Biomarker Consortium

GI Cancer

Pancreatic Cancer

DNA mismatch repair/microsatellite instability

DNA MMR is involved in preserving genomic fidelity by repairing DNA after mismatching errors after replication or recombination.

MMR is also involved in cell cycle regulation and apoptosis in response to DNA damage.

Four genes regulate MMR mechanisms, and the dimer proteins they form are responsible for mismatch recognition, insertion-deletion loops, base excision, and other functions. 

Biallelic inactivation of 1 or more MMR genes can result from either somatic or germline mutations or from epigenetic silencing.

Germline mutations in MMR genes are frequently associated with Lynch syndrome, which is known to increase the risk of several types of cancers.

Microsatellites are short tandem nucleotide repeats (1-6 nucleotides) scattered throughout the genome and prone to high rates of mutation.

The incidence of MMR-deficient (dMMR)/MSI-H pancreatic cancer ranges from 

MSI refers to a hypermutable phenotype that results when MMR genes are inactive or faulty.

MSI status is generally categorized into 3 types: high MSI (MSI-H), low MSI (MSI-L), and microsatellite stability (MSS).

Testing is recommended for patients with locally advanced or metastatic pancreatic cancer who are candidates for anticancer therapy.

Several techniques are used to test for the presence of dMMR including immunohistochemistry (IHC) or polymerase chain reaction (PCR)–based assays as well as next-generation sequencing (NGS) testing. IHC assays assess expression of MMR proteins, PCR evaluates tumor DNA for microsatellite repeats, and NGS identifies inactivating mutations in MMR genes. MSI-H status correlates with the loss expression in 2 of 4 MMR proteins and abnormal microsatellites in 2 or more regions.

 For patients with locally advanced or metastatic disease eligible for anticancer therapy, the NCCN Panel recommends testing for actionable somatic mutations, including fusions (ALK, NRG1, NTRK, ROS1, FGFR2, RET), mutations (BRAF, BRCA1/2, HER2, KRAS, PALB2), amplifications (HER2), MSI, dMMR, and TMB.

 The FDA has approved several immunotherapy agents for the treatment of patients with dMMR/MSI-H solid tumors.

 In 2023, pembrolizumab received approval for the treatment of adult and pediatric patients who have unresectable or metastatic MSI-H or dMMR solid tumors as determined by an FDA-approved test, who have experienced progression following prior treatment, and who have no satisfactory alternative treatment options.

Dostarlimab has also received accelerated approval for dMMR recurrent or advanced solid tumors with no satisfactory alternative treatment options based on findings from the GARNET trial (NCT02715284).

Pembrolizumab and dostarlimab are monoclonal antibodies that target the programmed death receptor-1 (PD-1), blocking its interaction with the ligands PD-L1 and PD-L2, thereby promoting anti-tumor activity.

Modrich P, Lahue R. Mismatch repair in replication fidelity, genetic recombination, and cancer biology. 

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Marti TM, Kunz C, Fleck O. DNA mismatch repair and mutation avoidance pathways. 

Bellacosa A. Functional interactions and signaling properties of mammalian DNA mismatch repair proteins. 

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Peters AC, Young LC, Maeda T, Tron VA, Andrew SE. Mammalian DNA mismatch repair protects cells from UVB-induced DNA damage by facilitating apoptosis and p53 activation. 

 2003;2:427-435. doi:10.1016/s1568-7864(03)00003-x

 1996;65:101-133. doi:10.1146/annurev.bi.65.070196.000533

Herman JG, Umar A, Polyak K, et al. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. 

 1998;95:6870-6875. doi:10.1073/pnas.95.12.6870

Hampel H, Frankel WL, Martin E, et al. Feasibility of screening for Lynch syndrome among patients with colorectal cancer. 

 2008;26:5783-5788. doi:10.1200/JCO.2008.17.5950

Lynch HT, de la Chapelle A. Hereditary colorectal cancer. 

 2003;348:919-932. doi:10.1056/NEJMra012242

Aaltonen LA, Salovaara R, Kristo P, et al. Incidence of hereditary nonpolyposis colorectal cancer and the feasibility of molecular screening for the disease. 

 1998;338:1481-1487. doi:10.1056/NEJM199805213382101

Hampel H, Frankel WL, Martin E, et al. Screening for the Lynch syndrome (hereditary nonpolyposis colorectal cancer). 

 2005;352:1851-1860.doi:10.1056/NEJMoa043146

Bonneville R, Krook MA, Chen HZ, et al. Detection of microsatellite instability biomarkers via next-generation sequencing. 

 2020;2055:119-132. doi:10.1007/978-1-4939-9773-2_5

Li K, Luo H, Huang L, Luo H, Zhu X. Microsatellite instability: a review of what the oncologist should know. 

 2020;20:16. doi:10.1186/s12935-019-1091-8

Hu ZI, Shia J, Stadler ZK, et al. Evaluating mismatch repair deficiency in pancreatic adenocarcinoma: challenges and recommendations. 

 2018;24(6):1326-1336. doi:10.1158/1078-0432.CCR-17-3099

NCCN. Clinical Practice Guidelines in Oncology. Pancreatic adenocarcinoma, version 1.2024. Accessed April 10, 2024. 

https://www.nccn.org/professionals/physician_gls/pdf/pancreatic.pdf

KEYTRUDA (pembrolizumab). Prescribing information. Merck & Co; 12018. Accessed April 10, 2024. 

https://www.merck.com/product/usa/pi_circulars/k/keytruda/keytruda_pi.pdf

JEMPERLI (dostarlimab). Prescribing information. GlaxoSmithKline; 2024. Accessed April 10, 2024. 

https://gskpro.com/content/dam/global/hcpportal/en_US/Prescribing_Information/Jemperli/pdf/JEMPERLI-PI-MG.PDF

FDA converts to full approval indication for KETRUDA (pembrolizumab) for certain adult and pediatric patients with advanced microsatellite instability-high (MSI-H) or mismatch repair deficient (dMMR) solid tumors. Press release. Merck. March 29, 2023. Accessed April 10, 2024. 

https://www.merck.com/news/fda-converts-to-full-approval-indication-for-keytruda-pembrolizumab-for-certain-adult-and-pediatric-patients-with-advanced-microsatellite-instability-high-msi-h-or-mismatch-repair-deficient/

FDA grants accelerated approval to dostarlimab-gxly for dMMR advanced solid tumors. FDA. Updated July 18, 2023. Accessed April 10, 2024. 

https://www.fda.gov/drugs/resources-information-approved-drugs/fda-grants-accelerated-approval-dostarlimab-gxly-dmmr-advanced-solid-tumors

MSI-H/dMMR

V-RAF murine sarcoma viral oncogene homolog B1 (BRAF)

 gene is located on chromosome 7, and its corresponding protein plays a role in the RAS-RAF-MEK-ERK (MAPK) signal transduction pathway.

MAPK enzymes are activated through interaction with growth factors, cytokines, and hormones.

More than a dozen known MAPK enzymes regulate cell differentiation, proliferation, and survival.

BRAF and its family of proteins are serine/threonine kinases that target other MAPK proteins via phosphorylation.

BRAF has 3 conserved regions (CRs) involved in protein function: CR1, CR2, and CR3.

CR1 and CR3 interact to form an autoinhibitory complex, whereas CR2 functions as a hinge for this complex.

Under normal conditions, RAS-GTP binds the CR1-CR3 complex and exposes the CR3 catalytic site for substrate activation.

Once activated, BRAF is localized to the cell membrane.

 is a major driver of gene alteration in many types of cancer, including pancreatic malignancies, and the V600E mutation has been best characterized as a constitutive active driver mutation.

can create a constitutively active protein that drives unregulated cell growth and division.

Pathogenic BRAF variants, including class I/II mutations, deletions, and fusions, are 

present in 2% to 4% of advanced pancreatic cancer cases, 

occurring more frequently in KRAS wild-type vs KRAS-mutant tumors (30% vs 1.5%, respectively).

BRAF V600E comprise approximately 17-28% of BRAF mutations in pancreatic cancer.

BRAF testing can be performed using immunohistochemistry (IHC) or, preferably, next-generation sequencing (NGS).

The National Comprehensive Cancer Network guidelines recommend testing for actionable somatic mutations including those involving 

 for all patients with advanced pancreatic cancer regardless of the presence of metastases.

The recommended testing method is NGS with an FDA-approved assay, although there is a growing consensus that RNA-based testing for fusion gene expression should be strongly considered as well.

V600E–mutant pancreatic cancer is dabrafenib plus trametinib.

Dabrafenib inhibits signals from the BRAF protein activated by the 

V600E mutation and prevents associated tumor growth.

Trametinib complements this mechanism by inhibiting mitogen-activated extracellular-regulated kinase 1 (MEK1) and MEK2 that is activated by the mutated gene.

The dual action prevents tumors from continuing to grow via the escape mechanism of MEK protein activating signals.

Learn more about Dabrafenib and Trametinib >

TAFINLAR (dabrafenib). Prescribing information. Novartis; 2024. Accessed March 11, 2024. 

https://www.novartis.com/us-en/sites/novartis_us/files/tafinlar.pdf

MEKINIST (trametinib). Prescribing information. Novartis; 2024. Accessed March 11, 2024. 

https://www.novartis.com/us-en/sites/novartis_us/files/mekinist.pdf

New study targets specific BRAF mutation. Let’s Win Pancreatic Cancer. July 27, 2023. Accessed March 11, 2024. 

https://letswinpc.org/research/target-braf-mutation/

Wan PTC, Garnett MJ, Roe SM, et al; Cancer Genome Project. Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. 

 2004;116(6):855-867. doi:10.1016/s0092-8674(04)00215-6

Cargnello M, Roux PP. Activation and function of the MAPKs and their substrates, the MAPK-activated protein kinases. 

 2011;75(1):50-83. doi:10.1128/MMBR.00031-10

Zaman A, Wu W, Bivona TG. Targeting oncogenic BRAF: past, present, and future. 

 2019;11(8):1197. doi:10.3390/cancers11081197

Allen MJ, Zhang A, Bavi P, et al. Molecular characterisation of pancreatic ductal adenocarcinoma with 

 fusions and review of the literature. J Clin Pathol. 2023;76(3):158-165. doi: 10.1136/jclinpath-2021-207781.

NCCN. Clinical Practice Guidelines in Oncology. Pancreatic adenocarcinoma, version 1.2024. Accessed June 11, 2024. 

Winstead E. Dabrafenib-trametinib combination approved for solid tumors with BRAF mutations. American Cancer Society. July 21, 2022. Accessed March 9, 2024. 

https://www.cancer.gov/news-events/cancer-currents-blog/2022/fda-dabrafenib-trametinib-braf-solid-tumors

BRAF V600E

Neurotrophic tropomyosin kinase receptors (NTRK)

Neurotrophic tropomyosin kinase receptors (NTRK) are a family of transmembrane proteins involved in neuronal development, proliferation, survival, and differentiation.

The genes NTRK1, NTRK2, and NTRK3 encode the proteins TRKA, TRKB, and TRKC, respectively.

TRK proteins are activated via neurotrophin ligands that trigger receptor dimerization and phosphorylation.

After activation, TRK proteins active signal transduction pathways RAS-RAF-MEK-ERK (MAPK), phosphatidylinositol-3-kinase (PI3K), phospholipase C-γ1, and others.

NTRK is a driver oncogene that promotes tumorigenesis via constitutive expression or increased kinase domain activity.

Gene fusions involve one of the three NTRK genes fusing the c-terminal with an n-terminal fusion partner, resulting in a chimeric protein that promotes solid tumor growth.

NTRK gene fusion mutations are rarely present in cancers (<1%) and have a similarly low prevalence in pancreatic cancer (0.34-0.8%)

Testing is recommended for patients with locally advanced or metastatic pancreatic cancer who are candidates for anticancer therapy

Testing can be performed via  immunohistochemistry (IHC) or via an FDA-approved or validated next-generation sequencing (NGS) assay; RNA assays are preferred over DNA assays for gene fusion detection.

It has been suggested that if immunohistochemistry (IHC) is used to detect NTRK gene fusions, then positive samples should be confirmed with RNA-NGS.

For patients with locally advanced or metastatic disease eligible for anticancer therapy, the NCCN Panel recommends testing for actionable somatic mutations, including fusions (ALK, NRG1, NTRK, ROS1, FGFR2, RET), mutations (BRAF, BRCA1/2, HER2, KRAS, PALB2), amplifications (HER2), MSI, dMMR, and TMB.

Larotrectinib and entrectinib are the two drugs currently approved by the FDA for treating NTRK gene fusion-positive solid tumors that are unresectable or metastatic.

They are both tropomyosin receptor tyrosine kinase inhibitors with slightly different molecular target profiles.

Larotrectinib was approved based on data from three phase I-II studies, with the primary endpoint overall response rate (ORR) and secondary endpoints duration of response (DOR), progression-free survival (PFS), and safety.

Based on outcomes data, larotrectinib was approved in 2018, with updated data published in 2020 that showed ORR 79% (95% CI 72-85) and 16% showing a complete response.

In 2019, the FDA approved entrectinib based on clinical data from phase I-II trials ALKA-372-001, STARTRK-1, and STARTRK-2.

 ORR was 57.4 (95% CI 43.2-70.8), DOR 10.4 months (95% CI 7.1-NR), and PFS 11.2 months (95% CI 8.0-14.9).

Larotrectinib and entrectinib are tyrosine kinase inhibitors specifically targeting TRKA, TRKB, and TRKC, anaplastic lymphoma kinase (ALK), and the proto-oncogene tyrosine-protein kinase 1 (ROS1).

Okamura R, Boichard A, Kato S, Sicklick JK, Bazhenova L, Kurzrock R. Analysis of 

 Alterations in Pan-Cancer Adult and Pediatric Malignancies: Implications for NTRK-Targeted Therapeutics. 

Manea CA, Badiu DC, Ploscaru IC, et al. A review of NTRK fusions in cancer. 

. 2022;79. doi:10.1016/j.amsu.2022.103893

Lange A, Lo HW. Inhibiting TRK Proteins in Clinical Cancer Therapy. 

. 2018;10(4):105. doi:10.3390/cancers10040105

Demols A, Rocq L, Perez-Casanova L, et al. A Two-Step Diagnostic Approach for 

 Gene Fusion Detection in Biliary Tract and Pancreatic Adenocarcinomas. 

. 2023;28(7):e520-e525. doi:10.1093/oncolo/oyad075

. 2023;76(3):158-165. doi:10.1136/jclinpath-2021-207781

National Comprehensive Cancer Network. NCCN guidelines version 1.2024: Pancreatic Adenocarcinoma. 

ROZLYTREK (entrectinib). Prescribing information. Genentech; 2019. Accessed May 5, 2024. 

https://www.gene.com/download/pdf/rozlytrek_prescribing.pdf

VITRAKVI (larotrectinib). Prescribing information. Loxo Oncology; 2018. Accessed May 5, 2024. 

https://labeling.bayerhealthcare.com/html/products/pi/vitrakvi_PI.pdf

Drilon A, Laetsch TW, Kummar S, et al. Efficacy of Larotrectinib in 

 Fusion–Positive Cancers in Adults and Children. 

. 2018;378(8):731-739. doi:10.1056/NEJMoa1714448

Demetri GD, Paz-Ares L, Farago AF, et al. Efficacy and safety of entrectinib in patients with NTRK fusion-positive (NTRK-fp) tumors: pooled analysis of STARTRK-2, STARTRK-1 and ALKA-372-001. 

. 2018;29:viii713. doi:10.1093/annonc/mdy424.017

NTRK fusions

 gene is a novel target for pancreatic solid tumors.

 is involved in developing the kidney and the nervous systems; it plays a vital role in cell development, proliferation, migration, and differentiation.

is located on chromosome 10, measures 60 kb, and contains 21 exons.

Under normal cellular conditions, the RET protein binds endogenous ligands that cause homodimerization, autophosphorylation, and activation of multiple signal transduction pathways, including JAK-STAT, PKA, MAPK, PI3K, PLCγ, and PKC.

Unlike many other receptor tyrosine kinases, RET does not bind directly to its ligands but to a ligand–coreceptor complex.

 Glial-line derived neurotrophic factor (GDNF), neurturin, persephin, and artemin are endogenous ligands that bind to GDNF family receptor-α (GFRα) coreceptors.

encodes a transmembrane tyrosine kinase with 3 domains: the intracellular, transmembrane, and extracellular domains.

Of interest to clinicians is the extracellular domain; this area contains a cysteine-rich domain and cadherin-like domains 1-4 (CDL1-4), which are mutation hotspots for the proto-oncogene.

 fusions cause oncogenesis in 1 of 2 primary ways: chimeric fusion with increased transcriptional control or upstream fusion of a homodimerization domain that results in ligand-independent autophosphorylation.

 fusions are uncommon in pancreatic cancer—they present in approximately 0.6% of tumor lines.

Pancreatic ductal adenocarcinoma (PDAC) cell lines with RET isoforms display increased tumor aggressiveness secondary to perineural invasion.

High RET expression is also associated with better overall survival in PDAC but increased tumor aggression and poorer prognosis.

Testing is typically performed via next generation sequencing (NGS), with RNA-based NGS being the preferred method due to improved detection of gene fusions.

The National Comprehensive Cancer Network guidelines do not make specific recommendations for 

gene fusions but broadly recommend gene fusion testing via next-generation sequencing (NGS) with RNA.

RNA-based testing has high sensitivity and specificity compared with other forms of testing, and it is generally recommended as the testing methodology for other types of cancers.

One drug—selpercatinib—is currently approved for treating 

 gene fusion–positive pancreatic cancer.

Selpercatinib received accelerated approval in 2022 for locally advanced or metastatic, tumor-agnostic cancers based on favorable efficacy and safety data.

 Overall response rate was 44% with a median duration of response of 24.5 months.

Selpercatinib binds to and inactivates wild-type 

 mutant isoforms, VEGFR1, VEGFR2, and FGFR1-3.

FDA D.I.S.C.O. Burst Edition: FDA approvals of Retevmo (selpercatinib) for adult patients with locally advanced or metastatic RET fusion-positive solid tumors, and Retevmo (selpercatinib) for adult patients with locally advanced or metastatic RET fusion-positive non-small cell lung cancer. FDA. November 7, 2022. Accessed April 1, 2024. 

https://www.fda.gov/drugs/resources-information-approved-drugs/fda-disco-burst-edition-fda-approvals-retevmo-selpercatinib-adult-patients-locally-advanced-or

RETEVMO (selpercatinib). Prescribing information. Eli Lilly and Company. 2024. Accessed June 12, 2024. 

https://uspl.lilly.com/retevmo/retevmo.html#pi

Zhao L, Wang N, Zhang D, Jia Y, Kong F. A comprehensive overview of the relationship between RET gene and tumor occurrence. 

 2023;13:1090757. doi:10.3389/fonc.2023.1090757

Ibanez CF. Structure and physiology of the RET receptor tyrosine kinase. 

 2013;5(2):a009134. doi:10.1101/cshperspect.a009134

Carlomagno F. Thyroid cancer: Role of RET and beyond. 

Belli C, Penault-Llorca F, Ladanyi M, et al. ESMO recommendations on the standard methods to detect RET fusions and mutations in daily practice and clinical research. 

 2021;32(3):337-350. doi:10.1016/j.annonc.2020.11.021

Drilon A, Hu ZI, Lai GGY, Tan DSW. Targeting RET-driven cancers: Lessons from evolving preclinical and clinical landscapes. 

 2018;15(3):151-167. doi:10.1038/nrclinonc.2017.175

Kato S, Subbiah V, Marchlik E, Elkin SK, Carter JL, Kurzrock R. RET aberrations in diverse cancers: next-generation sequencing of 4,871 patients. 

 2017;23(8):1988-1997. doi:10.1158/1078-0432.CCR-16-1679

Zhang T, Wang H, Cai Z, Zhang S, Jiang C. RET rearrangement-positive pancreatic cancer has remarkable response to pralsetinib: a case report. 

 2023;13:1078076. doi:10.3389/fonc.2023.1078076

Lian EY, Hyndman BD, Moodley S, Maritan SM, Mulligan LM. RET isoforms contribute differentially to invasive processes in pancreatic ductal adenocarcinoma. 

 2020;39(41):6493-6510. doi:10.1038/s41388-020-01448-z

NCCN. Clinical Practice Guidelines in Oncology. Pancreatic adenocarcinoma, version 1.2024. Accessed June 12, 2024. 

Properties of FDA-approved small molecule protein kinase inhibitors: A 2022 update. 

 2022;175:106037. doi:10.1016/j.phrs.2021.106037

Subbiah V, Wolf J, Konda B, et al. Tumour-agnostic efficacy and safety of selpercatinib in patients with RET fusion-positive solid tumours other than lung or thyroid tumours (LIBRETTO-001): a phase 1/2, open-label, basket trial. 

 2022;23(10):1261-1273. doi:10.1016/S1470-2045(22)00541-1

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