Purine and pyrimidine synthesis and metabolism disorders: Pathology review

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Case study0:00–1:51

Three kids are brought to the clinic by three very concerned mothers. The first one’s Carl, a 10 month old boy that, according to his mother, is always sick with bronchitis and diarrhea.
On physical examination, you notice that Carl is quite small for his age. Laboratory studies are obtained, showing an absolute lymphocyte count of 2,000 cells per cubic millimeter.
A sputum culture reveals that Carl’s bronchitis is caused by a fungal infection by Pneumocystis jirovecii. Next comes Mark, a 2 year old boy with aggressive and self-destructive behavior, such as constantly biting his lips, tongue, and fingers.
In addition, Mark doesn’t seem to be able to walk or speak a word. His mother tells you that her younger brother, so Mark’s uncle, was diagnosed with a rare disease that caused mental retardation, and she’s worried Mark may have it too.
Upon physical exam, you notice some orange sand-like deposits in his diapers. Laboratory studies show elevated levels of uric acid in his blood.
Finally, you see Laura, a 4 month old girl with a history of anemia that was diagnosed some days after birth. Since then, Laura has been on a bottle-feeding regimen with folate and vitamin B12 supplementation; however, her anemia is not getting any better.
On examination, you notice cloudy urine that left some residues on Laura’s diaper, so you ask for a urinalysis. Results revealed that the residues are orotic acid crystals.Based on the initial presentation, all three cases seemed to be due to purine and pyrimidine metabolism disorder.

Pathology1:51–3:44

But first, a bit of biochemistry review. Normally, each nucleotide can be broken down into a sugar that’s either a deoxyribose in DNA or a ribose in RNA, followed by one to three phosphate groups, and a nucleobase, which can be either a purine or a pyrimidine.
There are two purine bases, adenine and guanine; and three pyrimidine bases, cytosine, thymine, and uracil. Now, the nucleoside based on adenine and ribose is adenosine, and a nucleotide based on adenosine and one phosphate would be adenosine monophosphate, or AMP for short; whereas the same combination with a deoxyribose would be deoxyadenosine monophosphate, or dAMP; and the same naming convention applies to all the other nucleobases.
Now, there are two ways our cells can make nucleotides, one is de novo synthesis, meaning that they are made from scratch, and the other is via the salvage pathway, by recycling nucleotides.
Now, mutations in enzymes involved in these pathways lead to rare inherited disorders collectively called purine and pyrimidine metabolism disorders, the most important of which are severe combined immunodeficiency, Lesch-Nyhan syndrome, and orotic aciduria.Okay, then!

Severe Combined Immunodeficiency (SCID)3:44–8:31

Starting with severe combined immunodeficiency, or SCID for short. This affects the development of both B and T cells, so there’s combined antibody and T- cell deficiencies, which makes it the most severe form of primary immunodeficiencies.
In fact, the immune system is so dysfunctional that it is considered almost completely absent. Now, SCID can be caused by a variety of gene mutations.
For your exams, a very high yield one is an autosomal recessive mutation in the gene coding for the enzyme adenosine deaminase or ADA.
And this form of SCID is also called ADA-SCID. Now, normally, in the purine salvage pathway, ADA is required to degrade adenosine and deoxyadenosine into inosine and deoxyinosine.
As a consequence, with ADA deficiency, adenosine and deoxyadenosine build up, and these can be toxic to B and T lymphocytes.
In addition, the excess deoxyadenosine can get converted into deoxyadenosine monophosphate or dAMP, then deoxyadenosine diphosphate or dADP, and finally into deoxyadenosine triphosphate or dATP.
Accumulation of dATP leads to inhibition of the enzyme ribonucleotide reductase, which mediates the conversion of ribonucleotides to deoxynucleotides, before they can get incorporated into DNA.
The end result is an impaired DNA synthesis in B and T cells, which leads to failure in their maturation and proliferation.
Now, SCID usually presents in infancy as an extreme susceptibility to all kinds of bacterial, viral, and fungal infections.
Most importantly, these include opportunistic pathogens, such as Candida albicans, nontuberculous Mycobacteria or Pneumocystis jirovecii, which don’t usually cause serious infections in individuals with a healthy immune system.
For your exams, remember that oral candidiasis typically presents with an oral thrush that’s often described as “cottage cheese-like thrush”, isn’t painful and can be scraped away with a tongue depressor, leaving behind a red mucosal base which sometimes bleeds.
In addition, individuals often present with chronic diarrhea, and a failure to thrive. If left untreated, SCID has a high mortality rate in the first year of life.
Diagnosis of SCID in many countries is based on newborn screening tests. These measure T-cell receptor excision circles, or TRECs, in blood.
The presence of TRECs is a biomarker for normal T-cell development, so remember that in SCID, TRECs are absent. Laboratory tests are also required, showing an absolute lymphocyte count lower than 2500 cells per cubic millimeter, with T cells making up less than 20 percent of the total lymphocytes in flow cytometry.
Additional findings can include absence of thymic shadow on chest X-rays, as T cells maturation normally takes place in the thymus.
Finally, a lymph node biopsy shows absence of germinal centers, which is where mature B cells would normally proliferate to fight infections.
Finally, to find the specific form of SCID, genetic testing can be performed to look for the mutated gene.For treatment, hematopoietic stem cell transplantation is recommended before the age of 3 months.
Until then, these infants are often kept in a sterile environment to prevent infections. In addition, intravenous IgG infusions can be given about once a month.
Next, Lesch-Nyhan syndrome is caused by a mutation in the HPRT1 gene on the X chromosome. So, Lesch- Nyhan syndrome is an X-linked recessive disorder, which means that all carrier males develop the disease, because they only have one X chromosome and thus one HPRT1 gene available.

Lesch-Nyhan Syndrome8:31–13:39

On the other hand, females have two X chromosomes, so a single mutation makes them a carrier, and two mutations are needed to have the disease.
Now, the HPRT1 gene codes for an enzyme called hypoxanthine-guanine phosphoribosyl transferase or HGPRT for short. Normally, HGPRT works in the purine salvage pathway by converting guanine to GMP, as well as hypoxanthine, which is a naturally occurring purine derivative, to IMP.
In Lesch-Nyhan syndrome, the mutated HPRT1 gene means that there’s deficiency of the HGPRT enzyme. As a result, guanine and hypoxanthine cannot get recycled through the salvage pathway, and instead they get degraded into xanthine and then uric acid.
At the same time, to make up for the lack of recycling, the de novo purine synthesis pathway ramps up, which results in even more purines getting degraded to uric acid.
As a consequence, all that uric acid builds up in the blood, causing hyperuricemia. Symptoms of Lesch-Nyhan syndrome typically present during the first year of life.
At first, the kidneys try to compensate by increasing the uric acid excretion into the urine, which is called hyperuricosuria.
The excreted uric acid can precipitate and form small orange urate crystals that are passed with the urine. This can be described as “orange sand” in the diapers of affected infants with this disorder.
Sometimes, the uric acid forms larger urate crystals that get stuck in the urinary tract and cause intense pain and hematuria, or blood in the urine, as well as recurrent urinary tract infections.
Over time, in older children and adults, the kidneys can’t keep up, so the excess uric acid in blood begins to precipitate as crystals in tissues.
The urate crystals can particularly affect the interstitium of the kidney, causing urate nephropathy and ultimately kidney failure.
Urate crystals can also deposit in other areas, like under the skin of the elbows, earlobes, fingers and knees, appearing as chalky lumps or nodules, called tophi.
Crystals can also deposit within joints, particularly within the first metatarsal joint of the foot, or the big toe, causing a form of inflammatory arthritis called gout.
Classically, gout presents as attacks of severe joint pain, swelling, warmth, and redness that can last for days or weeks.For unknown reasons, the elevated levels of uric acid seems to cause a drop in the levels and activity of dopamine, a neurotransmitter in the brain.
As a result, these individuals usually have intellectual disability and aggressive behavior, often associated with self-mutilation.
In an exam question, look for clues such as head banging and finger or nail biting. Finally, individuals with Lesch-Nyhan syndrome may also have neuromuscular problems like hypotonia, or decreased muscle tone, or a delay in childhood milestones like walking and talking.
Another important neuromuscular problem is having dystonia or involuntary muscle contractions, as well as chorea, which is characterized by involuntary jerky movements.
The diagnosis of Lesch-Nyhan syndrome usually begins with detecting high uric acid levels in blood and urine, and is confirmed through genetic testing, looking for the mutation in the HPRT1 gene.
Treatment of Lesch-Nyhan syndrome involves reducing uric acid levels with allopurinol or febuxostat, which are medications that inhibit the degradation of hypoxanthine to uric acid.Orotic aciduria is an autosomal recessive disease that’s caused by a deficiency in the enzyme uridine monophosphate synthase, or UMPS for short.

Orotic Aciduria13:39–17:01

Normally, UMPS works in the de novo pyrimidine synthesis pathway, converting orotic acid to UMP. Deficiency in UMPS impairs pyrimidine synthesis and results in an increase of orotic acid in blood.
Ultimately, this excess orotic acid gets excreted through urine, giving them a characteristic cloudy appearance. And the problem with that is that orotic acid can form crystals in urine, which can obstruct the urinary tract.
In addition, affected children can present with physical and mental developmental delay, along with failure to thrive. For your exams, if a question mentions elevated orotic acid in urine, make sure you rule out ornithine transcarbamylase or OTC deficiency.
OTC deficiency is an X-linked disorder characterized by deficiency of the OTC enzyme, which results in a defect in the urea cycle, leading to an increase in orotic acid in the urine.
One way to tell the two apart is that OTC causes an excessive accumulation of nitrogen in the form of ammonia in the blood, which is known as hyperammonemia.
In orotic aciduria there is no hyperammonemia, but unlike OTC, it’s associated with megaloblastic anemia, which is a form of macrocytic anemia, with a mean corpuscular volume or MCV larger than 100 fL, and it's also characterized by the presence of megaloblasts.
Megaloblastic anemia is caused by impaired DNA synthesis during red blood cell production in the bone marrow, which leads to continuing cell growth without division.
And in orotic aciduria, this can occur due to the decreased pyrimidine synthesis. Also, bear in mind that megaloblastic anemia in orotic aciduria does not improve with folate and B12 supplementation.Diagnosis of orotic aciduria involves urinalysis revealing the presence of orotic acid in urine, as well as blood tests showing high orotic acid levels, megaloblastic anemia, and the absence of hyperammonemia.
Treatment for orotic aciduria involves giving uridine supplementation in the form of uridine monophosphate, UMP, or uridine triacetate.
The goal of uridine supplementation is to provide a substrate that bypasses the mutated enzyme and aids in pyrimidine synthesis.All right, as a quick recap… Purine and pyrimidine metabolism disorders are rare inherited disorders characterized by impairment in the de novo or salvage pathways for nucleotide synthesis.

Review17:01–19:47

ADA-SCID is an autosomal recessive form of severe combined immunodeficiency. The cause is a mutation in adenosine deaminase of the salvage pathway.
As a consequence, there’s accumulation of adenosine and deoxyadenosine, which can be toxic to B and T lymphocytes. SCID presents in infancy with various infections, and is diagnosed through screening tests showing decreased or absent TRECs in blood, or based on low total lymphocyte count on blood tests, and low percentage of T cells in flow cytometry.
For treatment, hematopoietic stem cell transplantation is recommended before the age of 3 months. Lesch-Nyhan syndrome is an X-linked recessive disorder characterized by deficiency of the HGPRT enzyme, which takes part in the purine salvage pathway.
The excess purines get degraded to uric acid, resulting in hyperuricemia and hyperuricosuria, which leads to urinary tract stones, gouty arthritis, intellectual disability, aggressive behavior, neuromuscular problems, and developmental delay.
Diagnosis of Lesch-Nyhan syndrome is confirmed through genetic testing, and treatment involves medications like allopurinol or febuxostat.
Finally, orotic aciduria is an autosomal recessive disease caused by a deficiency of the UMPS enzyme, which normally works in the de novo pyrimidine synthesis pathway, converting orotic acid to UMP.
As a result, orotic acid builds up in blood and gets excreted through urine. Symptoms include urinary tract obstruction, physical and mental developmental delay, and failure to thrive.
Diagnosis of orotic aciduria involves urinalysis revealing the presence of orotic acid in urine, as well as blood tests showing high orotic acid levels and megaloblastic anemia.
Treatment involves giving uridine supplementation. Okay, back to our cases.

Summary19:47–21:17

Carl is a 10 month old boy with chronic diarrhea and failure to thrive, who’s frequently sick with infections like bronchitis, and has a low absolute lymphocyte count.
These two findings should make you think he has some form of immunodeficiency. A sputum culture reveals Carl’s bronchitis is caused by Pneumocystis jirovecii, so diagnosis of SCID is likely.
Genetic testing was performed, revealing a mutation in ADA. Next, Mark is a 2 year old boy with aggressive behavior, self-mutilation, and a delay in childhood milestones.
Additionally, Mark has a family history for a rare disease that causes mental retardation. These findings, together with the orange sand-like deposits in his diaper, are characteristic for Lesch-Nyhan syndrome, which was confirmed through laboratory studies revealing hyperuricemia.
Finally, Laura is a 4 month old girl with a history of anemia that is not improving with folate and vitamin B12 supplementation.
Laura’s diaper has cloudy urine that has some residue, which turned out to be orotic acid crystals on urinalysis. So this is a pretty straight forward case of Orotic aciduria and she is started on infant formula containing
Purine and pyrimidine synthesis and metabolism disorders | Osmosis