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CANCER GENOMICS Powered By Docstoc
         A scale of the cancer problem
                  Chances to develop invasive cancer
Cancer type        Birth-39              40-59            Birth – death
All cancers,     1/69    1/52      1/12          1/11     1/2           1/3
                  Male/Female       Male/Female            Male/Female

Breast              1/229                 1/24                   1/8
Uterine corpus       1/567               1/288                  1/117
Uterine cervix      1/2097               1/138                  1/37
Prostate           <1/10000               1/48                   1/6
Lymphoma 1/591 1/1311            1/208           1/317   1/48           1/57
Lung           1/3060 1/3099     1/89            1/116   1/13           1/17
Colorectal 1/1508 1/1719         1/115           1/145   1/17           1/18
Melanoma 1/769           1/508   1/199           1/261   1/58           1/82
         Last 70 years statistics
                         GASTRIC CANCER -
                         down 4 times
                         REASON? – better nutrition?

                          LUNG CANCER – UP!!!
                          10 times (due to smoking
                          and air pollution)
        Last 70 years statistics
                        UTERINE CANCER
                        (including cervix) –
                        down 5 times due to
                        early diagnostics

                        GASTRIC CANCER -
                        down 4 times
                        … Same as in males….

                        LUNG CANCER – UP!!!
                        10 times (due to smoking
                        and air pollution)
   Does science help patients?
                 5-year survival rates
Cancer type      Years 74-76    Years 83-85   Year 92-97
Leukemia             35%              42%         46%
Prostate             68%              76%         97%
Breast               75%              79%         87%
Cancer type      Years 74-76    Years 83-85   Year 92-97
Pancreas              3%              3%           4%
Liver                 4%              6%           6%
Uterine corpus       89%              85%         86%
             Few things contribute

Early diagnosis                        Specific treatment

 Early check for relapse

                  NOT possible without understanding
                  of the state of genes in every given tumor
    Tumors are very polymorphic entities
         There is no such a thing like tumor in general;
          they all differ in their way to survive and kill
      Multiple systems of tumor classification exist

 ORGAN – based            TISSUE - based          WISDOM – based
    (trivial)             (histological)            (clinicians’
Breast cancer
Brain cancer              Sarcoma                 Grading/staging
                                              1   (metastase/invasion)
Liver cancer              Lymphoma
                                              2   Pace of progression
Colon cancer
                Mucinous cystadenocarcinoma       (slow of fast)
                   Carcinomas with spindle
                   and/or giant cells               (best working)
     ORGAN – based classification
Breast cancer as an example
                            Tumors can be derived
                        from ductal cells or lobular cells
                       Ductal carcinoma          Lobular carcinoma
                       in situ (DCIS)            in situ (LCIS)

                      malignant                          benign
                  High chances to become             Low chances to become
               Invasive carcinomas (ductal or lobular or even mixed)
                                    Very malignant
   inflammatory breast cancer, medullary carcinoma, mucinous carcinoma,
   Paget's disease of the nipple, Phyllodes tumor, and tubular carcinoma.
        TISSUE-based classification
malignant neoplasm of epithelial origin,
including internal epithelium
(bladder lining, pancreatic duct lining etc…. )

Adenocarcinoma                Squamous cell carcinoma (SCC)

From tissue/cells                   From pure lining cells
producing secret                    or from skin epithelium
– milk or mucous or enzymes

         Other small variants, like basal cell carcinoma etc.
    Sarcoma refers to cancer that originates
    in supportive and connective tissues
    such as bones, tendons, cartilage, muscle, and fat.
•Osteosarcoma or osteogenic sarcoma (bone)
•Chondrosarcoma (cartilage)
•Leiomyosarcoma (smooth muscle)
•Rhabdomyosarcoma (skeletal muscle)
•Mesothelial sarcoma or mesothelioma
      (membranous lining of body cavities)
•Fibrosarcoma (fibrous tissue)
•Angiosarcoma or hemangioendothelioma (blood vessels)
•Liposarcoma (adipose tissue)
•Glioma or astrocytoma (neurogenic connective tissue
                  found in the brain)
•Myxosarcoma (primitive embryonic connective tissue)
   cancers of the bone marrow (liquid phase)

  overproduction of immature lymphocytes, which
  do not perform as well as they should, therefore
       the patient is often prone to infection


              Mixed (polycytemia vera)
 tumors from the lymphocytes from lymph nodes
                      (solid tumors)
    Can be present in extranodal (non-lymph nodes) sites
             – stomach lymphoma, skin lymphoma.
   Lymphoma goes through the same stages of generalization
              (metastase) as any solid tumor

Hodgkin disease                     Non-Hodgkin lymphoma
• Mixed type of tumor,
  often it is derived from embryonic or stem cells

 The most common elements
       are components of
stratified squamous epithelium

Common types of cancer progression

  Adenoma                       Adenocarcinoma

   Papilloma              Squamous cell carcimoma

   Fibroma              Fibrosarcoma

   Lipoma               Liposarcoma

Glioma         Anaplastic glioma        Glioblastoma multiforme

Chronic leukemia          Remission with latent residual disease

                             Acute leukemic crisis (blast crisis)
      WISDOM – based classification of
BENIGN                   MALIGNANT

                                            Borders                No clear borders

                                             No invasion                Invasion

                                               Normal blood vessels

                                                           many leaky blood vessels cancer/cancer34.htm
           Histological picture of
           tumor malignisation cancer/cancer34.htm
TUMOR GRADES are based on
 degree of cell differentiation
tumor cells obtained from biopsy are
   evaluated by histopathologist
                        Grade I
 (Cells are slightly abnormal and well differentiated)
                      Grade II
(Cells are more abnormal and moderately differentiated)
                       Grade III
   (Cells are very abnormal and poorly differentiated)
                     Grade IV
       (Cells are immature and undifferentiated)
                 Tumor histology
• Metaplasia
  – Replacement of normal differentiated tissue by another
    (differentiated) type like epithelial to mesenchime
    transition in breast carcinoma progression
• Anaplasia
  – Loss of differentiated phenotype
• Dysplasia
  – Loss of tissue organisation
• Hyperplasia
  – Increase in cell division
             TUMOR STAGING
   Staging is the classification of the extent of
             the disease in the body.
Most common systems are TNM system and Numerical system

    The tumor, nodes, metastases (TNM) system
                 classifies cancer :
  -- by Tumor size,   T
  -- the degree of regional spread or Node
                      N                            M
  -- and presence/absence of distant Metastasis.
               Tumor (T)

T0      (No evidence of tumor)
(Carcinoma in situ
limited to surface cells)

(Increasing tumor size and involvement)
               Node (N)

N0 No lymph node involvement

Increasing degrees
of lymph node involvement
Lymph node involvement cannot be assessed
          Metastases (M)
M0 No evidence of distant metastases
M1 Evidence of distant metastases
                            Pancreatic carc. met. in liver

             Numerical system

Stage 0      Cancer in situ (limited to surface cells)
Stage 1      Cancer limited to the tissue of
          origin with evidence of tumor growth
Stage 2     Limited local spread of cancerous cells
Stage 3     Extensive local and regional spread
Stage 4          Distant metastasis
    Grading / Staging and prognosis

High-grade tumors progress faster      Late-stage tumors prognosis is worse

Radical                        Palliative
IDEAL GOAL:                  GOALS:
Completely eradicate tumor
                             Pain relief
                             Infection combat
Remove primary tumor         (especially important
(surgically)                 for leukemias and lymphomas)
or achieve tumor shrinkage
                             problems combat


Surgery           Chemotherapy

                Hormonal therapy
     Primary care for most of the tumors
     Ablastic principle (all cuts are done within normal
     tissue; can be PCR controlled)

     On the advanced stages surgery
     always used in combination with

-Not able to catch and remove micrometastases;
-Not able to deal with ascytic (liquid) tumors
 CHEMOTHERAPY is the treatment of
 cancer with drugs that can destroy cancer

 Ideal anticancer drug should be able to
 kill tumor cell and be harmless for any
 normal cell
No clear differences between normal and tumor cells
            side effects
  Only the rate of cell division makes tumor cell
        more prone to poisonous effect of
                   chemotherapy          (Cytoreduction)

    Normal cells with fast pace of divisions
      are also very susceptible to chemo

Side effects for BONE MARROW, COLON,
   SIDE EFFECTS of Chemotherapy

       Bone marrow toxicity –
infection and hemorrhage (bleeding)
                              Gut mucosa toxicity –
   Oral mucosa toxicity –
   mucositis (oral dryness)
                          Hair follicle toxicity –
                                 hair loss
   Genomics can help!

 Better understanding of differences
  between normal and tumor cells

    can help to invent new drugs
with increased tumor-specific action
       = tumor resistance
After rounds of chemotherapy and successful
shrinkage of tumor and/or remission tumor
cells become resistant to treatment

    Side effects prevail over benefits

   Clinician has to stop treatment
   and tumor start to grow again
 Genomics can help again!
Understanding of genomic changes during
       development of resistance

      can help prevent such changes
        or help invent new drugs
not producing common types of resistance
Traditional chemotherapeutic drugs

• I. Alkylating agents (e.g. cisplatin)
• II. Antimetabolites (e.g. Folate, purine or
  pyrimidine analogs)
• III. Plant derivates (vinca alcaloids,
  taxanes, etoposide)
• IV. Anti-tumoral Antibiotics
           Tumor could become resistant
   to any of this compounds or their combinations
               I. Alkylating agents:
        Nitrogen mustards, Nitrosoureas,
  Platinum agents (Cisplatin), Cyclophosphamides
      The alkylating agents react with everything;
            impair cell function by forming
  covalent bonds with the amino, carboxyl, sulfhydryl,
and phosphate groups in biologically important molecules
 Alkylating agents generally interact with DNA non-specifically:
         the more effective ones tend to crosslink DNA.

The electron-rich nitrogen at the N7 position of guanine
                         in DNA
       is particularly susceptible to alkylation.
                                        Alkylating agents
            Monoalkylation              interact with DNA

             Crosslinking                  Active even
           (Between strands)           for the resting cells
       chlorambucil and melphalan   (not cell cycle/phase-specific)

              Crosslinking             (damage cell now,
              (Same strand)          kill it during next cell

     Therefore Alkylating Agents can be used
    for the treatment of slow-growing tumors;
extensive damage of DNA will lead to cell death
   Nitrogen mustard – first chemotherapeutic
     substance (interstrand-linking agent)
   Nitrogen mustard drugs were developed from mustard gas,
      a war agent first used during the First World War at Ypres.
      Could penetrate all protective materials except urethan
                   One of the toxic-effects of exposure
      is the destruction of the bone marrow and white blood cells.

 Mustard gas                     Cure for cancer of the lymph glands –
                                          Hodgkin's Disease.

Nitrogen mustard
(Same strand-linking agent)

     than INTERstrand-linking agent!!

           because of two reasons
 (Same strand-linking agent)
1. Same strand cross-links formed are “harder" to repair
than cross-links between strands.
  2. Cisplatin is able to replace zinc(II) ion in zinc-finger containing
    transcription factors, directly destroying transcription regulation
Cisplatin Therapy Type of Cancer
Complete cure          Testicular cancer
Sensitive              Ovarian
Responsive             Bladder, Head & neck
Resistant              Cervix, Prostate, Esophegeal
Activity shown         Various, eg.: Non-small cell lung,
                       Ostegenic sarcoma, Hodgkins lymphoma
  Synergy shown in combination with 5-fluorouracil, cytarabine and bleomycin,
        That allows for greater flexibility in the design of drug regimens.
      Tumor could develop resistance to
             alkylating agents
Genomic changes in AA treated tumor cells may lead to:

-- Increase in ability of treated cells to repair DNA defects;
          -- Decrease in cellular permeability
                to the Alkylating drugs;

        -- Increase in glutathione synthesis
   conjugation with glutathione leads to chemical
          inactivation of alkylating agents
       (catalyzed by glutathione S-transferase)
          II. Antimetabolite agents:
1. Antimetabolites are structural analogs of the naturally
occurring metabolites involved in DNA and RNA synthesis.

     2. Antimetabolites exert their cytotoxic activity
  either by competing with normal metabolites for the
         catalytic or regulatory site of a key enzyme
         or by direct substituting for a nucleotide
     that is normally incorporated into DNA and RNA.

    3. Antimetabolites are most active in S phase cells
          and have little effect on cells in G0.
             Consequently, these drugs are
       most effective in rapidly dividing tumors
          Types of Antimetabolites:
      Folate analogs -- Methotrexate (MTX)
 (bind to catalytic site of dihydrofolate reductase DHFR)

  Purine analogs -- Mercaptopurine,Fludarabine
  (inhibits enzymes involved in purine metabolism)

Pyrimidine analogs -- Flurouracil (5-FU), Ara-C
  (inhibits enzymes involved in pyrimidine metabolism)
 Methotrexate (MTX)

                                              Looks very same
                                                to folic acid –
                                             necessary nutrient.

 DHFR like MTX          No production of      No THF-co-enzymes
more than folic acid   tetrahydrofolic acid for one-carbon transfer

                              No de novo purines and pyrimidines
 Broad range
                                                 No DNA synthesis
Treat leukemia, lymphomas, and osteosarcoma.
It is also used in the treatment of AIDS and rheumatoid arthritis
  Methotrexate (MTX) resistance as an
  example of antimetabolite resistance
   Genomic changes in MTX-treated tumor cells may lead to:

-- decrease in drug transport into the cell (less MTX)

         -- alteration in gene DHFR encoding
 dihydrofolate reductase enzyme with lower affinity for
         methotrexate (MTX-durable DHFR)

  -- quantitative increase in DHFR concentration
           by DHFR gene amplification,
     or by increased DHFR mRNA production
                    (more DHFR)
  III. Plant derivates (heterogenous group)
• Vinca alcaloids (Vinblastine, Vincristine)
from periwinkle plant Vinca rosea
(native to Madagaskar);

• Taxanes (Paclitaxel = Taxol and docetaxel = Taxotere) from
  needles of Pacific Yew plant Taxus brevifolia;

• Podophyllotoxin (etoposide) from
  Podophyllum peltatum (India)

• Camptothecins (topotecan, irinotecan)
  from Camptotheca acuminata (China)
 -- Mechanism of action = mitosis block:
 bind to tubulin and induce microtubule depolymerization (Disassembly)

               Cells are arrested at metaphase
           as no chromosome segregation possible

                            Red – anti-tubulin;
                           Green – anti-vimentin;
                               Blue -- DNA

Mouse 3T3 fibroblast (normal)                       3T3 after vincristine
Vinca alcaloids bind to tubulin dimers
at a specific recognition site on the protein.

Tubulin form paracrystaline aggregates
                                                 Mitotic spindles
Concentration of the free dimers is reduced      can not be formed

Equilibrium of growth/shrinkage of tubules shifted to the shrinkage


     Paclitaxel (Taxol)
  and docetaxel (Taxotere)

-- Mechanism of action = mitosis block:
       promote microtubule assembly and super stability,
   action is opposite to vinca alcaloids, but effect is the same
Bundling of accumulated, disorganised microtubule filaments.

                           + Taxol

 Used for treatment of otherwise resistant ovarian cancers
                and recurrent breast tumors
     Podophyllotoxin (etoposide) =
          Topo II inhibitor
of DNA

                                 Etoposide stabilizes
                                 TOPO II – DNA complex
                                 in “non-sealable” form

                                            Etoposide inhibit
Both ends of DNA can freely rotate          topoisomerase II
       within the enzyme                      that catalyses
                                           transient breaking
                                              and re-joining
                                           of ds DNA strands
                                        (DNA becomes damaged
(topotecan, irinotecan) =
    Topo I inhibitor
                topoisomerase I produces
         reversible single-strand breaks in DNA
          These single-strand breaks relieve torsional strains,
               and allow DNA replication to proceed.

         Topotecan binds to the topoisomerase I-DNA complex
                 and prevents ligation of the DNA strand,
     resulting in DNA breakage during the elongation and cell death

TOPO I is not required for the viability of cells (TOPO II can substitute).
       Therefore, TOPO I – negative cancer cells are viable
                      and resistant to topotecan
              IV. Antitumoral antibiotics
                  (produced by fungi)
        Doxorubicin (Adriamycin) and Daunorubicin
Produced by fungus
Streptomyces percetus var caesius.

Doxorubicin                                            Bleomycin
               Produced by Streptomyces verticillus
              as a mixture of small-molecular-weight
                  copper-chelating glycopeptides
    Doxorubicin (Adriamycin) and Daunorubicin

           Mechanisms of action:

   1) intercalation between DNA base pairs
and inhibition of DNA topoisomerases I and II.

2) Altering membrane fluidity and ion transport

  Active in Hodgkin's disease, non-Hodgkin's lymphomas, sarcomas,
       acute leukemia, and breast, lung, and ovarian carcinomas
Mechanisms of action - multiple:
1) binds to double- and single-stranded DNA
produces site-specific and non-specific SS and DS breaks
    ratio single:double = 10:1; Cleave DNA at G-C and G-T sequences;
DNA in open chromatin esp. sensitive (where genes are expressed)

     2) Makes non-covalent interstrand links

      3) Inhibits DNA reparation by suppression of DNA ligase

 Rapidly degraded by bleomycin                No bone marrow
           hydrolase                       and intestinal toxicity!!
     present in most tissues                (…Pulmonary fibrosis
      except skin and lung               and skin effects are strong...)
         Multidrug resistance phenomenon
              Is a membrane associated phenomenon
   that represents a serious obstacle to chemotherapy of cancer

             Cell that are treated with (let’s say) etoposide
                 and develop resistance to etoposide,
           simultaneously become resistant to Methotrexate

            MDR caused by induction of membrane proteins that
              effectively and (almost) non-specifically expel
                       small molecules from the cell!

     P-glycoprotein (170 kDa)               Other transporters
Belongs to traffic-ATPase superfamily
        of transport proteins
                                        BCRP, ABC 1,2,3 … etc….

                             This is an ATP-dependent
                             export pump (= efflux pump)
                             of broad specificity

                              This efflux pump expel
                              hydrophobic drugs,
                              natural products and peptides.

The transport function of P-glycoprotein can be blocked
       by the action of another group of compounds
 known as MDR modulators, or chemosensitizers
         cyclosporin A, verapamil, tamoxifen


Surgery         Chemotherapy

• General principle is the same – reduce a mass
    of rapidly dividing cells (cytoreduction
       principle, the same as for chemo)

   Side effects are the same as for chemo

      Difference – radiotherapy is regional.
      IR could be focused like a beam of light
       to a treated area (internal or external)
       Good for hormone-dependent tumors
Speaking generally, hormonal therapy can be discussed
         as trophic factor removal therapy

 Estrogens are trophic factors for breast
     epithelium and uterine epithelium

          Removal of estrogen
        from ER-positive tumors
      leads to stop of their growth
      Tamoxifen                     Tamoxifen mimics
                                    the action of estrogene
      (Nolvadex)                    and binds to estrogen receptor (ER).

The tamoxifen-ER complex dimerises

Than transported from the cytosol
into the cell's nucleus

The dimeric tamoxifen-ER complex
          binds to DNA

   DNA-tamox-ER complex is unable to function
in the same way as the DNA-estrogene-ER complex
   In reality mechanism is not known completely
             !!!! In other tissues of the body Tamoxifen
             plays exactly like estrogene itself !!!
Any intervention to enhance the body's natural ability
     to defend itself against malignant tumors.

   Cytokines: IFN-alpha, IL-2, Tumor necrosis factors (TNFs)

Monoclonal antibodies: anti-CD20 Rituximab for lymphomas,
          anti-HER2 trastuzumab (herceptin) for breast cancer

         Cancer Vaccines: cancer-specific antigens +
  other components boosting immunity (e.g. dendritic cell vaccines)

Surgery         Chemotherapy

          Hormonal therapy

IMMUNOTHERAPY           MODERN science-oriented
   Modern science for cancer treatment
   SURGERY – PCR assisted surgery
CHEMOTHERAPY – new target-specific drugs,
               tumor-specific delivery
  RADIOTHERAPY – normal (p53 positive) cell
    can be protected by p53 inhibitor pifithrin
     chemical inhibitors of hormone receptors
   IMMUNOTHERAPY – entirely modern area

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