Precision medicine for IBD

Precision medicine, also known as personalized medicine, is a key clinical goal for the effective treatment of heterogeneous, complex diseases such as inflammatory bowel disease (IBD), cancer, autoimmune diseases and COVID-19. 

Recent paper published in the journal Nature Communications describes a precision medicine approach - the integrated SNP (Single Nucleotide Polymorphism) Network Pipeline (iSNP). 

The iSNP tool will help to identify subtype of IBD for every patient based on their specific genetics. It could help to describe the individual pathogenesis story and find the best treatment.

Patients with Inflammatory Bowel Disease (IBD) develop the condition due to distinct and different mechanisms, determined by their genetics. The causes of IBD aren't understood but are linked to dysfunction of the immune system and how it reacts to food and the gut microbiome, including virome. 

For IBD, less than 10% of the identified SNPs are in coding regions of genes and over 90% of SNPs are in areas once thought to just be junk DNA, controlling and regulating the activity of the genes. The immune system functions by taking a wide range of different inputs that trigger different signaling networks within the cell, integrating these to produce a balanced, appropriate response, so a combination of even subtlest SNPs could disequilibrate the system. Understanding how they combine to influence intricately interlinked signals would fill in major gaps enabling personalized treatment. 

The iSNP workflow identifies patient clusters with distinct pathomechanisms. 

Patient data is layered with population-wide genomics and transcriptomics using. To achieve this, hidden proteins contributing to pathogenesis and key pathogenic pathways are identified and aligned with pathological processes in disease development. 

High-quality individual patient genetic information was used along with preprocessed and quality-controlled immunochip data. miRNA-TS identification algorithm MIRANDA was included in the pipeline along with other genetic analysis tools. A computer simulation of interactions, pathways and networks used databases of known and predicted interactions between proteins in the network.

There was not enough granularity in the clinical data to link all pathways with phenotypes and remove confounders such as recurrent corticosteroid therapy. Further work will need to be done on larger cohorts and with multi-omics datasets to confirm the potential for iSNP to be used for precision therapy based on patient-specific genetics.

REFERENCE

Johanne Brooks-Warburton et al, A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis, Nature Communications (2022). DOI: 10.1038/s41467-022-29998-8

Autoimmune diseases and COVID-19 vaccines

Autoimmune diseases occur when the immune system attacks the healthy body tissue within digestive track, joints, vasculature and other organ systems. This causes inflammation, pain, diminished mobility, fatigue, and other non-specific symptoms.  

Nearly 4% of the world’s population and 5-8% of U.S. is affected by an autoimmune diseases, the most common of which include type 1 diabetes, multiple sclerosis, rheumatoid arthritis, lupus, Crohn’s disease, and psoriasis. 

There is no evidence that any vaccines cause flares of autoimmune diseases, used to say doctors. However, there is limited data available since individuals with autoimmune diseases were excluded from phase I–III vaccine trials. And it is known that immunizations could cause flare ups (see, eg, this study of 2020/2021 flu vaccines). Preliminary data from smaller studies and case reports after emergency-use-authorization for SARS-CoV-2 suggest there is a possibility.

A case of a white 55-year-old male who has been in sustained remission from rheumatoid arthritis for more than 2 years describes him developing an acute flare of his rheumatoid arthritis 12 h after the second BNT162b2 vaccination (similarly to flares observed after COVID-19 infection). The patient was treated with intra-articular steroids with rapid improvement, and he is once again in clinical remission.

23-year-old woman who developed acute reactive arthritis on her left knee joint after COVID-19 vaccination with Sinovac CoronaVac was back on her feet in 2 days, after she was administered a single intra-articular injection of 1 ml compound betamethasone.

A 20-year-old man with a history of multiple sclerosis experienced acute myocarditis after the third dose of SARS-COV-2 vaccine (AstraZeneca vaccine). He had received the first and second dose of the SARS-COV-2 vaccine (Sinopharm vaccine) 5 and 4 months before.

More recently published, 27 case reports from Israel, US and UK described 17 flares and 10 new onset immune-mediated diseases. 23/27 received the BNT - 162b2 vaccine, 2/27 the mRNA-1273 and 2/27 the ChAdOx1 vaccines. The mean age was 54.4 ± 19.2 years and 55% of cases were female.

A study that compared 26 people with autoimmune disorders aged 24 to 89 (Rheumatoid arthritis, Crohn's disease, Psoriatic Arthritis, Sarcoidosis, Lupus, etc; none had been infected with SARS-CoV-2 prior to vaccination) with 42 healthy controls. Patients with autoimmune diseases had a marginal propensity towards more vaccine side effects compared with healthy controls: mild fatigue and myalgia were more frequent  (53.8% vs 43.2% and 42.3% vs 31.6%) and so was headache (38.5% vs 35.1%). Fever, on the other hand, was completely absent in patients with inflammatory diseases while being reported by 13.5% of the healthy cohort. Arthralgia was comparable in both groups. 

Researchers from two different rheumatology departments in Israel monitored 491 patients with autoimmune inflammatory rheumatic diseases (AIRD) and compared their reactions to 99 healthy controls. Shortly after receiving the vaccine, 1.2% of those with AIIRD (six patients total, age range: 36 to 61) developed their first case of shingles compared to none of the controls. Four of the six affected individuals had stable rheumatoid arthritis, one had Sjögren’s syndrome and another one had undifferentiated connective disease. Notably, one patient developed Herpes zoster despite being vaccinated for it two years prior to the reported event.

Multiple cases of apparent secondary immune thrombocytopenia (ITP), an unusual immune reaction triggered  after SARS‐CoV‐2 vaccination have been reported and reached public attention. 

One case was actually a flareup for a patient with a past medical history of  autoimmune bleeding disorder Immune thrombocytopenia (ITP). This patient received the first dose of SARS‐CoV‐2 mRNA‐1273 Moderna Covid‐19 vaccine 2 weeks prior to presentation. Three other individuals that experienced thrombocytopenia had known autoimmune conditions including hypothyroidism, Crohn's disease, or tested positive for anti‐thyroglobulin antibodies. Given that a small percentage of patients with lupus and antiphospholipid syndrome have been previously shown to display serum antibodies against PF-4 in association with thrombotic events constant vigilance is warranted.

Preliminary results of the COVID-19 Back to Normal study  show that some individuals with autoimmune diseases do experience flareups and higher frequency of adverse reactions such as enlarged lymph nodes. A smaller percentage of people claim they actually observed improvement in their autoimmune conditions after vaccinations You can help by submitting your observations about effects of vaccinations: https://forms.gle/5xs4XzFUFkhpa2TA9

REFERENCES

Buttari F, Bruno A, Dolcetti E, Azzolini F, Bellantonio P, Centonze D, Fantozzi R. COVID-19 vaccines in multiple sclerosis treated with cladribine or ocrelizumab. Multiple Sclerosis and Related Disorders. 2021 May 4:102983.

Geisen UM, Berner DK, Tran F, Sümbül M, Vullriede L, Ciripoi M, Reid HM, Schaffarzyk A, Longardt AC, Franzenburg J, Hoff P. Immunogenicity and safety of anti-SARS-CoV-2 mRNA vaccines in patients with chronic inflammatory conditions and immunosuppressive therapy in a monocentric cohort. Annals of the Rheumatic Diseases. 2021 Mar 24.

Furer V, Zisman D, Kibari A, Rimar D, Paran Y, Elkayam O. Herpes zoster following BNT162b2 mRNA Covid-19 vaccination in patients with autoimmune inflammatory rheumatic diseases: a case series. Rheumatology (Oxford, England). 2021 Apr 12.

Lee EJ, Cines DB, Gernsheimer T, Kessler C, Michel M, Tarantino MD, Semple JW, Arnold DM, Godeau B, Lambert MP, Bussel JB. Thrombocytopenia following Pfizer and Moderna SARS‐CoV‐2 vaccination. American Journal of Hematology. 2021 Feb 19.

Moutsopoulos HM. A recommended paradigm for vaccination of rheumatic disease patients with the SARS-CoV-2 vaccine. Journal of Autoimmunity. 2021 May 1:102649.

Terracina KA, Tan FK. Flare of rheumatoid arthritis after COVID-19 vaccination. The Lancet. Rheumatology. 2021 Mar 30. 

Toom S, Wolf B, Avula A, Peeke S, Becker K. Familial thrombocytopenia flare‐up following the first dose of mRNA‐1273 Covid‐19 vaccine. American Journal of Hematology. 2021 Feb 13.

Qi-jun An, De-an Qin & Jin-xian Pei (2021) Reactive arthritis after COVID-19 vaccination, Human Vaccines & Immunotherapeutics, DOI: 10.1080/21645515.2021.1920274

Watad A, De Marco G, Mahajna H, Druyan A, Eltity M, Hijazi N, Haddad A, Elias M, Zisman D, Naffaa ME, Brodavka M. Immune-Mediated Disease Flares or New-Onset Disease in 27 Subjects Following mRNA/DNA SARS-CoV-2 Vaccination. Vaccines. 2021 May;9(5):435.