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OPTIMARK project preliminary results on antigenicity and integrity in
non-tumor tissue samples
Cristina Villena Pulmonary Biobank Consortium CIBERES. Scientific coordinator
Spanish National Biobank Network – ISCIII. Coordinator
Spanish National Biobank Network
0001 CIBERES- H. U. SON ESPASES 0002 IDIS- C.H.U SANTIAGO 0004 CNIO 0006 FJD 0007 NAVARRABIOMED 0008 MD ANDERSON 0010 HOSPITAL RAMON Y CAJAL 0011 IMIM 0013 H12O 0014 F-CIEN 0016 IDIBAPS 0017 FISABIO 0018 CLINICA UNIVERSIDAD DE NAVARRA 0019 IDIVAL 0020 HOSPITAL UNIV. PUERTA DE HIERRO 0021 BIOBANCO VASCO 0023 ISPA 0024 IDIBELL 0025 IDIPAZ 0027 IRBLleida 0029 INSTITUTO INV. S. PERE VIRGILI 0032 INSTITUTO INV. BIOMED. LA CORUÑA (INIBIC) 0033 INSTITUTO INV. BIOMED. GIRONA DR.JOSEP TRUETA 0034 INSTITUTO INV. SANITARIA GALICIA SUR 0036 HOSPITAL SANT JOAN DE DEU 0037 H. U. FUNDACION ALCORCON 0038 IMIB
0039 INSTITUTO ARAGONES CIENCIAS SALUD 0040 INSTITUTO INV. SANIT. H. CLINICO SAN CARLOS 0041 BBSPA 0042 INSTITUTO INV. SANITARIA GREGORIO MARAÑON (IiSGM) 0043 H LA FE 0044 U Salamanca 0045 HUGTiP 0047 VHIR 0049 INCLIVA 0050 HOSPITAL DE LA PRINCESA 0051 FIVO XXXX ISCIII -BioNER
OPTIMARK project
1. Identify the pre-analytical variables more relevant in tissues, which could affect the clinical biomarkers development.
OBJECTIVES
2. Develop and validate a common procedure to clarify the potential use of the samples in research, especially those without pre-analytical control.
3. To allow collections to be available to the scientific and biotechnological community, with a very good control of their pre-analytical variables, so that they can evaluate the sensitivity of their developing biomarkers to these factors.
Retrospective phase: sample conservation time
If we are able to find a sensitivity biomarker with the sample age, probably we could use it to evaluate the impact of other pre-analytical factors.
Colon (n=104) Brain (57)
Lung (76) Breast (85)
Stomach (17) Endometrium (35)
374 patients (30-65 y.o.; in brain up to 75 y.o. without vascular pathology)
Healthy tissue (non-tumor)
Flash-frozen and FFPE paired samples.
Checking non other relevant pathologies in the organ selected.
B: extraction time between 5 to 10 years
control: extraction time <1 year
A: extraction time between 1 to 5 years
C: extraction time between 10 to 20 years
D: extraction time >20 years
Groups
Experimental design
Biobanks sample suppliers (10)*
Colon (5) Brain (3) Lung (3) Breast (4) Endometrium (1) Stomach (1)
RNA Integrity analysis (9) Antigenicity analysis
Flash frozen Slides FFPE
Biobanks stainers IHQ Vimentin (2)
Biobanks stainers IHQ CD31 (2)
Biobanks stainers IHQ Ki67 (2)
Scanning center (system 1)
Scanning center (system 2)
Scanning center (system 3)
(a) (b)
Nuclear Cytoplasm Membrane
Ki67 Vimentin CD31
TTF-1 SDHB Beta-catherin
FOS BCL-2
A A
Antigenicity Colon Ki67 (nucleus)
CONTROL CONTROL
Intensity: +++ red, ++ orange, + yellow, 0 blue
B B
C C
D
Intensity: +++ red, ++ orange, + yellow, 0 blue
Antigenicity Colon Ki67 (nucleus)
Analysis Antigenicity Colon Ki67 (nucleus)
Intensity: +++ red, ++ orange, + yellow, 0 blue
Antigenicity Endometrium CD31 (membrane)
CONTROL A
B C
Analysis Antigenicity CD31 (membrane)
0
20
40
60
80
100
120
140
160
180
Brain Lung Colon Breast Endometrium Stomach
Control
A
B
C
D
CD
31
Ave
rage
Po
siti
ve In
ten
sity
Intensity: +++ red, ++ orange, + yellow, 0 blue
Antigenicity Lung TTF-1 (nucleus)
CONTROL A
B C
Analysis Antigenicity Lung TTF-1 (nucleus)
Regarding... RNA Integrity Number (RIN)
Tissue Biobank N
(%)
Patient age
(years)*
Obtention Warm Ischemia
Time (min)*
Cold Ischemia
Time (min)*
Lung
1, 2 41
(21,1)
53 ± 10
Surgery
22 ± 10
22 ± 10
Brain
3, 4 27
(13,9)
67 ± 11
Post mortem
NA**
NA
Colon
4, 5, 6, 7 49
(25,3)
58 ± 9
Surgery
17 ± 2
16 ± 5
Breast
4, 5, 7, 8 34
(17,5)
50 ± 8
Surgery
NA
18 ± 6
Endometrium
9 26
(13,4)
53 ± 7
Surgery
NA
61 ± 38
Stomach
10 17
(8,8)
47 ± 12
Surgery
NA
229 ± 285
*Average ± SD, **Non available
194 paired tissue samples
RNA Integrity Number (RIN)
Endom. Lung Brain Colon Breast Stomach
Error barr: +/- 1 SD
less than 1 year old
1-5 years old
5-10 years old
10-20 years old
RIN
ave
rage
+/-
SD
Acknowledgments
Villena C, Almenara I, Artiga MJ, Bahamonde O, Bermudo R, Castro E, De la Puente R, Escámez T, Esteva-Socias M, Fraga M, Jauregui-Mosquera L, Martin-Arruti M, Morente M, Peiró-Chova L,
Pons DG, Rejón JD, Ruiz-Miró M, Vieiro P, Zazo S, Villar V y Rábano A on behalf of R&D working group of Spanish Biobank Platform
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