrM demonstrated reduced immune gene signature expression, although a signature associated with fibroblast-associated wound healing was elevated in BrM. Metrics of T and B cell receptor diversity were also reduced in BrM.CONCLUSIONSBrM harbored higher mutational burden and SNV-derived neoantigen expression along with reduced immune gene signature expression relative to primary TNBC. Further research will expand these findings to other breast cancer subtypes. Exploration of immunomodulatory approaches including vaccine applications and immune checkpoint inhibition to enhance anti-tumor immunity in TNBC BrM are warranted.

Analysis of Genomic Alterations Associated with Recurrence in Early Stage HER2-Positive Breast Cancer.

Simple SummaryThis study provides information about the genetic alterations associated with disease recurrence in early stage HER2-positive breast cancer. We found seven upregulated and two downregulated differentially expressed genes in patients with recurrence. In addition, the tumor inflammation signature score and the scores of six immune-related breast cancer signatures were decreased in patients with recurrence. Our study offers insight into the underlying genetic background of recurrence risk and can help to develop effective risk-adapted therapeutic strategies in early stage HER2-positive breast cancer.We aimed to compare gene expression in primary tumors of patients with recurrence and nonrecurrence to gain insight into the biology of high-risk HER2-positive early breast cancer. Patients who underwent curative resection and received adjuvant trastuzumab for HER2-positive early breast cancer were evaluated. Gene expression analyses were performed using NanoString Technologies’ nCounter Breast Cancer 360 Panel. PAM50 intrinsic subtypes and Breast Cancer Signatures including tumor inflammation signature (TIS) were evaluated. Of 247 patients, 28 (11.3%) had recurrence at a median follow-up of 54.2 months. Patients with pathological stage III, tumor size > 5 cm, axillary lymph node metastases, and hormone receptor-negativity were more frequently observed in the recurrent group compared with the nonrecurrent group. In patients with recurrence, seven genes were upregulated significantly, including WNT11, HAPLN1, FGF10, BBOX1, CXADR, NDP, and EREG, and two genes were downregulated, including CXCL9 and GNLY. TIS score was significantly lower in patients with recurrence compared with controls without recurrence. These findings suggest that activation of oncogenic signaling pathways related to cell proliferation, adhesion, cancer stemness, and noninflamed tumor microenvironment are associated with the risk of recurrence in early stage, HER2-positive breast cancer.

Comprehensive Analysis of the Immunogenomics of Triple-Negative Breast Cancer Brain Metastases From LCCC1419.

BackgroundTriple negative breast cancer (TNBC) is an aggressive variant of breast cancer that lacks the expression of estrogen and progesterone receptors (ER and PR) and HER2. Nearly 50% of patients with advanced TNBC will develop brain metastases (BrM), commonly with progressive extracranial disease. Immunotherapy has shown promise in the treatment of advanced TNBC; however, the immune contexture of BrM remains largely unknown. We conducted a comprehensive analysis of TNBC BrM and matched primary tumors to characterize the genomic and immune landscape of TNBC BrM to inform the development of immunotherapy strategies in this aggressive disease.MethodsWhole-exome sequencing (WES) and RNA sequencing were conducted on formalin-fixed, paraffin-embedded samples of BrM and primary tumors of patients with clinical TNBC (n = 25, n = 9 matched pairs) from the LCCC1419 biobank at UNC—Chapel Hill. Matched blood was analyzed by DNA sequencing as a comparison for tumor WES for the identification of somatic variants. A comprehensive genomics assessment, including mutational and copy number alteration analyses, neoantigen prediction, and transcriptomic analysis of the tumor immune microenvironment were performed.ResultsPrimary and BrM tissues were confirmed as TNBC (23/25 primaries, 16/17 BrM) by immunohistochemistry and of the basal intrinsic subtype (13/15 primaries and 16/19 BrM) by PAM50. Compared to primary tumors, BrM demonstrated a higher tumor mutational burden. TP53 was the most frequently mutated gene and was altered in 50% of the samples. Neoantigen prediction showed elevated cancer testis antigen- and endogenous retrovirus-derived MHC class I-binding peptides in both primary tumors and BrM and predicted that single-nucleotide variant (SNV)-derived peptides were significantly higher in BrM. BrM demonstrated a reduced immune gene signature expression, although a signature associated with fibroblast-associated wound healing was elevated in BrM. Metrics of T and B cell receptor diversity were also reduced in BrM.ConclusionsBrM harbored higher mutational burden and SNV-derived neoantigen expression along with reduced immune gene signature expression relative to primary TNBC. Immune signatures correlated with improved survival, including T cell signatures. Further research will expand these findings to other breast cancer subtypes in the same biobank. Exploration of immunomodulatory approaches including vaccine applications and immune checkpoint inhibition to enhance anti-tumor immunity in TNBC BrM is warranted.

Associations between circulating proteins and risk of breast cancer by intrinsic subtypes: a Mendelian randomisation analysis.

The aetiologic role of circulating proteins in the development of breast cancer subtypes is not clear. We aimed to examine the potential causal effects of circulating proteins on the risk of breast cancer by intrinsic-like subtypes within the Mendelian randomisation (MR) framework. MR was performed using summary statistics from two sources: the INTERVAL protein quantitative trait loci (pQTL) Study (1890 circulating proteins and 3301 healthy individuals) and the Breast Cancer Association Consortium (BCAC; 106,278 invasive cases and 91,477 controls). The inverse-variance (IVW)-weighted method was used as the main analysis to evaluate the associations between genetically predicted proteins and the risk of five different intrinsic-like breast cancer subtypes and the weighted median MR method, the Egger regression, the MR-PRESSO, and the MRLocus method were performed as secondary analysis. We identified 98 unique proteins significantly associated with the risk of one or more subtypes (Benjamini-Hochberg false discovery rate < 0.05). Among them, 51 were potentially specific to luminal A-like subtype, 14 to luminal B/Her2-negative-like, 11 to triple negative, 3 to luminal B-like, and 2 to Her2-enriched-like breast cancer (ntotal = 81). Associations for three proteins (ICAM1, PLA2R1 and TXNDC12) showed evident heterogeneity across the subtypes. For example, higher levels of genetically predicted ICAM1 (per unit of increase) were associated with an increased risk of luminal B/HER2-negative-like cancer (OR = 1.06, 95% CI = 1.03-1.08, BH-FDR = 2.43 × 10-4) while inversely associated with triple-negative breast cancer with borderline significance (OR = 0.97, 95% CI = 0.95-0.99, BH-FDR = 0.065, Pheterogeneity < 0.005). Our study found potential causal associations with the risk of subtypes of breast cancer for 98 proteins. Associations of ICAM1, PLA2R1 and TXNDC12 varied substantially across the subtypes. The identified proteins may partly explain the heterogeneity in the aetiology of distinct subtypes of breast cancer and facilitate the personalised risk assessment of the malignancy.

Molecular signatures of in situ to invasive progression for basal-like breast cancers: An integrated mouse model and human DCIS study

Ductal carcinoma in situ (DCIS) of the breast is a non-obligate precursor of Invasive Ductal Carcinoma (IDC) and thus the identification of features that may predict DCIS progression would be of potential clinical value. Experimental mouse models can be used to address this challenge by studying DCIS-to-IDC biology. Here we utilize single cell RNA sequencing (scRNAseq) on the C3Tag genetically engineered mouse model that forms DCIS-like precursor lesions and for which many lesions progress into end-stage basal-like molecular subtype IDC. We also perform bulk RNAseq analysis on 10 human synchronous DCIS-IDC pairs comprised of estrogen receptor (ER) positive and ER-negative subsets and utilize 2 additional public human DCIS data sets for comparison to our mouse model. By identifying malignant cells using inferred DNA copy number changes from the murine C3Tag scRNAseq data, we show the existence of cancer cells within the C3Tag pre-DCIS, DCIS, and IDC-like tumor specimens. These cancer cells were further classified into proliferative, hypoxic, and inflammatory subpopulations, which change in frequency in DCIS versus IDC. The C3Tag tumor progression model was also associated with increase in Cancer-Associated Fibroblasts and decrease in activated T cells in IDC. Importantly, we translate the C3Tag murine genomic findings into human DCIS where we find common features only with human basal-like DCIS, suggesting there are intrinsic subtype unique DCIS features. This study identifies several tumor and microenvironmental features associated with DCIS progression and may also provide genomic signatures that can identify progression-prone DCIS within the context of human basal-like breast cancers.

Clinical features and prognostic factors of breast cancer in young women: a retrospective single-center study.

This research aims to characterize the differences in clinical features and prognostic factors between younger and older breast cancer (BC) patients in China. All patients who were recently diagnosed with BC between January 1, 2015 and December 31, 2016 at Shanxi Province Cancer Hospital were recruited. We collected the epidemiological and clinical data as well as the follow-up information. Out of the 1968 BC patients who met the criteria for analysis, 227 (11.53%) were under 40years of age with a median age of 34years at diagnosis. All patients were classified into the age < 40, age 40-59, and age ≥ 60 groups. There were significant differences in the histology, tumor size, T stage, grade, and human epidermal growth factor receptor-2 (HER-2) levels among the three groups (all P < 0.05). The 5-year overall survival (OS) rates were 86.34%, 89.58%, and 84.84% for the age < 40, age 40-59, and age ≥ 60 groups, respectively. The TNM stage was the only predictor of clinical outcome in all BC patients. The prognostic value of intrinsic subtypes for OS was different among the three groups. Our study helped identify an age-related prognostic indicator of adverse events in BC patients and showed that young women with BC exhibited more aggressive clinical and pathological features. Our findings may facilitate clinical management and therapeutic interventions in young BC patients, especially in young women with a history of exposure to risk factors and age < 40years.

Identification of two intrinsic epithelial subtypes of colorectal cancer.

Identification of two intrinsic epithelial subtypes of colorectal cancer.

Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer

The consensus molecular subtype (CMS) classification of colorectal cancer is based on bulk transcriptomics. The underlying epithelial cell diversity remains unclear. We analyzed 373,058 single-cell transcriptomes from 63 patients, focusing on 49,155 epithelial cells. We identified a pervasive genetic and transcriptomic dichotomy of malignant cells, based on distinct gene expression, DNA copy number and gene regulatory network. We recapitulated these subtypes in bulk transcriptomes from 3,614 patients. The two intrinsic subtypes, iCMS2 and iCMS3, refine CMS. iCMS3 comprises microsatellite unstable (MSI-H) cancers and one-third of microsatellite-stable (MSS) tumors. iCMS3 MSS cancers are transcriptomically more similar to MSI-H cancers than to other MSS cancers. CMS4 cancers had either iCMS2 or iCMS3 epithelium; the latter had the worst prognosis. We defined the intrinsic epithelial axis of colorectal cancer and propose a refined ‘IMF’ classification with five subtypes, combining intrinsic epithelial subtype (I), microsatellite instability status (M) and fibrosis (F).

Role of Intrinsic Subtype Analysis with PAM50 in Hormone Receptors Positive HER2 Negative Metastatic Breast Cancer: A Systematic Review.

Endocrine therapy (ET), associated with CDK 4/6 inhibitors, represents the first choice of treatment for HR+/HER2- metastatic breast cancer (mBC). Primary or secondary endocrine resistance could develop; however validated biomarkers capable of predicting such a conditions are not available. Several studies have shown that HR+/HER2- mBC comprises five intrinsic subtypes. The purpose of this systematic review was to analyze the potential correlations between intrinsic subtype, efficacy of treatment, and patient outcome. Five papers that analyzed the intrinsic subtype with PAM50 assay in patients (pts) with HR+/HER2- mBC treated with ET (alone or in combination) within seven phase III clinical trials (EGF30008, BOLERO-2, PALOMA-2,3, MONALEESA-2,3,7) were identified. Non-luminal subtypes are more frequent in endocrine-resistant pts and in metastatic sites (vs. primary tumors), have less benefit from ET, and worse prognosis. Among these, HER2-enriched subtypes are similar to HER2+ tumors and benefit from the addition of anti-HER2 agents (lapatinib) and, for less clear reasons, of ribociclib (unconfirmed data for palbociclib and everolimus). Basal-like subtypes are similar to triple-negative tumors, making them more sensitive to chemotherapy. The intrinsic subtype is also not static but can vary over time with the evolution of the disease. Currently, the intrinsic subtype does not play a decisive role in the choice of treatment in clinical practice, but has potential prognostic and predictive value that should be further investigated.

Abstract CT026: The effect of intrinsic subtype on inhibition of tumor growth by anastrozole vs. fulvestrant vs. the combination: Results from the Alliance neoadjuvant endocrine therapy (NET) ALTERNATE trial

Abstract Introduction: The ALTERNATE trial randomized postmenopausal women with ER Allred 6-8 HER2- breast cancer to 6 months of NET with anastrozole (A), fulvestrant (F) or the combination (A+F). Biopsies were taken preNET and after 4-weeks(wks). Patients with Ki67 values &amp;gt;10% at 4-wks were offered triage to neoadjuvant chemotherapy. Patients with on-treatment Ki67 ≤ 10% who completed NET underwent surgery and Ki67 was reassessed. The primary endpoint was endocrine-sensitive disease rate (ESDR). ESD is defined as pCR or PEPI-0 residual disease (pT1-2, pN0, Ki67 ≤ 2.7%). We previously reported that the ESDR difference between the F-containing arms and the A arm was not &amp;gt;10% (ASCO 2020) and that baseline RNA-seq-based intrinsic subtypes predicted outcomes overall (SABCS 2021). Herein we describe relationships between PAM50 intrinsic subtype and Ki67 values by treatment arm because comparative drug effectiveness in adjuvant endocrine therapy studies in ER+ HER2- breast cancer can be predicted by the degree of Ki67 suppression (PMC3518447). Methods: 743 of the 1297 eligible patients (A: 264; F: 231; A+F: 248) had RNA extracted from preNET frozen tumor biopsies with &amp;gt;50% tumor content and subjected to RNA seq. Intrinsic subtypes were then assigned as LumA, LumB, and NonLum (Basal or HER2-E) using open-source PAM50-based informatics. Differences in the proportion with wk4 Ki67 &amp;gt; 10%, % change in wk4 ki67, and surgical CCCA (Ki67 ≤ 2.7%) rate (sxCCCA) between treatments and by intrinsic subtype was assessed using stratified logistic regression, Wilcoxon rank sum test, and Fisher’s exact test, respectively. Analysis of sxCCCA excluded those who failed to complete NET for reasons other than disease progression or early Ki67 &amp;gt;10%. Results: Amongst the 358 LumA cases there were no significant differences in Ki67-based endpoints between treatments. Among the 292 LumB cases, the wk4 ki67 &amp;gt; 10% rate was lower with A+F (19.4%) than A (43%) (P=0.0002) and was somewhat lower in F (31%) versus A (P=0.076). The % change in wk4 Ki67 in LumB cases, adjusted for baseline Ki67, showed markedly superior suppression for A+F versus A (-90% vs. -77%; P=&amp;lt;0.0001) and versus F (-90% vs. -80%; P=0.0026). Furthermore sxCCCA rates were significantly higher with A+F than A (53% vs. 25% P = &amp;lt;0.0001) and somewhat higher for F (37%) than A (p=0.068), indicating that superior antiproliferative effects for A+F persist after 6 months on therapy. Lack of Ki67 suppression in response to treatment was observed in the majority of 43 NonLum samples regardless of treatment. Conclusion: The combination of A+F was significantly more effective than either drug alone for the control of LumB breast cancer cell proliferation. This suggests that A+F may be a more effective adjuvant endocrine therapy than A alone in LumB disease. The lower Ki67 suppression with A alone also suggests that poorer outcome in some LumB tumors may be due to insufficient ER targeting rather than ER-independent tumor growth Support: U10CA180821, U10CA180882, U24CA196171, UG1CA189856, U10CA180868 (NRG), NCI BIQSFP, BCRF, Genentech, AstraZeneca. https://acknowledgments.alliancefound.org. (MJE) CPRIT RR140033, P50-CA186784, P50-CA58223, U01-CA214125, U24-CA210954, Gift from Ralph and Lisa Eads, McNair Scholarship. ClinicalTrials.gov Identifier: NCT01953588 Citation Format: Matthew J. Ellis, Meenakshi Anurag, Jeremy Hoog, Aranzazu Fernandez-Martinez, Cheng Fan, Richard Gibbs, Souzan Sanati, Kiran Vij, Mark Watson, Travis Dockter, Olwen Hahn, Joseph Guenther, Abigail Caudle, Erica Crouch, Amy Tiersten, Monica Mita, Wajeeha Razaq, Tina J. Hieken, Yang Wang, A. Marilyn Leitch, Gary W. Unzeitig, Eric Winer, Anna Weiss, Kelly Hunt, Ann H. Partridge, Charles M. Perou, Vera Suman, Cynthia X. Ma, Lisa A. Carey. The effect of intrinsic subtype on inhibition of tumor growth by anastrozole vs. fulvestrant vs. the combination: Results from the Alliance neoadjuvant endocrine therapy (NET) ALTERNATE trial [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr CT026.