Biomarkers of mismatch repair deficiency in colorectal cancer and cancer predisposition syndromes

PhD ThesisColorectal cancer (CRC) is the third most common cancer in Western societies and approximately 15% are mismatch repair deficient (MMRd). MMRd CRCs have a distinct prognosis, respond to immunotherapy, and occur at a high rate in patients with Lynch syndrome or constitutional mismatch repair deficiency (CMMRD). Detection of MMR deficiency, therefore, guides treatment and identification of associated cancerpredisposition syndromes. However, there is a need for novel biomarkers to detect MMRd CRC, and innovative assays to improve Lynch syndrome and CMMRD diagnosis. I assessed autoantibodies generated against MMRd CRCs as a liquid-biopsy biomarker for cancer detection, by analysing the sera of 464 Lynch syndrome gene carriers using a recently published, multiplex method. Although autoantibodies correlated with a history of CRC, a lack of signal from patients who developed CRC shortly after sampling suggests the method has poor sensitivity. Microsatellite instability (MSI) is an established biomarker of MMR deficiency. I used single molecule molecular inversion probes to develop a sequencing-based MSI assay with an automated results analysis, suitable as a companion diagnostic for immunotherapy, and for streamlined Lynch syndrome screening. The assay achieved 100% accuracy in 197 CRCs, and was robust to sample variables, including quantity, quality, and tumour cell content. Subsequently, I adapted the MSI assay to detect low-level MSI in non-neoplastic tissues of CMMRD patients. The assay separated all 32 CMMRD patients from 94 controls. For both CRC and CMMRD diagnostics, the MSI assay is cheaper and faster than current methods, and is scalable to large cohorts. These results suggest that the humoral immune response to MMRd CRCs cannot readily be used as a biomarker to detect disease, and that alternatives should be sought. However, the MSI assay could be deployed into clinical practice to meet the high demand for MMR deficiency testing of CRCs and to improve CMMRD diagnostics.the Barbour Foundatio

Pyrotechnic Actuator for Retracting Tubes Between MSL Subsystems

An apparatus, denoted the "retractuator" (a contraction of "retracting actuator"), was designed to help ensure clean separation between the cruise stage and the entry-vehicle subsystem of the Mars Science Laboratory (MSL) mission. The retractuator or an equivalent mechanism is needed because of tubes that (1) transport a heat-transfer fluid between the stages during flight and (2) are cut immediately prior to separation of the stages retractuator. The role of the retractuator is to retract the tubes, after they are cut and before separation of the subsystem, so that cut ends of the tubes do not damage thermal-protection coats on the entry vehicle and do not contribute to uncertainty of drag and consequent uncertainty in separation velocity

Is HLA type a possible cancer risk modifier in Lynch syndrome?

Lynch syndrome (LS) is the most common inherited cancer syndrome. It is inherited via a monoallelic germline variant in one of the DNA mismatch repair (MMR) genes. LS carriers have a broad 30% to 80% risk of developing various malignancies, and more precise, individual risk estimations would be of high clinical value, allowing tailored cancer prevention and surveillance. Due to MMR deficiency, LS cancers are characterized by the accumulation of frameshift mutations leading to highly immunogenic frameshift peptides (FSPs). Thus, immune surveillance is proposed to inhibit the outgrowth of MMR-deficient cell clones. Recent studies have shown that immunoediting during the evolution of MMR-deficient cancers leads to a counter-selection of highly immunogenic antigens. The immunogenicity of FSPs is dependent on the antigen presentation. One crucial factor determining antigen presentation is the HLA genotype. Hence, a LS carrier's HLA genotype plays an important role in the presentation of FSP antigens to the immune system, and may influence the likelihood of progression from precancerous lesions to cancer. To address the challenge of clarifying this possibility including diverse populations with different HLA types, we have established the INDICATE initiative (Individual cancer risk by HLA type, ), an international network aiming at a systematic evaluation of the HLA genotype as a possible cancer risk modifier in LS. Here we summarize the current knowledge on the role of HLA type in cancer risk and outline future research directions to delineate possible association in the scenario of LS with genetically defined risk population and highly immunogenic tumors.Peer reviewe

The "unnatural" history of colorectal cancer in Lynch syndrome : Lessons from colonoscopy surveillance

Individuals with Lynch syndrome (LS), one of the most common inherited cancer syndromes, are at increased risk of developing malignancies, in particular colorectal cancer (CRC). Regular colonoscopy with polypectomy is recommended to reduce CRC risk in LS individuals. However, recent independent studies demonstrated that a substantial proportion of LS individuals develop CRC despite regular colonoscopy. The reasons for this surprising observation confirmed by large prospective studies are a matter of debate. In this review, we collect existing evidence from clinical, epidemiological and molecular studies and interpret them with regard to the origins and progression of LS-associated CRC. Alongside with hypotheses addressing colonoscopy quality and pace of progression from adenoma to cancer, we discuss the role of alternative precursors and of immune system in LS-associated CRC. We also identify gaps in current knowledge and make suggestions for future studies aiming at improved CRC prevention for LS individuals.Peer reviewe

A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours

<div><p>Somatic mutations in mononucleotide repeats are commonly used to assess the mismatch repair status of tumours. Current tests focus on repeats with a length above 15bp, which tend to be somatically more unstable than shorter ones. These longer repeats also have a substantially higher PCR error rate, and tests that use capillary electrophoresis for fragment size analysis often require expert interpretation. In this communication, we present a panel of 17 short repeats (length 7–12bp) for sequence-based microsatellite instability (MSI) testing. Using a simple scoring procedure that incorporates the allelic distribution of the mutant repeats, and analysis of two cohort of tumours totalling 209 samples, we show that this panel is able to discriminate between MMR proficient and deficient tumours, even when constitutional DNA is not available. In the training cohort, the method achieved 100% concordance with fragment analysis, while in the testing cohort, 4 discordant samples were observed (corresponding to 97% concordance). Of these, 2 showed discrepancies between fragment analysis and immunohistochemistry and one was reclassified after re-testing using fragment analysis. These results indicate that our approach offers the option of a reliable, scalable routine test for MSI.</p></div

Constitutional Microsatellite Instability, Genotype, and Phenotype Correlations in Constitutional Mismatch Repair Deficiency

peer reviewed[en] BACKGROUND & AIMS: Constitutional mismatch repair deficiency (CMMRD) is a rare recessive childhood cancer predisposition syndrome caused by germline mismatch repair variants. Constitutional microsatellite instability (cMSI) is a CMMRD diagnostic hallmark and may associate with cancer risk. We quantified cMSI in a large CMMRD patient cohort to explore genotype-phenotype correlations using novel MSI markers selected for instability in blood. METHODS: Three CMMRD, 1 Lynch syndrome, and 2 control blood samples were genome sequenced to >120× depth. A pilot cohort of 8 CMMRD and 38 control blood samples and a blinded cohort of 56 CMMRD, 8 suspected CMMRD, 40 Lynch syndrome, and 43 control blood samples were amplicon sequenced to 5000× depth. Sample cMSI score was calculated using a published method comparing microsatellite reference allele frequencies with 80 controls. RESULTS: Thirty-two mononucleotide repeats were selected from blood genome and pilot amplicon sequencing data. cMSI scoring using these MSI markers achieved 100% sensitivity (95% CI, 93.6%-100.0%) and specificity (95% CI 97.9%-100.0%), was reproducible, and was superior to an established tumor MSI marker panel. Lower cMSI scores were found in patients with CMMRD with MSH6 deficiency and patients with at least 1 mismatch repair missense variant, and patients with biallelic truncating/copy number variants had higher scores. cMSI score did not correlate with age at first tumor. CONCLUSIONS: We present an inexpensive and scalable cMSI assay that enhances CMMRD detection relative to existing methods. cMSI score is associated with mismatch repair genotype but not phenotype, suggesting it is not a useful predictor of cancer risk

Constitutional mismatch repair deficiency syndrome with atypical features caused by a homozygous MLH1 missense variant (c.1918C>A, p.(Pro640Thr)): a case report

Constitutional mismatch repair deficiency (CMMRD) syndrome is a rare autosomal recessive genetic disorder caused by biallelic germline mutations in one of the mismatch repair genes. Carriers are at exceptionally high risk for developing, typically in early life, hematological and brain malignancies, as well as cancers observed in Lynch syndrome. We report a homozygous MLH1 missense variant (c.1918C&gt;A p.(Pro640Thr)) in a Tunisian patient with CMMRD syndrome and a family history of early-age colorectal cancer. The proband presented initially with colonic oligopolyposis and adenosquamous carcinoma of the caecum. He later developed several malignancies, including undifferentiated carcinoma of the parotid, grade 4 IDH-mutant astrocytoma, and ampulla of Vater adenocarcinoma. The patient was older than typical for this disease and had a remarkably prolonged survival despite developing four distinct aggressive malignancies. The current report highlights the challenges in assessing the pathogenicity of the identified variant and the remarkable phenotypic diversity in CMMRD

Retriever is a multiprotein complex for retromer-independent endosomal cargo recycling

Following endocytosis into the endosomal network, integral membrane proteins undergo sorting for lysosomal degradation or are retrieved and recycled back to the cell surface. Here we describe the discovery of an ancient and conserved multiprotein complex that orchestrates cargo retrieval and recycling and, importantly, is biochemically and functionally distinct from the established retromer pathway. We have called this complex 'retriever'; it is a heterotrimer composed of DSCR3, C16orf62 and VPS29, and bears striking similarity to retromer. We establish that retriever associates with the cargo adaptor sorting nexin 17 (SNX17) and couples to CCC (CCDC93, CCDC22, COMMD) and WASH complexes to prevent lysosomal degradation and promote cell surface recycling of α5β1 integrin. Through quantitative proteomic analysis, we identify over 120 cell surface proteins, including numerous integrins, signalling receptors and solute transporters, that require SNX17-retriever to maintain their surface levels. Our\ua0identification of retriever establishes a major endosomal retrieval and recycling pathway

Encyocratella Strand 1907

Encyocratella Strand, 1907 Encyocratella Strand 1907a: 556; Raven 1985: 152 (syn.). Revalidated. Xenodendrophila Gallon 2003: 405. Syn. n. Type species: Encyocratella olivacea Strand, 1907 by original designation. Diagnosis: Female and genus diagnosed as Xenodendrophila in Gallon (2003). The presence of leg spines, less developed tarsal and metatarsal scopulae, absence of lateral leg fringes (Figs. 10–11) and a broad, keeled embolus, readily distinguish Encyocratella males from those of Stromatopelma and Heteroscodra, the only other stromatopelmine genera. In males of both Stromatopelma and Heteroscodra the legs are aspinose, have laterally well­developed leg scopulae, distinct lateral leg fringes (Figs. 12–13) and thin, unkeeled emboli. In Encyocratella the ocular tubercle is oval and elevated (Figs. 14–15), whereas in both Stromatopelma and Heteroscodra it is broadly rectangular and weakly elevated (Figs. 16–17).Published as part of Gallon, Richard C., 2005, Encyocratella olivacea Strand, 1907, a senior synonym of Xenodendrophila gabrieli Gallon, 2003 (Araneae: Theraphosidae: Stromatopelminae) with a description of the male, pp. 45-56 in Zootaxa 1003 (1) on pages 46-47, DOI: 10.11646/zootaxa.1003.1.3, http://zenodo.org/record/504873