Daniel Alpern

Biological material pooling device for biological or biomolecule purification

Daniel Alpern, Riccardo Dainese, Bart Deplancke

The present invention concerns a biological material pooling device for biological or biomolecule purification comprising a receptacle including a first orifice comprising ordefining a rectangular opening, the receptacle being configured to receive at least one liquid through the first orifice, a second orifice located opposite the first orifice; and at least one side wall extending between the first orifice and the second orifice. The at least one side wall extends between the first orifice and the second orifice to define a tapered cavity or a cavity of decreasing cross-sectional area between the first orifice and the second orifice to guide and remove the at least one liquid out of the biological material pooling device.

2023

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Daniel Alpern, Riccardo Dainese, Bart Deplancke, Vincent Roland Julien Gardeux

The present invention relates generally to the field of nucleic acid sequencing and provides oligonucleotide molecules and barcodes contained therein. These oligonucleotide molecules and barcodes molecules are useful in sequencing to identify and resolve errors.

2023

Mammalian adipogenesis regulator (Areg) cells use retinoic acid signalling to be non- and anti-adipogenic in age-dependent manner

Daniel Alpern, Bart Deplancke, Radiana Ferrero, Horia Hashimi, Maria Litovchenko, Pernille Yde Rainer, Julie Marie Russeil, Magda Zachara

Adipose stem and precursor cells (ASPCs) give rise to adipocytes and determine the composition and plasticity of adipose tissue. Recently, several studies have demonstrated that ASPCs partition into at least three distinct cell subpopulations, including the enigmatic CD142(+) cells. An outstanding challenge is to functionally characterise this population, as discrepant properties, from adipogenic to non- and anti-adipogenic, have been reported for these cells. To resolve these phenotypic ambiguities, we characterised mammalian subcutaneous CD142(+) ASPCs across various experimental conditions, demonstrating that CD142(+) ASPCs exhibit high molecular and phenotypic robustness. Specifically, we find these cells to be firmly non- and anti-adipogenic both in vitro and in vivo, with their inhibitory signals also impacting adipogenic human cells. However, these CD142(+) ASPC-specific properties exhibit surprising temporal phenotypic alterations, and emerge only in an age-dependent manner. Finally, using multi-omic and functional assays, we show that the inhibitory nature of these adipogenesis-regulatory CD142(+) ASPCs (Aregs) is driven by specifically expressed secretory factors that cooperate with the retinoic acid signalling pathway to transform the adipogenic state of CD142(-) ASPCs into a non-adipogenic, Areg-like state.

WILEY2022

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

Daniel Alpern, Riccardo Dainese, Mustafa Demir, Bart Deplancke

The invention relates to methods for the preparation of method of preparation of cDNA library based on one or many RNA samples useful for efficient RNA sequencing and uses thereof. The invention further relates to related tools and kits useful in said method.

2022

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

Daniel Alpern, Elisa Cora, Bart Deplancke, Vincent Roland Julien Gardeux, Bastien Mangeat, Jörn Pezoldt, Julie Marie Russeil

Since its emergence in December 2019, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spread globally and become a major public health burden. Despite its close phylogenetic relationship to SARS-CoV, SARS-CoV-2 exhibits increased human-to-human transmission dynamics, likely due to efficient early replication in the upper respiratory epithelium of infected individuals. Since different temperatures encountered in the human upper and lower respiratory tract (37 degrees C and 33 degrees C, respectively) have been shown to affect the replication kinetics of several respiratory viruses, as well as host immune response dynamics, we investigated the impact of temperatures during SARS-CoV-2 and SARS-CoV infection using the primary human airway epithelial cell culture model. SARS-CoV-2, in contrast to SARS-CoV, replicated to higher titers when infections were performed at 33 degrees C rather than 37 degrees C. Although both viruses were highly sensitive to type I and type III interferon pretreatment, a detailed time-resolved transcriptome analysis revealed temperature-dependent interferon and pro-inflammatory responses specifically induced by SARS-CoV or SARS-CoV-2, which amplitude was inversely proportional to their replication efficiencies at 33 degrees C or 37 degrees C. These data provide crucial insight on pivotal virus-host interaction dynamics and are in line with characteristic clinical features of SARS-CoV-2 and SARS-CoV, as well as their respective transmission efficiencies.

PUBLIC LIBRARY SCIENCE2021

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

Daniel Alpern, Bart Deplancke, Julie Marie Russeil

Skeletal muscles are composed of gigantic cells called muscle fibers, packed with force-producing myofibrils. During development, the size of individual muscle fibers must dramatically enlarge to match with skeletal growth. How muscle growth is coordinated with growth of the contractile apparatus is not understood. Here, we use the large Drosophila flight muscles to mechanistically decipher how muscle fiber growth is controlled. We find that regulated activity of core members of the Hippo pathway is required to support flight muscle growth. Interestingly, we identify Dlg5 and Slmap as regulators of the STRIPAK phosphatase, which negatively regulates Hippo to enable post-mitotic muscle growth. Mechanistically, we show that the Hippo pathway controls timing and levels of sarcomeric gene expression during development and thus regulates the key components that physically mediate muscle growth. Since Dlg5, STRIPAK and the Hippo pathway are conserved a similar mechanism may contribute to muscle or cardiomyocyte growth in humans.

ELIFE SCIENCES PUBLICATIONS LTD2021

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Daniel Alpern, Antonio Carlos Alves Meireles Filho, Riccardo Dainese, Bart Deplancke, Vincent Roland Julien Gardeux, Jia Yuan Jiang, Gerard Llimos Aubach

Despite its popularity, chromatin immunoprecipitation followed by sequencing (ChIP-seq) remains a tedious (>2 d), manually intensive, low-sensitivity and low-throughput approach. Here, we combine principles of microengineering, surface chemistry, and molecular biology to address the major limitations of standard ChIP-seq. The resulting technology, FloChIP, automates and miniaturizes ChIP in a beadless fashion while facilitating the downstream library preparation process through on-chip chromatin tagmentation. FloChIP is fast (

NATL ACAD SCIENCES2020

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress

Daniel Alpern, Antoine Timothée Cherix, Bart Deplancke, Sriparna Ghosal, Jocelin Grosse, Rolf Gruetter, Julie Marie Russeil, Maria del Carmen Sandi Perez, Meltem Weger

Mitochondrial dysfunction was highlighted as a crucial vulnerability factor for the development of depression. However, systemic studies assessing stress-induced changes in mitochondria-associated genes in brain regions relevant to depression symptomatology remain scarce. Here, we performed a genome-wide transcriptomic study to examine mitochondrial gene expression in the prefrontal cortex (PFC) and nucleus accumbens (NAc) of mice exposed to multimodal chronic restraint stress. We identified mitochondria-associated gene pathways as most prominently affected in the PFC and with lesser significance in the NAc. A more detailed mitochondrial gene expression analysis revealed that in particular mitochondrial DNA-encoded subunits of the oxidative phosphorylation complexes were altered in the PFC. The comparison of our data with a reanalyzed transcriptome data set of chronic variable stress mice and major depression disorder subjects showed that the changes in mitochondrial DNA-encoded genes are a feature generalizing to other chronic stress-protocols as well and might have translational relevance. Finally, we provide evidence for changes in mitochondrial outputs in the PFC following chronic stress that are indicative of mitochondrial dysfunction. Collectively, our work reinforces the idea that changes in mitochondrial gene expression are key players in the prefrontal adaptations observed in individuals with high behavioral susceptibility and resilience to chronic stress.

2020

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

Daniel Alpern, Antonio Carlos Alves Meireles Filho, Bart Deplancke, Vincent Roland Julien Gardeux, David Hacker, Bastien Mangeat, Julie Marie Russeil

Despite its widespread use, RNA-seq is still too laborious and expensive to replace RT-qPCR as the default gene expression analysis method. We present a novel approach, BRB-seq, which uses early multiplexing to produce 3 cDNA libraries for dozens of samples, requiring just 2hours of hands-on time. BRB-seq has a comparable performance to the standard TruSeq approach while showing greater tolerance for lower RNA quality and being up to 25 times cheaper. We anticipate that BRB-seq will transform basic laboratory practice given its capacity to generate genome-wide transcriptomic data at a similar cost as profiling four genes using RT-qPCR.

2019

Daniel Alpern

Biological material pooling device for biological or biomolecule purification

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Mammalian adipogenesis regulator (Areg) cells use retinoic acid signalling to be non- and anti-adipogenic in age-dependent manner

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

A stromal cell population that inhibits adipogenesis in mammalian fat depots

Biological material pooling device for biological or biomolecule purification

Optimised set of oligonucleotides for bulk rna barcoding and sequencing

Method of preparation of cdna library useful for efficient mrna sequencing and uses thereof

Disparate temperature-dependent virus-host dynamics for SARS-CoV-2 and SARS-CoV in the human respiratory epithelium

A parallelized, automated platform enabling individual or sequential ChIP of histone marks and transcription factors

The Hippo pathway controls myofibril assembly and muscle fiber growth by regulating sarcomeric gene expression

BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing

Mitochondrial gene signature in the prefrontal cortex for differential susceptibility to chronic stress

A stromal cell population that inhibits adipogenesis in mammalian fat depots

Mammalian adipogenesis regulator (Areg) cells use retinoic acid signalling to be non- and anti-adipogenic in age-dependent manner