Neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER + /HER2- breast cancer: a randomized phase II trial

Domain: neuroscience
Published: 2026-04-08
Editorial outcome: minor_revision

Abstract
In PREDIX LumB patients with estrogen receptor positive and human epidermal growth factor receptor negative (ER+/HER2-) breast cancer > 20 mm and/or with lymph node metastasis were randomized 1:1 to receive either paclitaxel weekly for 12 weeks followed by palbociclib and endocrine therapy for 12 weeks (arm A), or the reverse sequence (arm B). Primary endpoint is objective radiologic response at 12 weeks (ORR12), and key secondary endpoints are ORR24, pathologic complete response, event-free survival, safety and correlative studies of tissue and circulating biomarkers. Whole exome sequencing and RNA sequencing were performed on baseline fresh frozen tissue samples. In total, 179 patients comprise the intention-to-treat population. There is no statistically significant difference between the two arms in ORR12 (59% vs 45%, p=0.058). An exploratory gene expression analysis identified differentially expressed genes and gene sets between responders and non-responders at 12 weeks. A predictive signature, CDKPredX, comprising 31 genes related to proliferation, ER signaling and immune activity was developed to identify patients resistant to chemotherapy but responding to palbociclib plus endocrine therapy (p interaction = 0.03). The predictive signature was independently validated in the CORALLEEN trial (p interaction = 0.048). Clinicaltrials.gov identifier: NCT02603679

Introduction
Inhibitors of cyclin dependent kinases 4 and 6 (CDK4/6i) are approved at both first and second line for the treatment of advanced estrogen receptor positive and human epidermal growth factor receptor 2 negative breast cancer (ER+/HER2- BC), based on the results of multiple randomized trials that have shown statistically and clinically significant prolongation of progression free and overall survival1. Their efficacy at the metastatic setting has inevitably led to their evaluation and subsequent approval in the adjuvant setting, where the addition to endocrine therapy of abemaciclib for two years or ribociclib for three years postoperatively has been shown to improve invasive disease-free and distant disease-free survival2,3. The uptake of CDK4/6i as preoperative treatment has been slower. CDK4/6i in combination with endocrine therapy has been compared with either endocrine therapy alone or with neoadjuvant chemotherapy4. Efficacy measured with traditional endpoints such as pathologic complete response (pCR) has not been encouraging and focus has shifted to biomarkers of response, such as complete cell cycle arrest (CCCA)5 or gene expression profiling-based risk classification6,7. Another clinically meaningful endpoint is tumor shrinkage to enable breast conserving surgery8, since similar objective radiologic response (ORR) rates to CDK4/6i plus endocrine therapy and chemotherapy are seen among patients with ER+/HER2- BC7, albeit with considerably less toxicity. However, the lack of predictive biomarkers undermines the implementation of neoadjuvant CDK4/6i6.

An overlooked aspect of CDK4/6i integration to the preoperative setting is its timing in relation to cytotoxic chemotherapy. The addition of the CDK4/6i trilaciclib to chemotherapy confers a protective effect on bone marrow progenitors, which has been shown in randomized trials to reduce myelotoxicity during treatment for small cell lung cancer9, and improves survival of patients with metastatic triple negative BC10. In the latter trial, trilaciclib was administered either simultaneously (arm B) or one day before chemotherapy (arm C) and in both cases efficacy improved over chemotherapy alone, an effect thought to be mediated by promotion of anti-tumor immunity. This hypothesis is in contrast with evidence on pancreatic cancer, where palbociclib after taxane chemotherapy augmented the cytotoxic effect by repressing DNA repair mechanisms, whereas palbociclib prior to chemotherapy mitigated its effect due to inhibition of tumor cell proliferation11. Considering the above, the identification of potential responders to preoperative CDK4/6i and the sequence of CDK4/6i and chemotherapy during preoperative treatment for ER+/HER2- BC may be of clinical importance12. The objectives of the randomized PREDIX LumB trial were to compare neoadjuvant paclitaxel with palbociclib and endocrine therapy in terms of objective response to treatment and to investigate their optimal sequence.

Here, we show the primary efficacy, safety and biomarker analyses of PREDIX LumB. There is no difference in terms of radiologic response between paclitaxel and palbociclib plus endocrine therapy, while the sequence of the treatments does not affect patient survival. In addition, we describe the development and validation of a transcriptomic biomarker that identifies breast tumors resistant to chemotherapy that retain sensitivity to palbociclib plus endocrine therapy.

Results
Patient characteristics
Between March 18th 2016 and July 29th 2021, 181 patients were enrolled in the trial. Two patients are excluded from all analyses, one because no protocol-mandated research core biopsy was obtained prior to treatment start and one because the results of the baseline computed tomography (CT) scans became available after treatment started and they showed disseminated disease. As such, the intention-to-treat (ITT) population comprises 179 patients. The available biopsy samples for translational analysis are summarized in Fig. 1.

The patients’ baseline characteristics are shown in Table 1. Baseline characteristics were mostly balanced, except for median Ki67 (arm A 30% versus arm B 25%). ~two thirds of all patients had histologically or cytologically verified lymph node metastasis prior to treatment start and more than 80% had progesterone receptor positive tumors.

Primary and secondary efficacy endpoints
In total, 51 patients treated with paclitaxel and 40 treated with palbociclib and endocrine therapy as first treatment attained an objective response. The difference between the two groups in terms of the primary endpoint of radiological response at 12 weeks (ORR12) was not statistically significant, 59% versus 45% (p=0.058). There was no statistically significant difference in radiological response at 24 weeks (ORR24) between the two arms (arm A 78% versus arm B 71%, p=0.293). Eight patients attained pCR, three in arm A and five in arm B (p=0.469). Residual cancer burden (RCB) class could be calculated for 132 patients, with most missing data due to pre chemotherapy removal of a positive sentinel node, which was routine practice during the earlier years of the trial. RCB 0/I was observed in 11 patients treated in arm A (n=3 RCB 0, n=8 RCB 1) versus 5 in arm B (n=5 RCB 0, p=0.073). The overall distribution of RCB classes differed between the two arms (p=0.023), with 59% in arm A versus 65% in arm B assessed as RCB-II and 24% versus 28% as RCB-III.

At the time of data cut-off (April 15th 2024), median follow-up time was 4.52 years (interquartile range, 3.39−5.59 years). There were 39 first events: 6 locoregional recurrences, 16 distant recurrences, 1 contralateral breast cancer, 7 disease progressions during neoadjuvant therapy, 7 second (new, non-breast) cancers and 2 deaths. There was no difference in terms of EFS between the two arms (HR=1.06, 95% CI 0.57–1.99, p=0.86). The corresponding five-year event-free survival (EFS) rates were 80.6% for arm A and 79.7% for arm B (Supplementary Fig. 1A). In addition, there were 24 post-surgery relapses, of which 7 were locoregional, 16 distant and 1 contralateral breast cancer. Relapse-free survival (RFS) did not differ between the two arms (HR=0.84, 95% CI 0.37–1.87, p=0.66; five-year rates 81.2% versus 86.0%; Supplementary Fig. 1B). Finally, there were 11 deaths, of which 6 breast cancer-related and 5 due to unrelated causes of death. No difference in overall survival (OS) between the two groups was observed (HR=1.22, 95% CI 0.37–4.01, p=0.74; five-year rates: 95.7% versus 93.2%; Supplementary Fig. 1C).

Histologic, imaging and molecular biomarkers of response to treatment
Baseline pathologist-read and digital Ki67, pathologist-read tumor infiltrating lymphocytes (TILs) and positron emission tomography/computed tomography (PET/CT) calculated maximal Standardized Uptake Values (SUVmax) were associated with likelihood of objective response at 12 weeks regardless of treatment arm (p >0.1 in all cases; Fig. 2A), although interaction between digital TILs and treatment arm was observed (p=0.037).

CCCA was not statistically significantly different between the two arms at surgery (p=0.080) or at 12 weeks (p=0.076). Higher digital Ki67 at 12 weeks was associated with lower likelihood of pCR only for patients treated with paclitaxel (OR=0.94, 95% CI 0.88–1.00, p=0.047), but not with palbociclib (OR=1.02, 95% CI 0.96–1.08, p=0.566; p interaction = 0.063).

At baseline there was no difference in median SUVmax according to PET/CT between the two treatment groups (5.0 versus 6.4, p=0.925). Metabolic activity was better suppressed during treatment with paclitaxel than with palbociclib (SUVmax week 12/baseline ratio 0.40 versus 0.53, corresponding to 60% versus 47% relative decrease, p=0.009). SUVmax week 12/baseline ratio was associated with likelihood of objective response at 24 weeks (OR=0.11, 95% CI 0.02–0.60, p=0.01) and pCR (OR=0.02, 95% CI 0.00–0.95, p=0.047). In all cases, no differential effect according to treatment was noted (p interaction >0.1).

The associations between likelihood of objective response at 12 weeks and intrinsic subtypes, risk of recurrence-subtype-proliferation (ROR-P) score groups, PI3K/AKT/mTOR pathway mutations and the integrative clusters are summarized in Fig. 2B. No interaction with treatment was observed for intrinsic subtype (p interaction = 0.064), ROR-P score groups (p interaction = 0.289), PI3K/AKT/mTOR pathway alterations (p interaction = 0.085), and integrative clusters (p interaction = 0.352). The same was true for mutations or copy number alterations of key genes involved in CDK4/6-Rb pathway (Supplementary Fig. 2).

Transcriptomic determinants of treatment response
Differential gene expression and gene set enrichment analyses of baseline RNA sequencing data revealed distinct molecular profiles associated with treatment response. Tumors from responders to paclitaxel exhibited upregulation of immune-related pathways and downregulation of estrogen receptor (ER)-related pathways. In contrast, responders to palbociclib and endocrine therapy showed enrichment of proliferation and cell cycle-related pathways (Supplementary Fig. 3). These findings were corroborated by analyses of relevant genes and molecular signatures. Lower expression levels of established ER-related gene signatures were associated with response to paclitaxel (Supplementary Fig. 4). A similar trend was observed in tumors with low proliferative activity, as indicated by low ROR-P scores and classification as the luminal A intrinsic subtype (Fig. 2).

Regarding the immune microenvironment, paclitaxel responders demonstrated expression patterns indicative of an anti-tumor immune response, including higher levels of antigen presentation (Supplementary Fig. 5), increased cytotoxic or effector T cells (Supplementary Fig. 6), and higher levels of humoral immunity (Supplementary Fig. 7). Similar associations were observed when assessing the immune-related modules derived in silico from the publicly available gene sets of the Breast Cancer 360™ (BC360) panel (Supplementary Fig. 8). As expected due to the study design involving treatment reassignment after 12 weeks, patients achieving RCB 0/1 had baseline tumors characterized by upregulated proliferation and immune-related pathways and downregulated ER-related gene sets (Supplementary Fig. 9). Importantly, the recurrence of these biological patterns in responders, regardless of the time point of assessment (week 12 or surgery), underscores the time-independent nature of treatment response biology.

Development and validation of CDKPredX predictor
To quantify the relationship between these biological phenotypes and treatment response, a metagene predictor termed CDKPredX was established. CDKPredX+ subgroup was defined by tumors with high levels of proliferation and ER pathway expression, and low levels of immune-related gene expression, and comprised 42 of the 163 patients (25.8%). CDKPredX+ was enriched for luminal B intrinsic subtype (p<0.001), exhibited high expression of the retinoblastoma loss-of-function signature (RBsig) (p<0.001) and was associated with non-lobular histology (p=0.026). These findings were further validated in the SCAN-B cohort (Supplementary Fig. 10). In our cohort, expression of RBsig was strongly correlated with E2F signature expression (R=0.97, p<0.001). There were no RB1 point mutations, while deep deletions of RB1 gene were a rare event (5/166 patients, 3%) (Supplementary Fig. 11). The clinicopathologic and molecular characteristics of the CDKPredX subgroups are summarized in Fig. 3A and Supplementary Table 1. Further exploratory analysis compared unscaled continuous 21-gene recurrence score distributions, computed using a research-based implementation, between CDKPredX-defined subgroups (Supplementary Fig. 12).

A statistically significant interaction between CDKPredX subgroups and treatment was observed (p interaction = 0.03; Fig. 3B), as the predictor selected responders to palbociclib plus endocrine treatment and resistant to chemotherapy. ORR12 for CDKPredX+ tumors was 47.8% for CDK4/6i and endocrine treatment versus 31.6% for chemotherapy (OR=1.99, 95% CI 0.57–7.38, p=0.288), and 43.3% versus 65.6%, respectively for CDKPredX- tumors (OR=0.4, 95% CI 0.19–0.83, p=0.015). This interaction was confirmed in the CORALLEEN trial (p interaction = 0.048; Fig. 3B), with the corresponding OR for the CDKPredX+ and CDKPredX- groups being OR=3, 95% CI 0.28−70.88 (p=0.395) in favor of palbociclib and endocrine therapy, and OR=0.19, 95% CI 0.04−0.71 (p=0.019) in favor of chemotherapy. This effect was noted regardless of menopausal status (Supplementary Fig. 13). CDKPredX+ was not statistically significantly associated with ORR24, RCB, pCR rates and time-to-failure endpoints in PREDIX LumB (Supplementary Figs. 14 and 15). The association of CDKPredX and PET/CT SUVmax with outcomes in the subgroup of interest of lobular tumors is shown in Supplementary Fig. 16.

The chemoresistance of CDKPredX+ patients was further confirmed in the I-SPY2 and SCAN-B cohorts. CDKPredX+ showed lower pCR rates to neoadjuvant chemotherapy with or without immunotherapy compared to CDKPredX- in I-SPY2 (OR=0.15, 95% CI 0.04–0.43, p=0.002) (Supplementary Fig. 17) and derived no benefit from adjuvant chemotherapy in SCAN-B trial (inverse probability treatment weighting-adjusted p=0.61). CDKPredX was not prognostic for long-term outcomes regardless of treatment (Supplementary Fig. 18).

Safety and health related quality of life
There were no differences between the two treatment groups in terms of any dose reduction (43.8% versus 50.0%, p=0.41), any dose delay (59.6% versus 51.1%, p=0.26) or treatment discontinuation of at least one part of the preoperative treatment (27.0% versus 34.4%, p=0.28) for arm A versus arm B, respectively. Specifically, in arm A 19.1% and 9.0% prematurely discontinued paclitaxel and palbociclib respectively, while the corresponding proportions of patients in arm B were 28.8% for paclitaxel and 5.5% for palbociclib. The most common adverse events of any grade during paclitaxel were peripheral sensory neuropathy, rash and fatigue and during palbociclib neutropenia and nausea. The most common grade 3/4 adverse events during paclitaxel were peripheral sensory neuropathy and neutropenia, and during palbociclib neutropenia (Table 2). There were no differences in adverse events of any grade or of grade 3/4 between the two treatment arms.

The summary of the patient reported outcomes is shown in Fig. 4. The response rate of the health-related quality of life (HRQoL) questionnaires was 98% at baseline and ranged from 82-94% during treatment up to one year postoperatively (18 months since enrollment to the trial). At baseline, there was no difference between the two treatment groups (Supplementary Fig. 19). HRQoL was better preserved under treatment with palbociclib than paclitaxel during the first 12 weeks, with a shift after treatment switch in several domains such as dyspnea, diarrhea, and hair loss (Fig. 4 and Supplementary Figs. 20 and 21). At the time of the first annual follow-up visit, patient-reported HRQoL had returned to baseline levels for most variables regardless of randomization arm. However, compared with Swedish general population normative data, moderate differences in cognitive function, social function and insomnia and small differences in role function, fatigue and financial problems were observed (Supplementary Fig. 22).

Methods
Study oversight
This study was approved by the Regional Ethical Committee in Stockholm (dnr 2014/1492-31/4) and the Swedish Medical Product Agency. All patients provided written informed consent before inclusion. The study was conducted according to the Declaration of Helsinki and the principles of good clinical practice and was registered with EudraCT number 2014-000810-72 and at the ClinicalTrials.gov website, identifier NCT02603679.

Study design and participants
PREDIX LumB is an academic, prospective, randomized, open-label, multicenter phase 2 trial which was conducted at three centers in Stockholm, Sweden (Karolinska University Hospital, Södersjukhuset and Capio S:t Göran Hospital). The trial protocol is available as supplementary material. The clinical trial is reported here under according to the Consolidated Standards of Reporting Trials (CONSORT) guidelines32 and the correlative analyses according to the Reporting Recommendations for Tumor Marker Prognostic Studies (REMARK) guidelines33.

Eligible patients were women and men over 35 years with Eastern Cooperative Oncology Group performance status 0 or 1, diagnosed with ER positive (ER≥10%, in accordance with the Swedish National Care Program for breast cancer) and HER2-negative BC, greater than 2cm in size and/or node-positive. Patients with at most two distant metastases that could be treated with curative intent could be enrolled. Adequate cardiac, renal and hepatic function, and no history of other malignancies during the past five years were required for inclusion to the study.

Randomization and masking
Patients were randomly assigned (1:1) into the two treatment groups described hereunder. Randomization was conducted at the Central Trial Office at Karolinska University Hospital by a web-based procedure (TENALEA, TransEuropean Network for Clinical Trial Services, Amsterdam, Netherlands). Random assignment was stratified by participating site. Random permuted blocks of different sizes (block size of 2 or 4) were used to allocate the patients to each treatment group. This was an open-label study, thus both participants and investigators were aware of the treatment assignment.

Procedures
Patients allocated to arm A received 12 cycles of paclitaxel 80 mg/m2 administered weekly and then switched to treatment for 12 weeks with palbociclib (125 mg/day during days 1–21 every 28 days) in combination with endocrine therapy which was selected at the treating physician’s discretion (anastrozole 1 mg/day or letrozole 2.5 mg/day or exemestane 25 mg/day or tamoxifen 20 mg/day). Premenopausal patients planned for treatment with an aromatase inhibitor received additional goserelin 3.6 mg every four weeks subcutaneously. Patients allocated to arm B were treated with the reverse sequence, first 12 weeks of palbociclib and endocrine therapy, followed by 12 cycles of weekly paclitaxel. In case of disease progression before the 12-week time point, patients could prematurely switch to the other treatment. Breast surgery was performed ~two weeks after the final cycle. All patients received three adjuvant cycles of epirubicin 75–100 mg/m2 and cyclophosphamide 600 mg/m2 every three weeks, followed by radiotherapy and endocrine therapy in accordance with national guidelines and local practice.

Patients were followed during treatment with office visits for clinical examination and routine laboratory assessments (complete blood count, serum chemistry) every four weeks during the neoadjuvant phase. Response to treatment was assessed with breast imaging at 12 (prior to treatment switch) and 24 weeks (before surgery), either with mammography and ultrasound or with magnetic resonance imaging (MRI) of the breasts. Fluorine 18–labeled fluorodeoxyglucose (18F-FDG) combined positron emission tomography/computed tomography (PET/CT) was performed at baseline within two weeks prior to treatment start and at the 12-week time point prior to treatment switch. Following intravenous FDG injection and a 60-minute uptake phase, a combined PET/CT scan was obtained from the thorax and regional lymph nodes to limit radiation exposure. Within the scope of this analysis, the evaluation of the combined PET/CT images was made by calculating the maximal Standardized Uptake Values (SUVmax).

Safety was assessed according to the National Cancer Institute Common Terminology Criteria for Adverse Events version 4.0. Health-related quality of life (HRQoL) was assessed using the European Organization for Research and Treatment of Cancer (EORTC) quality of life questionnaire C30 (QLQ-C30) and the breast cancer–specific BR23 questionnaire34,35. HRQoL forms were completed at baseline before randomization, every six weeks during treatment (four timepoints), three months after surgery and annually at follow-up visits.

After the end of adjuvant chemotherapy and radiotherapy, patients were followed according to protocol for up to ten years with annual office visits for physical examination, documentation of adverse events and collection of HRQoL (the latter during years 0–5), complete blood count, serum chemistry, breast imaging, and plasma and serum collection for research use. At the time of recurrence further plasma and serum samples were collected, while a metastatic biopsy for research use was recommended but not obligatory.

Outcomes
The primary endpoint of the study is the rates of locally assessed radiological response at 12 weeks (ORR12), defined as complete (complete resolution of all lesions) or partial response (reduction in size of at least 30% with no new lesions). Secondary efficacy endpoints include ORR at 24 weeks (ORR24); rates of locally assessed pCR, defined as absence of invasive carcinoma in the breast and axillary lymph nodes (ypT0/Tis, ypN0); pathologic response according to Residual Cancer Burden (RCB)36, event-free survival (EFS), defined as time from randomization to disease progression, disease recurrence (local, regional, or distant), contralateral BC, other malignancy, or death from any cause, whichever occurs first; relapse-free survival (RFS), defined as time from surgery to disease recurrence (local, regional, or distant), or death from any cause, whichever occurs first; and overall survival (OS), defined as time from randomization to death from any cause. The definitions of the time-to-failure endpoints are generally aligned with the standardized NeoSTEEP (Standardized Definitions for Efficacy End Points) definitions37. Other secondary endpoints include safety and HRQoL as described above, including comparison with Swedish general population normative HRQoL data using EORTC QLQ-C3038, and biomarker studies for markers of response and resistance to the study treatments.

Study assessments
Tissue collection. Tissue biospecimens were collected from the patients prior to the initiation of the neoadjuvant therapy, as specified in the study protocol. Up to five 14-gauge ultrasound-guided core needle tissue biopsies were collected. Three fresh-frozen (FF) tissue samples were stored directly at −80°C after collection. The remaining two samples were directly immersed into 10% neutral-buffered formalin for preparation of formalin-fixed paraffin-embedded (FFPE) tissue blocks. Biopsies at baseline on-treatment were obtained after the PET/CT scan. Biopsies on-treatment were obtained at a median time of four days from the last administered palbociclib dose at week 12 (arm B), while surgery was performed at a median time of twelve days from the last administered palbociclib dose (arm A). Whole peripheral blood was also collected before the initiation of neoadjuvant therapy in 4 ml EDTA tubes and stored at –80°C. Plasma and serum samples were collected at baseline and every six weeks during treatment, as well as during follow-up.

Hematoxylin & eosin staining and Ki67 immunohistochemistry. Whole tissue sections (4 μm thick) from FFPE research biopsies were stained by E.T. for hematoxylin and eosin (H&E) and Ki67 immunohistochemistry (IHC) (clone SP6, dilution 1:100). For immunohistochemistry, the IntelliPath FLX automated slide stainer was used (BioCare Medical, California, USA) according to manufacturer’s protocol. Slides were deparaffinized with xylene for 20 min and rehydrated through a series of graded ethanol to water solutions. Antigen retrieval was performed with Diva Decloaker (BioCare Medical) in a decloaking chamber (BioCare Medical) under pressure at 95°C for 15 min and cooled down in washing buffer. Peroxidase block, protein block, immunostaining, HRP-coupled detection, and DAB chromogen were carried out with MACH1 Universal HRP-Polymer Detection Kit (BioCare Medical) and counterstaining with hematoxylin (Intellipath hematoxylin, BioCare Medical). After dehydration with increasing ethanol concentration, the slides were mounted using Pertex (Histolab, Gothenburg, Sweden).

Manual evaluation of tumor infiltrating lymphocytes, immune aggregates and Ki67. Stromal tumor infiltrating lymphocytes (TILs) were assessed by a certified breast pathologist (W.S.), who was blinded to other clinicopathological and molecular characteristics, as the percentage of tumor stroma covered by infiltrating lymphocytes, according to the recommendations of the International TILs Working Group39. The presence of immune aggregates was assessed by E.T. as a binary variable. The aggregates could be localized either inside or outside the invasive cancer area. A figure of representative immune aggregation morphology can be found in Supplementary Fig. 23. Expression of Ki67 (clone 30-9) at the baseline diagnostic biopsy and the surgical specimen was assessed locally according to routine care at the time the trial was conducted as the percentage of tumor cells with positive nuclear staining counted in a hotspot with a minimum of 200 tumor cells.

Generation of digital images. Digital images were generated by E.T. through slide scanning at 40x magnification with the NanoZoomer-XR digital slide scanner (cat # 12000, Hamamatsu Photonics, Hamamatsu, Japan) and the NDP.scan software (Hamamatsu Photonics, Hamamatsu, Japan) and were saved in NDPI file format.

Digital image assessment. Digital images were processed with the QuPath software40. The invasive cancer area was annotated in H&E images by W.S. according to TILs Working Group guidelines and in IHC by C.B. A cell classifier algorithm41,42 was used to enumerate digital TILs (DTILs), and the variable easTILs% = TILs Cell Area/Stroma Area * 100 was calculated as a surrogate of the respective definition from the TILs Working Group for the visual assessment. Across timepoints, pathologist-read and digital TILs were weakly but statistically significantly correlated (Spearman’s rho=0.292, p<0.001). The expression of digital Ki67 (DKi67) was automatically enumerated, as previously described43–46, using the guideline from the International Ki67 in Breast Cancer Working Group (https://www.ki67inbreastcancerwg.org/). Regardless of the assessment method, complete cell cycle arrest (CCCA) was defined as Ki67 ≤ 2.7%30. Across timepoints, pathologist-read and digital Ki67 were moderately and statistically significantly correlated (Spearman’s rho=0.553, p<0.001).

Nucleic acid extraction, library preparation, and sequencing. Simultaneous isolation of bulk RNA and DNA from fresh-frozen tumor biopsies was performed by E.T. using the AllPrep DNA/RNA/Protein Mini Kit (cat # 80004, QIAGEN, Hilden, Germany) according to manufacturer’s instructions. Each fresh-frozen sample was first minced into small pieces on a petri dish on dry ice using sterile stainless steel scalpels No. 10 (cat # 0501, Swann-Morton, Sheffield, UK). The tissue pieces were disrupted and homogenized in a mixture of Buffer RLT with β-mercaptoethanol (cat # 125470100, Thermo Fisher Scientific, USA) using 2.8 mm and 1.4 mm zirconium oxide homogenization beads included in the Precellys® CK Mix Tissue Homogenizing Kit (cat # P000918-LYSK0-A, Bertin Corp. Maryland, US), reinforced tubes (cat # D1031-RFS, Benchmark Scientific, Sayreville, US) and the BeadBug microtube homogenizer (cat # D1030E, Benchmark Scientific, Sayreville, US). After complete tissue disruption and during the RNA purification process, DNA digestion was performed using the RNase-free DNase set (cat # 79254, QIAGEN, Hilden, Germany). RNA was eluted with RNase-free water while DNA was eluted with EB buffer (cat # 19086, QIAGEN, Hilden, Germany). Germline DNA was isolated from whole peripheral blood using the FlexiGene DNA kit (cat # 51206, QIAGEN, Hilden, Germany). All nucleic acids were collected in Eppendorf® Forensic DNA Grade Safe-Lock 1.5 mL microcentrifuge tubes (Eppendorf SE, Hamburg, Germany). Initial quality control of the extracted nucleic acids was performed right after elution of the tumor RNA and DNA samples followed by storage at –80°C. Quantification of RNA and DNA was performed by the Qubit 3.0 Fluorometer (cat # Q33216, Thermo Fisher Scientific, USA) using Qubit™ RNA BR Assay Kit (cat # Q10210) and Qubit™ dsDNA BR Assay Kit (cat # Q32850, Invitrogen, USA), respectively. Purity was assessed using the Nanodrop ND-1000 (Saveen Werner, Malmö, Sweden).

For library preparation, all nucleic acid samples were first prepared to a final concentration of 20 ng/μL, while the initial nucleic acid input was 100 ng. RNA libraries were prepared using the Illumina Stranded Total RNA library preparation kit with Ribo-Zero Plus treatment (cat # 20040525/20040529, Illumina Inc.). Unique dual indexes (cat # 20040553/20040554, Illumina Inc.) were used. The library preparation was performed according to the manufacturers’ protocol (cat # 1000000124514). DNA libraries were prepared using the Twist Library Preparation EF Kit 2.0 and Twist Comprehensive Exome probe panel (cat # 104207, # 103698 and # 101308/09/10/11, Twist Bioscience) with unique dual indexes. Library preparation was performed according to the manufacturer’s instructions (DOC-001239). Sequencing was carried out in the National Genomics Infrastructure (NGI) at the Science for Life Laboratory (SciLifeLab) Uppsala Sweden, using the NovaSeq X Plus system, with 150 bp paired-end read length, 25B flow cell and XLEAP-SBS sequencing chemistry. After initial quality control assessment, baseline samples with concentration at the time of extraction of less than 20 ng/μL were considered as low quantity samples and were excluded from downstream analyses.

Whole exome sequencing preprocessing. Whole-exome sequencing (WES) data were processed using the nf-core/sarek pipeline (v2.7)47 employing default settings except where otherwise specified below. Paired-end FASTQ files, from multiple sequencing lanes per sample, were merged prior to analysis. Reads were aligned to the GRCh38 reference genome using BWA-MEM2 (v2.0)48. Post-alignment processing included duplicate marking, base quality score recalibration, and generation of recalibrated BAM files using GATK (v4.1.7.0)49. The mean target coverages of WES for tumor and germline DNA samples were 325x and 180x, respectively. Extensive quality control metrics, including mapping rate, duplication rate, and on-target percentage, were generated to assess sequencing and variant-calling performance.

Somatic mutation calling. Somatic variant calling, including single nucleotide variants (SNVs) and insertions/deletions (indels), was performed in matched tumor-normal mode using GATK4 Mutect2 (v2.2)50, as implemented in the nf-core/sarek pipeline (v2.7). To mitigate common technical artifacts, a panel of normals (PoN) was created by running Mutect2 in tumor-only mode across all normal samples (n=170), followed by merging the resulting VCF files using GATK’s CreateSomaticPanelOfNormals. Mutect2 was then run on each tumor–normal sample pair using this PoN for site-level variant filtration. Variants were filtered using FilterMutectCalls with default parameters. Mutations that were present at a variant allele fraction (VAF) of less than 5%, had coverage of less than 25x in both tumor and normal samples, and were present in the gnomAD repository with a population allele frequency greater than or equal to 1% were removed. Somatic variants were annotated for potential functional effects using Ensembl Variant Effect Predictor (v113)51 and snpEff (v4.3.1)52. Annotated VCF files were converted into Mutation Annotation Format (MAF) using vcf2maf (v1.6.22)53. Downstream analyses were restricted to non-synonymous mutations. Tumor mutational burden (TMB) was computed as the sum of all the above filtered mutations per tumor divided by the total exonic target size (36.8 Mb). APOBEC enrichment scores were estimated based on the method described by Roberts et al.54 using the maftools R package (v2.22.0)55.

Copy number alteration analysis. Copy number alterations (CNAs) were inferred using the PureCN R package (v1.22.2)56. A mapping bias reference was generated based on the WES bait coordinates, excluding low mappability regions. Coverage normalization was performed using a curated pool of normal blood-derived BAM files. Germline SNPs were incorporated by re-calling variants with Mutect2 in tumor-normal mode, including PoN sites, to improve allele-specific copy number estimation. The analysis workflow included Tangent normalization and segmentation steps to estimate log2 copy number ratios and to determine major and minor allele copy numbers. Significant amplifications and deletions were then identified using the Genomic Identification of Significant Targets in Cancer (GISTIC 2.0) algorithm57, applying thresholds of +0.1 for amplifications and −0.1 for deletions, with a confidence level of 0.99. Genomic events with q-values below 0.25 were considered significant at the focal or arm level. Each gene was assigned a discrete copy number state from −2 to +2, corresponding to deep deletion (−2), loss (−1), neutral (0), gain (+1), and amplification (+2). These GISTIC 2.0-derived copy number states were used in downstream integrative analyses.

RNA sequencing preprocessing and gene abundance estimation. RNA sequencing (RNA-seq) data were processed using the nf-core/rnaseq pipeline (v3.3)58 employing default settings except where otherwise specified below. Paired-end FASTQ files from multiple sequencing lanes per sample were merged prior to analysis. Reads were aligned to the GRch38 reference genome using the STAR aligner (v2.6.1d)59. Samples exhibiting fewer than 75% of uniquely mapped reads were excluded to ensure data quality and reliability. Additional exclusions removed any libraries from patients not included in the intention-to-treat population or lacked primary endpoint data (ORR12). Only pretreatment biopsies (baseline samples) were retained for downstream analysis.

Transcript abundance was quantified by Salmon (v1.4.0)60. Gene-level expression counts were derived from the transcript-level estimates using the tximport R package (v1.34.0)61. Gene length normalization was performed by scaling each gene’s length to its geometric mean across all samples, and raw counts were then scaled by these normalized gene lengths to adjust for length biases and ensure comparability of gene counts. Effective library sizes were estimated from the scaled count matrix using the trimmed mean of M-values (TMM) normalization method via the edgeR package (v4.4.2), and log2-transformed for use as offsets for downstream differential expression analysis. For visualization and downstream exploratory analyses, gene-level expression values were calculated as Transcripts Per Million (TPM), and log2-transformed to stabilize variance. All downstream analyses were performed using the resulting log2-transformed, TMM-normalized TPM matrix (log2 TMM-TPM).

Gene expression outliers were identified by calculating the median Euclidean distance of each sample to all other samples based on log2-transformed gene abundance. Samples with median distances exceeding the 75th percentile plus three times the interquartile range (IQR) of all median distances were classified as outliers and excluded from downstream analyses. Finally, the remaining high-quality samples were retained for subsequent transcriptomic analysis (n=163).

Differential gene expression and gene set enrichment analysis. To identify genes with altered expression between patients based on their ORR12 status, differential expression analysis was conducted on the raw gene counts using DESeq2 R package (v1.46.0)62. Genes with very low counts (total raw counts ≤ 10 across all samples) were excluded prior to analysis to improve robustness. Differential expression was assessed using the Wald test, and genes with an adjusted p value threshold of 0.05 (Benjamini–Hochberg correction) and an absolute log2 fold change cutoff of 0.5 were considered differentially expressed. Genes were ranked based on enrichment scores calculated as –log10 (p value) * sign(log2 (FoldChange)), integrating directionality and statistical significance for pre-ranked GSEA. Gene Set Enrichment Analysis (GSEA) was performed using the fgsea R package (v1.32.0) with a minimum gene set size of 10 and a maximum of 500, using annotated Hallmark gene sets from the Molecular Signatures Database (MSigDB, v2024.1)63. Resulting gene sets were filtered to retain only those with an adjusted p value < 0.05. Normalized enrichment scores (NES) of these significant pathways were used to explore biological processes and signaling pathways associated with the observed gene expression patterns63. In addition, Reactome64 pathway enrichment analysis was performed using the ReactomePA R package (v1.50.0) with an adjusted p value < 0.05. Enrichment maps were generated with the enrichplot R package (v1.26.6), incorporating pairwise pathway similarity to cluster related terms and displaying the top 25 enriched categories.

To further investigate treatment outcomes, differential expression analysis was also performed according to RCB status. As patients had received comparable therapies, the DESeq2 model included RCB status, treatment arm, and their interaction. Genes were ranked and subjected to pre-ranked GSEA with the Hallmark MSigDB gene sets, as described above, to identify pathways associated with RCB.

Intrinsic Subtyping and Risk of Recurrence (ROR) Estimation. Starting from the STAR-Salmon quantified data, upper-quartile normalization and log2-transformation were applied using edgeR package in accordance with65. Gene-centering and intrinsic subtype/ROR calculation were then performed in a single step using the BS_ssBC() function from BreastSubtypeR (v1.2.066) with the parameters s = “ER.v2” and Subtype=TRUE. This function implements the subgroup-specific centering method67, using ER+/HER2- reference quantiles65, and automatically outputs: (a) intrinsic subtype assignment (Basal-like, HER2-Enriched, Luminal A, Luminal B), reassigning any sample whose highest correlation is to the Normal-like centroid to its next highest correlation among the four target centroids, and (b) risk of recurrence-subtype-proliferation (ROR-P) score68.

Estrogen receptor (ER)-related signatures. The ESR1 module, comprising 131 genes correlated with ESR1 expression, was calculated as the average expression of these genes69. The ER-related gene expression module of the 21-gene Recurrence Score, including 4 ER-related genes, was computed to capture ER signaling70. The SET ER/PR index, based on 18 genes, was applied to measure transcription associated with ESR1 and PGR expression71. In addition, a research-based, in silico implementation of the ER signaling module from the NanoString Breast Cancer 360™ (BC360) panel was performed using the publicly available gene set provided by NanoString Technologies. For all signatures, samples were dichotomized at the median into high and low expression groups.

Immune-related signatures and immune cell deconvolution. Immune activity was assessed using complementary approaches. The Immunophenoscore (IPS) was computed using the hacksig R package (v0.1.2)72. The IPS provides a quantitative measure of tumor immunogenicity by aggregating biomarker scores across four categories: MHC molecules, immunomodulators, effector cells, and suppressor cells. The Danaher et al. immune cell signature method was applied according to the original publication73, which quantifies 14 immune cell populations by averaging the expression of predefined marker genes for each subset. A tumor-infiltrating lymphocyte (TIL) score was further derived as the mean of selected immune cell scores. Immune cell abundances were also estimated using the Microenvironment Cell Populations-counter (MCP-counter) method, implemented according to the original method to quantify eight immune and two stromal populations74. In addition, we performed a research-based, in silico implementation of the immune-related modules available from the NanoString Breast Cancer 360™ (BC360) panel using the publicly available gene set. The 14-gene immunoglobulin B-cell (IGG) signature was applied to capture humoral immune activity, reflecting processes such as lymphocyte maturation, CD4⁺ and B-cell activation and survival, germinal center differentiation, immunoglobulin production, chemotaxis, and regulation of B-, T-, and NK-cell activity75, A 9-gene and a 12-chemokine signature were applied to capture the presence of tertiary lymphoid structures (TLS)76,77. Beyond these signatures, expression levels of selected immune-related single genes, including human leukocyte antigens (HLA-A, HLA-B, HLA-C, HLA-E, HLA-F, HLA-G, HLA-H, HLA-J, HLA-K, HLA-L) and CD274, were also assessed. All immune-related signatures were subsequently organized into four functional categories: antigen presentation, T cell activity, B cell activity, and BC360-based immune modules. For all signatures, deconvolution-derived cell types, and single-gene measures, samples were dichotomized into high and low groups using the cohort median as a cut-off.

Rb loss-of-function (RBsig) scoring. The gene expression signature of Rb loss-of-function (RBsig), incorporating 87 genes that are correlated with E2F1 and E2F2 expression, was calculated for each sample as the average expression of these genes78. Samples with RBsig scores greater or equal to the cohort median were classified as “RBsig-high”, and those below the median as “RBsig-low”.

Integrative clusters. Integrative cluster (IntClust) subtypes, derived from gene expression and copy number data, were computed using the iC10 package (v2.0.2)79 for samples with both data types available. IntClusts associated with the ER-positive subtype were grouped into low- (IntClusts 3, 4, 7 and 8) and high-risk (IntClusts 1, 2, 6 and 9) subgroups based on their prognostic profiles, as described in80.

Development and validation of the CDKPredX metagene. A three-module metagene predictor (CDKPredX) was developed, using a proliferation-related mitosis kinase metagene score (Pr), the ER-related module of the 21-gene Recurrence Score (Er), and an immune-related kinase metagene score (Im), as they were defined in81. For each module, gene-level expression values (log2 TMM-TPM) were averaged across all module genes to yield a single module score per sample. Samples were dichotomized into high or low activity groups for each module using module-specific thresholds: the lower quartile for Pr, and the median for Er and Im. Samples with high Pr, high Er, and low Im were defined as the CDKPredX+ subgroup and the remaining as CDKPredX-. This stratification was then correlated with clinical outcomes.

The CDKPredX predictor was subsequently tested in three external validation cohorts using the same cutoffs. The first, CORALLEEN, is a prospective, multicenter, randomized, parallel-group, non-comparative phase II clinical trial. The trial’s primary analysis and gene expression data have been previously presented6,7. Only patients with RNA samples available at baseline were included in the current analysis, and no quality control steps were applied to the validation cohort data. The neoadjuvant I-SPY2 trial27 and the adjuvant SCAN-B observational study82 are publicly available and have been previously described in detail, including gene expression data.

Statistics and reproducibility
This analysis concerns the primary and secondary efficacy endpoints of PREDIX LumB, as well as safety and HRQoL analysis, and protocol-predefined biomarker assessments (PET/CT, TILs, Ki67, gene expression and genomic alterations). The sample size was determined for an explorative comparison of objective response rates after 12 weeks of neoadjuvant treatment. Assuming a 40% ORR12 in arm A (12 courses of weekly paclitaxel), and a 20% absolute improvement in arm B, a two-sided alpha = 0.10 and 80% power required 166 patients (83 per treatment arm). The goal was thus to randomize between 180 and 200 patients in the trial83.

Binary outcomes were compared using Fisher’s exact test. Continuous variables were compared using the Wilcoxon rank-sum test. Spearman’s rank correlation coefficients (with 95% bootstrap confidence intervals) quantified associations between continuous biomarkers. Logistic regression models – reporting odds ratios (ORs) with 95% confidence intervals (CIs) and Wald p values – assessed predictors of objective response. Time-to-event endpoints (EFS, RFS, OS) were censored at last follow-up and displayed via Kaplan–Meier curves; the log-rank test evaluated unadjusted differences. Multivariable Cox proportional hazards models – reporting hazard ratios (HRs) with 95% CIs and Wald p values – examined time to failure. Adjusted survival curves for the observational SCAN-B cohort were generated using the Inverse Probability of Treatment Weighting (IPTW) method, adjusted for age, size, lymph node status, and grade. Continuous biomarkers (e.g., Ki67, DKi67, TILs, DTILs, SUVmax) entered models as continuous covariates. Associations between clinicopathologic/molecular characteristics and CDKPredX subgroups were tested with Pearson’s chi-squared test. HRQoL scales were analyzed via linear regression, presenting mean differences with 95% CIs and p-values. All p-values were two-sided, and the level of significance was set to 5%. Analyses were performed using Stata v17 (StataCorp, College Station, TX, USA) and R v4.4.3.

Peer review rounds
[{"round": 1, "reviewer_comments": {"reviewer_1": "This is an interesting translational analysis from a randomized trial (PREDIX LumB) that attempts to identify a gene-expression signature (CDKPredX, 31 genes) predicting differential response to frontline paclitaxel versus palbociclib+endocrine therapy in ER+/HER2– breast cancer. The concept of using gene signature to select patients more likely to benefit from a CDK4/6 inhibitor-based therapy vs chemotherapy in the neoadjuvant setting is clinically relevant and of potential importance to the field.\nWe suggest the following points for clarification and discussion:\n• Validation cohorts (Lines 70-71, 224, 233, 236-237): The authors state that the predictive signature was independently validated in the CORALLEN trial. While CORALLEEN is an appropriate external cohort, the two trials differ substantially in regimen, primary endpoints, patient population, and timing of assessments, which complicates interpretation of “validation.” The same caveat applies to the SCAN-B and I-SPY2 cohorts. We suggest that the authors explicitly acknowledge and discuss these differences.\n• Sequential therapy discussion (Lines 101-105): The discussion of sequential CDK4/6i and chemotherapy in pancreatic cancer is interesting. Are there similar reports or pre-clinical evidence for breast cancer? (eg. PMID: 30635336)\n• Subtype-specific results (Figure 2B): In the forest plot, luminal A subtype appears to favor chemotherapy, whereas luminal B favors palbociclib plus endocrine therapy, which is the opposite of what might be expected given low proliferative activity of luminal A tumors and high proliferative activity of luminal B tumors. Is there a possible explanation or hypothesis to address these results?\n• Primary endpoint interpretation (Lines 274-276): The authors report no difference between chemotherapy and CDK4/6i plus endocrine therapy for the primary endpoint of ORR12 – Was the study statistically powered to detect small differences? Based on pre-specified effect size, alpha, and sample size calculation, please clarify whether this constitutes a negative trial per protocol, or whether the analysis may be underpowered. Is the ORR12 the right primary endpoint in this situation? 12 weeks of neoadjuvant ET may not be sufficient to see changes in tumor activity, and at same time, 12 weeks of weekly paclitaxel might not represent the ideal neoadjuvant chemotherapy regimen. Authors can add this in the study caveats.\n• The use of neoadjuvant ET is well established for post-menopausal women and is usually performed without the use of CDK4/6i. They acknowledge this in the discussion (338-340). Have authors considered validation of CDKPredX in ET alone and how that differentiate outcomes among the two treatment modalities? This can really help highlighting the utility of CDKPredX, enabling the identification of patients who can benefit from the addition of CDK4/6 to ET alone.\n• Comparison with Oncotype DX: Since Oncotype DX is the most widely use genomic assay in ER+/HER- disease, and both Oncotype and CDKPredX contain proliferation/ER-related signals, it would be informative to explore the correlation between the two signatures. If feasible, trial outcomes (chemotherapy vs. CDK4/6i+ET response) could be stratified by both Oncotype score categories (e.g., <26 vs. ≥26) and CDKPredX, which would enhance clinical interpretability.\n• The use of neoadjuvant ET is not well established for pre-menopausal women. Based on the most recent discrepancy of oncotype predictive value for pre-menopausal women in the TailorX and RXPonder trials, how does CDKPredX performs in the two populations of pre- and post-menopausal women. PREDIX LumB have included both populations and interpretation may be complicated due to small sample size.\n• The authors mentioned at the end of discussion that a prospective trial is undergoing to test CDKPredX as a single sample predictor. Is there a NCT number available for the trial? In what setting/population trial will run?", "reviewer_2": "Dear Dr. Matikas et al,\nI read the manuscript titled \"Randomized trial of neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER+/HER2- breast cancer (PREDIX LumB): Primary analysis and development of the CDKPredX metagene predictor” with great interest. The manuscript reports on the results of a randomized clinical trial in early stage hormone receptor positive and Her2 negative (ER+/Her2-) breast cancer with a particular emphasis on the development of a novel predictive signature to identify patients that would respond to a CDK4/6 inhibitor + endocrine therapy. Overall, it is a well written manuscript that requires minimal editing.\nKey strengths of the submitted manuscript include:\n1. Innovative hypothesis. The authors investigated a preoperative sequential strategy of endocrine therapy (ET) + palbociclib preceding or following chemotherapy. The trial was designed for superiority Arm B (ET + palbociclib preceding paclitaxel). Although this preoperative strategy does not have the prospect of broader clinical adoption/application, it was a relatively “clean” experiment to deduce their novel predictive signature.\n2. Well conducted clinical trial with long follow up that captured at least early recurrences.\n3. In-depth correlative studies.\n4. Development of a signature of response to ET + CDK4/6 inhibitors challenging the paradigm that all HR+/Her2- breast cancers respond to CDK4/6 inhibitors propelled by the preconception that RB1 mutations are rare in breast cancer and RB1 mutations constitute the only mechanism of resistance to CDK4/6 inhibitors. I note the limited potential clinical application of the predictor:\nA. neoadjuvant CDK4/6 inhibitors do not constitute standard of care. The authors appropriately discuss the potential application of this predictor to conduct such biomarker informed studies.\nB. the predictor cannot be leveraged to identify luminal B early stage tumors that can forego chemotherapy, which constitutes a pressing and enduring question in the clinic. In other words, could patients with CDKPredX+ tumors forego chemotherapy and pursue treatment with ER + CDK4/6 inhibitors alone?\nThe manuscript has several limitations:\n1. The protocol therapy called for adjuvant epirubicin + cyclophosphamide x 3 cycles in both arms. The authors do not report how many patients in each arm received adjuvant chemotherapy. Imbalances in adjuvant therapy may bias at least short term outcomes. The manuscript (which otherwise elaborately reports on the results of a prospective clinical trial) can benefit by adding the schema of the trial as a main figure.\n2. The study used overall response rate at 12 weeks (ORR12) as its primary endpoint. Assessing ORR, especially in the 20-24% of patients with lobular carcinoma can be extremely problematic. I acknowledge that this limitation plagues all studies conducted in this setting. A subgroup analysis of ORR, PET response, and RCB in the patients with invasive lobular carcinoma would be of great interest.\n3. It should be reported in the manuscript how temporally close to the 12 week biopsy and especially definitive surgery patients were allowed to take palbociclib. We know from the NeoPalANA trial that Ki67 rebounds upon discontinuation of the CDK4/6 inhibitor. Potential Ki67 rebound may skew CCCA assessments.\n4. How do the authors reconcile that CDKPredX+ tumors frequently harbor a high retinoblastoma loss-of-function signature? Is it because RBsig is not identical to RB1 loss? What is the association or overlap of RBsig-high and RB1 loss?\n5. The CDKPredX signature is a synthesis of preexistent modules that capture features that individually were associated with differential response. The investigators did not incorporate any differential weights for the individual modules of the predictor and I am wondering whether such a strategy would enhance the discriminatory capacity of the predictor.\n6. Note that the development of a predictor of response to CDK4/6 inhibitors is not new (https://pubmed.ncbi.nlm.nih.gov/28566333/) and prior efforts have been undertaken to identify patients who will respond to CDK4/6 inhibitors in the metastatic setting, albeit these investigations focused on individual genes of the cell cycle circuitry rather than signatures.\n7. Editorial note: lines 323 – 324: “…settings where CDK4/6i have an established role, albeit concerning all-comers thus leading to both unnecessary toxicity and high costs for patients unlikely to respond.” Needs to be rephrased.", "reviewer_3": "I co-reviewed this manuscript with one of the reviewers who provided the listed reports. This is part of the Nature Communications initiative to facilitate training in peer review and to provide appropriate recognition for Early Career Researchers who co-review manuscripts.", "reviewer_4": "Overall, this is an important paper and generally well-written. However, the authors should use more careful language around statistical significance, and several points require elaboration and explanation.\n1. P4, L63-64: The analysis of the primary outcome does not indicate “no difference” in ORR_12. The two proportions, 59% vs. 45%, are meaningfully different, and the p-value (0.06) is borderline significant. It is not reasonable to say these results indicate “no difference” in the two arms on the primary outcome.\na. This issue is repeated several times, where “no difference” is claimed despite scientifically meaningful differences, e.g., L135-136, L234, L239.\n2. P4, L70-71: The ORs in PREDIX LumB were reported – the same should be done for CORALLEEN to gauge similarity and thus the interpretation of the validation.\n3. P7, L125: P-values should not be provided for Table 1 as they are not meaningful.\n4. P9, L163-164: The p-value for digital TILs was < 0.05, which contradicts the statement that all interaction p-values were at least 0.1.\n5. P9, L166-168: Here (and elsewhere) care is needed to note that we cannot talk about associations with pCR rates, or ORR, as each individual can experience a pCR or a response, not a rate. For instance, in this line, “lower pCR rates” should be replaced with “lower likelihood of pCR”.\n6. P9, L173-175: It is not clear the units for these odds ratios – are they per 1 unit change in the ratio (i.e., for a 100% change vs. a 0% change)?\n7. P10, L202-205: What does “no associations” mean in this case? Supplementary Figure 7 indicates statistically significant associations of arm with ORR by (e.g.) immunoglobulin signature, so there are not “no associations”. Perhaps this refers to interactions, not associations?\n8. P10, L198-208: In general, while the interactions are not significant, there is a pattern of indications of a larger effect for “high” values of the signatures – this is worth noting, particularly since the study was not designed to look for these associations, so they may be underpowered.\n9. P11, L228-229: Does this interaction relate to the outcome of objective response?\n10. P12, L232-233: The ORR_12 proportions should also be reported for the CDKPredX- subgroup.\n11. P12, L234-235: CDKPredX+ seems to be associated with ORR_24 and RCB, albeit not statistically significantly.\n12. P12, L237-238: “…low pCR rates…” compared to what?\n13. P12, L237-241: This statement is about chemoresistance, but notes that treatment in I-SPY2 was chemotherapy and/or immunotherapy – perhaps the “or” is a typo? Also, is the adjuvant treatment setting from SCAN-B relevant?\n14. P12, L241-242: CDKPredX seems to have a suggestion of being prognostic for OS.\n15. P13, L260-261: There is not “no difference” (e.g., constipation is borderline), but I would advise against using p-values to compare a range of baseline variables.\n16. P14, L291-293: The claim “not predictive” does not seem correct as some interactions in Table 2B (and perhaps other places) were borderline significant.\n17. P19, L395-396: How many people switched treatment prematurely?\n18. P33, L726-735: It should be made clear that the thresholds used to create CDKPredX (that is, the medians and quartiles) were fixed before validation.\n19. P33, L726-735: Presumably only individuals with all the requisite samples for the three modules were included in the derivation and evaluation of CDKPredX – how many was that in PREDIX LumB?\n20. P33, L741-743: Please clarify if SCAN-B concerned the adjuvant or neoadjuvant setting.\n21. P34, L763-765: Please clarify that IPTW is needed because SCAN-B is an observational study and please note whether IPTW was used in any other analyses. Also please indicate which variables were used in the IPTW model.\n22. Table 2A: Please explain why paclitaxel and palbociclib are listed in both Arms A and B.\n23. Table 2A: What is the p-value comparing?"}, "author_response": "We thank the reviewers for their valuable comments. We have performed revisions in the manuscript according to their suggestions. Please find hereunder our responses to the reviewers’ comments, with the comment appearing in regular text and our reply following in bold text. The revised manuscript has been uploaded in two forms, one clean and one where all the changes to the manuscript are marked with the tracked changes tool.\n******\nReviewer #1 (Remarks to the Author):\n1. This is an interesting translational analysis from a randomized trial (PREDIX LumB) that attempts to identify a gene-expression signature (CDKPredX, 31 genes) predicting differential response to frontline paclitaxel versus palbociclib+endocrine therapy in ER+/HER2– breast cancer. The concept of using gene signature to select patients more likely to benefit from a CDK4/6 inhibitor-based therapy vs chemotherapy in the neoadjuvant setting is clinically relevant and of potential importance to the field. We suggest the following points for clarification and discussion:\nWe thank the reviewer for these comments.\n2. Validation cohorts (Lines 70-71, 224, 233, 236-237): The authors state that the predictive signature was independently validated in the CORALLEN trial. While CORALLEEN is an appropriate external cohort, the two trials differ substantially in regimen, primary endpoints, patient population, and timing of assessments, which complicates interpretation of “validation.” The same caveat applies to the SCAN-B and I-SPY2 cohorts. We suggest that the authors explicitly acknowledge and discuss these differences.\nWe agree with the reviewer that these differences comprise a study limitation, which we now acknowledge in the revised discussion (lines 350-353): “Finally, although we took appropriate steps to externally validate our findings, we acknowledge that differences between the study cohorts in terms of chemotherapy regimens, administered CDK4/6 inhibitor in CORALLEEN, study endpoints and methods of assessment of response may have influenced our results.” The rarity of transcriptomic datasets from randomized comparisons between chemotherapy and CDK4/6i + endocrine therapy however meant that we needed to make pragmatic decisions when we validated the gene signature.\n3. Sequential therapy discussion (Lines 101-105): The discussion of sequential CDK4/6i and chemotherapy in pancreatic cancer is interesting. Are there similar reports or pre-clinical evidence for breast cancer? (eg. PMID: 30635336)\nWe thank the reviewer for providing us with this highly relevant reference, which we now include to the revised manuscript. Our initial and now our updated literature search has not identified any further breast cancer-specific studies.\n4. Subtype-specific results (Figure 2B): In the forest plot, luminal A subtype appears to favor chemotherapy, whereas luminal B favors palbociclib plus endocrine therapy, which is the opposite of what might be expected given low proliferative activity of luminal A tumors and high proliferative activity of luminal B tumors. Is there a possible explanation or hypothesis to address these results?\nWe thank the reviewer for this comment. Firstly, we cannot exclude the possibility that this is a chance finding, considering the wide confidence intervals and our inability to validate this analysis in CORALLEEN where all enrolled patients per study inclusion criteria had Luminal B tumors. In addition, the smaller NEOPAL trial enrolled patients with mostly Luminal B tumors (88%), precluding any meaningful comparison of efficacy between CDK4/6i+endocrine treatment versus chemotherapy per subtype, although the descriptive analysis doesn’t point towards any differential efficacy (PMID: 30307466). Finally, CDK4/6i have proven efficacy against Luminal B disease both at the metastatic (PMID: 37939142) and adjuvant settings (increased absolute benefit from abemaciclib with higher Ki67 in monarchE, although no predictive value of Ki67 was shown), while taxane monotherapy preoperatively seems to retain its activity against Luminal A tumors (PMID: 37833133).\n5. Primary endpoint interpretation (Lines 274-276): The authors report no difference between chemotherapy and CDK4/6i plus endocrine therapy for the primary endpoint of ORR12 – Was the study statistically powered to detect small differences? Based on pre-specified effect size, alpha, and sample size calculation, please clarify whether this constitutes a negative trial per protocol, or whether the analysis may be underpowered. Is the ORR12 the right primary endpoint in this situation? 12 weeks of neoadjuvant ET may not be sufficient to see changes in tumor activity, and at same time, 12 weeks of weekly paclitaxel might not represent the ideal neoadjuvant chemotherapy regimen. Authors can add this in the study caveats.\nWe agree with the reviewer that these are significant limitations, which we acknowledge in the discussion (lines 334-342 of the revised manuscript): “The relatively small sample size of this randomized trial was in line with prior trials studying neoadjuvant CDK4/6i, however it may have been insufficient to detect small differences between administered treatments or associations of biomarkers with outcomes, whereas the trial was not powered for comparing the two treatment sequences for time-to-failure outcomes. Other limitations that should be acknowledged are the short treatment duration of 12 weeks with palbociclib and endocrine therapy which may have been insufficient to exert its full antitumoral effect and the relatively short follow-up considering the long natural history of ER+/HER2- BC, although it’s one of the longest reported among neoadjuvant CDK4/6i trials.”\n6. The use of neoadjuvant ET is well established for post-menopausal women and is usually performed without the use of CDK4/6i. They acknowledge this in the discussion (338-340). Have authors considered validation of CDKPredX in ET alone and how that differentiate outcomes among the two treatment modalities? This can really help highlighting the utility of CDKPredX, enabling the identification of patients who can benefit from the addition of CDK4/6 to ET alone.\nWe thank the reviewer for this suggestion, which we have also considered. We have applied and received approval to run the signature on the transcriptomic dataset of the PALLAS trial on adjuvant palbociclib, which is expected during the latter part of 2026. We should however underscore the fact that CDKPredX was designed to reveal chemoresistance while CDK4/6i + endocrine treatment activity is retained, and not to discern the relative contribution of palbociclib or endocrine therapy, a limitation we had already acknowledged in the discussion (lines 343-345): “Furthermore, due to the design of PREDIX LumB it is not possible to discern the relative contributions of palbociclib or endocrine therapy to treatment effect and biomarker associations”.\n7. Comparison with Oncotype DX: Since Oncotype DX is the most widely use genomic assay in ER+/HER- disease, and both Oncotype and CDKPredX contain proliferation/ER-related signals, it would be informative to explore the correlation between the two signatures. If feasible, trial outcomes (chemotherapy vs. CDK4/6i+ET response) could be stratified by both Oncotype score categories (e.g., <26 vs. ≥26) and CDKPredX, which would enhance clinical interpretability.\nWe conducted the above analysis according to the reviewer’s comment. Since Oncotype DX had not been performed for any of the study participants, we instead ran the research version of RS from the genefu R package. There was weak but statistically significant correlation between CDKPredX and RS (r=0.17, p=0.035), with CDKPredX+ tumors having higher RS (Wilcoxon p=0.036), which was expected since both signatures include ER and proliferation genes. We then used both the proposed by the package risk cutoffs for RS, as well as the approach described in PMID: 37059742, to divide patients to high and low RS risk groups as the commercial Oncotype DX assay would. Both approaches yielded almost identical results. However, most patients in the cohort had RS high risk as shown in the table below, precluding any meaningful analysis due to low number of patients with RS low disease.\nCDKPredX+ CDKPredX-\nRS high 38 100\nRS low 4 21\n8. The use of neoadjuvant ET is not well established for pre-menopausal women. Based on the most recent discrepancy of oncotype predictive value for pre-menopausal women in the TailorX and RXPonder trials, how does CDKPredX performs in the two populations of pre- and post-menopausal women. PREDIX LumB have included both populations and interpretation may be complicated due to small sample size.\nWe performed additional exploration per menopausal status as suggested by the reviewer, which is presented below. In summary, we saw no evidence of differential associations of CDKPredX with treatment effect in premenopausal versus postmenopausal women. Due to smaller patient groups, confidence intervals were wide but the point estimates remained unchanged. In support of our findings are also the results of the RIBOLARIS trial presented at ESMO 2025, where neoadjuvant CDK4/6i + endocrine treatment showed initial efficacy among premenopausal patients, as measured by the proportion of patients with ROR low at surgery.\n9. The authors mentioned at the end of discussion that a prospective trial is undergoing to test CDKPredX as a single sample predictor. Is there a NCT number available for the trial? In what setting/population trial will run?\nThe trial is under design, while we await decisions on our applications for academic funding which is why we only briefly mention the study. Patients with ER+/HER2- breast cancer and an indication for neoadjuvant therapy will be randomized to either standard chemotherapy, or to CDKPredX-driven treatment selection (CDK4/6i+ET for positive and chemotherapy for negative patients). In total 230 patients will be randomized. The study will not start before funding is secured and CDKPredX is appropriately developed as a single sample predictor, which is why it’s not yet registered.\nReviewer #2 (Remarks to the Author):\nI read the manuscript titled \"Randomized trial of neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER+/HER2- breast cancer (PREDIX LumB): Primary analysis and development of the CDKPredX metagene predictor” with great interest.\nThe manuscript reports on the results of a randomized clinical trial in early stage hormone receptor positive and Her2 negative (ER+/Her2-) breast cancer with a particular emphasis on the development of a novel predictive signature to identify patients that would respond to a CDK4/6 inhibitor + endocrine therapy. Overall, it is a well written manuscript that requires minimal editing.\nKey strengths of the submitted manuscript include:\n1. Innovative hypothesis. The authors investigated a preoperative sequential strategy of endocrine therapy (ET) + palbociclib preceding or following chemotherapy. The trial was designed for superiority Arm B (ET + palbociclib preceding paclitaxel). Although this preoperative strategy does not have the prospect of broader clinical adoption/application, it was a relatively “clean” experiment to deduce their novel predictive signature.\n2. Well conducted clinical trial with long follow up that captured at least early recurrences.\n3. In-depth correlative studies.\n4. Development of a signature of response to ET + CDK4/6 inhibitors challenging the paradigm that all HR+/Her2- breast cancers respond to CDK4/6 inhibitors propelled by the preconception that RB1 mutations are rare in breast cancer and RB1 mutations constitute the only mechanism of resistance to CDK4/6 inhibitors. I note the limited potential clinical application of the predictor:\nA. neoadjuvant CDK4/6 inhibitors do not constitute standard of care. The authors appropriately discuss the potential application of this predictor to conduct such biomarker informed studies.\nB. the predictor cannot be leveraged to identify luminal B early stage tumors that can forego chemotherapy, which constitutes a pressing and enduring question in the clinic. In other words, could patients with CDKPredX+ tumors forego chemotherapy and pursue treatment with ER + CDK4/6 inhibitors alone?\nWe thank the reviewer for their thoughtful analysis. We agree with the criticisms under comment #4, essentially that we only demonstrate clinical validity but not clinical utility, which is why we plan a prospective randomized trial where decision on neoadjuvant chemotherapy will depend on CDKPredX (see our response to Reviewer 1, comment #9).\nThe manuscript has several limitations:\n1. The protocol therapy called for adjuvant epirubicin + cyclophosphamide x 3 cycles in both arms. The authors do not report how many patients in each arm received adjuvant chemotherapy. Imbalances in adjuvant therapy may bias at least short term outcomes. The manuscript (which otherwise elaborately reports on the results of a prospective clinical trial) can benefit by adding the schema of the trial as a main figure.\nInformation on adjuvant EC has now been added to Table 1, per the reviewer’s suggestion. In short, EC administration was well-balanced (82 versus 82 patients completed three cycles, 3 versus 2 fewer than three and 3 versus 4 did not receive EC).\n2. The study used overall response rate at 12 weeks (ORR12) as its primary endpoint. Assessing ORR, especially in the 20-24% of patients with lobular carcinoma can be extremely problematic. I acknowledge that this limitation plagues all studies conducted in this setting. A subgroup analysis of ORR, PET response, and RCB in the patients with invasive lobular carcinoma would be of great interest.\nWe agree with the reviewer that lobular cancer comprises a subgroup of interest in this study, which is why we have added all requested analyses in the new Supplementary Figure 14.\n3. It should be reported in the manuscript how temporally close to the 12 week biopsy and especially definitive surgery patients were allowed to take palbociclib. We know from the NeoPalANA trial that Ki67 rebounds upon discontinuation of the CDK4/6 inhibitor. Potential Ki67 rebound may skew CCCA assessments.\nWe have now added this information to the methods section (lines 466-469) in accordance with the reviewer’s request. Median time from last administered palbociclib dose to biopsy at 12 weeks (arm B) was four days, while median time from last administered palbociclib dose to surgery (arm A) was twelve days.\n4. How do the authors reconcile that CDKPredX+ tumors frequently harbor a high retinoblastoma loss-of-function signature? Is it because RBsig is not identical to RB1 loss? What is the association or overlap of RBsig-high and RB1 loss?\nWe thank the reviewer for this highly relevant comment. The RBsig predicts E2F activity in this largely RB1 wild type cohort (only 3% had RB1 loss). This information has now been added to the main text (lines 221-223 of the revised manuscript): “In our cohort, expression of RBsig was strongly correlated with E2F signature expression (R=0.97, p<0.001). There were no RB1 point mutations, while deep deletions of RB1 gene were a rare event (5/166 patients, 3%) (Supplementary Figure 11)” and to Supplementary Figure 11.\n5. The CDKPredX signature is a synthesis of preexistent modules that capture features that individually were associated with differential response. The investigators did not incorporate any differential weights for the individual modules of the predictor and I am wondering whether such a strategy would enhance the discriminatory capacity of the predictor.\nWe agree with the approach the reviewer suggests in their comment. Applying and validating different weights, potentially removing genes and developing a single sample predictor are our plans for the immediate future. We also refer to our response to Reviewer 1, comment #6.\n6. Note that the development of a predictor of response to CDK4/6 inhibitors is not new (https://pubmed.ncbi.nlm.nih.gov/28566333/) and prior efforts have been undertaken to identify patients who will respond to CDK4/6 inhibitors in the metastatic setting, albeit these investigations focused on individual genes of the cell cycle circuitry rather than signatures.\nWe agree with the reviewer and we have now clarified our claim in the discussion that “CDKPredX is, to our knowledge, the first transcriptomic signature to predict resistance to chemotherapy while the effect of CDK4/6i and endocrine therapy is retained or even enriched”, replacing thus the previously stated more generic term “biomarker”.\n7. Editorial note: lines 323 – 324: “…settings where CDK4/6i have an established role, albeit concerning all-comers thus leading to both unnecessary toxicity and high costs for patients unlikely to respond.” Needs to be rephrased.\nWe have now rewritten the phrase to improve clarity as such (lines 325-329 of the revised manuscript): “Further studies will shed light on the clinical validity and utility of CDKPredX at the adjuvant and metastatic settings where CDK4/6i have an established role, albeit concerning all-comers without biomarker-driven patient selection. This lack of precision may lead to both unnecessary toxicity and high costs for patients unlikely to respond.”\nReviewer #3 (Remarks to the Author):\n1. I co-reviewed this manuscript with one of the reviewers who provided the listed reports. This is part of the Nature Communications initiative to facilitate training in peer review and to provide appropriate recognition for Early Career Researchers who co-review manuscripts.\nWe thank the reviewer for their contribution and wish them all the best with their future career.\nReviewer #4 (Remarks to the Author)\nOverall, this is an important paper and generally well-written. However, the authors should use more careful language around statistical significance, and several points require elaboration and explanation.\n1. P4, L63-64: The analysis of the primary outcome does not indicate “no difference” in ORR_12. The two proportions, 59% vs. 45%, are meaningfully different, and the p-value (0.06) is borderline significant. It is not reasonable to say these results indicate “no difference” in the two arms on the primary outcome. This issue is repeated several times, where “no difference” is claimed despite scientifically meaningful differences, e.g., L135-136, L234, L239.\nWe agree with the reviewer that the phrasing is unclear, since we cannot exclude with limited sample size and power the existence of a true difference in efficacy between the two arms. For clarity, we now specify in all instances that no statistically significant differences between the comparator groups were observed.\n2. P4, L70-71: The ORs in PREDIX LumB were reported – the same should be done for CORALLEEN to gauge similarity and thus the interpretation of the validation.\nSince we had already surpassed the word limit in the abstract by more than 10%, we have now opted to remove all odds ratios from the abstract and instead add the CORALLEEN odds ratios to the main text in the results section (besides Figure 3B).\n3. P7, L125: P-values should not be provided for Table 1 as they are not meaningful.\nRemoved, according to the reviewer’s request.\n4. P9, L163-164: The p-value for digital TILs was < 0.05, which contradicts the statement that all interaction p-values were at least 0.1.\nWe thank the reviewer for this comment, however we did not claim otherwise – in the original phrase we only commented on pathologist-read TILs. We have now added a phrase on digital TILs for clarity.\n5. P9, L166-168: Here (and elsewhere) care is needed to note that we cannot talk about associations with pCR rates, or ORR, as each individual can experience a pCR or a response, not a rate. For instance, in this line, “lower pCR rates” should be replaced with “lower likelihood of pCR”.\nCorrected throughout the manuscript, according to the reviewer’s request.\n6. P9, L173-175: It is not clear the units for these odds ratios – are they per 1 unit change in the ratio (i.e., for a 100% change vs. a 0% change)?\nExactly, they represent per 1 unit change of the ratio, which can be >1 in case of increased SUVmax at 12 weeks compared to baseline.\n7. P10, L202-205: What does “no associations” mean in this case? Supplementary Figure 7 indicates statistically significant associations of arm with ORR by (e.g.) immunoglobulin signature, so there are not “no associations”. Perhaps this refers to interactions, not associations?\nIn supplementary figure 7 all confidence intervals cross 1 and all p values including tests for interaction are >0.05. The immunoglobulin signature comes closest, with high signature correlating with response to paclitaxel (OR=0.45, 95% CI 0.18-1.09, p=0.081). Although we agree with the reviewer’s first comment on associations and statistical significance, at the preset level of significance we could not claim statistically significant associations.\n8. P10, L198-208: In general, while the interactions are not significant, there is a pattern of indications of a larger effect for “high” values of the signatures – this is worth noting, particularly since the study was not designed to look for these associations, so they may be underpowered.\nWe agree with the reviewer’s observation on these consistent trends, especially when it comes to immune-related and endocrine-related signatures. This is exactly the reason behind the inclusion of specific gene modules to CDKPredX during its development.\n9. P11, L228-229: Does this interaction relate to the outcome of objective response?\nExactly, we have now expanded the results to clarify (lines 232-235): “This interaction was confirmed in the CORALLEEN trial (p interaction= 0.048; Figure 3B), with the corresponding OR for the CDKPRedX+ and CDKPredX- groups being OR=3, 95% CI 0.28−70.88 (p=0.395) in favor of palbociclib and endocrine therapy, and OR=0.19, 95% CI 0.04−0.71 (p=0.019) in favor of chemotherapy.”\n10. P12, L232-233: The ORR_12 proportions should also be reported for the CDKPredX- subgroup.\nAdded these results as requested by the reviewer, see our response to comment #9.\n11. P12, L234-235: CDKPredX+ seems to be associated with ORR_24 and RCB, albeit not statistically significantly.\nEspecially in the case of RCB, it is difficult to say due to the, expectedly, few patients that achieved RCB 0/1. ORR was numerically lower in the CDKPredX+, but as the 24 reviewer noted the difference was not statistically significant.\n12. P12, L237-238: “…low pCR rates…” compared to what?\nWe now clarify that the comparison was versus CDKPredX- in the trial, as shown in Supplementary Figure 12.\n13. P12, L237-241: This statement is about chemoresistance, but notes that treatment in I-SPY2 was chemotherapy and/or immunotherapy – perhaps the “or” is a typo? Also, is the adjuvant treatment setting from SCAN-B relevant?\nWe have changed to “chemotherapy with or without immunotherapy” since it more accurately describes the I-SPY2 study. We used the adjuvant SCAN-B cohort for three reasons: to validate the biologic correlations of CDKPredX, to more accurately study the prognostic value of the signature, if any, in a very large cohort, and to add a layer of validation concerning chemoresistance of CDKPredX+.\n14. P12, L241-242: CDKPredX seems to have a suggestion of being prognostic for OS.\nWe agree, which is why we further investigated its prognostic value in the much larger SCAN-B cohort which unfortunately showed no such signs (Supplementary Figure 16).\n15. P13, L260-261: There is not “no difference” (e.g., constipation is borderline), but I would advise against using p-values to compare a range of baseline variables.\nWe appreciate the reviewer’s suggestion. The reason why we present baseline p values despite the randomized nature of the trial is to confirm that missingness in the HRQoL questionnaires was not informative. We would caution against overinterpretation of the borderline p values since we did not control the familywise error rate in these analyses.\n16. P14, L291-293: The claim “not predictive” does not seem correct as some interactions in Table 2B (and perhaps other places) were borderline significant.\nAlthough we agree with the reviewer’s observation, no other finding could be reproduced in the CORALLEEN dataset except for CDKPredX, either due to lack of data (TILs, PET/CT) or negative results (gene associations).\n17. P19, L395-396: How many people switched treatment prematurely?\nRates of treatment switch due to early discontinuation of paclitaxel (arm A) and palbociclib (arm B) are given under the Safety section of the results (19.1% and 5.5%, respectively).\n18. P33, L726-735: It should be made clear that the thresholds used to create CDKPredX (that is, the medians and quartiles) were fixed before validation.\nWe confirm that the same cutoffs were applied to all cohorts. This is now explicitly stated in the updated methods.\n19. P33, L726-735: Presumably only individuals with all the requisite samples for the three modules were included in the derivation and evaluation of CDKPredX – how many was that in PREDIX LumB?\nIn total, 163/179 patients from the PREDIX LumB ITT population had baseline transcriptomic data and are included in all CDKPredX analyses, as described in the patient flowchart in Figure 1.\n20. P33, L741-743: Please clarify if SCAN-B concerned the adjuvant or neoadjuvant setting.\nAdded to the methods section, as requested by the reviewer.\n21. P34, L763-765: Please clarify that IPTW is needed because SCAN-B is an observational study and please note whether IPTW was used in any other analyses. Also please indicate which variables were used in the IPTW model.\nAdded all requested information to the Statistical analysis section of Methods. In the IPTW model we adjusted for age, size, lymph node status, and grade.\n22. Table 2A: Please explain why paclitaxel and palbociclib are listed in both Arms A and B.\nSince all patients switched treatment per study design, all patients from both arms were exposed to both medications. Adverse events during the respective time periods are reported in the Table.\n23. Table 2A: What is the p-value comparing?\nDifferences between the two arms in terms of cumulative adverse events.\nOn behalf of all the authors,\nAlexios Matikas, Associate Professor of Oncology\nDepartment of Oncology – Pathology\nKarolinska Institutet and University Hospital\n17164 Stockholm, Sweden\ntel: +46 767823322\ne-mail: alexios.matikas@ki.se"}, {"round": 2, "reviewer_comments": {"reviewer_1": "please incorporate the analyses suggested by R#1, #7 and #8, in the supplementary results.", "reviewer_2": "Dear Dr. Matikas et al,\nI reviewed thoroughly the revised manuscript and the responses to my comments. My comments are adequately addressed and I deem that the revisions and small additions made to the manuscript render it suitable for publication. Most importantly, it is gratifying that a prospective clinical trial to establish the clinical utility of CDKPredX is under design and the development of this biomarker will not remain just an academic exercise.", "reviewer_3": "I co-reviewed this manuscript with one of the reviewers who provided the listed reports. This is part of the Nature Communications initiative to facilitate training in peer review and to provide appropriate recognition for Early Career Researchers who co-review manuscripts.", "reviewer_4": "I thank the authors for their responses and edits. I have no further comments."}, "author_response": "Re: Revised manuscript entitled \"Randomized trial of neoadjuvant palbociclib and endocrine therapy versus chemotherapy in ER+/HER2- breast cancer (PREDIX LumB): Primary analysis and development of the CDKPredX metagene predictor\" Ms. Ref. No.: NCOMMS-25-68309\nWe thank the reviewers for their valuable comments. We have performed revisions in the manuscript according to their suggestions. Please find hereunder our responses to the reviewers’ comments, with the comment appearing in regular text and our reply following in bold text. The revised manuscript has been uploaded in two forms, one clean and one where all the changes to the manuscript are marked with the tracked changes tool.\n******\nReviewer #1 (Remarks to the Author):\nPlease incorporate the analyses suggested by R#1, #7 and #8, in the supplementary results:\nThese analyses have now been added to the manuscript, in the new Supplementary Figures 12 and 13.\nReviewer #2 (Remarks to the Author):\nDear Dr. Matikas et al,\nI reviewed thoroughly the revised manuscript and the responses to my comments. My comments are adequately addressed and I deem that the revisions and small additions made to the manuscript render it suitable for publication. Most importantly, it is gratifying that a prospective clinical trial to establish the clinical utility of CDKPredX is under design and the development of this biomarker will not remain just an academic exercise\nWe thank the reviewer for their comments.\nReviewer #3 (Remarks to the Author):\nI co-reviewed this manuscript with one of the reviewers who provided the listed reports. This is part of the Nature Communications initiative to facilitate training in peer review and to provide appropriate recognition for Early Career Researchers who co-review manuscripts.\nWe thank the reviewer for their contribution and wish them all the best with their future career.\nReviewer #4 (Remarks to the Author)\nI thank the authors for their responses and edits. I have no further comments.\nWe thank the reviewer for their comment.\nOn behalf of all the authors,\nAlexios Matikas, Associate Professor of Oncology\nDepartment of Oncology – Pathology\nKarolinska Institutet and University Hospital\n17164 Stockholm, Sweden\ntel: +46 767823322\ne-mail: alexios.matikas@ki.se"}]

Decision letter