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.

Stereo-EEG tailored resection in a child with presumed perinatal post-stroke epilepsy: The complex organization of epileptogenic zone.

Introduction: Only a few studies have focused on tailored resection in post-stroke epilepsy, in which hemispherectomy and hemispherotomy are the most recognized treatments. Case description: We describe the case of a patient with drug-resistant, presumed perinatal, post-stroke epilepsy and moderate right hemiparesis. The seizures were stereotyped, both spontaneous and induced by sudden noises and somatosensory stimuli. Considering the discordant anatomic-electro-clinical data - left perisylvian malacic lesion with electrical onset over the left mesial fronto-central leads - and the patient's functional preservation, SEEG was performed. SEEG revealed sub-continuous abnormalities in the perilesional regions. Several seizures were recorded, with onset over the premotor area, rapidly involving the motor and insular-opercular regions. We decided for a combined surgical approach, SEEG-guided radiofrequency thermocoagulation, on the fronto-mesial structure but also on the central operculum, followed by resective surgery including only the fronto-mesial structures. Discussion and conclusion: The SEEG allowed to localize the epileptogenic zone far away from the anatomical lesion but connected to part of it. A combined surgical approach tailored on SEEG results allowed a good outcome (Engel Ib) without additional deficits.

PEOPLE (NCT03447678), a first-line phase II pembrolizumab trial, in negative and low PD-L1 advanced NSCLC: clinical outcomes and association with circulating immune biomarkers.

BACKGROUND: The PEOPLE trial aimed to identify new immune biomarkers in negative and low programmed death-ligand 1 (PD-L1) (0%-49%) advanced non-small-cell lung cancer (aNSCLC) patients treated with first-line pembrolizumab. Here we report the main outcomes and the circulating immune biomarkers analysis. PATIENTS AND METHODS: The primary endpoint of this phase II trial was the identification of immune biomarkers associated with progression-free survival (PFS). Overall survival (OS), objective response rate (ORR), disease control rate (DCR), duration of response (DoR) and safety were secondary endpoints. Absolute cell counts for 36 subsets belonging to innate and adaptive immunity were determined by multiparametric flow cytometry in peripheral blood at baseline and at first radiologic evaluation. An orthoblique principal components-based clustering approach and multivariable Cox regression model adjusted for clinical variables were used to analyze immune variables and their correlation with clinical endpoints. RESULTS: From May 2018 to October 2020, 65 patients were enrolled. After a median follow-up of 26.4 months, the median PFS was 2.9 months [95% confidence interval (CI) 1.8-5.6 months] and median OS was 12.1 months (95% CI 8.7-17.1 months). The ORR was 21.5%, DCR was 47.7% and median DoR was 14.5 months (95% CI 6.4-24.9 months). Drug-related grade 3-4 adverse events were 9.2%. Higher T cell and natural killer (NK) cell count at baseline and at the first radiologic evaluation were associated with improved PFS, DCR and OS. On the contrary, higher myeloid cell count at baseline or at the first radiologic evaluation was significantly associated with worse OS and DCR. CONCLUSIONS: Circulating immune biomarkers can contribute to predict outcomes in negative and low PD-L1 aNSCLC patients treated with first-line single-agent pembrolizumab.

The lung immuno-oncology prognostic score (LIPS-3): a prognostic classification of patients receiving first-line pembrolizumab for PD-L1 ≥ 50% advanced non-small-cell lung cancer.

BACKGROUND: To stratify the prognosis of patients with programmed cell death-ligand 1 (PD-L1) ≥ 50% advanced non-small-cell lung cancer (aNSCLC) treated with first-line immunotherapy. METHODS: Baseline clinical prognostic factors, the neutrophil-to-lymphocyte ratio (NLR), PD-L1 tumour cell expression level, lactate dehydrogenase (LDH) and their combination were investigated by a retrospective analysis of 784 patients divided between statistically powered training (n = 201) and validation (n = 583) cohorts. Cut-offs were explored by receiver operating characteristic (ROC) curves and a risk model built with validated independent factors by multivariate analysis. RESULTS: NLR < 4 was a significant prognostic factor in both cohorts (P < 0.001). It represented 53% of patients in the validation cohort, with 1-year overall survival (OS) of 76.6% versus 44.8% with NLR > 4, in the validation series. The addition of PD-L1 ≥ 80% (21% of patients) or LDH < 252 U/l (25%) to NLR < 4 did not result in better 1-year OS (of 72.6% and 74.1%, respectively, in the validation cohort). Eastern Cooperative Oncology Group (ECOG) performance status (PS) of 2 [P < 0.001, hazard ratio (HR) 2.04], pretreatment steroids (P < 0.001, HR 1.67) and NLR < 4 (P < 0.001, HR 2.29) resulted in independent prognostic factors. A risk model with these three factors, namely, the lung immuno-oncology prognostic score (LIPS)-3, accurately stratified three OS risk-validated categories of patients: favourable (0 risk factors, 40%, 1-year OS of 78.2% in the whole series), intermediate (1 or 2 risk factors, 54%, 1-year OS 53.8%) and poor (>2 risk factors, 5%, 1-year OS 10.7%) prognosis. CONCLUSIONS: We advocate the use of LIPS-3 as an easy-to-assess and inexpensive adjuvant prognostic tool for patients with PD-L1 ≥ 50% aNSCLC.

Focal lesions induce large-scale percolation of sleep-like intracerebral activity in awake humans.

Focal cortical lesions are known to result in large-scale functional alterations involving distant areas; however, little is known about the electrophysiological mechanisms underlying these network effects. Here, we addressed this issue by analysing the short and long distance intracranial effects of controlled structural lesions in humans. The changes in Stereo-Electroencephalographic (SEEG) activity after Radiofrequency-Thermocoagulation (RFTC) recorded in 21 epileptic subjects were assessed with respect to baseline resting wakefulness and sleep activity. In addition, Cortico-Cortical Evoked Potentials (CCEPs) recorded before the lesion were employed to interpret these changes with respect to individual long-range connectivity patterns. We found that small structural ablations lead to the generation and large-scale propagation of sleep-like slow waves within the awake brain. These slow waves match those recorded in the same subjects during sleep, are prevalent in perilesional areas, but can percolate up to distances of 60 mm through specific long-range connections, as predicted by CCEPs. Given the known impact of slow waves on information processing and cortical plasticity, demonstrating their intrusion and percolation within the awake brain add key elements to our understanding of network dysfunction after cortical injuries.

Single-arm, open label prospective trial to assess prediction of the role of ERCC1/XPF complex in the response of advanced NSCLC patients to platinum-based chemotherapy.

BACKGROUND: Platinum-based therapy, combined or not with immune checkpoint inhibitors, represents a front-line choice for patients with non-small-cell lung cancer (NSCLC). Despite the improved outcomes in the last years for this malignancy, only a sub-group of patients have long-term benefit. Excision repair cross-complementation group 1 (ERCC1) has been considered a potential biomarker to predict the outcome of platinum-based chemotherapy in NSCLC. However, the ERCC1 gene is transcribed in four splice variants where the isoform 202 was described as the only one active and able to complex Xeroderma pigmentosum group F-complementing protein (XPF). Here, we prospectively investigated if the active form of ERCC1, as assessed by the ERCC1/XPF complex (ERCC1/XPF), could predict the sensitivity to platinum compounds. PATIENTS AND METHODS: Prospectively enrolled, patients with advanced NSCLC treated with a first-line regimen containing platinum were centrally evaluated for ERCC1/XPF by a proximity ligation assay. Overall survival (OS), progression-free survival (PFS) and objective response rate (ORR) were analyzed. RESULTS: The absence of the ERCC1/XPF in the tumor suggested a trend of worst outcomes in terms of both OS [hazard ratio (HR) 1.41, 95% confidence interval (CI) 0.67-2.94, P = 0.373] and PFS (HR 1.61, 95% CI 0.88-3.03, P = 0.123). ORR was marginally influenced in ERCC1/XPF-negative and -positive groups [odds ratio (stable disease + progressive disease versus complete response + partial response) 0.87, 95% CI 0.25-3.07, P = 0.832]. CONCLUSION: The lack of ERCC1/XPF complex in NSCLC tumor cells might delineate a group of patients with poor outcomes when treated with platinum compounds. ERCC1/XPF absence might well identify patients for whom a different therapeutic approach could be necessary.

Choosing wisely first line immunotherapy in non-small cell lung cancer (NSCLC): what to add and what to leave out.

Immunotherapy has dramatically changed the therapeutic scenario in treatment naïve advanced non-small cell lung cancer (NSCLC). While single agent pembrolizumab has become the standard therapy in patients with PD-L1 expression on tumor cells ≥ 50%, the combination of pembrolizumab or atezolizumab and platinum-based chemotherapy has emerged as an effective first line treatment regardless of PD-L1 expression both in squamous and non-squamous NSCLC without oncogenic drivers. Furthermore, double immune checkpoint inhibition has shown promising results in treatment naïve patients with high tumor mutational burden (TMB). Of note, the presence of both negative PD-L1 expression and low TMB may identify a subgroup of patients who has little benefit from immunotherapy combinations and for whom the best treatment option may still be platinum-based chemotherapy. To date, first-line single agent immune checkpoint blockade has demonstrated limited activity in EGFR mutated NSCLC and the combination of immunotherapy and targeted agents has raised safety concerns in both EGFR and ALK positive NSCLC patients. Finally, in EGFR mutated or ALK rearranged NSCLC, atezolizumab in combination with platinum-based chemotherapy and bevacizumab is emerging as a potential treatment option upon progression to first line tyrosine kinase inhibitors.

Multiple time courses of somatosensory responses in human cortex.

Here we show how anatomical and functional data recorded from patients undergoing stereo-EEG can be used to decompose the cortical processing following nerve stimulation in different stages characterized by specific topography and time course. Tibial, median and trigeminal nerves were stimulated in 96 patients, and the increase in gamma power was evaluated over 11878 cortical sites. All three nerve datasets exhibited similar clusters of time courses: phasic, delayed/prolonged and tonic, which differed in topography, temporal organization and degree of spatial overlap. Strong phasic responses of the three nerves followed the classical somatotopic organization of SI, with no overlap in either time or space. Delayed responses presented overlaps between pairs of body parts in both time and space, and were confined to the dorsal motor cortices. Finally, tonic responses occurred in the perisylvian region including posterior insular cortex and were evoked by the stimulation of all three nerves, lacking any spatial and temporal specificity. These data indicate that the somatosensory processing following nerve stimulation is a multi-stage hierarchical process common to all three nerves, with the different stages likely subserving different functions. While phasic responses represent the neural basis of tactile perception, multi-nerve tonic responses may represent the neural signature of processes sustaining the capacity to become aware of tactile stimuli.

Comparative study of oncoplastic versus non-oncoplastic breast conserving surgery in a group of 211 breast cancer patients.

OBJECTIVE: Breast conserving surgery (BCS) followed by radiotherapy is the standard of care for most patients with early breast cancers; however, the aesthetic outcomes of this procedure is not always desirable. Oncoplastic breast surgery is an innovative approach that aims at the safe and effective treatment of the cancerous lesion while achieving the best possible aesthetic outcome. The aim of this study was to evaluate and compare oncoplastic and non-oncoplastic procedures. PATIENTS AND METHODS: A retrospective observational study was conducted on a group of patients who underwent oncoplastic or non-oncoplastic breast surgery at the Breast Unit of the University of Rome Tor Vergata. RESULTS: Out of 211 patients, 154 (73%) underwent non-oncoplastic surgery, while 61 (27%) underwent an oncoplastic procedure. The percentage of patients requiring re-excision was twice greater for women in the non-oncoplastic group: 12.9% vs. 6.5% in the oncoplastic group. The rate of complications was higher in the oncoplastic group compared to the non-oncoplastic one (4.9% vs. 1.3%). The size of the tumor, the number of the patients receiving post-operative radiation, the interval between surgery and radiotherapy and follow-up were similar between the two groups. CONCLUSIONS: Oncoplastic surgery represents a valid alternative to breast conserving surgery for patients with breast cancer, with only minimal differences in long-term complications and similar results in terms of local recurrence and number of metastasis.

A method for the assessment of time-varying brain shift during navigated epilepsy surgery.

PURPOSE: Image guidance is widely used in neurosurgery. Tracking systems (neuronavigators) allow registering the preoperative image space to the surgical space. The localization accuracy is influenced by technical and clinical factors, such as brain shift. This paper aims at providing quantitative measure of the time-varying brain shift during open epilepsy surgery, and at measuring the pattern of brain deformation with respect to three potentially meaningful parameters: craniotomy area, craniotomy orientation and gravity vector direction in the images reference frame. METHODS: We integrated an image-guided surgery system with 3D Slicer, an open-source package freely available in the Internet. We identified the preoperative position of several cortical features in the image space of 12 patients, inspecting both the multiplanar and the 3D reconstructions. We subsequently repeatedly tracked their position in the surgical space. Therefore, we measured the cortical shift, following its time-related changes and estimating its correlation with gravity and craniotomy normal directions. RESULTS: The mean of the median brain shift amount is 9.64 mm ([Formula: see text] mm). The brain shift amount resulted not correlated with respect to the gravity direction, the craniotomy normal, the angle between the gravity and the craniotomy normal and the craniotomy area. CONCLUSIONS: Our method, which relies on cortex surface 3D measurements, gave results, which are consistent with literature. Our measurements are useful for the neurosurgeon, since they provide a continuous monitoring of the intra-operative sinking or bulking of the brain, giving an estimate of the preoperative images validity versus time.

Fertility drugs and breast cancer risk.

PURPOSE OF INVESTIGATION: Female infertility is a widespread problem in Western countries. During past years, an association between ovarian stimulation in unfertile women and breast cancer risk has been hypothesized. OBJECTIVE: Purpose of the present investigation was to comment the most updated studies about an eventual relationship between fertility drugs and breast cancer risk. MATERIALS AND METHODS: The authors performed a review of the current literature regarding the possible association between the use of fertility drugs and the enhanced risk of breast cancer. They searched digital databases including Pubmed, EMBASE, and the Cochrane Library. The literature search was performed using various combinations of keywords. They carefully analyzed only the full versions of all relevant studies. RESULTS: Using various combination of keywords, the authors examined 930 papers. They considered only papers written in English. With these criteria they selected the studies that had been discussed in detail on the text. CONCLUSION: None of the works commented provides an indisputable evidence about a link between ovarian stimulation and breast cancer risk. On the contrary, most of them actually suggest a lack of interaction between them or even a protective role of ovarian stimulation.

Surgical treatment of cavernoma-related epilepsy.

Cerebral cavernous malformations (CCMs) are frequently associated with a seizure disorder, and the risk of developing drug-resistant epilepsy (DRE) is substantial, especially for temporal lobe lesions. This article includes a review of the literature on the surgical treatment of epilepsy associated to CCMs in the magnetic resonance imaging (MRI) era, as well as an analysis of the Authors' experience in this field. It is concluded that microsurgery is a valuable treatment option, which may provide excellent results on seizures, with 76% of patients on average being seizure-free after surgery. Nevertheless, the optimal surgical strategy to achieve seizure control has not been clearly identified, and several attitudes have been reported in the literature. The choice of lesionectomy, associated or not to removal of surrounding hemosiderin, versus resections extended to epileptogenic cortex depends on the accurate scrutiny of several factors, which should be investigated through an adequate epileptological presurgical workup. This should include an epilepsy-oriented brain MRI study, integrated by an appropriate neurophysiological and clinical assessment, and if needed by other functional evaluations. Besides representing the optimal option in CCM-related DRE cases, microsurgery should be considered also at seizure presentation or in cases with recent-onset sporadic seizures, to protect the patient from both the possible development of drug resistance and the risk of haemorrhage.

Penile length is a very important factor for cosmesis, function and psychosexual development in patients affected by hypospadias: Results from a long-term longitudinal cohort study.

Few studies of long-term outcome of hypospadias treatment in terms of voiding, surgical complications, sexual functioning, intimate relationships and cosmetic results have been investigated and contrasting results have been obtained so far. The aim of our study is to investigate the long-term outcome of urinary and sexual function, cosmesis and the quality of intimate relationships in a series of hypospadias. In this study, 42 patients who underwent surgery for hypospadias were prospectively followed for 15 years. Medical records provided the hypospadias data, the number of reconstructive operations and the reconstruction technique that was used. Patients underwent physical examination, including penile length measurement and completed International Prostatic Symptoms Score (I-PSS), International Index Of Erectile Function (IIEF 15) and the Penile Perception Score questionnaire (PPPS). Twenty patients agreed to participate in the study. At the enrolment, the median value of HOSE was 13, as regards PPPS, 18/20 (90%) were satisfied, while in 1998 only 80% were satisfied. No significant statistical difference has been reported from the results obtained at enrolment and those obtained at follow-up, in terms of PPPS (P = 0.81), IPSS and IIEF-15. Penile length was 6.5 cm flaccid and 10.5 cm stretched. Our data show how cosmesis, function and psychosexual development for these patients are highly connected to surgical outcome, which is understood to be a decrease in penile size.

Multi-trajectories automatic planner for StereoElectroEncephaloGraphy (SEEG).

PURPOSE: StereoElectroEncephaloGraphy (SEEG) is done to identify the epileptogenic zone of the brain using several multi-lead electrodes whose positions in the brain are pre-operatively defined. Intracranial hemorrhages due to disruption of blood vessels can cause major complications of this procedure ([Formula: see text]1%). In order to increase the intervention safety, we developed and tested planning tools to assist neurosurgeons in choosing the best trajectory configuration. METHODS: An automated planning method was developed that maximizes the distance of the electrode from the vessels and avoids the sulci as entry points. The angle of the guiding screws is optimized to reduce positioning error. The planner was quantitatively and qualitatively compared with manually computed trajectories on 26 electrodes planned for three patients undergoing SEEG by four neurosurgeons. Quantitative comparison was performed computing for each trajectory using (a) the Euclidean distance from the closest vessel and (b) the incidence angle. RESULTS: Quantitative evaluation shows that automatic planned trajectories are safer in terms of distance from the closest vessel with respect to manually planned trajectories. Qualitative evaluation performed by four neurosurgeons showed that the automatically computed trajectories would have been preferred to manually computed ones in 30% of the cases and were judged good or acceptable in about 86% of the cases. A significant reduction in time required for planning was observed with the automated system (approximately 1/10). CONCLUSION: The automatic SEEG electrode planner satisfied the essential clinical requirements, by providing safe trajectories in an efficient timeframe.

Hippocampal sleep spindles preceding neocortical sleep onset in humans.

The coexistence of regionally dissociated brain activity patterns -with some brain areas being active while other already showing sleep signs- may occur throughout all vigilance states including the transition from wakefulness to sleep and may account for both physiological as well as pathological events. These dissociated electrophysiological states are often characterized by multi-domain cognitive and behavioral impairment such as amnesia for events immediately preceding sleep. By performing simultaneous intracerebral electroencephalographic recordings from hippocampal as well as from distributed neocortical sites in neurosurgical patients, we observed that sleep spindles consistently occurred in the hippocampus several minutes before sleep onset. In addition, hippocampal spindle detections consistently preceded neocortical events, with increasing delays along the cortical antero-posterior axis. Our results support the notion that wakefulness and sleep are not mutually exclusive states, but rather part of a continuum resulting from the complex interaction between diffuse neuromodulatory systems and intrinsic properties of the different thalamocortical modules. This interaction may account for the occurrence of dissociated activity across different brain structures characterizing both physiological and pathological conditions.

Circulating tumor cells in metastatic colorectal cancer: do we need an alternative cutoff?

PURPOSE: To assess the prognostic and predictive value of circulating tumor cells (CTCs) in metastatic colorectal cancer (mCRC) irrespective of detection level. MATERIALS AND METHODS: We evaluated the prognostic and predictive significance of CTC count at baseline and under treatment in 119 mCRC subjects and compared the standard cutoff (≥3 CTCs/7.5 mL to ≥1 CTCs/7.5 mL). RESULTS: An overall comparison was made between patients with 0, 1-2 and ≥3 CTC (median PFS 8, 4 and 5 months, respectively). Two poor prognostic groups were found, including patients with ≥1 CTCs before and during treatment and patients with 0 CTC at baseline who converted to ≥1 CTCs (p = 0.014). CONCLUSIONS: The presence of at least 1 CTC at baseline count is predictive for poor prognosis in mCRC patients. Patients with 1-2 CTC should be switched from the favorable prognostic group--conventionally defined by the presence of <3 CTC--to the unfavorable, deserving a more careful monitoring.

Epileptic motor behaviors during sleep: anatomo-electro-clinical features.

BACKGROUND: Sleep-related complex motor seizures have long been considered pathognomonic features of Nocturnal Frontal Lobe Epilepsy (NFLE). In recent years, these manifestations have also been reported to have a temporal or insular origin. METHOD: We describe 40 drug-resistant epileptic patients with complex motor seizures during sleep, submitted to presurgical stereo-EEG (SEEG) evaluation and seizure-free after surgical resection of the epileptogenic zone. RESULTS: In a significant proportion (30%) of these patients, seizures arose from extra-frontal regions, including mainly the temporal lobe and the insular cortex, but also the parietal and occipital lobes. In patients with extra-frontal epilepsy, when complex motor behaviors appeared, SEEG revealed that the ictal discharge involved the cingulate and the frontal regions. Finally, at histology, Taylor's focal cortical dysplasia (TFCD) was the most common finding (90% of patients), independent of the site of seizure onset. CONCLUSION: As previously reported by other studies, this histologic substrate may be a major determinant of sleep-related seizures in drug-resistant epileptic patients.

Cysts of the canal of Nuck: ultrasound and magnetic resonance imaging findings.

Cyst of the canal of Nuck is a rare cause of inguinal swelling in woman. We report a case of a cyst of the canal of Nuck in which sonography showed a tubular cystic structure with internal septae localized within the inguinal canal. Magnetic resonance examination demonstrated that the mass was hypointense on T1-weighted and hyperintense on T2-weighted series and that there were fine hypointense septae inside the mass on the T2-weighted sequence. Diagnosis of cyst of the canal of Nuck was confirmed by surgery and subsequent histopathologic evaluation.