Artificial intelligence for predictive biomarker discovery in immuno-oncology: a systematic review

BACKGROUND

The widespread use of immune checkpoint inhibitors (ICIs) has revolutionised treatment of multiple cancer types. However, selecting patients who may benefit from ICI remains challenging. Artificial intelligence (AI) approaches allow exploitation of high-dimension oncological data in research and development of precision immuno-oncology.

MATERIALS AND METHODS

We conducted a systematic literature review of peer-reviewed original articles studying the ICI efficacy prediction in cancer patients across five data modalities: genomics (including genomics, transcriptomics, and epigenomics), radiomics, digital pathology (pathomics), and real-world and multimodality data.

RESULTS

A total of 90 studies were included in this systematic review, with 80% published in 2021-2022. Among them, 37 studies included genomic, 20 radiomic, 8 pathomic, 20 real-world, and 5 multimodal data. Standard machine learning (ML) methods were used in 72% of studies, deep learning (DL) methods in 22%, and both in 6%. The most frequently studied cancer type was non-small-cell lung cancer (36%), followed by melanoma (16%), while 25% included pan-cancer studies. No prospective study design incorporated AI-based methodologies from the outset; rather, all implemented AI as a post hoc analysis. Novel biomarkers for ICI in radiomics and pathomics were identified using AI approaches, and molecular biomarkers have expanded past genomics into transcriptomics and epigenomics. Finally, complex algorithms and new types of AI-based markers, such as meta-biomarkers, are emerging by integrating multimodal/multi-omics data.

CONCLUSION

AI-based methods have expanded the horizon for biomarker discovery, demonstrating the power of integrating multimodal data from existing datasets to discover new meta-biomarkers. While most of the included studies showed promise for AI-based prediction of benefit from immunotherapy, none provided high-level evidence for immediate practice change. A priori planned prospective trial designs are needed to cover all lifecycle steps of these software biomarkers, from development and validation to integration into clinical practice.

Case report: a giant cell-rich gnathic bone lesion in a child with pycnodysostosis

Pycnodysostosis is a skeletal dysplasia characterized by short stature, generalized osteosclerosis, acro-osteolysis, and recognizable facial features. Oral manifestations are commonly described and include a high-arched palate with dental crowding and malocclusion, hypoplastic enamel, and retained deciduous teeth with impacted permanent teeth, and there is an increased risk of developing osteomyelitis of the jaw. We report here the history of a 9-year-old male with the typical facial and skeletal phenotype of pycnodysostosis but novel oral features. He presented with bilateral progressive facial swelling, which caused functional impairment with chewing and contributed to his severe obstructive sleep apnea (OSA). The severity of his OSA required surgical intervention, and the lesions were resected. Extensive bone remodeling and replacement by fibrous tissue were noted on submucosal dissection, and bilateral subtotal maxillectomies were required. The histopathology of the biopsied lesion was consistent with a giant cell-rich lesion. Genetic testing identified a pathogenic homozygous variant in the CTSK gene, c.953G > A, p. (Cys318Tyr). The proband had a good postsurgical response with sustained improvement in his sleep OSA. We present here the history and clinical characteristics of a patient with typical features of pycnodysostosis and an unusual presentation and histopathology of gnathic bone lesions. This report adds to the body of literature on this rare condition and also highlights the finding of giant cell-rich lesions of the gnathic bones. Giant cell-rich lesions in pycnodysostosis have previously been reported in two cases in the literature. While there is not enough evidence to support a certain association with pycnodysostosis, it is prudent to consider regular oral dental reviews in affected individuals to identify pathology early and avoid such life-threatening complications.

Observations during the COVID-19 pandemic in chronic heart failure patients with complex devices in a tertiary care cardiac centre using the HeartLogic software

Funding Acknowledgements

Type of funding sources: None.

Introduction

Decompensation of heart failure leading (HF) to hospitalisation is the single most important drain on healthcare resources when managing patients with left ventricular systolic dysfunction. Cardiac resynchronisation therapy with/without defibrillators (CRT-P/D) decreases hospitalisation due to HF and improves survival while implantable cardiac defibrillators (ICD"s) have a favourable effect on the former. Proprietary software algorithms embedded in these complex devices give an early warning to clinicians when decompensation of HF is imminent allowing preventative action to be undertaken.

HeartLogic (HL) is one such new algorithm in Boston Scientific CRT-D/ICD devices using multiple sensors to track 5 physiological parameters, combining them into one composite Index, with an Alert being triggered if the Index is >16. The COVID-19 pandemic, due to multiple reasons, resulted in a significant decrease in availability of routine HF services in the United Kingdom, especially during the initial lockdown period from 23rd March to 1st July 2020.

Aim

To assess the impact of the COVID-19 pandemic, using HL, in patients with HF and complex devices. 

Materials and Methods

Retrospective analysis of patients in a tertiary care cardiac centre in whom the HL software had been activated in March/April 2019 (n = 49) and comparison of those with (Group A n = 21) and without (Group B n = 28) an Alert (HLA) during the COVID-19 pandemic. 

Results (Table): Whole cohort n = 49. Age:  72 ± 12 years, Median: 75, Range: 36-95. 36/49 (73.5%) males. Type of device implanted: Resonate X4 CRT-D: 28/49 (57.1%); Momentum CRT-D: 8/49 (16.3%); Resonate ICD: 13/49 (26.5%). Ischaemic aetiology of HF: 35/49 (71.4%), Total duration of HL monitoring: 632 ± 7 days (median: 632; range: 626-672).  There was no difference in the age, gender, and type of device implanted between Group A and Group B. Over nearly ∼1 year of monitoring in each of the groups, Group A had more unstable HF with 10/21 (47.6%) having their first HLA during the pandemic. Multiple HLA"s, longer period in HLA and those with ischaemic aetiology of HF were higher in Group A. 17/40 (42.5%) HLA"s in Group A were within the first lockdown period (March - July). 24/28 (85.7%) patients in Group B had no HLA"s either before or during the pandemic. There was no difference in the HLA score between Groups A and B.

Conclusion

In this limited group of patients with a medium term follow-up, using the HeartLogic software, patients with ischaemic aetiology of HF and those with more HLA"s prior to the pandemic did worse than those who no HLA"s. First HLA"s, multiple alerts and longer duration of alerts in this group of patients suggests a lack of access to adequate HF services during the pandemic. It has implications with regard to how HF services are configured in future whenever resources are constrained.

Teaching Visually Impaired Children to Make Distance Judgments from a Tactile Map

This article reports on two experiments that investigated 59 children's ability to estimate distances from a map. In Experiment 1, totally blind children, children with residual vision, and sighted children were given a map showing the position of three objects on a path, two of which were present on the actual path. The children were asked to use the map to work out the position of the third object. The visually impaired children performed less well than did the sighted children, and an analysis of the children's strategies indicated that the majority of visually impaired children did not know an effective way to work out distances from the map. In Experiment 2, the visually impaired children were given a brief training in how to calculate distances from a map and then they were retested. After training, the children's performance improved.

Can Visually Impaired Children Use Tactile Maps to Estimate Directions?

This article reports on three experiments in which totally blind children and children with residual vision were asked to estimate directions between landmarks in a large-scale layout of objects. The children experienced the layout either directly, by walking around it, or indirectly by examining a tactile map. The authors found that the use of tactile maps considerably facilitated the performance of the totally blind children. The theoretical and practical implications of these findings are discussed.

Lactating mothers infected with Ebola virus: EBOV RT-PCR of blood only may be insufficient

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[2+3] Cycloaddition Reactions of Azido Metal Complexes and Crystal Structure of the Cycloadduct of (Ρh3Ρ)2Pd(Ν3)2 with Benzonitrile

Cycloaddition reactions of (R3P) 2M(N3)2 (M = Pd, Pt) with organic nitriles, thiocyanates, isothiocyanates, dimethylacetylenedicarboxylate and carbon disulphide are described; an X-ray analysis of the crystal structure of bis (5-phenyltetrazolato) -bis (triphenylphosphine) palladium (II) is summarised and related to isomerism of the complex in solution.

Experimental validation of a novel compact focusing scheme for future energy-frontier linear lepton colliders

A novel scheme for the focusing of high-energy leptons in future linear colliders was proposed in 2001 [P. Raimondi and A. Seryi, Phys. Rev. Lett. 86, 3779 (2001)]. This scheme has many advantageous properties over previously studied focusing schemes, including being significantly shorter for a given energy and having a significantly better energy bandwidth. Experimental results from the ATF2 accelerator at KEK are presented that validate the operating principle of such a scheme by demonstrating the demagnification of a 1.3 GeV electron beam down to below 65 nm in height using an energy-scaled version of the compact focusing optics designed for the ILC collider.

ROCK1 & 2 perform overlapping and unique roles in angiogenesis and angiosarcoma tumor progression

The serine/threonine protein kinase paralogs ROCK1 & 2 have been implicated as essential modulators of angiogenesis; however their paralog-specific roles in endothelial function are unknown. shRNA knockdown of ROCK1 or 2 in endothelial cells resulted in a significant disruption of in vitro capillary network formation, cell polarization, and cell migration compared to cells harboring non-targeting control shRNA plasmids. Knockdowns led to alterations in cytoskeletal dynamics due to ROCK1 & 2-mediated reductions in actin isoform expression, and ROCK2-specific reduction in myosin phosphatase and cofilin phosphorylation. Knockdowns enhanced cell survival and led to ROCK1 & 2-mediated reduction in caspase 6 and 9 cleavage, and a ROCK2-specific reduction in caspase 3 cleavage. Microarray analysis of ROCK knockdown lines revealed overlapping and unique control of global transcription by the paralogs, and a reduction in the transcriptional regulation of just under 50% of VEGF responsive genes. Finally, paralog knockdown in xenograft angiosarcoma tumors resulted in a significant reduction in tumor formation. Our data reveals that ROCK1 & 2 exhibit overlapping and unique roles in normal and dysfunctional endothelial cells, that alterations in cytoskeletal dynamics are capable of overriding mitogen activated transcription, and that therapeutic targeting of ROCK signaling may have profound impacts for targeting angiogenesis.

GPR55, a G-protein coupled receptor for lysophosphatidylinositol, plays a role in motor coordination

The G-protein coupled receptor 55 (GPR55) is activated by lysophosphatidylinositols and some cannabinoids. Recent studies found prominent roles for GPR55 in neuropathic/inflammatory pain, cancer and bone physiology. However, little is known about the role of GPR55 in CNS development and function. To address this question, we performed a detailed characterization of GPR55 knockout mice using molecular, anatomical, electrophysiological, and behavioral assays. Quantitative PCR studies found that GPR55 mRNA was expressed (in order of decreasing abundance) in the striatum, hippocampus, forebrain, cortex, and cerebellum. GPR55 deficiency did not affect the concentrations of endocannabinoids and related lipids or mRNA levels for several components of the endocannabinoid system in the hippocampus. Normal synaptic transmission and short-term as well as long-term synaptic plasticity were found in GPR55 knockout CA1 pyramidal neurons. Deleting GPR55 function did not affect behavioral assays assessing muscle strength, gross motor skills, sensory-motor integration, motor learning, anxiety or depressive behaviors. In addition, GPR55 null mutant mice exhibited normal contextual and auditory-cue conditioned fear learning and memory in a Pavlovian conditioned fear test. In contrast, when presented with tasks requiring more challenging motor responses, GPR55 knockout mice showed impaired movement coordination. Taken together, these results suggest that GPR55 plays a role in motor coordination, but does not strongly regulate CNS development, gross motor movement or several types of learned behavior.

Daily bathing with octenidine on an intensive care unit is associated with a lower carriage rate of meticillin-resistant Staphylococcus aureus

Routine daily bathing of intensive care (ICU) patients with topical chlorhexidine reduces meticillin-resistant Staphylococcus aureus (MRSA) acquisition. The aim of this study was to investigate whether repeated five-day cycles of daily topical octenidine could result in a similar effect. This was a two-year retrospective, uncontrolled study in a mixed medical and surgical ICU/high dependency unit, demonstrating a 76% reduction in MRSA acquisition but no significant reduction in all ICU-acquired bacteraemias. Chlorhexidine use is increasing but resistance is being reported. This pilot study found a similar reduction in MRSA acquisition with octenidine as an alternative to chlorhexidine. Further study is required to establish causality.

Enriched rearing improves behavioral responses of an animal model for CNV-based autistic-like traits

Potocki-Lupski syndrome (PTLS; MIM #610883), characterized by neurobehavioral abnormalities, intellectual disability and congenital anomalies, is caused by a 3.7-Mb duplication in 17p11.2. Neurobehavioral studies determined that ∼70-90% of PTLS subjects tested positive for autism or autism spectrum disorder (ASD). We previously chromosomally engineered a mouse model for PTLS (Dp(11)17/+) with a duplication of a 2-Mb genomic interval syntenic to the PTLS region and identified consistent behavioral abnormalities in this mouse model. We now report extensive phenotyping with behavioral assays established to evaluate core and associated autistic-like traits, including tests for social abnormalities, ultrasonic vocalizations, perseverative and stereotypic behaviors, anxiety, learning and memory deficits and motor defects. Alterations were identified in both core and associated ASD-like traits. Rearing this animal model in an enriched environment mitigated some, and even rescued selected, neurobehavioral abnormalities, suggesting a role for gene-environment interactions in the determination of copy number variation-mediated autism severity.

Randomized controlled trial of atorvastatin in clinically isolated syndrome: the STAyCIS study

OBJECTIVE

To test efficacy and safety of atorvastatin in subjects with clinically isolated syndrome (CIS).

METHODS

Subjects with CIS were enrolled in a phase II, double-blind, placebo-controlled, 14-center randomized trial testing 80 mg atorvastatin on clinical and brain MRI activity. Brain MRIs were performed quarterly. The primary endpoint (PEP) was development of ≥ 3 new T2 lesions, or one clinical relapse within 12 months. Subjects meeting the PEP were offered additional weekly interferon β-1a (IFNβ-1a).

RESULTS

Due to slow recruitment, enrollment was discontinued after 81 of 152 planned subjects with CIS were randomized and initiated study drug. Median (interquartile range) numbers of T2 and gadolinium-enhancing (Gd) lesions were 15.0 (22.0) and 0.0 (0.0) at baseline. A total of 53.1% of atorvastatin recipients (n = 26/49) met PEP compared to 56.3% of placebo recipients (n = 18/32) (p = 0.82). Eleven atorvastatin subjects (22.4%) and 7 placebo subjects (21.9%) met the PEP by clinical criteria. Proportion of subjects who did not develop new T2 lesions up to month 12 or to starting IFNβ-1a was 55.3% in the atorvastatin and 27.6% in the placebo group (p = 0.03). Likelihood of remaining free of new T2 lesions was significantly greater in the atorvastatin group compared with placebo (odds ratio [OR] = 4.34, p = 0.01). Likelihood of remaining free of Gd lesions tended to be higher in the atorvastatin group (OR = 2.72, p = 0.11). Overall, atorvastatin was well tolerated. No clear antagonistic effect of atorvastatin plus IFNβ-1a was observed on MRI measures.

CONCLUSION

Atorvastatin treatment significantly decreased development of new brain MRI T2 lesion activity, although it did not achieve the composite clinical and imaging PEP.

CLASSIFICATION OF EVIDENCE

This study provided Class II evidence that atorvastatin did not reduce the proportion of patients with CIS meeting imaging and clinical criteria for starting immunomodulating therapy after 12 months, compared to placebo. In an analysis of a secondary endpoint (Class III), atorvastatin was associated with a reduced risk for developing new T2 lesions.

Current thyroglobulin autoantibody (TgAb) assays often fail to detect interfering TgAb that can result in the reporting of falsely low/undetectable serum Tg IMA values for patients with differentiated thyroid cancer

CONTEXT

Specimens have thyroglobulin antibody (TgAb) measured prior to thyroglobulin (Tg) testing because the qualitative TgAb status (positive or negative) determines risk for Tg assay interference, and the quantitative TgAb concentration serves as a surrogate tumor marker for differentiated thyroid cancer.

OBJECTIVE

This study assessed the reliability of four TgAb methods to detect interfering TgAb [as judged from abnormally low Tg immunometric assay (IMA) to Tg RIA ratios] and determine whether between-method conversion factors might prevent a change in method from disrupting TgAb monitoring.

METHODS

Sera from selected and unselected TgAb-negative and TgAb-positive differentiated thyroid cancer patients had serum Tg measured by both IMA and RIA and TgAb measured by a reference method and three additional methods.

RESULTS

The Tg IMA and Tg RIA values were concordant when TgAb was absent. Tg IMA to Tg RIA ratios below 75% were considered to indicate TgAb interference. Manufacturer-recommended cutoffs were set in the detectable range, and when used to determine the presence of TgAb misclassified many specimens displaying Tg interference as TgAb negative. False-negative misclassifications were virtually eliminated for two of four methods by using the analytical sensitivity (AS) as the detection limit for TgAb. Relationships between values for different specimens were too variable to establish between-method conversion factors.

CONCLUSIONS

Many specimens with interfering TgAb were misclassified as TgAb negative using manufacturer-recommended cutoffs. It is recommended that assay AS limits be used to detect TgAb to minimize false-negative misclassifications. However, for two of four assays, AS limits failed to detect interfering TgAb in 20-30% of cases. TgAb methods were too qualitatively and quantitatively variable to establish conversion factors that would allow a change in method without disrupting serial TgAb monitoring.

Altered ultrasonic vocalization and impaired learning and memory in Angelman syndrome mouse model with a large maternal deletion from Ube3a to Gabrb3

Angelman syndrome (AS) is a neurobehavioral disorder associated with mental retardation, absence of language development, characteristic electroencephalography (EEG) abnormalities and epilepsy, happy disposition, movement or balance disorders, and autistic behaviors. The molecular defects underlying AS are heterogeneous, including large maternal deletions of chromosome 15q11–q13 (70%), paternal uniparental disomy (UPD) of chromosome 15 (5%), imprinting mutations (rare), and mutations in the E6-AP ubiquitin ligase gene UBE3A (15%). Although patients with UBE3A mutations have a wide spectrum of neurological phenotypes, their features are usually milder than AS patients with deletions of 15q11–q13. Using a chromosomal engineering strategy, we generated mutant mice with a 1.6-Mb chromosomal deletion from Ube3a to Gabrb3, which inactivated the Ube3a and Gabrb3 genes and deleted the Atp10a gene. Homozygous deletion mutant mice died in the perinatal period due to a cleft palate resulting from the null mutation in Gabrb3 gene. Mice with a maternal deletion (m−/p+) were viable and did not have any obvious developmental defects. Expression analysis of the maternal and paternal deletion mice confirmed that the Ube3a gene is maternally expressed in brain, and showed that the Atp10a and Gabrb3 genes are biallelically expressed in all brain sub-regions studied. Maternal (m−/p+), but not paternal (m+/p−), deletion mice had increased spontaneous seizure activity and abnormal EEG. Extensive behavioral analyses revealed significant impairment in motor function, learning and memory tasks, and anxiety-related measures assayed in the light-dark box in maternal deletion but not paternal deletion mice. Ultrasonic vocalization (USV) recording in newborns revealed that maternal deletion pups emitted significantly more USVs than wild-type littermates. The increased USV in maternal deletion mice suggests abnormal signaling behavior between mothers and pups that may reflect abnormal communication behaviors in human AS patients. Thus, mutant mice with a maternal deletion from Ube3a to Gabrb3 provide an AS mouse model that is molecularly more similar to the contiguous gene deletion form of AS in humans than mice with Ube3a mutation alone. These mice will be valuable for future comparative studies to mice with maternal deficiency of Ube3a alone.