Table 2 Pre-treatment cell cycle, immune, growth factor receptor or epithelial gene expression, distribution and associations with PFS

From: Baseline cell cycle and immune profiles indicate CDK4/6 inhibitor response in metastatic HR + /HER2- breast cancer

  

Total PFS cohort

First-line PFS cohort

  

Mean gene expression

Gene association with PFS of the combined cohort (n = 95)

Mean gene expression

Gene association with PFS of the combined cohort (n = 80)

Pre-treatment gene set

Pre-treatment gene

Short PFS (n = 27)

Long PFS (n = 68)

HR

p-value

Short PFS (n = 17)

Long PFS (n = 63)

HR

p-value

Cell cycle

CCND1

11.2

11.08

1.02

0.8

11.27

11.08

1.00

1.00

CDK4

8.9

8.66

1.76

0.08

8.79

8.67

1.42

0.3

CDK6

7.06

6.87

1.43

0.06

6.88

6.86

1.31

0.2

RB1

8.02

8.00

1.03

0.8

8.08

8.01

1.05

0.8

E2F1

6.62

6.28

1.57

*0.01

6.50

6.30

1.44

0.08

CCNA2

7.62**

7.11

1.6

*0.03

7.52

7.14

1.31

0.3

CCNE2

7.71*

7.33

1.56

*0.03

7.61

7.35

1.30

0.3

CDK2

8.06

8.01

1.03

0.9

7.97

8.03

0.68

0.4

CCNB1

8.56**

7.97

1.56

*0.03

8.43*

8.00

1.21

0.4

MKI67

7.82**

7.16

1.6

*0.01

7.68*

7.18

1.37

0.1

Immune

CD163

9.22

8.64

1.32

*0.02

9.25

8.61

1.29

0.05

CD3d

6.23

5.97

0.9

0.4

6.04

6.18

0.98

0.9

CD8a

6.57

6.59

0.96

0.7

6.71

6.58

1.03

0.8

FOXP3

3.83

4.14

1.01

1.0

3.85

4.09

1.06

0.6

TNFRSF4

4.5

4.93*

0.89

0.3

4.47

4.90

0.92

0.5

PDCD1

4.36

4.45

1.02

0.9

4.45

4.42

1.12

0.4

CD274

5.82

5.71

1.29

0.1

5.81

5.68

1.36

0.1

Growth factor receptor

ESR1

10.86

11.48

0.93

0.3

10.57

11.44

0.87

0.1

ESR2

4.16

4.28

1.10

0.4

4.17

4.17

1.17

0.2

FGFR2

7.22

7.85*

0.86

0.3

7.15

7.79*

0.79

0.1

FGFR4

6.69**

5.83

1.15

0.09

6.4

5.88

1.07

0.5

IGFR1

8.14

9.35***

0.7

***0.0003

8.13

9.36**

0.71

**0.002

PI3KR

9.26

9.73*

0.77

0.05

9.3

9.76

0.79

0.1

PGR

5.55

6.82*

0.87

*0.02

6.24

6.76

0.93

0.3

Epithelial

EPCAM

9.14*

8.7

1.12

0.4

9.03

8.72

1.02

0.9

KRT14

4.55

5.66*

0.86

*0.03

5.24

5.65

0.89

0.1

PTTG2

7.66**

7.08

2.14

***0.0008

7.73**

7.09

2.05

**0.005

ZEB1

7.31

7.64*

0.63

0.06

7.34

7.65*

0.70

0.2

  1. Mean gene expression was determined by targeted RNA-seq analyses to calculate differential gene expression and association with PFS. Differential gene expression of the total stratified PFS cohort (left) or the first-line CDK4/6i (right) patient cohort with short or long PFS was determined by Wald tests and significant differential gene expression is bolded. Univariate Cox proportional-HR determined pre-treatment gene associations with PFS of the combined short and long patient cohorts. Significant gene associations are bolded. *p < 0.05; **p < 0.01; ***p < 0.001. HR hazard regression, PFS progression-free survival.
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