WO2022136252A1

WO2022136252A1 - Methods for prognosis the humoral response of a subject prior to vaccination

Info

Publication number: WO2022136252A1
Application number: PCT/EP2021/086754
Authority: WO
Inventors: Behazine Combadiere; Elena GONÇALVES
Original assignee: INSERM (Institut National de la Santé et de la Recherche Médicale); Sorbonne Universite
Priority date: 2020-12-21
Filing date: 2021-12-20
Publication date: 2022-06-30

Abstract

The present invention represents the first systems biology approach to investigate the volunteers' immune predisposition to respond to a vaccination (proteins trimer GP160 SOSIP), assessed by their blood transcriptome profile; specifically, that related to their B cell differentiation stages. That is, inventors investigated the host gene expression in blood by a microarray approach before vaccination. The objective was to examine their potential involvement in an effective SOSIP neutralizing antibody (Nabs) response during a randomized phase lb clinical study. This trial immunized 6 HIV seronegative subjects by the intramuscular route with SOSIP -HIV clade B vaccine. Inventors found that gene expression of a group of genes (detected through mRNA nucleic acids in blood) are overexpressed at baseline in subjects with the highest antibody response compared to the subjects with the lowest antibody response, and therefore may be considered as good biomarkers to assess the humoral immune response of a subject to a vaccine. Accordingly, the present invention relates to methods and kits for predicting the humoral response of a subject prior to vaccination. More specifically present invention relates to methods for assessing the humoral response of a subject to a vaccine through detection in a blood sample of specific RNAs.

Description

METHODS FOR PROGNOSIS THE HUMORAL RESPONSE OF A SUBJECT

PRIOR TO VACCINATION

FIELD OF THE INVENTION:

The present invention relates to methods and kits for predicting the humoral response of a subject prior to vaccination. More specifically present invention relates to methods for assessing the humoral response of a subject to a vaccine through detection in a blood sample of specific RNAs.

BACKGROUND OF THE INVENTION:

Systems biology has been successfully used to investigate the fundamental innate immune mechanisms orchestrating protective adaptive responses after the perturbation of vaccination against yellow fever (Gaucher et al., 2008; Querec et al., 2009), HIV (Ehrenberg et al., 2019), Ebola (Rechtien et al., 2017), and influenza (Nakaya et al., 2011). An important challenge, however, is to analyze individual baseline human health characteristics to help identify those at higher risk of infection despite vaccination. Until now, only a few studies have looked for candidate traits associated with vaccine responsiveness and partially predicting the humoral response to vaccination against influenza (Furman et al., 2014; Parvandeh et al., 2019; Team and Consortium, 2017; Tsang et al., 2014). No study has examined the interrelations between each individual's immunological state, their microbiota at baseline, and the impact of both on their vaccine-induced immune responses. As the most successful vaccines act through the production of antibodies (Plotkin, 2010), identifying specific individual characteristics of the genome at baseline should enhance our ability for dividing vaccinees into “high responders” or “low responders” in terms of humoral response (Tsang, 2015). Such predictive markers might serve as a potential diagnostic tool that assists vaccine development by taking into account the interindividual heterogeneity of immune responses.

Accordingly, there remains an unmet need in the art for specific and more rapid prognostic test for predicting the humoral response of a subject prior to vaccination, reflecting the immunological status of the patient. SUMMARY OF THE INVENTION:

The present invention relates to an in vitro method for assessing a subject’s humoral immune response to a vaccine, said method, comprising the step of (a) measuring in a sample obtained from said subject prior to the administration of said vaccine the level of one or more gene expression level selected from a group of genes consisting of: IGLV8-61, BLK, EBF1 and IFNal6 gene b) wherein the level of one or more gene expression of step a) is positively correlated with the humoral immune response of said subject.

Another object of the invention relates to a kit, comprising:

- at least a mean for determining one or more gene expression level selected from a group of gene consisting of: IGLV8-61, BLK, EBF1 and IFNal6 gene and

- instructions for use. for use to assess a subject’s humoral immune response to a vaccine.

DETAILED DESCRIPTION OF THE INVENTION:

Prognostic methods according to the invention

Inventor’s work represents the first systems biology approach to investigate the volunteers' immune predisposition to respond to Recombinant HIV-1 trimeric gpl40 Env proteins (ConM SOSIP gpl40) vaccination, assessed by their blood transcriptome profile; specifically, that related to their B cell differentiation stages. That is, they investigated the host gene expression in blood by a microarray approach a before vaccination. The objective was to examine their potential involvement in an effective MVA-B neutralizing antibody (Nabs) response during the European EM SOSIP study phase lb clinical study. This trial immunized 6 HIV seronegative subjects aged from 18 to 45 years by the intramuscular route with SOSIP formulated in (Monophosphoryl lipid A MPLA) adjuvant vaccine. Inventors analyzed their baseline transcriptomic signature in blood to assess their potential association with the intensity of the Nabs response.

In other words, the inventors found that gene expression of a group of genes of the invention (detected through mRNA nucleic acids in blood) are overexpressed at baseline in subjects with the highest antibody response compared to the subjects with the lowest antibody response, and therefore may be considered as good biomarkers to assess the humoral immune response of a subject to a vaccine.

This minimal marker set identified by the inventors, may be used as prognoses tool alone or in combination with bacterial abundance and diversity scores. These results thus set- up the basis for the development of a rapid functional specific prognostic test for predicting the humoral response of a subject prior to vaccination with an antigen.

Thus, the present invention relates to an in vitro method for assessing a subject’s humoral immune response to a vaccine, said method, comprising the step of (a) measuring in a sample obtained from said subject prior to the administration of said vaccine, the level of one or more gene expression level selected from a group of genes consisting of: IGLV8-61, BLK, EBF1 and IFNal6 gene b) wherein the level of one or more gene expression of step a) is positively correlated with the humoral immune response of said subject.

In some embodiments, the said method is performed in vitro or ex vivo.

In particular embodiments the prognostic method of the invention comprising the step of comparing said level of one or more gene expression to a control reference value wherein:

- a high level of one or more gene expression compared to said control reference value is predictive that said subject is a high risk to be a “high responder” to said vaccine

- a low level of one or more gene expression compared to said control reference value is predictive that said subject is a high risk to be a “low responder” to said vaccine

The term “subject” as used herein refers to a mammalian, such as a rodent (e.g. a mouse or a rat), a feline, a canine or a primate. In a preferred embodiment, said subject is a human subject.

The subject according to the invention can be a healthy subject or a subject suffering from a given disease such as infectious disease prior to the vaccination of said subject with an antigen.

As used herein, the term "infectious disease" refers to a condition in which an infectious organism or agent is present in a detectable amount in the blood or in a normally sterile tissue or normally sterile compartment of a subject. Infectious organisms and agents include viruses, mycobacteria, bacteria, fungi, and parasites. The terms encompass both acute and chronic infections, as well as sepsis. In a particular embodiment the infectious organism is a virus or a bacteria that is responsible of infection such as:

Example of viral infections: Adenoviridae (ie Adenovirus); Herpesviridae (Herpes simplex, type 1, Herpes simplex, type 2, Varicella-zoster virus, Epstein-Barr virus, Human cytomegalovirus, Human herpesvirus, type 8); Papillomaviridae (Human papillomavirus); Polyomaviridae (BK virus, JC virus); Poxviridae (Smallpox); Hepadnaviridae (Hepatitis B virus); Parvoviridae (Parvovirus Bl 9); Astroviridae (Human astrovirus) Caliciviridae (Norwalk virus); Picomaviridae (coxsackievirus, hepatitis A virus, poliovirus rhinovirus) ;Coronaviridae (Severe acute respiratory syndrome-related coronavirus, strains: Severe acute respiratory syndrome virus, Severe acute respiratory syndrome coronavirus 2); Flaviviridae (Hepatitis C virus, yellow fever virus, dengue virus, West Nile virus, TBE virus, Zika virus); Matonaviridae (Rubella virus); Hepeviridae (Hepatitis E virus); Retroviridae (Human immunodeficiency virus (HIV)); Orthomyxoviridae (Influenza virus); Arenaviridae (Lassa virus); Bunyaviridae (Crimean-Congo hemorrhagic fever virus, Hantaan virus); Filoviridae (Ebola virus, Marburg virus); Paramyxoviridae (Measles virus, Mumps virus, Parainfluenza virus); Pneumoviridae (Respiratory syncytial virus); Rhabdoviridae (Rabies virus) ; Unassigned (Hepatitis D); Reoviridae (Rotavirus, Orbivirus, Coltivirus, Banna virus)

In a particular embodiment the viral infection is Coronaviridae (Severe acute respiratory syndrome-related coronavirus, strains: Severe acute respiratory syndrome virus, Severe acute respiratory syndrome coronavirus 2) and Retroviridae (Human immunodeficiency virus (HIV)).

As used herein the term “humoral immune response” means the immune response involving the transformation of B cells into plasma cells that produce and secrete antibodies to a specific antigen. In the context of the present invention “assessing a subject’s humoral immune response to a vaccine” means detecting antibody response, in particular neutralizing antibody response, after immunization with an antigen, against a pathogen (infectious agent, or tumor cells). Humoral immunity prevents infection and can be of different kinds. It is characterized, for example, by neutralizing antibodies responses induced after vaccination. These functional antibodies are the main actors of protective immunity, they are able to neutralize the ability of the virus to penetrate or replicate in cells. Antibodies can belong to different immunoglobulin classes and subclasses including for example serum IgG and mucosal IgG and IgA. These Ig can also act in other ways by opsonization or complement activation, involving serum immune regulatory proteins for pathogen elimination. Other ways to defend oneself is antibody-dependent cell-mediated virus inhibition (ADCVI) and antibody-dependent cell-mediated-cytotoxicity (ADCC). This is one of the mechanisms by which antibodies act to limit and contain infection. It’s carried out by natural killer cells (NK) through different proteins: perforins (pore-forming proteins), granzymes (serine proteases), reactive oxygen intermediates, and cytokines. These cells lysis an infected cell labeled with antibody bound to antigen present on the membrane.

The term "protective humoral immunity" as used herein, means a humoral immune response that confers the essential component of protection against a pathogen. The term "sterilizing humoral immunity" as used herein, means a humoral immune response that prevents the establishment of any detectable infection by a pathogen.

The term "long-lasting humoral immunity" as used herein, means that some aspect of humoral immunity is detectable three months after antigen administration, such as, for example, antibodies elicited by the antigen. Suitable methods of antibody detection include, but are not limited to, such methods as ELISA, immunofluorescence (IF A), focus reduction neutralization tests (FRNT), immunoprecipitation, and Western blotting.

The term "neutralizing humoral response" as used herein, means that the antibodies elicited during humoral immunity directly block the ability of a pathogen to infect cells.

The term "quick response" as used herein, means that protective humoral immunity is conferred within three weeks of antigen administration. The term "very quick response" as used herein, means that protective humoral immunity is conferred within one week of antigen administration.

A “responder to a vaccine” means that after vaccination of a subject, the serum antibody titer against the targeted antigen of said subject is sufficient to adequately clear the disease (infectious disease or tumor) and exhibit an efficient immune humoral activity. In such a case, then one can conclude that said patient has a greater proportion of immune B cells which induce an efficient immune humoral response in particular a neutralizing antibody response. Tests for determining the serum antibody titer are well known to the person skilled in the art. For example, a GFP Neutralizing assay (as described in example section) to detect an anti-antigen neutralizing activity in a serum of subjects collected 8 days after vaccination based on GFP detection by flow cytometry can be used.

Another example, according to the US FDA Guidance for Industry document, having a hemagglutinin inhibition (HI) antibody titer of 1 :40 against influenza (seroprotection) or a fourfold increase in HI titer following influenza vaccination (sero-conversion) are considered protective.

A "vaccine composition" or a “vaccine”, once it has been administered to a subject or an animal, elicits a protective immune response against said one or more antigen(s) which is (are) comprised herein. Accordingly, the vaccine composition according to the present invention, once it has been administered to the subject or the animal, induces a protective immune response against, for example, a microorganism, or to efficaciously protect the subject or the animal against infection.

A variety of substances can be used as antigens in a compound or formulation, of immunogenic or vaccine type. For example, attenuated and inactivated viral and bacterial pathogens, purified macromolecules, polysaccharides, toxoids, recombinant antigens, organisms containing a foreign gene from a pathogen, synthetic peptides, polynucleic acids (DNA, RNA), antibodies and tumor cells can be used to prepare (i) an immunogenic composition useful to induce an immune response in an individual or (ii) a vaccine useful for treating a pathological condition.

An antigen is additionally capable of being recognized by the immune system and/or being capable of inducing a humoral immune response and/or cellular immune response leading to the activation of B- and/or T-lymphocytes. An antigen can have one or more epitopes or antigenic sites (B- and T- epitopes)

Therefore, a wide variety of antigens to produce a vaccine composition useful for inducing an immune response in an individual can be used.

Those skilled in the art will be able to select an antigen appropriate for treating a particular pathological condition and will know how to determine whether an isolated antigen is favored in a particular vaccine formulation.

An isolated antigen can be prepared using a variety of methods well known in the art. A gene encoding any immunogenic polypeptide can be isolated and cloned, for example, in bacterial, yeast, insect, reptile or mammalian cells using recombinant methods well known in the art and described, for example in Sambrook et al., Molecular cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, New York (1992) and in Ansubel et al., Current Protocols in Molecular Biology, John Wiley and Sons, Baltimore, MD (1998). A number of genes encoding surface antigens from viral, bacterial and protozoan pathogens have been successfully cloned, expressed and used as antigens for vaccine development. For example, the major surface antigen of hepatitis B virus, HbsAg, the P subunit of choleratoxin, the enterotoxin of E. coh. the circumsporozoite protein of the malaria parasite, and a glycoprotein membrane antigen from Epstein-Barr virus, as well as tumor cell antigens, have been expressed in various well-known vector/host systems, purified and used in vaccines.

A pathologically aberrant cell may also be used in a vaccine composition according to the invention can be obtained from any source such as one or more individuals having a pathological condition or ex vivo or in vitro cultured cells obtained from one or more such individuals, including a specific individual to be treated with the resulting vaccine.

As used herein, the term “sample “or "biological sample" as used herein refers to any biological sample of a subject and can include, by way of example and not limitation, bodily fluids and/or tissue extracts such as homogenates or solubilized tissue obtained from a subject. Tissue extracts are obtained routinely from tissue biopsy. In a particular embodiment regarding the prognostic method according to the invention, the biological sample is a body fluid sample (such blood sample) or tissue biopsy of said subject.

In preferred embodiments, the body fluid sample is a blood sample. The term “blood sample” means a whole blood sample obtained from a subject (e.g. an individual for which it is interesting to determine whether a gene expression level can be identified).

The term “prior to the administration of (said) vaccine” means that the level of one or more gene expression level selected from a group of gene consisting of: IGLV8-61, BLK, EBF1 and IFNal6 gene, is measured at least 30, 29, 28, 27, 26, 25, 24, 23, 22, 21, 20, 19, 18, 17, 16, 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0 day prior the administration of the vaccine. Preferably the level of one or more gene expression level selected from a group of gene consisting of: IGLV8-61, BLK, EBF1 and IFNal6 gene, is measured at least 15, 14, 13, 12, 11, 10, 9, 8, 7, 6, 5, 4, 3, 2, 1, 0 days prior the administration of the vaccine.

In a particular embodiment, when the antigen is administered twice or more (prime and boost type administration) the term “prior to the administration of vaccine” means that the level of one or more gene expression level selected from a group of gene consisting of: IGLV8-61, BLK, EBF1 and IFNal6 gene, is measured prior first and/or subsequent antigen administration. In the present EM SOSIP study, the level of one or more gene expression level selected from a group of gene consisting of: IGLV8-61, BLK, EBF1 and IFNal6 gene before 1^st and 2^nd antigen administration is the equivalent (the baselines are not significantly different between VI and V6).

As used herein, the term " IFNal6" also known as “Interferon alpha-16” or “IFN alpha 16”, has its general meaning in the art and refers to a cytokine that in humans is encoded by the IFNA16 gene (Gene ID: 3449). Produced by macrophages, IFN-alpha 16 have antiviral activities. Interferon alpha 16 stimulates the production of two enzymes: a protein kinase and an oligoadenylate synthetase. The sequence of said protein may be found with the NCBI Reference: NM_002173 and NP_002164.

As used herein, the term "IGLV8-61", also known as “Immunoglobulin lambda variable 8-61” has its general meaning in the art refers to a protein that in humans is encoded by the IGLV8-61gene (gene ID 28774). V region of the variable domain of immunoglobulin light chains that participates in the antigen recognition. Immunoglobulins, also known as antibodies, are membrane-bound or secreted glycoproteins produced by B lymphocytes. The antigen binding site is formed by the variable domain of one heavy chain, together with that of its associated light chain. Thus, each immunoglobulin has two antigen binding sites with remarkable affinity for a particular antigen. The variable domains are assembled by a process called V-(D)-J rearrangement and can then be subjected to somatic hypermutations which, after exposure to antigen and selection, allow affinity maturation for a particular antigen

The sequence of said gene may be found with the NCBI Reference: NG 000002 and NC_000022 (Reference GRCh38.pl3 Primary Assembly).

As used herein, the term BLK (Tyrosine-protein kinase BLK) also known as “B lymphocyte kinase” “BLK proto-oncogene” or “Src family tyrosine kinase” has its general meaning in the art and refers to an enzyme that in humans is encoded by the B LK gene (Gene ID: 640). BLK gene encodes a nonreceptor tyrosine-kinase of the src family of protooncogenes that are typically involved in cell proliferation and differentiation. The protein has a role in B-cell receptor signaling and B-cell development. The protein also stimulates insulin synthesis and secretion in response to glucose and enhances the expression of several pancreatic beta-cell transcription factors.

The sequence of said protein may be found with the NCBI Reference: NM_001715/NM_001330465 (isoform 1 and isoform 2) and NP_001317394/NP_001706 ((isoform 1 and isoform 2).

As used herein, the term EBF1 also known as “Early B-Cell Factor 1” “or “Transcription factor COE1” has its general meaning in the art and refers to a protein that in humans is encoded by the EBF1 gene (Gene ID: 1879). The transcription factor EBF1 controls the expression of key proteins required for B cell differentiation, signal transduction and function (Treiber, T. et al (2010). Immunity. 32 (5): 714-725.; Hagman J. et al (2012). Current Topics in Microbiology and Immunology. 356: 17-38.). The crucial role of this factor is shown in the regulation of expression of SLAM family co-receptors in B-cells (Schwartz, A. et al. (2016). Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms. 1859 (10): 1259-1268).

The sequence of said protein may be found with the NCBI Reference: NM_001290360 and NP_001277289 (isoform 1)/ NM_024007 and NP_076870 (isoform 2)/ NM_182708 and NP_874367 (isoform 3)/ NM_001324101 and NP_001311030 (isoform 4)/ NM_001324103 and NP_001311032 (isoform 5)/ NM_001324106 and NP_001311035 (isoform 6)/ NM_001324107 and NP_001311036 ((isoform 7)/ NM_001324108 and NP_001311037 (isoform 8)/ NM_001324109 and NP_001311038 (isoform 9)/ NM_001324111 and NP_001311040 (isoform 10)/ NM_001364155 and NP_001351084 (isoform 11)/ NM_001364156 and NP_001351085 (isoform 13)/ NM_001364157 and NP_001351086 (isoform 14)/ NM_001364158 and NP_001351087 (isoform 15)/ NM_001364159 and NP_001351088 (isoform 16). The inventors have found biomarkers (gene expression level selected from a group of gene) associated with subject’s humoral immune response to a vaccine and have identified 4 biomarkers which could be used separately or in combination.

Thus, in one aspect, the present invention provides an in vitro method for assessing a subject’s humoral immune response to a vaccine, comprising the step of (a) measuring in a sample obtained from said subject prior to the administration of said vaccine, the level of one or more gene expression level selected from a group of genes consisting of: IFNal6, IGLV8- 61, BLK, and EBF1 gene and b) wherein the level of one or more gene expression of step a) is positively correlated with the humoral immune response of said subject.

In preferred embodiments, a plurality of gene expression level biomarkers (i.e., one or more than one gene expression level biomarkers) is used in the method of prognosis. In other words, the method of the invention may comprise steps of: measuring in the biological sample plurality of gene expression level biomarkers, between one, two, three; four, gene expression level biomarker selected from a group of gene consisting of: IFNal6, IGLV8-61, BLK, and EBF1 gene present in the biological sample.

In particular embodiments, the method of prognosis is performed using the four different gene expression level biomarkers including the IFNal6, IGLV8-61, BLK, and EBF1 gene.

Measuring the expression level of a gene can be performed by a variety of techniques well known in the art.

Typically, the expression level of a gene may be determined by determining the quantity of mRNA. Methods for determining the quantity of mRNA are well known in the art. For example, the nucleic acid contained in the samples (e.g., blood, cell or tissue prepared from the patient) is first extracted according to standard methods, for example using lytic enzymes or chemical solutions or extracted by nucleic-acid-binding resins following the manufacturer's instructions. The extracted mRNA is then detected by hybridization (e. g., Northern blot analysis, in situ hybridization) and/or amplification (e.g., RT-PCR).

Other methods of Amplification include ligase chain reaction (LCR), transcription- mediated amplification (TMA), strand displacement amplification (SDA) and nucleic acid sequence-based amplification (NASBA).

Nucleic acids having at least 10 nucleotides and exhibiting sequence complementarity or homology to the mRNA of interest herein find utility as hybridization probes or amplification primers. It is understood that such nucleic acids need not be identical, but are typically at least about 80% identical to the homologous region of comparable size, more preferably 85% identical and even more preferably 90-95% identical. In certain embodiments, it will be advantageous to use nucleic acids in combination with appropriate means, such as a detectable label, for detecting hybridization.

Typically, the nucleic acid probes include one or more labels, for example to permit detection of a target nucleic acid molecule using the disclosed probes. In various applications, such as in situ hybridization procedures, a nucleic acid probe includes a label (e.g., a detectable label). A “detectable label” is a molecule or material that can be used to produce a detectable signal that indicates the presence or concentration of the probe (particularly the bound or hybridized probe) in a sample. Thus, a labelled nucleic acid molecule provides an indicator of the presence or concentration of a target nucleic acid sequence (e.g., genomic target nucleic acid sequence) (to which the labelled uniquely specific nucleic acid molecule is bound or hybridized) in a sample. A label associated with one or more nucleic acid molecules (such as a probe generated by the disclosed methods) can be detected either directly or indirectly. A label can be detected by any known or yet to be discovered mechanism including absorption, emission and/ or scattering of a photon (including radio frequency, microwave frequency, infrared frequency, visible frequency and ultra-violet frequency photons). Detectable labels include colored, fluorescent, phosphorescent and luminescent molecules and materials, catalysts (such as enzymes) that convert one substance into another substance to provide a detectable difference (such as by converting a colorless substance into a colored substance or vice versa, or by producing a precipitate or increasing sample turbidity), haptens that can be detected by antibody binding interactions, and paramagnetic and magnetic molecules or materials.

Particular examples of detectable labels include fluorescent molecules (or fluorochromes). Numerous fluorochromes are known to those of skill in the art, and can be selected, for example from Life Technologies (formerly Invitrogen), e.g., see, The Handbook — A Guide to Fluorescent Probes and Labeling Technologies). Examples of parti cularfluorophores that can be attached (for example, chemically conjugated) to a nucleic acid molecule (such as a uniquely specific binding region) are provided in U.S. Pat. No. 5,866, 366 to Nazarenko et al., such as 4-acetamido-4'-isothiocyanatostilbene-2,2' disulfonic acid, acridine and derivatives such as acridine and acridine isothiocyanate, 5-(2'-aminoethyl) aminonaphthalene- 1 -sulfonic acid (EDANS), 4-amino -N- [3 vinylsulfonyl)phenyl]naphthalimide-3,5 disulfonate (Lucifer Yellow VS), N-(4-anilino-l- naphthyl)mal eimide, antllranilamide, Brilliant Yellow, coumarin and derivatives such as coumarin, 7-amino-4-methylcoumarin (AMC, Coumarin 120), 7-amino-4- trifluoromethylcouluarin (Coumarin 151); cyanosine; 4',6-diarninidino-2-phenylindole (DAPI); 5',5"dibromopyrogallol-sulfonephthalein (Bromopyrogallol Red); 7 -diethylamino -3 (4'-isothiocyanatophenyl)-4-methylcoumarin; diethylenetriamine pentaacetate; 4,4'- diisothiocyanatodihydro-stilbene-2,2'-disulfonic acid; 4,4'-diisothiocyanatostilbene-2,2'- disulforlic acid; 5-[dimethylamino] naphthal ene-1 -sulfonyl chloride (DNS, dansyl chloride); 4-(4'-dimethylaminophenylazo)benzoic acid (DABCYL); 4-dimethylaminophenylazophenyl- 4'-isothiocyanate (DABITC); eosin and derivatives such as eosin and eosin isothiocyanate; erythrosin and derivatives such as erythrosin B and erythrosin isothiocyanate; ethidium; fluorescein and derivatives such as 5-carboxyfluorescein (FAM), 5-(4,6diclllorotriazin-2- yDarninofluorescein (DTAF), 2'7'dimethoxy-4'5'-dichloro-6-carboxyfluorescein (JOE), fluorescein, fluorescein isothiocyanate (FITC), and QFITC Q(RITC); 2',7'-difluorofluorescein (OREGON GREEN®); fluorescamine; IR144; IR1446; Malachite Green isothiocyanate; 4- methylumbelliferone; ortho cresolphthalein; nitrotyrosine; pararosaniline; Phenol Red; B- phycoerythrin; o-phthaldialdehyde; pyrene and derivatives such as pyrene, pyrene butyrate and succinimidyl 1 -pyrene butyrate; Reactive Red 4 (Cibacron Brilliant Red 3B-A); rhodamine and derivatives such as 6-carboxy-X-rhodamine (ROX), 6-carboxyrhodamine (R6G), lissamine rhodamine B sulfonyl chloride, rhodamine (Rhod), rhodamine B, rhodamine 123, rhodamine X isothiocyanate, rhodamine green, sulforhodamine B, sulforhodamine 101 and sulfonyl chloride derivative of sulforhodamine 101 (Texas Red); N, N,N',N' -tetramethyl - 6-carboxyrhodamine (TAMRA); tetramethyl rhodamine; tetramethyl rhodamine isothiocyanate (TRITC); riboflavin; rosolic acid and terbium chelate derivatives. Other suitable fluorophores include thiol -reactive europium chelates which emit at approximately 617 mn (Heyduk and Heyduk, Analyt. Biochem. 248:216-27, 1997; J. Biol. Chem. 274:3315- 22, 1999), as well as GFP, LissamineTM, di ethylaminocoumarin, fluorescein chlorotriazinyl, naphthofluorescein, 4,7-dichlororhodamine and xanthene (as described in U.S. Pat. No. 5,800,996 to Lee et al.) and derivatives thereof. Other fluorophores known to those skilled in the art can also be used, for example those available from Life Technologies (Invitrogen; Molecular Probes (Eugene, Oreg.)) and including the ALEXA FLUOR® series of dyes (for example, as described in U.S. Pat. Nos. 5,696,157, 6, 130, 101 and 6,716,979), the BODIPY series of dyes (dipyrrom etheneboron difluoride dyes, for example as described in U.S. Pat. Nos. 4,774,339, 5,187,288, 5,248,782, 5,274,113, 5,338,854, 5,451,663 and 5,433,896), Cascade Blue (an amine reactive derivative of the sulfonated pyrene described in U.S. Pat. No. 5,132,432) and Marina Blue (U.S. Pat. No. 5,830,912). In addition to the fluorochromes described above, a fluorescent label can be a fluorescent nanoparticle, such as a semiconductor nanocrystal, e.g., a QUANTUM DOTTM (obtained, for example, from Life Technologies (QuantumDot Corp, Invitrogen Nanocrystal Technologies, Eugene, Oreg.); see also, U.S. Pat. Nos. 6,815,064; 6,682,596; and 6,649, 138). Semiconductor nanocrystals are microscopic particles having size-dependent optical and/or electrical properties. When semiconductor nanocrystals are illuminated with a primary energy source, a secondary emission of energy occurs of a frequency that corresponds to the handgap of the semiconductor material used in the semiconductor nanocrystal. This emission can he detected as colored light of a specific wavelength or fluorescence. Semiconductor nanocrystals with different spectral characteristics are described in e.g., U.S. Pat. No. 6,602,671. Semiconductor nanocrystals that can he coupled to a variety of biological molecules (including dNTPs and/or nucleic acids) or substrates by techniques described in, for example, Bruchez et al., Science 281 :20132016, 1998; Chan et al., Science 281 :2016- 2018, 1998; and U.S. Pat. No. 6,274,323. Formation of semiconductor nanocrystals of various compositions are disclosed in, e.g., U.S. Pat. Nos. 6,927, 069; 6,914,256; 6,855,202; 6,709,929; 6,689,338; 6,500,622; 6,306,736; 6,225,198; 6,207,392; 6,114,038; 6,048,616; 5,990,479; 5,690,807; 5,571,018; 5,505,928; 5,262,357 and in U.S. Patent Publication No. 2003/0165951 as well as PCT Publication No. 99/26299 (published May 27, 1999). Separate populations of semiconductor nanocrystals can he produced that are identifiable based on their different spectral characteristics. For example, semiconductor nanocrystals can he produced that emit light of different colors based on their composition, size or size and composition. For example, quantum dots that emit light at different wavelengths based on size (565 mn, 655 mn, 705 mn, or 800 mn emission wavelengths), which are suitable as fluorescent labels in the probes disclosed herein are available from Life Technologies (Carlshad, Calif.).

Additional labels include, for example, radioisotopes (such as ³ H), metal chelates such as DOTA and DPTA chelates of radioactive or paramagnetic metal ions like Gd3+, and liposomes.

Detectable labels that can he used with nucleic acid molecules also include enzymes, for example horseradish peroxidase, alkaline phosphatase, acid phosphatase, glucose oxidase, beta-galactosidase, beta-glucuronidase, or beta-lactamase.

Alternatively, an enzyme can he used in a metallographic detection scheme. For example, silver in situ hybridization (SISH) procedures involve metallographic detection schemes for identification and localization of a hybridized genomic target nucleic acid sequence. Metallographic detection methods include using an enzyme, such as alkaline phosphatase, in combination with a water-soluble metal ion and a redox-inactive substrate of the enzyme. The substrate is converted to a redox-active agent by the enzyme, and the redoxactive agent reduces the metal ion, causing it to form a detectable precipitate. (See, for example, U.S. Patent Application Publication No. 2005/0100976, PCT Publication No. 2005/ 003777 and U.S. Patent Application Publication No. 2004/ 0265922). Metallographic detection methods also include using an oxido-reductase enzyme (such as horseradish peroxidase) along with a water-soluble metal ion, an oxidizing agent and a reducing agent, again to form a detectable precipitate. (See, for example, U.S. Pat. No. 6,670,113).

Probes made using the disclosed methods can be used for nucleic acid detection, such as ISH procedures (for example, fluorescence in situ hybridization (FISH), chromogenic in situ hybridization (CISH) and silver in situ hybridization (SISH)) or comparative genomic hybridization (CGH).

In situ hybridization (ISH) involves contacting a sample containing target nucleic acid sequence (e.g., genomic target nucleic acid sequence) in the context of a metaphase or interphase chromosome preparation (such as a cell or tissue sample mounted on a slide) with a labeled probe specifically hybridizable or specific for the target nucleic acid sequence (e.g., genomic target nucleic acid sequence). The slides are optionally pretreated, e.g., to remove paraffin or other materials that can interfere with uniform hybridization. The sample and the probe are both treated, for example by heating to denature the double stranded nucleic acids. The probe (formulated in a suitable hybridization buffer) and the sample are combined, under conditions and for sufficient time to permit hybridization to occur (typically to reach equilibrium). The chromosome preparation is washed to remove excess probe, and detection of specific labeling of the chromosome target is performed using standard techniques.

For example, a biotinylated probe can be detected using fluorescein-labeled avidin or avidin-alkaline phosphatase. For fluorochrome detection, the fluorochrome can be detected directly, or the samples can be incubated, for example, with fluorescein isothiocyanate (FITC)-conjugated avidin. Amplification of the FITC signal can be affected, if necessary, by incubation with biotin-conjugated goat antiavidin antibodies, washing and a second incubation with FITC-conjugated avidin. For detection by enzyme activity, samples can be incubated, for example, with streptavidin, washed, incubated with biotin-conjugated alkaline phosphatase, washed again and pre-equilibrated (e.g., in alkaline phosphatase (AP) buffer). For a general description of in situ hybridization procedures, see, e.g., U.S. Pat. No. 4,888,278. Numerous procedures for FISH, CISH, and SISH are known in the art. For example, procedures for performing FISH are described in U.S. Pat. Nos. 5,447,841; 5,472,842; and 5,427,932; and for example, in Pirlkel et al., Proc. Natl. Acad. Sci. 83:2934-2938, 1986; Pinkel et al., Proc. Natl. Acad. Sci. 85:9138-9142, 1988; and Lichter et al., Proc. Natl. Acad. Sci. 85:9664-9668, 1988. CISH is described in, e.g., Tanner et al., Am. .1. Pathol. 157: 1467- 1472, 2000 and U.S. Pat. No. 6,942,970. Additional detection methods are provided in U.S. Pat. No. 6,280,929.

Numerous reagents and detection schemes can be employed in conjunction with FISH, CISH, and SISH procedures to improve sensitivity, resolution, or other desirable properties. As discussed above probes labeled with fluorophores (including fluorescent dyes and QUANTUM DOTS®) can be directly optically detected when performing FISH. Alternatively, the probe can be labeled with a nonfluorescent molecule, such as a hapten (such as the following non-limiting examples: biotin, digoxigenin, DNP, and various oxazoles, pyrrazoles, thiazoles, nitroaryls, benzofurazans, triterpenes, ureas, thioureas, rotenones, coumarin, courmarin-based compounds, Podophyllotoxin, Podophyllotoxin-based compounds, and combinations thereof), ligand or other indirectly detectable moiety. Probes labeled with such non-fluorescent molecules (and the target nucleic acid sequences to which they bind) can then be detected by contacting the sample (e.g., the cell or tissue sample to which the probe is bound) with a labeled detection reagent, such as an antibody (or receptor, or other specific binding partner) specific for the chosen hapten or ligand. The detection reagent can be labeled with a fluorophore (e.g., QUANTUM DOT®) or with another indirectly detectable moiety, or can be contacted with one or more additional specific binding agents (e.g., secondary or specific antibodies), which can be labeled with a fluorophore.

In other examples, the probe, or specific binding agent (such as an antibody, e.g., a primary antibody, receptor or other binding agent) is labeled with an enzyme that is capable of converting a fluorogenic or chromogenic composition into a detectable fluorescent, colored or otherwise detectable signal (e.g., as in deposition of detectable metal particles in SISH). As indicated above, the enzyme can be attached directly or indirectly via a linker to the relevant probe or detection reagent. Examples of suitable reagents (e.g., binding reagents) and chemistries (e.g., linker and attachment chemistries) are described in U.S. Patent Application Publication Nos. 2006/0246524; 2006/0246523, and 2007/ 01 17153.

It will be appreciated by those of skill in the art that by appropriately selecting labelled probe-specific binding agent pairs, multiplex detection schemes can he produced to facilitate detection of multiple target nucleic acid sequences (e.g., genomic target nucleic acid sequences) in a single assay (e.g., on a single cell or tissue sample or on more than one cell or tissue sample). For example, a first probe that corresponds to a first target sequence can he labelled with a first hapten, such as biotin, while a second probe that corresponds to a second target sequence can be labelled with a second hapten, such as DNP. Following exposure of the sample to the probes, the bound probes can he detected by contacting the sample with a first specific binding agent (in this case avidin labelled with a first fluorophore, for example, a first spectrally distinct QUANTUM DOT®, e.g., that emits at 585 mn) and a second specific binding agent (in this case an anti-DNP antibody, or antibody fragment, labelled with a second fluorophore (for example, a second spectrally distinct QUANTUM DOT®, e.g., that emits at 705 mn). Additional probes/binding agent pairs can beadded to the multiplex detection scheme using other spectrally distinct fluorophores. Numerous variations of direct, and indirect (one step, two step or more) can he envisioned, all of which are suitable in the context of the disclosed probes and assays.

Probes typically comprise single-stranded nucleic acids of between 10 to 1000 nucleotides in length, for instance of between 10 and 800, more preferably of between 15 and 700, typically of between 20 and 500. Primers typically are shorter single-stranded nucleic acids, of between 10 to 25 nucleotides in length, designed to perfectly or almost perfectly match a nucleic acid of interest, to be amplified. The probes and primers are “specific” to the nucleic acids they hybridize to, i.e. they preferably hybridize under high stringency hybridization conditions (corresponding to the highest melting temperature Tm, e.g., 50 % formamide, 5x or 6x SCC. SCC is a 0.15 M NaCl, 0.015 M Na-citrate).

The nucleic acid primers or probes used in the above amplification and detection method may be assembled as a kit. Such a kit includes consensus primers and molecular probes. A preferred kit also includes the components necessary to determine if amplification has occurred. The kit may also include, for example, PCR buffers and enzymes; positive control sequences, reaction control primers; and instructions for amplifying and detecting the specific sequences.

In a particular embodiment, the methods of the invention comprise the steps of providing total RNAs extracted from blood and subjecting the RNAs to amplification and hybridization to specific probes, more particularly by means of a quantitative or semi- quantitative RT-PCR.

In another preferred embodiment, the expression level is determined by DNA chip analysis. Such DNA chip or nucleic acid microarray consists of different nucleic acid probes that are chemically attached to a substrate, which can be a microchip, a glass slide or a microsphere-sized bead. A microchip may be constituted of polymers, plastics, resins, polysaccharides, silica or silica-based materials, carbon, metals, inorganic glasses, or nitrocellulose. Probes comprise nucleic acids such as cDNAs or oligonucleotides that may be about 10 to about 60 base pairs. To determine the expression level, a sample from a test subject, optionally first subjected to a reverse transcription, is labelled and contacted with the microarray in hybridization conditions, leading to the formation of complexes between target nucleic acids that are complementary to probe sequences attached to the microarray surface. The labelled hybridized complexes are then detected and can be quantified or semi-quantified. Labelling may be achieved by various methods, e.g. by using radioactive or fluorescent labelling. Many variants of the microarray hybridization technology are available to the man skilled in the art (see e.g. the review by Hoheisel, Nature Reviews, Genetics, 2006, 7:200- 210).

Expression level of a gene may be expressed as absolute expression level or normalized expression level. Typically, expression levels are normalized by correcting the absolute expression level of a gene by comparing its expression to the expression of a gene that is not a relevant for determining the cancer stage of the patient, e.g., a housekeeping gene that is constitutively expressed. Suitable genes for normalization include housekeeping genes such as theactin gene ACTB, ribosomal 18S gene, GUSB, PGK1, TBP, HPRT1 and TFRC. TATA-binding protein (TBP) and hypoxanthine phosphoribosyl transferase 1 (HPRT1) were used as reference genes in the present study. This normalization allows the comparison of the expression level in one sample, e.g., a patient sample, to another sample, or between samples from different sources.

The man skilled in the art also understands that the same technique of assessment of the expression level of a gene should of course be used for obtaining the reference value and thereafter for assessment of the expression level of a gene of a patient subjected to the method of the invention.

Said reference control values may be determined in regard to the level of gene expression biomarker present in blood samples taken from one or more healthy subject(s) or in a control population.

In one embodiment, the method according to the present invention comprises the step of comparing said level of humoral immune response to a vaccine -specific gene expression level biomarkers (“Biomarkerl”: IFNal6 gene and/or “Biomarker2”: IGLV8-61 gene and/or “Biomarker3”: BLK gene and/or “Biomarker4”: EBF1 gene) to a control reference value wherein a high level of “humoral immune response to a vaccine -specific” gene expression biomarkers (“Biomarker 1”: IFNal6 gene and/or “Biomarker2”: IGLV8-61 gene and/or “Biomarker3”: BLK gene and/or “Biomarker4”: EBF1 gene) compared to said control reference value is predictive of a high risk to be a “high responder” to said vaccine and a low “humoral immune response to a vaccine -specific” gene expression biomarkers (Biomarkerl”: IFNal6 gene and/or “Biomarker2”: IGLV8-61 gene and/or “Biomarker3”: BLK gene and/or “Biomarker4”: EBF1 gene) compared to said control reference value is predictive of a high risk to be a “low responder” to said vaccine.

The control reference value may depend on various parameters such as the method used to measure the level humoral immune response to a vaccine -specific gene expression level biomarkers (“Biomarkerl”: IFNal6 gene and/or “Biomarker2”: IGLV8-61 gene and/or “Biomarker3”: BLK gene and/or “Biomarker4”: EBF1 gene) or the gender of the subject.

Control reference values are easily determinable by the one skilled in the art, by using the same techniques as for determining the level of gene expression biomarker in a blood sample previously collected from the patient under testing.

A “reference value” can be a “threshold value” or a “cut-off value”. Typically, a "threshold value" or "cut-off value" can be determined experimentally, empirically, or theoretically. A threshold value can also be arbitrarily selected based upon the existing experimental and/or clinical conditions, as would be recognized by a person of ordinary skilled in the art. The threshold value has to be determined in order to obtain the optimal sensitivity and specificity according to the function of the test and the benefit/risk balance (clinical consequences of false positive and false negative). Typically, the optimal sensitivity and specificity (and so the threshold value) can be determined using a Receiver Operating Characteristic (ROC) curve based on experimental data. Preferably, the person skilled in the art may compare the level of gene expression biomarkers (“Biomarkerl”: IFNal6 gene and/or “Biomarker2”: IGLV8-61 gene and/or “Biomarker3”: BLK gene and/or “Biomarker4”: EBF1 gene) with a defined threshold value. In one embodiment of the present invention, the threshold value is derived from the gene expression level (or ratio, or score) determined in a blood sample derived from one or more subjects who are responders (to the method according to the invention). In one embodiment of the present invention, the threshold value may also be derived from gene expression level (or ratio, or score) determined in a blood sample derived from one or more subjects or who are non-responders. Furthermore, retrospective measurement of the gene expression level (or ratio, or scores) in properly banked historical subject samples may be used in establishing these threshold values. For instance in the ConM SOSIP+MPLA vaccination study and with the expression level of IFNal6, IGLV8-61, BLK, and/or EBF1 gene assessed by microarray hybridation, the ROC curve analysis revealed that choosing a cut-off value at 5 unit expression of IFNal6 mRNA, and/or at 9 unit expression of IGLV8-61 mRNA and/or at 8 unit expression of BLK, and/or at 7 unit expression of EBF1 mRNA levels allowed to effectively discriminate responders from / non responders blood sample and which could be used as predetermined reference level for IFNal6, IGLV8-61, BLK, and/or EBF1.

"Risk" in the context of the present invention, relates to the probability that an event will occur over a specific time period, as in humoral immune response of a subject to a vaccine, and can mean a subject's "absolute" risk or "relative" risk. Absolute risk can be measured with reference to either actual observation post-measurement for the relevant time cohort, or with reference to index values developed from statistically valid historical cohorts that have been followed for the relevant time period. Relative risk refers to the ratio of absolute risks of a subject compared either to the absolute risks of low risk cohorts or an average population risk, which can vary by how clinical risk factors are assessed. Odds ratios, the proportion of positive events to negative events for a given test result, are also commonly used (odds are according to the formula p/(l-p) where p is the probability of event and (1- p) is the probability of no event) to no conversion. Alternative continuous measures, which may be assessed in the context of the present invention, include time to humoral immune response of a subject to a vaccine risk reduction ratios.

"Risk evaluation," or "evaluation of risk" in the context of the present invention encompasses making a prediction of the probability, odds, or likelihood that an event (humoral immune response of a subject to a vaccine) may occur, the rate of occurrence of the event or conversion from one state to another, i.e., from a “high responder” to said vaccine to “low responder” to said vaccine. Risk evaluation can also comprise prediction of future clinical parameters, traditional laboratory risk factor values, or other indices of “humoral response”, such as cellular population determination in peripheral tissues, in serum or other fluid, either in absolute or relative terms in reference to a previously measured population. The methods of the present invention may be used to make continuous or categorical measurements of the risk of an event (humoral immune response of a subject to a vaccine), thus prognosing and defining the risk spectrum of a category of subjects defined as being “high responder” to a vaccine. In the categorical scenario, the invention can be used to discriminate between normal and other subject cohorts at higher risk to be “high responder” to said vaccine. In other embodiments, the present invention may be used so as to help to discriminate those having “high responder” to a vaccine from “low responder” to said vaccine

Kit for performing the method of the invention

A further object of the invention relates to kits for performing the methods of the invention, wherein said kits comprise means for measuring the expression level of one or more gene expression level selected from a group of gene consisting of: IGLV8-61, BLK, EBF1 and IFNal6 gene of the invention in the sample obtained from the patient for use to assess a subject’s humoral immune response to a vaccine.

In a particular embodiment, the kit for performing the method of the invention comprise means for measuring the gene expression levels of IFNal6, IGLV8-61, BLK, and EBF1 gene.

Accordingly, the present invention also relates to a kit of the invention comprising means for determining the expression level of one or more gene expression level selected from a group of gene consisting of IGLV8-61, BLK, EBF1 and IFNal6 gene.

In one embodiment, the present invention relates to a kit for use to assess a subject’s humoral immune response to a vaccine, comprising:

- at least a means for determining the expression level of one or more gene expression level selected from a group of gene consisting of IGLV8-61, BLK, EBF1 and IFNal6 gene and

- instructions for use.

In a particular embodiment, the kit for use comprising:

- amplification primers and/or probe for determining the expression level one or more gene expression level selected from a group of gene consisting of IGLV8-61, BLK, EBF1 and IFNal6 gene,

- instructions for use.

The kits may include probes, primers macroarrays or microarrays as above described. For example, the kit may comprise a set of probes as above defined, usually made of DNA, and that may be pre-labelled. Alternatively, probes may be unlabelled and the ingredients for labelling may be included in the kit in separate containers. The kit may further comprise hybridization reagents or other suitably packaged reagents and materials needed for the particular hybridization protocol, including solid-phase matrices, if applicable, and standards. Alternatively the kit of the invention may comprise amplification primers that may be prelabelled or may contain an affinity purification or attachment moiety. The kit may further comprise amplification reagents and also other suitably packaged reagents and materials needed for the particular amplification protocol.

Therapeutic method

The invention also relates to a method for vaccinating a subject in need thereof with an antigen wherein prior to vaccination, the level of one or more gene expression level selected from a group of gene consisting of IFNal6, IGLV8-61, BLK and EBF1 gene obtained from said subject have been detected by one of method of the invention.

Another object of the present invention is a method for vaccinating a subject comprising prior to vaccination the steps of a) providing a blood sample from a subject, b) detecting the level of one or more gene expression level selected from a group of gene consisting of IFNal6, IGLV8-61, BLK and EBF1 gene obtained from said subject, c) comparing the level determined in step b) with a reference value and if level determined at step b) is higher than the reference value, vaccinating the subject with antigen.

Another object of the present invention is an antigen for use in a method for vaccinating a subject in need thereof, wherein prior to vaccination, the level of one or more gene expression level selected from a group of gene consisting of IFNal6, IGLV8-61, BLK and EBF1 gene obtained from said subject have been detected by one of method of the invention.

The invention will be further illustrated by the following figures and examples. However, these examples and figures should not be interpreted in any way as limiting the scope of the present invention.

FIGURES:

Figure 1: Vaccination protocol enrolling healthy volunteers aged (18-45) with given informed consent. Each participant will receive the immunogens according to the vaccination schedule (Visit (V)), Week (W). Three injections of vaccine were performed at V0 (W0) and V6 (W12) and VI 1 (W24). Transcriptomic analysis for gene expression were performed at V0 and V6 and serum titres of neutralising antibodies to virus expressing ConM were performed at V14 (W26). Figure 2: Correlation between biomarkers and neutralizing antibodies

Figure 3: ROC gene Nab: IGLV8-61, EBF1, IFNal6 and BLK. ROC curves show the specificity and the sensitivity of the logistic regression models, i.e., the proportion of correctly predicted responders and nonresponders, respectively. A) The logistic regression based on single level of IGLV8, B) EBF1, C) BLK and D) IFNal6. E) The logistic regression is based on the expression of 4 genes IGLV8, EBF1, IFNal6 and BLK.

Figure 4: Spearman correlation between gene expression and age of healthy donors. mRNA were extracted from frozen Peripheral Blood Mononuclear Cells (PBMC) samples isolatd from healthy donors ages (n=16, age range = 23-61 yo, median 40.5 yo). A) RT-PCR were performed using specific primers for each genes. Gene expression was normalized to the mean of actin and GAPDH expression and presented as 1/delta CT. B) Spearman rank correlation test with significance defined by a P-value <0.05.

EXAMPLE 1:

Methods:

The identification of new biomarkers in vaccination is essential to making it possible to predict the degree of protection a vaccine will provide against the relevant infectious disease. We thus identify biomarkers by transcriptomic analysis of gene expression before the vaccine intervention (prime and boost) particularly those involved in B cell development (BLK, IGLV8, IFNal6, EBF1) predictive of humoral responses. We based our analyses on healthy (n=6) participants in a randomized clinical study who were vaccinated with ConM SOSIP + MPLA adjuvant (see figure 1). We investigated the host whole-blood transcriptome at two baselines of injection (W0, W12) to assess the likelihood of their involvement in an effective HIV-neutralizing antibody response (Nab) at W26 vaccination.

Result:

The levels of Nab responses were positively correlated with all 4 biomarkers expression at baseline (W0, W12). The level of biomarkers at both baselines and known to be involved in B cell differentiation predict the level of responses to the vaccine by measurement of anti-HIV Nabs (see figure 2 and 3A,B,C,D, E).

EXAMPLE 2:

Methods:

Immunosenescence is a series of age-related changes that affect the immune system increasing vulnerability to infectious diseases and response to vaccine including decreased humoral responses during ageing (Ciocca, Michela et al., Frontiers in immunology vol. 12 690534 (2021); Nikolich-Zugich, Janko. Nature immunology vol. 19,1 (2018): 10-19). Identified biomarkers analysis during ageing in healthy adults validate likelihood of their involvement in immune responses to antigens. Result:

The levels of all 4 gene expression (BLK, IGLV8, IFNal6, EBF1) were negatively correlated with age in healthy adults. The level of biomarkers at known to be involved in B cell differentiation waning during ageing that is associated with immunosenescence (see figure 4A,B).

REFERENCES:

Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present disclosure.

Table 1: mRNA used in the present invention

Claims

- 27 -WO 2022/136252 PCT/EP2021/086754 CLAIMS:

1. An in vitro method for assessing a subject’s humoral immune response to a vaccine, said method, comprising the step of (a) measuring in a sample obtained from said subject prior to the administration of said vaccine, the level of one or more gene expression level selected from a group of gene consisting of: IFNal6, IGLV8-61, BLK, and EBF1 gene and b) wherein the level of one or more gene expression of step a) is positively correlated with the humoral immune response of said subject to said vaccine.

2. The in vitro method according to claim 1 comprising the step of comparing said level of one or more gene expression to a control reference value wherein:

3. The in vitro method according to any one of claim 1 to 2, wherein the sample is a blood sample.

4. The in vitro method according to any one of claim 1 or 3, wherein the level of one or more gene expression is determined at mRNA level.

5. The in vitro method according to any one of claim 1 or 4, wherein the level of the gene expression is determined with one, two, three, four gene selected from the group consisting of IGLV8-61, BLK, EBF1 and IFNal6 gene.

6. The in vitro method according to any one of claim 1 or 5, wherein the vaccine contains an antigen selected from the group consisting of attenuated and inactivated viral and bacterial pathogens, purified macromolecules, polysaccharides, toxoids, recombinant antigens, organisms containing a foreign gene from a pathogen, synthetic peptides, polynucleic acids (DNA, RNA), antibodies and tumor cells.

7. A kit, comprising:

8. A kit for use according to claim 7, comprising:

- amplification primers and/or probe for determining one or more gene expression level selected from a group of gene consisting of: IFNal6, IGLV8-61, BLK, and EBF1 gene,

- instructions for use.

9. Method for vaccinating a subject in need thereof with an antigen wherein prior to vaccination, the level of one or more gene expression level selected from a group of gene consisting of: IFNal6IGLV8-61, BLK and EBF1 gene obtained from said subject, have been detected by one of the methods of claim 1 to 6.