Identification and validation of a machine learning model of complete response to radiation in rectal cancer reveals immune infiltrate and TGFß as key predictors.

BACKGROUND: It is uncertain which biological features underpin the response of rectal cancer (RC) to radiotherapy. No biomarker is currently in clinical use to select patients for treatment modifications. METHODS: We identified two cohorts of patients (total N = 249) with RC treated with neoadjuvant radiotherapy (45Gy/25) plus fluoropyrimidine. This discovery set included 57 cases with pathological complete response (pCR) to chemoradiotherapy (23%). Pre-treatment cancer biopsies were assessed using transcriptome-wide mRNA expression and targeted DNA sequencing for copy number and driver mutations. Biological candidate and machine learning (ML) approaches were used to identify predictors of pCR to radiotherapy independent of tumour stage. Findings were assessed in 107 cases from an independent validation set (GSE87211). FINDINGS: Three gene expression sets showed significant independent associations with pCR: Fibroblast-TGFß Response Signature (F-TBRS) with radioresistance; and cytotoxic lymphocyte (CL) expression signature and consensus molecular subtype CMS1 with radiosensitivity. These associations were replicated in the validation cohort. In parallel, a gradient boosting machine model comprising the expression of 33 genes generated in the discovery cohort showed high performance in GSE87211 with 90% sensitivity, 86% specificity. Biological and ML signatures indicated similar mechanisms underlying radiation response, and showed better AUC and p-values than published transcriptomic signatures of radiation response in RC. INTERPRETATION: RCs responding completely to chemoradiotherapy (CRT) have biological characteristics of immune response and absence of immune inhibitory TGFß signalling. These tumours may be identified with a potential biomarker based on a 33 gene expression signature. This could help select patients likely to respond to treatment with a primary radiotherapy approach as for anal cancer. Conversely, those with predicted radioresistance may be candidates for clinical trials evaluating addition of immune-oncology agents and stromal TGFß signalling inhibition. FUNDING: The Stratification in Colorectal Cancer Consortium (S:CORT) was funded by the Medical Research Council and Cancer Research UK (MR/M016587/1).

Assessing kinetics and recruitment of DNA repair factors using high content screens.

Repair of genetic damage is coordinated in the context of chromatin, so cells dynamically modulate accessibility at DNA breaks for the recruitment of DNA damage response (DDR) factors. The identification of chromatin factors with roles in DDR has mostly relied on loss-of-function screens while lacking robust high-throughput systems to study DNA repair. In this study, we have developed two high-throughput systems that allow the study of DNA repair kinetics and the recruitment of factors to double-strand breaks in a 384-well plate format. Using a customized gain-of-function open-reading frame library ("ChromORFeome" library), we identify chromatin factors with putative roles in the DDR. Among these, we find the PHF20 factor is excluded from DNA breaks, affecting DNA repair by competing with 53BP1 recruitment. Adaptable for genetic perturbations, small-molecule screens, and large-scale analysis of DNA repair, these resources can aid our understanding and manipulation of DNA repair.

In-depth Clinical and Biological Exploration of DNA Damage Immune Response as a Biomarker for Oxaliplatin Use in Colorectal Cancer.

PURPOSE: The DNA damage immune response (DDIR) assay was developed in breast cancer based on biology associated with deficiencies in homologous recombination and Fanconi anemia pathways. A positive DDIR call identifies patients likely to respond to platinum-based chemotherapies in breast and esophageal cancers. In colorectal cancer, there is currently no biomarker to predict response to oxaliplatin. We tested the ability of the DDIR assay to predict response to oxaliplatin-based chemotherapy in colorectal cancer and characterized the biology in DDIR-positive colorectal cancer. EXPERIMENTAL DESIGN: Samples and clinical data were assessed according to DDIR status from patients who received either 5-fluorouracil (5-FU) or 5FUFA (bolus and infusion 5-FU with folinic acid) plus oxaliplatin (FOLFOX) within the FOCUS trial (n = 361, stage IV), or neoadjuvant FOLFOX in the FOxTROT trial (n = 97, stage II/III). Whole transcriptome, mutation, and IHC data of these samples were used to interrogate the biology of DDIR in colorectal cancer. RESULTS: Contrary to our hypothesis, DDIR-negative patients displayed a trend toward improved outcome for oxaliplatin-based chemotherapy compared with DDIR-positive patients. DDIR positivity was associated with microsatellite instability (MSI) and colorectal molecular subtype 1. Refinement of the DDIR signature, based on overlapping IFN-related chemokine signaling associated with DDIR positivity across colorectal cancer and breast cancer cohorts, further confirmed that the DDIR assay did not have predictive value for oxaliplatin-based chemotherapy in colorectal cancer. CONCLUSIONS: DDIR positivity does not predict improved response following oxaliplatin treatment in colorectal cancer. However, data presented here suggest the potential of the DDIR assay in identifying immune-rich tumors that may benefit from immune checkpoint blockade, beyond current use of MSI status.

TEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts.

Eukaryotic topoisomerase 1 (TOP1) regulates DNA topology to ensure efficient DNA replication and transcription. TOP1 is also a major driver of endogenous genome instability, particularly when its catalytic intermediate-a covalent TOP1-DNA adduct known as a TOP1 cleavage complex (TOP1cc)-is stabilised. TOP1ccs are highly cytotoxic and a failure to resolve them underlies the pathology of neurological disorders but is also exploited in cancer therapy where TOP1ccs are the target of widely used frontline anti-cancer drugs. A critical enzyme for TOP1cc resolution is the tyrosyl-DNA phosphodiesterase (TDP1), which hydrolyses the bond that links a tyrosine in the active site of TOP1 to a 3' phosphate group on a single-stranded (ss)DNA break. However, TDP1 can only process small peptide fragments from ssDNA ends, raising the question of how the ~90 kDa TOP1 protein is processed upstream of TDP1. Here we find that TEX264 fulfils this role by forming a complex with the p97 ATPase and the SPRTN metalloprotease. We show that TEX264 recognises both unmodified and SUMO1-modifed TOP1 and initiates TOP1cc repair by recruiting p97 and SPRTN. TEX264 localises to the nuclear periphery, associates with DNA replication forks, and counteracts TOP1ccs during DNA replication. Altogether, our study elucidates the existence of a specialised repair complex required for upstream proteolysis of TOP1ccs and their subsequent resolution.

Non-familial cardiomyopathies in Lebanon: exome sequencing results for five idiopathic cases.

BACKGROUND: Cardiomyopathies affect more than 0.5% of the general population. They are associated with high risk of sudden cardiac death, which can result from either heart failure or electrical abnormalities. Although different mechanisms underlie the various types of cardiomyopathies, a principal pathology is common to all and is usually at the level of the cardiac muscle. With a relatively high incidence rate in most countries, and a subsequent major health burden on both the families and governments, cardiomyopathies are gaining more attention by researchers and pharmaceutical companies as well as health government bodies. In Lebanon, there is no official data about the spectrum of the diseases in terms of their respective prevalence, clinical, or genetic profiles. METHODS: We used exome sequencing to unravel the genetic basis of idiopathic cases of cardiomyopathies in Lebanon, a relatively small country with high rates of consanguineous marriages. RESULTS: Five cases were diagnosed with different forms of cardiomyopathies, and exome sequencing revealed the presence of already documented or novel mutations in known genes in three cases: LMNA for an Emery Dreifuss Muscular Dystrophy case, PKP2 for an arrhythmogenic right ventricle dysplasia case, and MYPN for a dilated cardiomyopathy case. Interestingly two brothers with hypertrophic cardiomyopathy have a novel missense variation in NPR1, the gene encoding the natriuretic peptides receptor type I, not reported previously to be causing cardiomyopathies. CONCLUSION: Our results unravel novel mutations in known genes implicated in cardiomyopathies in Lebanon. Changes in clinical management however, require genetic profiling of a larger cohort of patients.

The Muscle-Bound Heart.

Hypertrophic cardiomyopathy (HCM) is a familial cardiac disease manifested in a wide phenotype and diverse genotype and, thus, presenting unpredictable risks mainly on young adults. Extensive studies are being conducted to categorize patients and link phenotype with genotype for a better management and control of the disease with all its complications. Because the full mechanisms behind HCM are still not revealed, therapeutics are not definitive. Further research is to be conducted for the generation of a complete picture and directed therapy for HCM.

Catecholaminergic Polymorphic Ventricular Tachycardia.

Catecholaminergic polymorphic ventricular tachycardia (CPVT) is a challenging and serious disease with a high incidence of sudden cardiac deaths. Patients with CPVT should not be exposed to physical or emotional exertion that might induce ventricular tachycardia. This article presents a case with CPVT and discusses the clinical features of the disease, its genetic background, and the management of CPVT.

Comparison of the performance of the Cepheid Xpert HemosIL Factor II and Factor V and the ViennaLab FV-PTH-MTHFR StripAssay kits for molecular thrombophilia profiling.

AIMS: To compare the performance of two assays used for the detection of mutations/polymorphisms in the Factor V, Factor II, and methylenetetrahydrofolate reductase genes among patients referred for the management of a thrombotic event. MATERIALS AND METHODS: We tested 40 different patient samples using two assays, the ViennaLab FV-PTH-MTHFR StripAssay and the Cepheid Xpert HemosIL. RESULTS: The two assays were 100% concordant in their produced results with no samples failing the testing procedures in both. CONCLUSION: This is the first report to evaluate the performance of the ViennaLab FV-PTH-MTHFR StripAssay and the Cepheid Xpert HemosIL. Both assays can be introduced to the operation of molecular diagnostic laboratories to cover the referrals from different disciplines, especially in tertiary care centers with emergency departments.

Laboratory referral rates of genetic tests for thrombophilia workup in a major referral center.

AIMS: The rate of laboratory referrals for thrombophilia patients' genetic workup was assessed and compared among the medical and surgical specialties and subspecialties at a major tertiary care center in Lebanon. METHODS: DNA extraction was performed using the PEL-FREEZ extraction kit (PEL-FREEZ; DYNAL) and the Factor V, prothrombin, and methylenetetrahydrofolate reductase genotypic profiles were done using the FV-PTH-MTHFR StripAssay kit (ViennaLab) that employs a polymerase chain reaction-reverse hybridization method. A total of 2238 referred cases were analyzed. RESULTS: Around 42.23% of all referred cases turned out to have a thrombosis-associated mutation. Referrals from medical and surgical specialties were almost equal. In the surgical specialty, most referrals came from the department of Obstetrics and Gynecology, while in the medical speciality, most of the workup referrals originated from the Hematology/Oncology physicians. However, low referral rates were reported from the emergency department and family medicine practitioners. CONCLUSION: Genetic testing for thrombophilia workup is gaining more importance among the different medical and surgical specialties and is worth being introduced into the offered test lists of all established molecular diagnostics laboratories.