Defining resistance mechanisms to CDK4/6 inhibition in hormone receptor-positive HER2-negative metastatic breast cancer (MBC) through a machine learning approach applied to circulating tumor DNA (ctDNA)

3055

Background: Although cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) are a primary treatment for hormone receptor-positive/HER2 negative MBC, data regarding resistance mechanisms are still an unmet need. The aim of the study was to highlight new resistance pathways using machine learning (ML) to detect multiparametric patterns in complex datasets. Methods: The study retrospectively analyzed a cohort of 610 hormone receptor positive HER2 negative MBC patients (pts) at Northwestern University, Massachusetts General Hospital and Washington University in St. Louis between 2015-2020 with baseline ctDNA testing by Guardant360. Pathways were defined based on previous work (Sanchez-Vega F et al, Cell. 2018) (i.e., RTK, RAS, RAF, MEK, NRF2, ER, WNT, MYC, P53, cell cycle, notch, PI3K). Only pathogenic variants according to OncoKB were included in the models. Associations among single nucleotide (SNVs) and copy number (CNVs) variations, pathway classification and previous exposure to CDK4/6i were explored through logistic regression and Gradient boosted machines (GBMs) ML algorithm. Results: at baseline, 322 pts (52.8%) were previously treated with CDK4/6i. The most detected pathway alterations were SNVs in PI3K (37.1%), P53 (31.8%), ER (29.2%) and RTK (22.3%). After stepwise logistic regression, RB1, NF1 and ESR1 SNVs were associated with previous exposure to CDK4/6i (respectively OR: 3.55 P = 0.017; OR: 3.06 P = 0.026 and OR: 1.82 P < 0.001), while SNVs in the ER pathway were associated with CDK4/6i (1.56 P < 0.001). Two GBMs models were designed based on gene variants (training AUC: 0.695, cross validation AUC: 0.631) and oncogenic pathways (training AUC: 0.713, cross validation AUC: 0.619). The highest relative importance (RI) was observed for ESR1 SNVs (RI: 35.35), TP53 SNVs (RI: 11.33), NF1 SNVs (RI: 3.45), SMAD4 SNVs (RI: 3.39) and RB1 SNVs (RI: 3.33). Alterations at a pathway level with the highest RI were ER SNVs (RI: 33.50), P53 SNVs (RI: 14.98), PI3K SNVs (RI: 14.40), RTK SNVs (RI: 10.55), RTK CNVs (RI: 10.26), cell cycle CNVs (RI: 6.99), cell cycle SNVs (RI: 6.77) and RAS SNVs (RI: 6.54). Of the previously highlighted pathway alterations, a significant impact on PFS after ctDNA collection was observed among de novo pts treated with CDK4/6i (165 pts) for ER SNVs (P < 0.0001), RTK SNVs (P = 0.0011), RTK CNVs (P = 0.0006), Cell cycle CNVs (P = 0.0010) and Cell cycle SNVs (P = 0.0143). No impact was observed on PFS for pts who had not received a CDK4/6i-based regimen. Conclusions: The combination of ctDNA-based datasets and machine learning algorithms defined novel resistance pathways for patients treated with CDK4/6i. Although preliminary, these results suggest that alterations of the ER, RTK and Cell cycle pathways might be crucial to optimize treatment strategy and drug development.

Landscape of GATA3 mutations identified from circulating tumor DNA clinical testing and their impact on disease outcomes in estrogen receptor-positive (ER+) metastatic breast cancers treated with endocrine therapies

1065

Background: The GATA3 gene encodes for a transcription factor (TF) that plays a pivotal role in the development of breast tissue. Breast tumors with lower GATA3 expression have worse prognosis compared to tumors with higher expression. However, the consequences of somatic GATA3 mutations ( GATA3mut) on clinical outcomes in metastatic breast cancer (MBC) remain poorly understood. Further, GATA3 TF interferes with FOXA1 and ER to enhance transcription of ER-responsive genes, but the role of GATA3mut in altering downstream transcriptional activity and its effects on response to anti-estrogens remains unclear. Methods: We retrospectively identified ctDNA next-generation sequencing results from 101 ER+/HER2- patients with MBC treated with either selective estrogen receptor degraders (SERDs) alone or a combination of SERDs and CDK4/6 inhibitors at Massachusetts General Hospital (Boston, MA) and Northwestern University (Chicago, IL). Associations between GATA3mut, patient and tumor characteristics, and prior treatments were assessed using logistic regression. Clinical outcomes were estimated through Cox proportional hazards regression. Results: GATA3mut were observed in 13 patients (13%), each with a single GATA3 variant. These mutations were detected in exon 4 (M294K), exon 5 that includes Zn-finger-2 motif (T327fs, R331fs, N334K, D336fs, c.925-3_925-2del splice acceptor variant), and exon 6 (K358fs, P409fs, M416fs, G431fs, M439fs, V440fs). All mutations except for M294K were insertion/deletion frameshift mutations that result in either elongation or truncation of the protein, potentially with heterogenous downstream effects. GATA3mut were the only detectable alteration in 4 patients. The most commonly co-occurring mutations with GATA3mut were ESR1mut in 7/13 (53.8%) and PIK3CAmut in 6/13 (46%) patients. Presence of GATA3mut was associated with prior exposure to chemotherapy (OR = 1.09, 95%CI [1.01 - 1.10], p = 0.03). Patients with GATA3mut tumors had shorter PFS compared to GATA3wild tumors (4.1 vs. 6.7 months, in both univariate and multivariate analysis controlled for presence of ESR1mut: HR = 2.22 95%CI [1.12 – 4.38], p = 0.02). OS was also significantly shorter in patients harboring GATA3mut compared to GATA3wild (14.1 vs. 27.1 months, multivariate analysis: HR = 2.30 95%CI [1.04 – 5.11], p = 0.04). Conclusions: GATA3mut in breast cancer tend to be grouped within exons 5 and 6, and they likely contribute to acquired resistance to endocrine-based therapies in MBC. Our study showed that patients with GATA3mut ER+ MBC have worse prognosis compared to those who were GATA3wild. Larger studies are needed to further stratify and ascertain functional effects of different GATA3 mutations and explore GATA3 gene or its translational product as a possible druggable target.

Uncovering the differential impact of ESR1 and PIK3CA codon variants on the clinical phenotype of metastatic breast cancer (MBC) through circulating tumor DNA (ctDNA) next-generation sequencing (NGS)

1033

Background: The exposure to endocrine therapy (ET) can induce the onset of ESR1 gene alterations that have an impact on not only treatment resistance but also clinical phenotype. We previously demonstrated the potential of liquid biopsy in describing the metastatic behavior of MBC. The aim of this study was to explore the different clinical phenotype across the main ESR1 and PIK3CA codon variants. Methods: The study retrospectively analyzed a cohort of 501 MBC patients (pts) characterized for ctDNA through NGS before treatment start at Northwestern University (Chicago, IL), Massachusetts General Hospital (Boston, MA), CRO National Cancer Institute (Aviano, IT) and ASUFC Hospital (Udine, IT) between 2014 and 2020. Associations between clinical characteristics and ESR1 and PIK3CA codon variants were explored through logistic regression corrected for sites and ESR1/ PIK3CA status. Survival was tested through Cox regression both for progression-free survival (PFS) and overall survival (OS). Results: Of the total 501 pts, 289 (58%) were diagnosed with hormone-receptor positive (HRpos) MBC, 114 (23%) with HER2-positive MBC, and 93 (19%) with triple-negative MBC. ESR1 mutations were detected in 71 pts (14%) and PIK3CA in 154 pts (31%). The most represented ESR1 gene mutations were found in codons 380 (9%), 536 (23%), 537 (34%), and 538 (34%), while alterations in codons 542 (19%), 545 (21%), and 1047 (60%) were the most common for PIK3CA. As expected, ESR1 mutations were found only in HRpos pts previously exposed to ET (P < 0.001). No significant differences were observed for PIK3CA. After multivariable analysis, ESR1mutations were confirmed as highly associated with liver and bone metastases (OR 3.31, P < 0.001 and OR 5.09, P < 0.001). Moreover, an association with lung (OR 2.07, P = 0.010) was observed in this cohort. After multivariable analysis, codon 537 mutations were associated with bone involvement (OR 12.97, P = 0.014), codon 538 with liver (OR 4.73, P = 0.010), and codon 536 with soft tissue (OR 5.84, P = 0.006) and liver (OR 4.06, P = 0.048). PIK3CA mutations were associated with bone (OR 2.61, P < 0.001) and lung metastases (OR 1.62, P = 0.044). Specifically, codon 1047 mutations were the primary driver (OR 3.14, P = 0.001 and OR 1.97, P = 0.019). In HRpos MBC, baseline mutations in ESR1 codon 537 and 538 had a negative impact on OS (HR 3.73, P < 0.010 and HR 2.99, P < 0.021), while 380 and 536 had a negative impact on PFS (HR 18.98, P < 0.001 and HR 2.60, P = 0.015). No impact was observed across PIK3CA gene variants. Conclusions: This study showed the different tumor biology across ESR1 and PIK3CA gene variants. As novel selective estrogen receptor degraders (SERDS) and PIK3CA inhibitors are gaining momentum as new ET options in MBC, these results highlight the future pivotal role of ctDNA NGS in refining tumor biology characterization.

Analysis of the typical unified lattice Boltzmann models and a comprehensive multiphase model for convection-diffusion problems in multiphase systems

The present paper analyzes the typical unified lattice Boltzmann (LB) models for different convection-diffusion (CD) problems in multiphase systems. The CD problems in multiphase systems can be roughly classified into three groups: CD problems with a continuous scalar value and a continuous flux, a discontinuous scalar value and a continuous flux, a continuous scalar value and a discontinuous flux. The characteristics of the corresponding unified LB models for the three kinds of CD problems are analyzed and the equivalence between the LB models based on different perspectives or numerical schemes is revealed. Finally, a comprehensive multiphase LB model (CMLBM) capable of solving different isotropic and anisotropic CD problems in multiphase systems is proposed. Four typical CD problems in multiphase systems are calculated to validate the CMLBM; the results show that it performs well against the typical isotropic and anisotropic CD problems in multiphase systems.

Rhein inhibits renal tubular epithelial cell hypertrophy and extracellular matrix accumulation induced by transforming growth factor beta1

AIM

To investigate the effects of rhein on cell hypertrophy and accumulation of extracellular matrix (ECM) in the renal tubular epithelial cells.

METHODS

LLC-PK1 cells were incubated with transforming growth factor beta1 (TGFbeta1) 2 microg/L for 24 h to induce cell hypertrophy and production of ECM. To evaluate the effects of rhein on inhibiting the action of TGFbeta1, cell volume, cellular protein level, and [3H]leucine incorporation in LLC-PK1 cells treated with rhein at different concentrations were measured. In addition, the [3H]proline incorporation, level of fibronectin (FN) in supernatant, and mRNA expression of collagen IV and FN were also detected in rhein treated cells.

RESULTS

The cell volume, cellular protein content, and [3H]leucine incorporation were markedly increased in LLC-PK1 cells after TGFbeta1 stimulation as compared with control (P < 0.01), and this TGFbeta1-stimulated cell hypertrophy was ameliorated by rhein. It was observed that TGFbeta1 not only increased the production of FN and [3H]proline incorporation in LLC-PK1 cells (P < 0.01), but also enhanced the mRNA expression of collagen IV and FN. Rhein significantly decreased the protein production and mRNA expression of ECM in LLC-PK1 cells stimulated by TGFbeta1.

CONCLUSION

Rhein can inhibit cell hypertrophy and ECM accumulation in LLC-PK1 cells induced by TGFbeta1, which may partly account for the role of rhein in preventing and retarding the progression of diabetic nephropathy.

Radiographic findings in cotton textile workers and the relationship to cigarette smoking

A group of 140 cotton textile workers from Shanghai, Shandong, Guangxi, and Beijing have had their chest radiographs taken using similar requirements. Most had come from the preparatory departments of cotton mills and had a history of exposure to cotton dust for at least 20 years. As controls, 140 healthy individuals with no dust exposure were matched with respect to sex, age, and smoking history. All the radiographs were read according to the ILO International Pneumoconiosis Classification, and the manifestations belonging to categories 0/0 and 0/1 were grouped as "normal," whereas categories 1/0, 1/1, and 1/2 and above as "abnormal." There was no significant difference in X-ray abnormalities between cotton textile workers and controls (P greater than 0.05). But when the data on the cotton textile workers and controls were combined, an appreciable difference in the incidence of radiographic abnormalities was found between smokers and non-smokers (P less than 0.001). Cotton dust exposure may induce nonspecific interstitial pulmonary changes, but these changes were exaggerated by cigarette smoking. These two factors appeared to have an additive effect on the pulmonary X-ray findings.