Wenzlau et al. 10.1073/pnas.0705894104.

Supporting Information

Files in this Data Supplement:

SI Table 1
SI Figure 7
SI Figure 8
SI Figure 9
SI Figure 10




SI Figure 7

Fig. 7. Relationship of ZnT8A levels to GADA, IA2A, and IAA. Assays with ZnT8 constructs were compared with GADA, IA2A, and IAA on the same new-onset T1D samples. Results of linear regression analyses are shown together with a quadrant showing negative and positive in each assay (left lower quadrant, double negative; upper right quadrant, double positive).





SI Figure 8

Fig. 8. Relationship of ZnT8A levels to age at diabetes onset. New-onset T1D subjects ranging from <1 yr to 18 yr old were grouped in 2-yr intervals to illustrate the level of Zn C-terminal autoreactivity. Prevalence of antibodies to ZnT C-terminal and N/C constructs in relation to one another and to GADA, IA2A, and IAA is shown for the samples in Fig. 5.





SI Figure 9

Fig. 9. Levels of ZnT8A in prediabetic subjects. ZnT8 C-terminal autoreactivity is shown for 27 prediabetic subjects followed to T1D onset grouped by age up to 4 yr and a 2-yr countdown to diagnosis ( Dx, Dx-1, and Dx-2).





SI Figure 10

Fig. 10. Individual progression of autoantibodies in prediabetic subjects. ZnT8 C-terminal levels are shown for 10 individuals who were followed from <1 yr to the onset of diabetes. ZnT8A and IAA are grouped (Upper) as are GADA and IA2A (Lower). Autoreactivity in each is indexed as the log10 SD score The area below 4 SD is shaded to denote the cutoff for statistical significance. For each individual, the relationship to the diabetic first-degree relative, gender, HLA-DR genotype, and age at diabetes onset (Dx) is recorded above each. Individuals from the newborn cohort (NEC) have no family history of T1D and were selected on the basis of HLA-DR genotype alone.





Table 1. Candidate autoantigens

Rank A

Gene

Unigene

Pancreas abundance per 106 clones

Pancreas specificity (% global)

Islet abundance (ln Affx signal)

Rank B

1

INS

Hs.89832

1,5426.0

98.6

14.93

1

2

IAPP

Hs.142255

1,564.0

99.6

12.02

9

3

SGNE1

(7B2)

Hs.156540

1,884.0

50.7

12.93

5

4

SLC30A8

(ZNT8)

Hs.532270

830.0

81.7

8.74

29

5

PSKN1

Hs.522640

1,047.0

44.3

9.17

28

6

GNAS

Hs.125898

4,600.0

9.4

13.70

3

7

CPE

Hs.75360

1,811.0

19.0

12.62

6

8

GAD2

(GAD65)

Hs.231829

356.0

75.9

4.95

50

9

TM4SF4

Hs.133527

565.0

43.3

10.27

19

10

G6PC2

(IGRP)

Hs.283963

260.0

84.7

4.78

51

11

CEL

Hs.533258

428.0

39.8

14.41

2

12

NKX2.2

Hs.516922

187.0

90.3

8.60

30

13

CHGB

Hs.516874

791.0

15.1

11.81

11

14

ERO1LB

Hs.558519

439.0

26.4

9.78

23

15

PC2

Hs.315186

434.0

23.6

7.06

44

16

IPF1

(PDX1)

Hs.32938

91.0

100.0

2.74

62

17

PAX6

Hs.591993

292.0

28.9

10.11

20

18

SCGN

Hs.116428

187.0

43.2

9.50

25

19

INSM1

Hs.89584

178.0

42.5

9.43

26

20

PC1

Hs.78977

224.0

29.6

10.40

18

21

APLP1

Hs.74565

328.0

15.5

7.26

43

22

SCG3

Hs.232618

210.0

24.0

9.26

27

23

CFTR

Hs.489786

200.0

20.5

9.98

22

24

SCG2

Hs.516726

278.0

13.8

11.59

12

25

KRT17

Hs.2785

2,276.0

1.7

10.90

16

26

PTPRN

(IA2)

Hs.89655

150.0

18.1

8.02

39

27

PPPIR1A

Hs.505662

141.0

19.3

8.08

38

28

CRB3

Hs.150319

104.0

26.1

7.47

42

29

ATP2A3

Hs.513870

269.0

9.3

3.61

58

30

ChGA

Hs.150793

292.0

8.3

11.83

10

31

KCNMB2

Hs.478368

123.0

14.2

5.34

48

32

REG3G

Hs.447084

73.0

23.7

10.80

17

33

SEZ6L2

Hs.6314

136.0

10.5

5.32

49

34

HSP90AB1

Hs.509736

898.0

1.4

12.99

4

35

FXYD2

Hs.413137

54.0

21.6

8.33

32

36

PTPRN2

(IA2ß)

Hs.490789

182.0

6.0

6.08

46

37

CLU

Hs.436657

512.0

1.9

12.19

8

38

REG3A

Hs.567312

178.0

4.2

12.42

7

39

SYT13

Hs.436643

68.0

9.2

8.22

36

40

HMGN3

Hs.77558

128.0

3.9

11.28

13

41

ICA1

(ICA69)

Hs.487561

86.0

5.7

7.87

40

42

SNAP25

Hs.167317

160.0

3.0

8.35

31

43

TMEM54

Hs.534521

50.0

7.3

8.32

33

44

TOB1

Hs.531550

82.0

3.7

10.07

21

45

ENO2

Hs.511915

109.0

2.4

11.26

15

46

IMO38

(MRPS31)

Hs.154655

73.0

3.4

8.18

37

47

SORL1

Hs.368592

95.0

2.5

9.70

24

48

CNTN1

Hs.567249

41.0

4.8

5.94

47

49

NPY

Hs.1832

27.0

6.7

4.35

55

50

TTFG3

Hs.82961

45.0

4.0

4.08

56

51

LYPD5

Hs.44289

31.0

5.8

1.91

68

52

EPHB3

Hs.26988

27.0

5.5

2.23

67

53

RAMP2

Hs.514193

18.0

7.0

2.47

64

54

INPP5E

Hs.120998

27.0

4.5

7.52

41

55

SYP

Hs.75667

27.0

4.0

4.59

52

56

HPN

Hs.182385

31.0

3.3

8.26

34

57

GLIPR1

Hs.591034

36.0

1.8

8.25

35

58

PRPH

Hs.37044

27.0

2.1

4.46

54

59

XPO4

Hs.507452

27.0

2.1

2.35

65

60

WBSCR14

(MLXIPL)

Hs.520446

18.0

2.7

3.68

57

61

GJA4

Hs.296310

18.0

2.5

3.46

59

62

CEACAM1

Hs.512682

27.0

1.6

4.50

53

63

SOX17

Hs.98367

13.0

2.6

2.50

63

64

IGF1

Hs.160562

27.0

1.1

2.34

66

65

SOX13

Hs.201671

13.0

1.1

3.05

61

66

SYTL4

Hs.522054

9.0

0.7

6.80

45

67

PROM 1

Hs.479220

9.0

0.3

11.27

14

68

GAD1

(GAD67)

Hs.420036

4.0

0.5

3.28

60

This list was compiled by multidimensional analysis of microarray data initially using the human Novartis Gene Atlas V2 as a source of information on islet specificity of gene expression in man. This data was complemented from Affymetrix HGI133 Plus 2.0 analyses of human fetal pancreas. Islet cell type specificity was deduced from Affymetrix MOE430 microarrays of pancreatic endocrine tumor and ductal cell lines compared with islets and sorted b-cells. In the final analysis, pancreas specificity was evaluated from Unigene expression profiles of each gene of interest and islet abundance from microarray results. In Rank A, genes are listed in descending order according to the index (pancreas abundance ´ pancreas specificity) derived from the Unigene expression profiles. Normalized islet microarray data is expressed on a ln2 scale and descending rank shown as Rank B. Known autoantigens are in bold type, and the candidate under study is boxed.