Molecular Hemepath

Question 1

RUNX1

Answer 1

Subunit of core binding factor (CBF), a key transcriptional regulator of normal hematopoiesis

Target of the RUNX1-RUNX1T1 translocation (one of the three automatic AML mutations) and can also be mutated in general AML with recurrent genetic abnormalities (PROVISIONAL category AML with mutated RUNX1).

Congenital mutations may cause thrombocytopenia and predisposition to MDS.

Question 2

JAK1

Answer 2

Janus Kinase 1

Often associated with lymphoid malignancies

Question 3

DNMT3A

Answer 3

DNA methlytransferase 3-alpha

Recurrently mutated in AML. Often these are cytogenetically normal as their proliferative lesion is present on the epigenetic level.

Question 4

NOTCH1

Answer 4

Notch receptor (Notch juxtacrine signal -> gamma secretase -> NCID -> nuclear translocation -> proliferative signaling)

Question 5

IDH2

Answer 5

Isocitrate dehydrogenase 2

Mutations in the two isocitrate dehydrogenase enzymes involved in cytoplasmic (IDH1) and mitochondrial (IDH2) conversion of alpha-ketoglutarate to D-2-hydroxyglutarate have been described as mutually exclusive in many of these cancer types. The most frequent mutation in IDH2 is R172 and is associated with poorer overall prognosis in AML patients, however its utility as a prognostic marker in MDS is still under debate.

The most frequent mutations involve R132 (IDH1) and R172 (IDH2) involve the active site and result in neomorphic enzyme activity.

Question 6

NRAS

Answer 6

One of the forms of cellular RAS.

Like other RAS variants, often mutated in cancer. The amino acid positions G12, G13 and Q61 account for the overwhelming majority of these mutations.

Question 7

TET2

Answer 7

Tet oncogene / Tet methylcytosine dioxygenase

Part of the IDH1/2-TET2-WT1 axis. WT TET2 inhibits cell proliferation in a WT1-dependent manner.

Catalyzes the conversion of methylcytosine to 5-hydroxymethylcytosine. Involved in myelopoiesis and defects are associated with MPN/AML, as well as lymphoid neoplasms. Some germline variants associated with immunodeficiency as well.

Carries an unfavorable prognosis in AML.

Question 8

PTPN11

Answer 8

Protein tyrosine phosphatase non-receptor type 11, aka SHP2/SH-2 containing tyrosine phosphatase-2

Regulator of mitogenic, growth, and transcriptional activities. Can be associated with juvenile myelomonocytic leukemia, as well as other AMLs.

Poor prognostic factor in AML.

Question 9

ETV6

Answer 9

TLE oncogene / ETS Variant Transcription Factor 6

Required for hematopoiesis and vascular growth. Known to be involved in a large number of chromosomal rearrangements associated with leukemia and congenital fibrosarcoma.

Frequently mutated in AML.

Congenital mutations may cause thrombocytopenia, macrocytosis, and a predisposition to MDS and AML.

Question 10

FLT3

Answer 10

Fms Related Receptor Tyrosine Kinase 3

Mutations that result in the constitutive activation of this receptor result in acute myeloid leukemia and acute lymphoblastic leukemia.

Often found to have internal tandem duplications (ITDs) in AML (present in ~25% of AML cases). Tyrosine kinase domain mutations (TKDs) present in ~10% of AML cases). Since this is such a potent monogenic etiology, these AMLs are often cytogenetically normal.

Question 11

NPM1

Answer 11

Nucleophosmin 1

Phosphoprotein that shuttles between the nucleolus, nucleus, and cytoplasm, chaperoning ribosomal proteins and core histones from the nucleus to the cytoplasm. Involved in centrosome duplication, protein chaperoning, and cell proliferation. Known to sequester the tumor suppressor ARF in the nucleolus, protecting it from degradation until it is needed.

AML with mutated NPM1 is an entity in the WHO classification of AML and it is highly recommended to test for this in cytogenetically normal AML.

Question 12

GATA2

Answer 12

GATA Binding Protein 2

Member of the GATA family of Zinc finger TFs. Involved in stem cell maintenance with key roles in hematopoietic development. GATA2 mutations are associated with a variety of inherited and acquired immune disorders including myelodysplastic syndrome and acute myeloid leukemia.

Maintenance GATA2 expression has been implicated as a requirement in KRAS-driven non-small cell lung cancer. Preclinical models have indicated therapeutic benefit from targeting GATA2-mediated pathways in the context of KRAS-driven NSCLC.

Congenital mutations are associated with MonoMAC syndrome (monocytosis, mycobacterial infections, MDS) and Emberger syndrome (lymphadenopathy, deafness, MDS).

Question 13

NFE2L3

Answer 13

Leucine zipper-family transcription factor overexpressed in several malignancies.

Important associations are fibrosarcomatous osteosarcoma and several types of lymphoma: Hodgkin’s and Mantle cell lymphoma, as well as occasional other Non-Hodgkin’s lymphomas.

Question 14

BCOR

Answer 14

Bcl6 Corepressor

Self-descriptive name. Found in AML (often associated with RUNX1 anomalies, some with normal karyotype) and various lymphomas.

Question 15

STAG2

Answer 15

Stromal Antigen 2, part of the cohesin complex.

Regulates the separation of sister chromatids during cell division. Mutations in STAG2 have been observed in MDS, AML, bladder cancer, and other cancers.

Inactivation of cohesin may be a cause of aneuploidy in cancer

Question 16

KMT2A

Answer 16

Lysine (K)-specific methyltransferase 2A, aka MLL, is a gene that encodes a protein that functions as a transcriptional coactivator.

The protein is involved in cellular processes including the regulation of gene expression and hematopoiesis. Fusions, rearrangements, missense mutations, nonsense mutations, silent mutations, frameshift insertions and deletions, and in-frame deletions are observed in cancers such as intestinal cancer, skin cancer, and stomach cancer, but also MDS, AML, other heme processes. Altered in 4.3% of all cancers

Question 17

IKZF1

Answer 17

IKAROS family zinc finger 1

Encodes a transcription factor protein that functions in chromatin remodeling and the regulation of lymphocyte differentiation. Fusions, missense mutations, nonsense mutations, silent mutations, whole gene deletions, and frameshift deletions and insertions are observed in cancers such as hematopoietic and lymphoid cancers, lung cancer, and skin cancer.

IKZF1 is altered in 2.23% of all cancers

Question 18

ERG

Answer 18

ETS-related gene. A member of the ETS family of transcription factors, which are key regulators of proliferation, differentiation, angiogenesis, and cell survival.Also derived from from avian erythroblastosis virus.

Regulates the differentiation and maturation of myeloid cells. Clinically, ERG histochemistry is often used as a marker of endothelial differentiation.

Question 19

IDH1

Answer 19

Isocitrate dehydrogenase 1

Mutations in the two isocitrate dehydrogenase enzymes involved in cytoplasmic (IDH1) and mitochondrial (IDH2) conversion of alpha-ketoglutarate to D-2-hydroxyglutarate have been described as mutually exclusive in many of these cancer types.

The most frequent mutation in IDH1 is R132, which is associated with worse outcome, shorter overall survival, and normal karyotype in MDS and AML. However, in glioblastoma and astrocytoma, patients with IDH1 mutations have shown better overall survival than patients with wild-type IDH1

Question 20

DDX41

Answer 20

DEAD-box protein (Asp-Glu-Ala-Glu). These are RNA helicases that are involved in RNA secondary structure changes (translation initiation, splicing, ribisome and splicosome assembly).

This DEAD-box interacts with several spliceosome elements, and is also thought to recognize cyclic di-GMP and di-AMP, resulting in innate immue regulation.

Mutations of this gene are involved in both MDS and myeloid/lymphoid malignancy.

Congenital mutations are associated with monocytosis and increased risk of MDS and AML.

Question 21

TERC

Answer 21

Encodes the RNA component of human telomerase (“TTAGGG”).

Congenital mutations associated with IPF and dyskeratosis congenita. Dyskeratosis congenita is a syndrome of dyskeratosis (abnormal pigmentation, nail changes, oral leukoplakia) and bone marrow failure.

Mutations may be found in numerous types of malignancy.

Question 22

MPL W515L/K

Answer 22

MPL encodes the thrombopoietin receptor

The W515K and W515L mutations are associated with myeloproliferative neoplasms, in particular essential thrombasthemia and primary myelofibrosis. Rarely, the mutations of hereditary thrombocytosis (W515S and W515A) can be causes of these disorders as well.

These mutations cause both cytokine-independent growth and hyper-TPO sensitivity in cell lines, primarily by means of activating JAK-STAT/ERK/Akt signal pathways.

Question 23

Mutations in hereditary thrombocytosis

Answer 23

MPL encodes the thrombopoietin receptor

While MPL W515L and MPL W515K are the main acquired mutations in ET and PMF, a range of W515 mutations and other MPL/TPO-R mutations can cause hereditary thrombocytosis

Of course, some mutations in this receptor can also cause hereditray thrombocytopenia

Question 24

The t(11:19) KMT2A-MLLT1 rearrangement is found in. . .

Answer 24

. . . AML and ALL

Question 25

The t(9;11) KMT2A-MLLT3 rearrangement is found in. . .

Answer 25

. . . a special WHO class of AML

Question 26

PIK3CA

Answer 26

Codes for the protein p110 alpha, the catalytic subunit of PI3K.

Often found in tumors of epithelial origin

Question 27

IDH1/2-TET2-WT1 axis in AML

Answer 27

WT1 is found mutated in a mutually exclusive manner with respect to IDH1/2 and TET2.

WT1 is a TF that acts as a TSG, and it is induced/aided in DNA binding by TET2. TET2 is in turn regulated by cellular metabolism via IDH1/2.

Mutations in IDH1/2 that result in production of 2HG, which inhibits TET2. LoF mutations in either TET2 or WT1, often affecting association of these proteins or DNA binding, result in loss of cellular differentiation and pro-apoptotic signals.

Question 28

del(1p36)

Answer 28

Often found as an acquired feature in hematologic (diffuse-type follicular lymphoma, CML transformation) and neurologic malignancies (glioblatoma, neuroblastoma)

1p36 contains several tumor suppressor genes: CHD5, CAMTA1, KIF1B, CASZ1, miR-34a

Congenitally, causes intellectual disability.

Question 29

Molecular progression in myeloma

Answer 29

Question 30

CALR

Answer 30

Calreticulin

Multifunctional Ca²⁺-sensitive second messenger protein. Found mutated in essential thrombasthenia and primary myelofibrosis.

Type I mutation: 52bp deletion

Type II mutation: 5bp insertion

Question 31

CSFR3

Answer 31

Colony stimulating factor receptor 3

Receptor for G-CSF. Signals via JAK and SRC pathways.

Acquired GoF mutations cause chronic neutrophilic leukemia. Congenital LoF mutations cause severe congenital neutropenia. Rarely CSFR3 is found mutated in de novo AML.

Question 32

ASXL1

Answer 32

Sex combs-like 1

Transcriptional suppressor. Frequently found mutated in myeloid neoplasms including MDS, MPN, MDS/MPN, and AML.

Question 33

SRSF2

Answer 33

Serine/arginine-rich splicing factor 2

pre-mRNA splicing factor. Found mutated in MDS and MPN, but especially in MDS/MPN overlap syndromes.

Question 34

RPL/RPS genes

Answer 34

Ribosomal protein L and S genes

Congenital mutations in these genes are causative for Diamond-Blackfan anemia.

Usually these will present as isolated aplastic anemia with syndromic features, but may present as bone marrow failure.

Question 35

DKC1

Answer 35

Dyskeratosis congenita-1 aka dyskerin pseudouridine synthase-1

Involved in telomere maintenance, along with hTERT, TERC, and GAR1.

Congenital mutations in DKC1 cause dyskeratosis congenita, characterized by bone marrow failure, pulmoanry fibrosis, oral leukoplakia, dystropic nails, hyperpigmentation, and cirrhosis.

Question 36

GAR1

Answer 36

GAR1 Ribonucleoprotein

A small nucleolar RNP (snoRNP) that is both involved in RNA processing and telomere maintenance, along with hTERT, TERC, and DKC1.

Reportedly can be mutated in congenital bone marrow failiure.

Question 37

Fanconi anemia genes

Answer 37

Question 38

Early MDS mutations

Answer 38

These tend to be mutations that promote self-renewal, leading to expansion of the MDS clone

SF3B1, SRSF2, U2AF1, ZRSR2

Epigenetic modifiers: TET2, DNMT3A

Question 39

U2AF1

Answer 39

U2 small nuclear auxilliary factor 1

Has a role in enhancer-dependent splicing.

Commonly mutated in MDS and AML.

Question 40

ZRSR2

Answer 40

Zinc finger CCCH-type, RNA binding motif and serine/arginine rich 2

Transcription factor

Often found in MDS, AML, and CMML.

Question 41

Chromothripsis

Answer 41

The complex karyotype that results from cellular crisis events

Question 42

Kataegis

Answer 42

A pattern of localized hypermutations

These tend to be C→T or C→G mutations

Occurs near sites of somatic chromosome rearrangements

Likely occurs during a single replication event and is highly associated with malignancy. It is thought that APOBEC family of adenosine deaminases is responsible for C→T mutations and that translesional DNA syntesis polymerase produces both C→T and C→G mutations.

Question 43

PHF6

Answer 43

Epigenetic regulator important for neurodevelopment and hematopoiesis. Serves as a tumor suppressor, with deletions implicated in T-lymphoblastic leukemia and myeloid neoplasms.

PHF6 mutation occurs early in T-LL leukemogenesis:
PHF6 -> NOTCH1 -> TLX1/TLX3
Meanwhile, it occurs late in myeloid leukemogenesis:
RUNX1 -> PHF6