Biology subjects

Ferreira, C. S.

Publications and source records attributed to Ferreira, C. S..

7 recordsLinked to original sources

bioRxiv2024

Identification of Cellular Signatures Associated with Chinese Hamster Ovary (CHO) Cell Adaptation for Secretion of Antibodies

The secretory capacity of Chinese hamster ovary (CHO) cells remains a fundamental bottleneck in the manufacturing of protein-based therapeutics. Unconventional biological drugs with complex structures and processing requirements are particularly problematic. Although engineered vector DNA elements can achieve rapid and high-level therapeutic protein production, a high metabolic and protein folding burden is imposed on the host cell. Cellular adaptations to these conditions include differential gene expression profiles that can in turn influence the productivity and quality control of recombinant proteins. In this study, we used quantitative transcriptomics and proteomics analyses to investigate how biological pathways change with antibody titre. Gene and protein expression profiles of CHO pools and clones producing a panel of different monoclonal and bispecific antibodies were analysed during fed-batch production. Antibody-expressing CHO pools were heterogeneous, resulting in few discernible genetic signatures. Clonal lines derived from these pools, selected for high and low production, yielded a small number of differentially expressed proteins that correlated with productivity and were shared across biotherapeutics. However, the dominant feature associated with higher protein production was transgene copy number and resulting mRNA expression level. Moreover, variability between clones suggested that the process of cellular adaptation is variable with diverse cellular changes associated with individual adaptation events.

bioengineering↗

bioRxiv2023

Tumor-agnostic transcriptome-based classifier identifies spatial infiltration patterns of CD8+ T cells in the tumor microenvironment and predicts clinical outcome in early- and late-phase clinical trials

BackgroundThe immune status of a patients tumor microenvironment (TME) may guide therapeutic interventions with cancer immunotherapy and help identify potential resistance mechanisms. Currently, patients immune status is mostly classified based on CD8+ tumor-infiltrating lymphocytes. An unmet need exists for comparable and reliable precision immunophenotyping tools that would facilitate clinical treatment-relevant decision-making and the understanding of how to overcome resistance mechanisms. MethodsWe systematically analyzed the CD8 immunophenotype of 2023 patients from 14 phase I-III clinical trials using immunohistochemistry (IHC) and additionally profiled gene expression by RNA-sequencing (RNA-seq). CD8 immunophenotypes were classified by pathologists into CD8-desert, CD8-excluded or CD8-inflamed tumors using CD8 IHC staining in epithelial and stromal areas of the tumor. Using regularized logistic regression, we developed an RNA-seq-based classifier as a surrogate to the IHC-based spatial classification of CD8+ tumor-infiltrating lymphocytes in the TME. ResultsThe CD8 immunophenotype and associated gene expression patterns varied across indications as well as across primary and metastatic lesions. Melanoma and kidney cancers were among the strongest inflamed indications, while CD8-desert phenotypes were most abundant in liver metastases across all tumor types. A good correspondence between the transcriptome and the IHC-based evaluation enabled us to develop a 92-gene classifier that accurately predicted the IHC-based CD8 immunophenotype in primary and metastatic samples (area under the curve (AUC) inflamed = 0.846; excluded = 0.712; desert = 0.855). The newly developed classifier was prognostic in The Cancer Genome Atlas (TCGA) data and predictive in lung cancer: patients with predicted CD8-inflamed tumors showed prolonged overall survival (OS) versus patients with CD8-desert tumors (hazard ratio [HR] 0.88; 95% confidence interval [CI]: 0.80-0.97) across TCGA, and longer OS upon immune checkpoint inhibitor administration (phase III OAK study) in non-small-cell lung cancer (HR 0.75; 95% CI: 0.58-0.97). ConclusionsWe provide a new precision immunophenotyping tool based on gene expression that reflects the spatial infiltration patterns of CD8+ lymphocytes in tumors. The classifier enables multiplex analyses and is easy to apply for retrospective, reverse translation approaches as well as for prospective patient enrichment to optimize the response to cancer immunotherapy. HIGHLIGHTSO_ST_ABSWhat is already known on this topicC_ST_ABST-cell infiltration, most commonly classified based on CD8+ T cell immunohistochemistry (IHC) staining, and various tumor microenvironment (TME)-specific resistance mechanisms, can impact response rates to cancer immunotherapy. What this study addsOur data provide new insights into the impact of tumor excision location and indication on the immune composition of the TME. We developed a transcriptome-based classifier that could accurately predict different spatial CD8+ T-cell infiltration patterns in the TME. We demonstrate the prognostic and predictive value of the classifier across independent patient cohorts (phase I to phase III trials). How this study might affect research, practice or policyOur new RNA-based tool provides a surrogate read-out for spatial IHC-based CD8 infiltration patterns, is easy to use and broadly applicable for both retrospective and prospective patient enrichment to enhance the effectiveness of cancer immunotherapy.

cancer biology↗

bioRxiv2022

Reconstructing Spatio-Temporal Trajectories of Visual Object Memories in the Human Brain

Our understanding of how information unfolds when we recall events from memory remains limited. In this study, we investigate whether the reconstruction of visual object memories follows a backward trajectory along the ventral visual stream with respect to perception, such that their neural feature representations are gradually reinstated from late areas close to the hippocampus backwards to lower-level sensory areas. We use multivariate analyses of fMRI activation patterns to map high-and low-level features of the object memories onto the brain during retrieval, and EEG-fMRI fusion to track the temporal evolution of the reactivated patterns. Participants studied new associations between verbs and randomly paired object images in an encoding phase, and subsequently recalled the objects when presented with the corresponding verb cue. Decoding reactivated memory features from fMRI activity revealed that retrieval patterns were dominated by conceptual features, represented in comparatively late visual and parietal areas. Representational-similarity-based fusion then allowed us to map the EEG patterns that emerged at each given time point of a trial onto the spatially resolved fMRI patterns. This fusion suggests that memory reconstruction proceeds from anterior fronto-temporal to posterior occipital and parietal regions, partly in line with a semantic-to-perceptual gradient. A linear regression on the peak time points of reactivated brain regions statistically confirms that the temporal progression is reversed with respect to encoding in ventral stream areas. Together, the results shed light onto the spatio-temporal trajectories along which memories and their constituent features are reconstructed during associative retrieval. Significance statementIn our work, we combined EEG and fMRI to investigate which features of a visual object are reactivated when recalled from episodic memory, and how the memory reconstruction stream unfolds over time and across the brain. Our findings suggest that with respect to perception, memory retrieval follows a backwards information trajectory along a conceptual-to-perceptual gradient, and additionally relays retrieved information to multimodal fronto-parietal brain regions. These findings address the fundamental question of whether memories are more or less complete and truthful reconstructions of past events, or instead are subject to systematic biases that prioritise some types of features over others. Our data suggests that episodic memory retrieval is a dynamic and highly reconstructive process with clear prioritisation of abstract-conceptual over detailed-perceptual information.

neuroscience↗

bioRxiv2020

Dynamic targeting enables domain-general inhibitory control over action and thought by the prefrontal cortex.

Successful self-control requires the ability to stop unwanted actions or thoughts. Stopping is regarded as a central function of inhibitory control, a mechanism enabling the suppression of diverse mental content, and strongly associated with the prefrontal cortex. A domain-general inhibitory control capacity, however, would require the region or regions implementing it to dynamically shift top-down inhibitory connectivity to diverse target regions in the brain. Here we show that stopping unwanted thoughts and stopping unwanted actions engage common regions in the right anterior dorsolateral and right ventrolateral prefrontal cortex, and that both areas exhibit this dynamic targeting capacity. Within each region, pattern classifiers trained to distinguish stopping actions from making actions also could identify when people were suppressing their thoughts (and vice versa) and could predict which people successfully forgot thoughts after inhibition. Effective connectivity analysis revealed that both regions contributed to action and thought stopping, by dynamically shifting inhibitory connectivity to motor area M1 or to the hippocampus, depending on the goal, suppressing task-specific activity in those regions. These findings support the existence of a domain-general inhibitory control mechanism that contributes to self-control and establish dynamic inhibitory targeting as a key mechanism enabling these abilities.

neuroscience↗

bioRxiv2019

Autobiographical memory reactivation in empathy

Empathy relies on the ability to mirror and to explicitly infer others inner states. Theoretical accounts suggest that memories play a role in empathy but direct evidence of a reactivation of autobiographical memories (AM) in empathy is yet to be shown. We addressed this question in two experiments. In experiment 1, electrophysiological activity (EEG) was recorded from 28 participants who performed an empathy task in which targets for empathy were depicted in contexts for which participants either did or did not have an AM, followed by a task that explicitly required memory retrieval of the AM and non-AM contexts. The retrieval task was implemented to extract the neural fingerprints of AM and non-AM contexts, which were then used to probe data from the empathy task. An EEG pattern classifier was trained and tested across tasks and showed evidence for AM reactivation when participants were preparing their judgement in the empathy task. Participants self-reported higher empathy for people depicted in situations they had experienced themselves as compared to situations they had not experienced. A second independent fMRI experiment replicated this behavioural finding and showed the predicted activation in the brain networks underlying both AM retrieval and empathy: precuneus, posterior parietal cortex, superior and inferior parietal lobule and superior frontal gyrus. Together, our study reports behavioural, electrophysiological and fMRI evidence that robustly supports the involvement of AM reactivation in empathy.

neuroscience↗

bioRxiv2018

Testing the fast consolidation hypothesis of retrieval-mediated learning

The testing-effect, or retrieval-mediated learning, is one of the most robust effects in memory research. It shows that actively and repeatedly retrieving information, compared to merely restudying it, improves long-term retention. Surprisingly, little is known about the neurocognitive mechanisms underlying this phenomenon. Attempting to fill this gap, a recent framework proposed that retrieval acts as a fast memory consolidation mechanism, stabilizing memories through online reactivation, similar to memory replay during offline (e.g. sleep) consolidation. In this fMRI study, we empirically tested the predictions derived from this framework.\n\nWe predicted that reactivation during retrieval allows memories to become embedded in neocortex, creating an additional route to access the memory trace and rendering it less hippocampus-dependent. Participants encoded scene-object pairs and either retrieved or restudied the objects over two sessions, two days apart. We analysed univariate and multivariate changes in brain activity specific to retrieval but not restudy, and tested whether the predicted changes occur rapidly within a session, or evolve slowly, across the two days.\n\nResults showed that medial prefrontal cortex activation increased across retrieval trials within one session, consistent with a fast consolidation account. Hippocampal activity decreased across sessions, suggesting a slower mechanism. Moreover, Representational Similarity Analyses (RSA) showed that consecutive retrieval attempts strengthen both higher-level semantic and episode-specific information in parietal areas, both across but not within sessions. Our findings suggest that retrieval supports the online creation of a neocortical trace, which becomes increasingly relevant at long delays when hippocampus-dependent episodic details would otherwise have faded.\n\nSignificance statementRepeated remembering strengthens memories much more so than repeated learning. The aim of this study was to shed light onto the poorly understood neurocognitive underpinnings of retrieval-mediated learning. We tested a novel framework proposing that a memorys stabilization via retrieval relies on mechanisms akin to those involved in offline systems consolidation. Observing the retrieval-induced neural pattern changes across different timescales, we find that retrieval stabilizes semantic and episodic aspects of the original memories, and produces increases in prefrontal activity and decreases in hippocampal activity that are consistent with the consolidation view, but not necessarily with a fast acting mechanism. Our findings inform cognitive theories of the testing effect, suggesting that retrieval produces its benefits by interacting with hippocampal-neocortical consolidation mechanisms.

neuroscience↗

bioRxiv2018

Theta oscillations show impaired interference detection in the elderly during selective memory retrieval

Seemingly effortless tasks, such as recognizing faces and retrieving names, become significantly harder as people get older. These age-related difficulties may be partially due to the concurrent activation of related competitors. However, it remains unclear whether older adults struggle with detecting an early interference signal or with suppressing irrelevant competitors once competition is detected. To investigate this question, we used the retrieval practice paradigm, shown to elicit interference, while recording electrophysiological activity in young and older adults. In two experiments, young participants showed the typical Retrieval Induced Forgetting (RIF) effect whereas the elderly did not. Neurally, young adults were more capable to detect interference than the older, as evidenced by an increase in mid-frontal theta power (~4-8Hz). This efficient interference detection allowed young adults to recruit inhibitory mechanisms that overcome competition, as traced by a theta power reduction across retrieval cycles. No such reduction was found for the elderly, indicating that the lack of an early interference detection signal renders older adults unable to recruit memory selection mechanisms, eliminating RIF.\n\nAUTHORS NOTEThis research was supported by the doctoral research grants AP2009-2215 to C.S.F and BES-2013-066842 to M.J.M.; by grants PSI2012-33625; PSI2015-65502-C2-1-P from the Spanish Ministry of Economy and Competiveness, and by the Economic Council of the Andalusian Government P08-HUM-03600-Feder and P12-CTS-2369-Feder to T.B.\n\nDeclaration of interestThe authors have no conflicts of interest to disclose

neuroscience↗