Claude Perreault - Academia.edu (original) (raw)

Papers by Claude Perreault

STEM CELLS Translational Medicine, 2020

7 Introduction Rapid T cell reconstitution following hematopoietic stem cell transplantation is e... more 7 Introduction Rapid T cell reconstitution following hematopoietic stem cell transplantation is essential for protection against infections and has been associated with lower incidence of chronic graftvs-host disease (cGVHD), relapse, and transplant-related mortality (TRM). Although cord blood (CB) transplants are associated with lower rates of cGVHD and relapse, their low stem cell content results in slower immune reconstitution and higher risk of graft failure, severe infections, and TRM. Objective Recently, results of a phase I/II trial revealed that single UM171-expanded CB transplant allowed the use of smaller CB units without compromising engraftment. The present study assessed T cell reconstitution and immune function in patients transplanted with UM171-expanded CB grafts. Methods We performed a retrospective analysis of a cohort of 20 patients treated with UM171-expanded CB and compared it to a contemporary cohort of 12 patients treated in the same institution who received unmanipulated CB transplant with similar conditioning regimens. We used flow cytometry and T cell receptor (TCR) sequencing to evaluate T cell reconstitution, and we used virus-specific ELISpot assays to evaluate T cell function in the first year post-transplantation. We also categorized infectious events according to the definitions of infection severity in the “Bone and Marrow Transplant Clinical Trials Network Technical Manual of Procedures,” Version 3.0, and report the mean cumulative count of infectious events for each cohort. Results While median T cell dose in graft was at least 2 to 3 times lower for the cohort of patients treated with UM171-expanded CB, numbers and phenotype of T cells at 3, 6, and 12 months post-transplant were similar between the two cohorts. TCR sequencing analyses revealed that UM171 patients had greater T cell diversity and higher numbers of clonotypes at 12 months post-transplant. This was associated with higher counts of naïve T cells and recent thymic emigrants, suggesting active thymopoiesis and correlating with the demonstration that UM171 expands common lymphoid progenitors in vitro. UM171 patients also showed rapid virus-specific T cell reactivity. Most importantly, UM171 patients showed a significantly reduced incidence of severe infections, especially for bacterial and viral infections (Figure 1). Discussion These results suggest that UM171 patients benefit from rapid T cell reconstitution, which likely contributes to the absence of moderate/severe cGVHD, infection-related mortality and late TRM observed in this cohort. STEM CELLS TRANSLATIONAL MEDICINE | StemCellsTM.com © AlphaMed Press 2020 CLINICAL TRIALS— HEMATOPOIETIC STEM CELL THERAPY

ArXiv, 2018

Representation learning is at the heart of what makes deep learning effective. In this work, we i... more Representation learning is at the heart of what makes deep learning effective. In this work, we introduce a new framework for representation learning that we call "Holographic Neural Architectures" (HNAs). In the same way that an observer can experience the 3D structure of a holographed object by looking at its hologram from several angles, HNAs derive Holographic Representations from the training set. These representations can then be explored by moving along a continuous bounded single dimension. We show that HNAs can be used to make generative networks, state-of-the-art regression models and that they are inherently highly resistant to noise. Finally, we argue that because of their denoising abilities and their capacity to generalize well from very few examples, models based upon HNAs are particularly well suited for biological applications where training examples are rare or noisy.

Transplantation and Cellular Therapy, 2021

, UM171-expanded cord blood transplants support robust T cell reconstitution with low rates of se... more , UM171-expanded cord blood transplants support robust T cell reconstitution with low rates of severe infections,

SSRN Electronic Journal, 2020

Combining RNA-sequencing, ribosome profiling, and mass spectrometry, we elucidate the contributio... more Combining RNA-sequencing, ribosome profiling, and mass spectrometry, we elucidate the contribution of non-canonical translation to the proteome and MHC class I immunopeptidome. Remarkably, of 14,498 proteins identified in three human B cell lymphomas, 2,503 are unannotated. Of these, 28% are new isoforms, and 72% are cryptic proteins encoded by ostensibly noncoding regions (60%) or frameshifted canonical genes (12%). Cryptic proteins are translated as efficiently as canonical proteins, have more predicted disordered residues and lower stability and critically, generate MHC-I peptides 5-fold more efficiently per translation event. Translating 5’ “untranslated” regions selectively hindered downstream translation of genes involved in transcription, translation and anti-viral responses. Novel protein isoforms showed strong enrichment for signaling pathways dysregulated in cancer. Only a small fraction of cryptic proteins detected in the proteome contribute to the MHC-I immunopeptidome, demonstrating the high preferential access of cryptic defective ribosomal products to the class I pathway.

MHC-I associated peptides (MAPs) play a central role in the elimination of virus-infected and neo... more MHC-I associated peptides (MAPs) play a central role in the elimination of virus-infected and neoplastic cells by CD8 T cells. However, accurately predicting the MAP repertoire remains difficult, because only a fraction of the transcriptome generates MAPs. In this study, we investigated whether codon arrangement (usage and placement) regulates MAP biogenesis. We developed an artificial neural network called Codon Arrangement MAP Predictor (CAMAP), predicting MAP presentation solely from mRNA sequences flanking the MAP coding regions, while excluding the MAP-coding codons per se. CAMAP predictions were significantly more accurate when using codon sequences than amino acid sequences. Furthermore, predictions were independent of mRNA expression and MAP binding affinity to MHC-I molecules, and applied to several cell types and species. Combining MAP binding affinity, transcript expression level and CAMAP scores was particularly useful to ameliorate predictions of MAP derived from lowly ...

Genome Medicine, 2020

Background Endogenous retroelements (EREs) constitute about 42% of the human genome and have been... more Background Endogenous retroelements (EREs) constitute about 42% of the human genome and have been implicated in common human diseases such as autoimmunity and cancer. The dominant paradigm holds that EREs are expressed in embryonic stem cells (ESCs) and germline cells but are repressed in differentiated somatic cells. Despite evidence that some EREs can be expressed at the RNA and protein levels in specific contexts, a system-level evaluation of their expression in human tissues is lacking. Methods Using RNA sequencing data, we analyzed ERE expression in 32 human tissues and cell types, including medullary thymic epithelial cells (mTECs). A tissue specificity index was computed to identify tissue-restricted ERE families. We also analyzed the transcriptome of mTECs in wild-type and autoimmune regulator (AIRE)-deficient mice. Finally, we developed a proteogenomic workflow combining RNA sequencing and mass spectrometry (MS) in order to evaluate whether EREs might be translated and gene...

Journal of Proteome Research, 2020

Cancer Immunology Research, 2020

High-grade serous ovarian cancer (HGSC), the principal cause of death from gynecologic malignanci... more High-grade serous ovarian cancer (HGSC), the principal cause of death from gynecologic malignancies in the world, has not significantly benefited from advances in cancer immunotherapy. Although HGSC infiltration by lymphocytes correlates with superior survival, the nature of antigens that can elicit anti-HGSC immune responses is unknown. The goal of this study was to establish the global landscape of HGSC tumor-specific antigens (TSA) using a mass spectrometry pipeline that interrogated all reading frames of all genomic regions. In 23 HGSC tumors, we identified 103 TSAs. Classic TSA discovery approaches focusing only on mutated exonic sequences would have uncovered only three of these TSAs. Other mutated TSAs resulted from out-of-frame exonic translation (n = 2) or from noncoding sequences (n = 7). One group of TSAs (n = 91) derived from aberrantly expressed unmutated genomic sequences, which were not expressed in normal tissues. These aberrantly expressed TSAs (aeTSA) originated pr...

Frontiers in Immunology, 2020

During gestation, sex hormones cause a significant thymic involution which enhances fertility. Th... more During gestation, sex hormones cause a significant thymic involution which enhances fertility. This thymic involution is rapidly corrected following parturition. As thymic epithelial cells (TECs) are responsible for the regulation of thymopoiesis, we analyzed the sequential phenotypic and transcriptomic changes in TECs during the postpartum period in order to identify mechanisms triggering postpartum thymic regeneration. In particular, we performed flow cytometry analyses and deep RNA-sequencing on purified TEC subsets at several time points before and after parturition. We report that pregnancy-induced involution is not caused by loss of TECs since their number does not change during or after pregnancy. However, during pregnancy, we observed a significant depletion of all thymocyte subsets downstream of the double-negative 1 (DN1) differentiation stage. Variations in thymocyte numbers correlated with conspicuous changes in the transcriptome of cortical TECs (cTECs). The transcriptomic changes affected predominantly cTEC expression of Foxn1, its targets and several genes that are essential for thymopoiesis. By contrast, medullary TECs (mTECs) showed very little transcriptomic changes in the early postpartum regenerative phase, but seemed to respond to the expansion of single-positive (SP) thymocytes in the late phase of regeneration. Together, these results show that postpartum thymic regeneration is orchestrated by variations in expression of a well-defined subset of cTEC genes, that occur very early after parturition.

Science Translational Medicine, 2018

A proteogenomic method identifies potentially actionable tumor-specific antigens and shows that m... more A proteogenomic method identifies potentially actionable tumor-specific antigens and shows that most of them are not coded by classic exons.

Frontiers in immunology, 2017

Thymic aging precedes that of other organs and is initiated by the gradual loss of thymic epithel... more Thymic aging precedes that of other organs and is initiated by the gradual loss of thymic epithelial cells (TECs). Based on culture and transplantation assays, recent studies have reported on the presence of thymic epithelial progenitor cells (TEPCs) in young adult mice. However, the physiological role and properties of TEPC populations reported to date remain unclear. Using an label-retention assay, we previously identified a population of quiescent but non-senescent TECs. The goals of this study were therefore (i) to evaluate the contribution of these quiescent TECs to thymic regeneration following irradiation-induced acute thymic injury and (ii) to characterize their phenotypic and molecular profiles using flow cytometry, immunohistology, and transcriptome sequencing. We report that while UEA1 cells cycle the most in steady state, they are greatly affected by irradiation, leading to cell loss and proliferative arrest following acute thymic involution. On the opposite, the UEA1 su...

Journal of Clinical Investigation, 2016

Scientific Reports, 2016

Based on transcriptomic analyses of thousands of samples from The Cancer Genome Atlas, we report ... more Based on transcriptomic analyses of thousands of samples from The Cancer Genome Atlas, we report that expression of constitutive proteasome (CP) genes (PSMB5, PSMB6, PSMB7) and immunoproteasome (IP) genes (PSMB8, PSMB9, PSMB10) is increased in most cancer types. In breast cancer, expression of IP genes was determined by the abundance of tumor infiltrating lymphocytes and high expression of IP genes was associated with longer survival. In contrast, IP upregulation in acute myeloid leukemia (AML) was a cell-intrinsic feature that was not associated with longer survival. Expression of IP genes in AML was IFN-independent, correlated with the methylation status of IP genes, and was particularly high in AML with an M5 phenotype and/or MLL rearrangement. Notably, PSMB8 inhibition led to accumulation of polyubiquitinated proteins and cell death in IPhigh but not IPlow AML cells. Co-clustering analysis revealed that genes correlated with IP subunits in non-M5 AMLs were primarily implicated i...

Leukemia, 2016

Pre-clinical studies have shown that injection of allogeneic T cells primed against a single mino... more Pre-clinical studies have shown that injection of allogeneic T cells primed against a single minor histocompatibility antigen (MiHA) could cure hematologic cancers (HC) without causing any toxicity to the host. However, translation of this approach in humans has been hampered by the paucity of molecularly defined human MiHAs. Using a novel proteogenomic approach, we have analyzed cells from 13 volunteers and discovered a vast repertoire of MiHAs presented by the most common HLA haplotype in European Americans: HLA-A*02:01;B*44:03. Notably, out of 46000 MiHAs, we have identified a set of 39 MiHAs that share optimal features for immunotherapy of HCs. These 'optimal MiHAs' are coded by common alleles of genes that are preferentially expressed in hematopoietic cells. Bioinformatic modeling based on MiHA allelic frequencies showed that the 39 optimal MiHAs would enable MiHA-targeted immunotherapy of practically all HLA-A*02:01;B*44:03 patients. Further extension of this strategy to a few additional HLA haplotypes would allow treatment of almost all patients.

Nature Communications, 2016

In view of recent reports documenting pervasive translation outside of canonical protein-coding s... more In view of recent reports documenting pervasive translation outside of canonical protein-coding sequences, we wished to determine the proportion of major histocompatibility complex (MHC) class I-associated peptides (MAPs) derived from non-canonical reading frames. Here we perform proteogenomic analyses of MAPs eluted from human B cells using high-throughput mass spectrometry to probe the six-frame translation of the B-cell transcriptome. We report that ∼10% of MAPs originate from allegedly noncoding genomic sequences or exonic out-of-frame translation. The biogenesis and properties of these ‘cryptic MAPs’ differ from those of conventional MAPs. Cryptic MAPs come from very short proteins with atypical C termini, and are coded by transcripts bearing long 3′UTRs enriched in destabilizing elements. Relative to conventional MAPs, cryptic MAPs display different MHC class I-binding preferences and harbour more genomic polymorphisms, some of which are immunogenic. Cryptic MAPs increase the ...

Journal of immunology (Baltimore, Md. : 1950), 2015

Establishment of self-tolerance in the thymus depends on promiscuous expression of tissue-restric... more Establishment of self-tolerance in the thymus depends on promiscuous expression of tissue-restricted Ags (TRA) by thymic epithelial cells (TEC). This promiscuous gene expression (pGE) is regulated in part by the autoimmune regulator (AIRE). To evaluate the commonalities and discrepancies between AIRE-dependent and -independent pGE, we analyzed the transcriptome of the three main TEC subsets in wild-type and Aire knockout mice. We found that the impact of AIRE-dependent pGE is not limited to generation of TRA. AIRE decreases, via non-cell autonomous mechanisms, the expression of genes coding for positive regulators of cell proliferation, and it thereby reduces the number of cortical TEC. In mature medullary TEC, AIRE-driven pGE upregulates non-TRA coding genes that enhance cell-cell interactions (e.g., claudins, integrins, and selectins) and are probably of prime relevance to tolerance induction. We also found that AIRE-dependent and -independent TRA present several distinctive featu...

Scientific Reports, 2013

In order to gain novel insights into thymus biology, we analysed the whole transcriptome of corti... more In order to gain novel insights into thymus biology, we analysed the whole transcriptome of cortical and medullary thymic epithelial cells (cTECs and mTECs) and of skin epithelial cells (ECs). Consistent with their ability to express ectopic genes, mTECs expressed more genes than other cell populations. Out of a total of 15,069 genes expressed in TECs, 25% were differentially expressed by at least 5-fold in cTECs vs. mTECs. Genes expressed at higher levels in cTECs than mTECs regulate numerous cell functions including cell differentiation, cell movement and microtubule dynamics. Many positive regulators of the cell cycle were overexpressed in skin ECs relative to TECs. Our RNA-seq data provide novel systems-level insights into the transcriptional landscape of TECs, highlight substantial divergences in the transcriptome of TEC subsets and suggest that cell cycle progression is differentially regulated in TECs and skin ECs. I n all vertebrates, the thymus is necessary and sufficient for production of classic adaptive T cells 1,2. There are no thymus substitutes in the animal kingdom and T cells generated extrathymically (e.g., in oncostatin Mtransgenic mice) are poorly functional: they cause severe autoimmunity and are unable to eliminate pathogens 2-5. The key components of the thymus are cortical and medullary thymic epithelial cells (cTECs and mTECs) which play several essential functions 6. During their intrathymic journey, which takes around 3 weeks, thymocytes undergo numerous reciprocal interactions with TECs located in seven functional zones 7-9. TECs produce chemokines that attract bone marrow derived hematopoietic progenitors, as well as interleukin (IL)-7 and the notch ligand DLL4 that induce thymocyte proliferation and differentiation 10,11. Furthermore, cTECs and mTECs express unique sets of ligands that mould the repertoire of antigen receptors expressed by thymocytes 6,12,13. The cells that induce the positive selection of thymocytes are primarily cTECs, whereas mTECs are instrumental in negative selection. Recent studies have highlighted several factors that regulate TEC development, maintenance and function including microRNAs, the transcription factor Foxn1 and Wnt signaling 14-18. Nonetheless, despite the capital role of TECs, our understanding of TEC biology is quite rudimentary. For instance, it is not yet known whether cTECs and mTECs are maintained by unipotent or bipotent progenitors in postnatal thymi, and what might be the extent of divergence in the functional program of these two TEC populations 6,7. In addition, while TECs display considerable proliferative potential 19 , it remains unclear why the number of TECs decreases rapidly with age, thereby leading to progressive thymic insufficiency 5,20,21. The transcriptome is a critical component of systems-level understanding of cell biology and it can be reliably tackled in its entirety in freshly harvested primary cells. In line with this, microarray analyses of several immune cell populations by the Immunological Genome Project Consortium have yielded fundamental insights into the biology of lymphocytes, dendritic cells and macrophages (http://www.immgen.org/index_content.html). As a first step to gain novel insights into TEC biology, we therefore decided to analyse the whole transcriptome of cTECs, mTECs and skin epithelial cells (ECs). We inferred that including skin ECs in our analyses would enable us to better appreciate the extent of divergence between the transcriptomes of mTECs and cTECs. In addition, we surmised that comparing the transcriptome of skin ECs vs. TECs might yield some clues as to why precocious agerelated hypocellularity impinges on TECs but not skin ECs. We elected to analyse gene expression using RNA-seq rather than microarrays because RNA-seq has higher sensitivity and dynamic range coupled to lower technical variations 22,23. We report that the transcriptomes of mTECs and cTECs present numerous substantial differences that may have far-reaching biological consequences. In addition, we found that many positive regulators of cell division are repressed in TECs relative to skin ECs. Our RNA-seq data offer a valuable resource to the community that can be mined to explore multiple questions.

Nature Communications, 2014

For decades, the global impact of genomic polymorphisms on the repertoire of peptides presented b... more For decades, the global impact of genomic polymorphisms on the repertoire of peptides presented by major histocompatibility complex (MHC) has remained a matter of speculation. Here we present a novel approach that enables high-throughput discovery of polymorphic MHC class I-associated peptides (MIPs), which play a major role in allorecognition. On the basis of comprehensive analyses of the genomic landscape of MIPs eluted from B lymphoblasts of two MHC-identical siblings, we show that 0.5% of non-synonymous single nucleotide variations are represented in the MIP repertoire. The 34 polymorphic MIPs found in our subjects are encoded by bi-allelic loci with dominant and recessive alleles. Our analyses show that, at the population level, 12% of the MIP-coding exome is polymorphic. Our method provides fundamental insights into the relationship between the genomic self and the immune self and accelerates the discovery of polymorphic MIPs (also known as minor histocompatibility antigens).