Posts Tagged ‘associated-with’

The history of primary myelofibrosis dates back to 1951 and the description of four distinct clinicopathologic entities that came to be known as myeloproliferative neoplasms (MPNs): chronic myeloid leukemia (CML), polycythemia vera, essential thrombocythemia, and myelofibrosis.

Discovery of the Philadelphia (Ph) chromosome in 1960 paved the way to identification of BCR/ABL as the principal genetic driver of CML. Another 45 years passed before the discovery of a first genetic driver of non-Ph MPNs, a mutation in the Janus kinase 2 (JAK2) gene, which occurs in 50-60% of myelofibrosis cases.

"The identification of that particular pathway was foundational, and it has changed the face of how we treat patients," said James Rossetti, DO, of the University of Pittsburgh. "The JAK2 mutation is not present in everyone with myelofibrosis, and there are other mutations as well."

A second key mutation in myelofibrosis, the myeloproliferative leukemia proto-oncogene (MPL, also known as thrombopoietin receptor), was identified in 2006. Subsequent studies have shown that the mutation occurs in 5-10% of cases.

Researchers identified a third key driver in 2013: calreticulin gene (CALR). The mutation is associated with about 25% of myelofibrosis cases.

Most studies have shown that JAK2, MPL, and CALR are mutually exclusive and do not occur together. However, a few studies have shown co-occurrence of the three key mutations. Even though JAK2, MPL, and CALR usually do not occur together, numerous other mutations have been identified in association with the three primary mutations. As many as 80% of patients with myelofibrosis have one or more other mutations.

Historically, myelofibrosis treatment was palliative in nature, aimed at relieving specific symptoms. The discovery of the JAK2 driver mutation has transformed treatment. Since 2011 four JAK2 inhibitors have received FDA approval: ruxolitinib (Jakafi), fedratinib (Inrebic), pacritinib (Vonjo), and momelotinib (Ojjaara). All four drugs demonstrated ability to reduce splenomegaly, a major clinical manifestation of myelofibrosis, as well as symptoms.

Some of the co-occurring mutations are targetable, creating interest in combination therapies that simultaneously target different signaling pathways, said Aaron Gerds, MD, of the Cleveland Clinic. One such combination was evaluated in a clinical trial that paired a JAK2 inhibitor with an IDH2 inhibitor.

"These were all patients that had very advanced disease, blast counts that were increasing and their disease was at or heading towards the point of an acute leukemia," he said. "We were able to -- with two pills, no IVs, no chemotherapy -- control the disease in these patients. A pretty remarkable event."

Such targeted combinations offer the potential to improve patients' lives, Gerds added.

Genetic testing has become standard for patients with myelofibrosis. Recognizing that mutations other than JAK2, MPL, and CALR might be present, clinicians will request a myeloid mutation panel that can identify a variety of mutations but also identify "triple negative" patients -- those who do not have JAK2, MPL, or CALR mutations. That subgroup accounts for about 10% of patients with myelofibrosis.

Triple-negative patients have a less favorable prognosis but receive the same type of clinical care as patients with mutations.

"Ruxolitinib, which is the only drug that so far has demonstrated an association with improved survival, as well as improved quality of life ... is used in all patients, regardless of the mutation underpinnings," said Gary Schiller, MD, of the University of California Los Angeles.

The four JAK2 inhibitors differ in their approach to disrupting JAK/STAT signaling. Genetic testing has yet to provide many clues to guide the selection of the different agents.

"The complicated molecular details probably don't inform us very much, except for the younger patient who's a potential recipient of allogeneic bone marrow transplant," said Schiller. "There the [genetic] mix might be important. But in terms of how you choose among the available therapies, right now, we often look at other factors, particularly the blood counts."

Mutation testing could play a role in developing new treatment strategies, particularly novel combination.

"BCL2 inhibition is one that is continuing to be explored, and PI3K inhibition is another," said Rossetti. "There are other pathways that we know are intimately linked to certain parts of the disease, and those studies are ongoing, usually with the backbone of JAK inhibition as sort of the gold standard for disease."

A number of mutations already have proven informative for prognosis. For example, SRSF2, ASXL1, and U2AF1-Q157 mutations predict shorter survival. RAS/CBL mutations predict resistance to ruxolitinib. Type 1-like CALR mutation is associated with better survival.

"We are certainly hopeful that in the future, mutations carry therapeutic information, and we've already seen a few examples of that," said Gerds. "If we see a JAK mutation, it helps us in the diagnosis, but if we see other mutations like ASXL1 or U2AF1, we know that those patients have disease that can be more aggressive over time. Thus, we're thinking more about curative therapies upfront, even allogeneic bone marrow transplant."

Charles Bankhead is senior editor for oncology and also covers urology, dermatology, and ophthalmology. He joined MedPage Today in 2007. Follow

Disclosures

Gerds disclosed relationships with AstraZeneca, E.R. Squibb & Sons, Celgene, MorphoSys, GSK, and Incyte.

Rossetti disclosed relationships with BeiGene, AstraZeneca, and CTI BioPharma.

Schiller disclosed relationships with CTI BioPharma, Sanofi-Aventis, Celgene, Agios, Novartis, Stemline Therapeutics, Jazz Pharmaceuticals, Karyopharm, Blueprint Medicine, and E.R. Squibb & Sons.

Read the original post:
Genetics and Genetic Testing to Inform Myelofibrosis Clinical Management - Medpage Today

Familial adenomatous polyposis (FAP) is an autosomal dominant disorder resulting from germline mutations in the APC gene. The APC gene, comprising 15 exons and encoding a protein with 2843 amino acids, is implicated in ~80% of FAP cases1. Extensive genetic analysis has revealed germline variants in FAP patients, and most APC mutations are found in the 5 half of the coding region. Genotypephenotype correlations have been reported for small-nucleotide alterations, including frameshift and nonsense mutations2,3. Large genomic deletions and duplications have been identified using multiplex ligation-dependent probe amplification (MLPA)4. Whole-genome array comparative genomic hybridization (aCGH) was used to identify a large deletion involving the middle portion of the long arm of chromosome 55. Here, we report a case of an FAP patient with intellectual disability that was attributed to a large deletion involving 5q22.2.

The proband was a 28-year-old female who was referred to the emergency hospital with acute abdominal pain. Computed tomography (CT) demonstrated perforation of the descending colon, multiple colorectal polyps, multiple liver metastases and lymph node swelling. She underwent left hemicolectomy, and the subsequent histological diagnosis was moderately differentiated adenocarcinoma (pT4a, pStage IVa). Chemotherapy was selected for treatment of the residual metastasis. Colonoscopy revealed advanced colon cancer with multiple adenomatous polyps (>100). Head CT revealed an osteoma in her skull, and the phenotype was subsequently defined as Gardners syndrome.

The patient had slight intellectual disability without developmental delay or neurogenic abnormalities. She and her mother requested comprehensive genomic panel (CGP) analysis (OncoGuideTM NCC oncopanel, Sysmex, Hyogo, Japan) of surgically resected colon cancer tissue after providing informed consent. This test can detect mutations in 124 genes and differentiate between germline and somatic mutations. The pathogenic mutations detected were KRAS G13D, PIC3CA H1047R, and TP53 M169fs*2, but no targeted therapy was recommended by the expert panel. No germline findings were reported, but whole APC gene deletion was suspected due to the low amplicon depth of the APC gene in both the tumor tissue and blood samples (Fig. S1).

According to her familial history (Fig. 1), her mother (II-3) was treated for sporadic colon cancer. She refused genetic testing due to receiving cancer chemotherapy. Her son (IV-1), whose intelligence was slightly low, had a single-parent history because his father was not identified.

The arrow indicates the patients who underwent genetic counseling. A closed circle indicates an individual with colorectal cancer. Colorectal polyposis was observed in the proband (III-1) but not in her ancestors.

After genetic counseling, aCGH (GenetiSure Dx Postnatal Assay, Agilent, Tokyo, Japan) was performed for further genetic testing. Notably, aCGH revealed the loss of chromosome 5 (chr5) q22.1-q22.2 (Fig. 2), the loss of chr3 p24.1-p23, and the gain of chr15 q15.3. The chr5 deletion included the entire APC gene (chr5:112043195-112181936 in GRCh37) located at 5q22.2 (Fig. S2), according to the Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources (DECIPHER, https://www.deciphergenomics.org).

A heterozygous 5q22 deletion was detected. The minimal and maximal deletion positions in GRCh37 (start_stop) were 111143360_112213143 and 111118900_112239978, respectively.

This case in which the entire APC gene was deleted, as determined by aCGH, is rare. Chromosome 5p22.1-22.2 deletion causes 1Mb of heterozygous loss, including the APC gene, which was reported as a cytogenetically detected deletion in previous reports. Previously, karyotyping and fluorescence in situ hybridization were used to detect large submicroscopic genomic deletions, and aCGH was used to detect high-resolution copy number variants in whole chromosomes6. aCGH is sensitive and comprehensive, allowing detection of multiple variations, and annotations by specialists are needed. DECIPHER catalogs common copy number changes, enabling the identification of potentially pathogenic variants. aCGH can also be used for sequencing targeted genes. For FAP patients, germline APC variants are identified by direct sequencing using next-generation sequencing (NGS) and MLPA5. Sequencing has been used to detect APC gene variants, but ~20% of FAP patients do not carry these variants. MLPA is useful for detecting whole or large APC gene copy number variants in mutation-negative FAP patients. There are several case reports in which germline variants of FAP were examined via aCGH7,8,9,10.

Our young patient with advanced colon cancer derived from multiple colorectal polyposis was diagnosed with FAP according to the clinical features. A CGP was performed using NGS for cancer precision medicine in this patient. Because metastatic colon cancer is treated by chemotherapy, somatic genomic analysis with CGP was also conducted to determine the optimal chemotherapy regimen. Next, we used NGS to determine the sequence of 100bp amplicons of 124 cancer-related genes from cancer tissue and peripheral blood. A large APC deletion was not detected by this targeted sequence, although both the somatic and germline amplicon depths of the APC gene were slightly low. A large number of APC variants have already been deposited in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/). For several FAP patients in which germline APC variants were not found, investigations of copy number variations have been performed. The genotypephenotype correlation of patients with chromosome 5q deletions has been discussed10. A classical FAP phenotype is associated with a mutation in codons 1681250 or codons 14001580. A severe phenotype is caused by a mutation in codons 12501464. A more attenuated form is associated with mutations in three regions: the 5 region of the APC gene, the alternative splicing region in exon 9, and the extreme 3 end of the gene11.

Whole or partial APC gene deletions can be detected with recently developed genetic techniques9,10,12. MLPA and aCGH are candidates for confirming large deletions or duplications, and the latter genetic test was chosen for our patient. In our patient, two chromosomal losses and one gain were detected. The advantage of chromosomal analysis is that it can reveal unexpected genetic changes even in separate chromosomes. The CGH database includes some patients with large deletions in chromosomal region 5q22, including the APC gene. In a very recent case report, aCGH was utilized to identify a large 19.85Mb deletion12. A case series with a literature review described a patient with intellectual disability and a colon neoplasm with an interstitial deletion of 5q identified by aCGH. Colorectal cancers are observed in some patients with 5q deletions, yet examination of colorectal polyposis in this context is limited. Among the primary dysmorphisms and symptoms linked to 5q deletions, the predominant manifestation identified in the analysis of 12 patients was mental retardation12. The cases documented in both the literature and the DECIPHER database are characterized by common clinical features, including predisposition to cancer, intellectual disability, and neurodevelopmental delay. Patients with these congenital changes should undergo genetic testing, including G-band, fluorescence in situ hybridization (FISH), and aCGH. aCGH offers high resolution, allowing for the detection of changes at the chromosomal level. This high sensitivity is particularly valuable when conventional methods, such as karyotyping or FISH, may not provide detailed information about genomic alterations. Moreover, this approach allows researchers and clinicians to explore potential genetic factors beyond the well-known APC genes. In the near future, long-read sequencing of large deletions may enable us to obtain detailed genomic information13. Additional clinical information is needed to establish the genotypephenotype correlations associated with the 5q22.2 deletion that includes the whole APC gene. The published cases have raised the question of whether whole APC deletion induces colorectal polyposis. Casper et al. reported a case of Gardner syndrome attributable to a substantial interstitial deletion of chromosome 5q, offering a comprehensive review of published cases9. Until 2014, 16 patients with FAP resulting from chromosome 5q deletions were documented, with all but one patient presenting with classic adenomatous polyposis rather than the profuse form. Most of these deletions were de novo alterations, consistent with our reported case in which the patients mother (II-3) exhibited sporadic colon cancer without polyposis. In the familial lineage (Fig. 1), our patients son (IV-1) carried a deletion in the 5q22.1-22.2 region, mirroring the genomic alteration of his mother (III-1). However, the genetic inheritance pattern of this large deletion is unclear. Meticulous follow-up of the young boy is important for addressing this issue.

In conclusion, this study describes a rare FAP patient characterized by a large deletion of chromosome 5q22.1-22.2 identified through comprehensive genomic analysis. The genetic variant was suspected by CGP and eventually identified by aCGH. These findings emphasize the importance of advanced genetic techniques in identifying complex genomic variations and suggest a need for additional research to elucidate the specific features associated with whole-APC gene deletions.

Link:
Genomic insights into familial adenomatous polyposis: unraveling a rare case with whole APC gene deletion and ... - Nature.com