Appunti Medicina Interna (Internal Medicine, Biomolecular Basis of Organ Pathologies)

DNA-MMR - DNA mismatch repair genes

HNPCC hereditary nonpolyposis colorectal cancer (Lynch syndrome) ->

• 0.8%-1% of CRC
• rare (if any) colon adenomas
• 45% develops other cancers in other parts of the colon and/or in other organs within 10 yrs from -> first CRC in particular females (e.g. endometrial cancer)
• microsatellite instability (MSI) mismatch repair genes and MI work together to increase the probability of developing cancer
• MMR mutations (MLH1, MSH2, etc.) in > 95% of cases

Lynch syndrome has an early onset + can have multiple locations since every colonocyte can start the cancer and, unlike FAP, it is predominant in right colon more difficult to control (FAP is more located in the left colon, rectum/sigmoid, and is easier to control)

adenomas are either few or absent (not important for cancer development) + it is transmitted through an autosomal dominant mechanism and has a strong association with endometrial cancer (usually starts 10 yrs later)

Do you diagnose HNPCC? Amsterdam Criteria 3, 2, 1, 1, 0 for Lynch syndrome:

1. At least ≥ 3 family members affected by CRC
2. At least ≥ 2 generations involved
3. At least ≥ 1 CRC patient 1° degree relative of at least ≥ 2 family members
4. At least ≥ 1 CRC patient diagnosed before 50 yrs
5. ≥ FAP excluded

A family is affected by the Lynch syndrome if at least 3 family members are affected by CRC. These 3 family members need to have an involvement of at least 2 generations. Additionally, at least 1 of the patients with CRC is a first-degree relative of at least 2 other members of the same family, and at least 1 patient had the CRC diagnosis before he/she was 50 years old. Finally, no FAP diagnosis (colonoscopy, > 20 adenomas indicates FAP) should be present. All criteria need to be matched to diagnose HNPCC.

The Amsterdam Criteria have now been improved by the Bethesda Criteria.

MMR genes:

MMR is a system for recognizing and repairing erroneous insertion, deletion, and misincorporation of bases that can arise during

DNA replication/recombination, and repairing some forms of DNA damage

➢ hMSH 2 and 6 (human mutS homolog 2 and 6), hMLH1 and 3 (human mutL homolog 1 and 3), hPMS 1 and 2 (human postmitotic segregation 1 and 2), hEXO1 (human exonuclease 1)

➢ in HNPCC (mutation/allelic loss) and 20% of sporadic CRC (promoter region methylation/loss of imprinting – LOI)

➢ genomic imprinting is an epigenetic phenomenon that causes genes to be expressed in a parent-of-origin-specific manner; most imprinted genes in mammals are involved in the control of embryonic growth and development

DNA structure

DNA is made up of molecules called nucleotides

➢ each nucleotide contains a phosphate group, a sugar group (deoxyribose) and a nitrogen base

o 4 nitrogen bases: adenine (A), thymine (T), guanine (G) and cytosine (C)

➢ the order of these bases determines the genetic code

when we associate A-T, we have 11.1 Å of distance between the two chains of DNA whilst when we have G->C we have a distance of

10.8 Å these distances stay constant throughout the human genomeif there is a mistake (e.g. A-G pairing) there will be a larger distance between the two chains while if wehave a T-C pairing the distance will shorten, so we need a system of proteins able to identify the distancebetween the two chainsthese proteins like hMSH6 and hMSH2 are in the shape of hands with thumb and fingers running along theDNA chains: when they find something wrong, e.g. T-C pairings, they et too close not touching the two→chains any longer what do they do? they simply stopwhen hMSH stop, they get linked to hMLH1 and hMLH3 and once they get linked to these, they are also→linked to hPMS1 and hPMS2 this complex of proteins can be enriched with energy (ATP)➢ when the protein system is enriched with ATP and they are precisely located into the spot wherethere is an abnormal association of bases, then hEXO1 arrives and physically cuts the DNA in thatparticular spot; after that there is thepossibility for repairing and the correct base can be put in the position ➢ these proteins control the DNA at every time microsatellite instability (MSI) microsatellite are repeated sequences of DNA that can be made of repeating units of one to six base pairs in length ➢ MSI length is highly variable from person to person and contributes to the individual DNA“fingerprint” each individual has microsatellites of a set length ➢ the most common microsatellite in humans is a dinucleotide repeat of the nucleotides C and A, which occurs tens of thousands of times across the genome INTERNAL MEDICINE 5 – 20/03/2023 gut microbiota no germs can be stained with hematoxylin-eosin ➔ 95% of cells of human body are bacteria and 5% eukaryotic ➔ 1000-1150 bacterial species identified →most bacteria are associated with the GI tract intestinal microbiota the number of bacteria associated to the GI tract is higher than the total number of subjects on the planet ➢ where are the

bacteria? mostly colon, esophagus, mouth, skin, stomach and vagina

two types of microbiota

• one is constant for our life
• one that changes over time

IBS patients have more fungi than healthy patients

childbirth delivery shapes the GI microbiota

• cesarean: GI microbiota of the newborn is similar to the skin microbiota of the mother
• vaginal: GI microbiota of newborn is similar to the vagina microbiota of the mother

aging is also associated with changes in microbiota and loss of variety

→subject-specificity of the microbiota in the human body forensic identification using skin bacterial communities

if the mother takes antibiotics during pregnancy, then the baby has a higher probability of developing chronic inflammatory disease of the GI tract

diseases associated with dysbiosis

• changes in microbiota
• atherosclerosis, obesity, insulin resistance, multiple sclerosis, IBD, IBS

70% of immune system is underneath the gut mucosa

digestive and gynecological disorders often overlap

If you treat the urinary infection with antibiotics, you have an increase in the number of fungi in the body, especially in the vagina and GI tract.

An increase in antibiotic resistance is also a consequence.

The better thing to do when you have a urinary infection is to cure the cause, such as gut dysbiosis and the weakening of the barriers (membranes).

Fibers protect the gut mucosa and give it butyric acid.

If you do not eat enough fibers, you have butyric acid depletion.

Non-digestible fibers cannot be digested due to the lack of specific enzymes, but they are digested by the gut microbiota.

The gut produces 5 liters of mucus every day.

There are two types of mucus: one thick, attached to the mucosa, and one not so thick in the gut lumen.

The GI tract is the largest body's surface in contact with the environment, thanks to villi and crypts.

Underneath the GI tract, we have the largest immune system, the largest endocrine system, and the second largest neurologic system.

INTERNAL MEDICINE 6 - 22/03/2023

gut

– membrane and response of your system →immune system response is not always a defense response, it could be also an excessive response. Sometimes the mistake is not in the “attacking team” but a genetic predisposition to over-respond to a normal attack, e.g. allergies.
➔ Allergens are there and they are not pathological conditions. They are external situations, such as food allergens. So, food allergens are not pathological situations and many germs in the gut microbiota are not pathological by themselves. They become pathological when their membrane is not normally functioning and when the immune system over-reacts.
So, many young people have lots of allergies. It is a common thought that food allergens would affect the gut, pollens would affect respiratory → airways, chemicals would affect the skin. However, the immune system does NOT work like this. The immune system looks for aggressive antigens wherever they can be found: when the membrane is not strong enough to defend allergens from the immune system,

The immune system would react to an example of nickel allergy to earrings in the following levels:

1. First level: first you have a reaction to, for example, earrings with nickel
2. Second level: disorders in alimentary canal, e.g. gastro-esophageal reflux, diarrhea, constipation
3. Third level: SNAS (systemic nickel allergy syndrome) memory loss, fatigue chronic syndrome

What happens in the gut doesn't stay in the gut: 70% of the immune system of our body is in the gut.

If we get inflamed in this immune system, the body may have side effects, similar to side effects of coeliac disease.

If you inflame the gut, then all your body will be inflamed.

Bologna salmonella outbreak, 1994:

Salmonella enteritidis D contaminated tuna sauce was distributed to main city schools.

Juvenile individuals with non-completely formed gut membrane were exposed to a severe dysbiosis.

Data collected: antibiotic therapy can be dangerous even in the case of bacterial infections.

Kids were treated by an infusion with water, without any further.

change in the gut microbiota, did much better compared to the kids treated with antibiotics with a further modification. The gut microbiota tends to arrange itself in most of the cases. Follow-up for 16 years, kids who got salmonella had an increased probability of developing chronic pain in their abdomen for the rest of their life. This is due to a severe dysbiosis mechanism that can lead to chronic disorder in the gut. Genes that predispose people to be sensitive to dysbiosis are genes involved either in the epithelial barrier or in the immune response. People genetically predisposed to respond in a proper way or in an abnormal way to dysbiosis. For example, epithelial barrier function (CDH1) and innate immune response to enteric bacteria TLR9 and IL-6. If you have a leaky and inflamed gut barrier, you have passage of germs through the barrier. Germs arrive in the bloodstream so they can enter in contact with the immune system cells. A leaky gut would allow germs/antigens to get in touch with thediseases➢ an increase in the incidence of autoimmune diseases➢ an increase in allergies and asthma